1
|
Lysakovskaia K, Devadas A, Schwalb B, Lidschreiber M, Cramer P. Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition. Nat Struct Mol Biol 2025:10.1038/s41594-025-01486-9. [PMID: 39934431 DOI: 10.1038/s41594-025-01486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 01/07/2025] [Indexed: 02/13/2025]
Abstract
Metazoan gene transcription by RNA polymerase II (Pol II) is regulated in the promoter-proximal region. Pol II can undergo termination in the promoter-proximal region but whether this can contribute to transcription regulation in cells remains unclear. Here we extend our previous multiomics analysis to quantify changes in transcription kinetics during a human cell type transition event. We observe that upregulation of transcription involves an increase in initiation frequency and, at a set of genes, a decrease in promoter-proximal termination. In turn, downregulation of transcription involves a decrease in initiation frequency and an increase in promoter-proximal termination. Thus, promoter-proximal termination of Pol II contributes to the regulation of human gene transcription.
Collapse
Affiliation(s)
- Kseniia Lysakovskaia
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Arjun Devadas
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| |
Collapse
|
2
|
Sun L, Fu X, Xiao Z, Ma G, Zhou Y, Hu H, Shi L, Li D, Jauch R, Hutchins AP. BRD8 Guards the Pluripotent State by Sensing and Maintaining Histone Acetylation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2409160. [PMID: 39656858 PMCID: PMC11792058 DOI: 10.1002/advs.202409160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Revised: 11/21/2024] [Indexed: 12/17/2024]
Abstract
Epigenetic control of cell fates is a critical determinant to maintain cell type stability and permit differentiation during embryonic development. However, the epigenetic control mechanisms are not well understood. Here, it is shown that the histone acetyltransferase reader protein BRD8 impairs the conversion of primed mouse EpiSCs (epiblast stem cells) to naive mouse ESCs (embryonic stem cells). BRD8 works by maintaining histone acetylation on promoters and transcribed gene bodies. BRD8 is responsible for maintaining open chromatin at somatic genes, and histone acetylation at naive-specific genes. When Brd8 expression is reduced, chromatin accessibility is unchanged at primed-specific genes, but histone acetylation is reduced. Conversely, naive-specific genes has reduced repressive chromatin marks and acquired accessible chromatin more rapidly during the cell type conversion. It is shown that this process requires active histone deacetylation to promote the conversion of primed to naive. This data supports a model for BRD8 reading histone acetylation to accurately localize the genome-wide binding of the histone acetyltransferase KAT5. Overall, this study shows how the reading of the histone acetylation state by BRD8 maintains cell type stability and both enables and impairs stem cell differentiation.
Collapse
Affiliation(s)
- Li Sun
- Department of Systems BiologySouthern University of Science and TechnologyShenzhen518055China
| | - Xiuling Fu
- Department of Systems BiologySouthern University of Science and TechnologyShenzhen518055China
| | - Zhen Xiao
- Department of Systems BiologySouthern University of Science and TechnologyShenzhen518055China
| | - Gang Ma
- Department of Systems BiologySouthern University of Science and TechnologyShenzhen518055China
| | - Yibin Zhou
- Department of Systems BiologySouthern University of Science and TechnologyShenzhen518055China
| | - Haoqing Hu
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
- Centre for Translational Stem Cell BiologyHong KongSARChina
| | - Liyang Shi
- Department of Systems BiologySouthern University of Science and TechnologyShenzhen518055China
| | - Dongwei Li
- Key Laboratory of Biological Targeting DiagnosisTherapy and Rehabilitation of Guangdong Higher Education InstitutesThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhou510799China
| | - Ralf Jauch
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongHong KongSARChina
- Centre for Translational Stem Cell BiologyHong KongSARChina
| | - Andrew Paul Hutchins
- Department of Systems BiologySouthern University of Science and TechnologyShenzhen518055China
| |
Collapse
|
3
|
Ma G, Fu X, Zhou L, Babarinde IA, Shi L, Yang W, Chen J, Xiao Z, Qiao Y, Ma L, Ou Y, Li Y, Chang C, Deng B, Zhang R, Sun L, Tong G, Li D, Li Y, Hutchins AP. The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cells. Nat Cell Biol 2025; 27:232-245. [PMID: 39789220 DOI: 10.1038/s41556-024-01595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 12/11/2024] [Indexed: 01/12/2025]
Abstract
The nuclear matrix, a proteinaceous gel composed of proteins and RNA, is an important nuclear structure that supports chromatin architecture, but its role in human pluripotent stem cells (hPSCs) has not been described. Here we show that by disrupting heterogeneous nuclear ribonucleoprotein U (HNRNPU) or the nuclear matrix protein, Matrin-3, primed hPSCs adopted features of the naive pluripotent state, including morphology and upregulation of naive-specific marker genes. We demonstrate that HNRNPU depletion leads to increased chromatin accessibility, reduced DNA contacts and increased nuclear size. Mechanistically, HNRNPU acts as a transcriptional co-factor that anchors promoters of primed-specific genes to the nuclear matrix with POLII to promote their expression and their RNA stability. Overall, HNRNPU promotes cell-type stability and when reduced promotes conversion to earlier embryonic states.
Collapse
Affiliation(s)
- Gang Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xiuling Fu
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Lulu Zhou
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Isaac A Babarinde
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liyang Shi
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenting Yang
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jiao Chen
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhen Xiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yu Qiao
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Lisha Ma
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuhao Ou
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuhao Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chen Chang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Boping Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ran Zhang
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Guoqing Tong
- Department of Reproductive Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dongwei Li
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Yiming Li
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China.
| | - Andrew P Hutchins
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| |
Collapse
|
4
|
Zhang Z, Hu X, Sun Y, Lei L, Liu Z. Early inhibition of BRD4 facilitates iPSC reprogramming via accelerating rDNA dynamic expression. BMC Biol 2024; 22:195. [PMID: 39256730 PMCID: PMC11389306 DOI: 10.1186/s12915-024-01997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/28/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND iPSC reprogramming technology exhibits significant promise in the realms of clinical therapeutics, disease modeling, pharmaceutical drug discovery, and various other applications. However, the extensive utilization of this technology has encountered impediments in the form of inefficiency, prolonged procedures, and ambiguous biological processes. Consequently, in order to improve this technology, it is of great significance to delve into the underlying mechanisms involved in iPSC reprogramming. The BET protein BRD4 plays a crucial role in the late stage of reprogramming; however, its precise function in the early stage remains unclear. RESULTS Our study aims to investigate BRD4's role in the early stages of iPSC reprogramming. Our investigation reveals that early inhibition of BRD4 substantially enhances iPSC reprogramming, whereas its implementation during the middle-late stage impedes the process. During the reprogramming, ribosome DNA expression initially increases before decreasing and then gradually recovers. Early inhibition of BRD4 improved the decline and restoration of rDNA expression in the early and middle-late stages, respectively. Additionally, we uncovered the mechanism of BRD4's regulation of rDNA transcription throughout reprogramming. Specifically, BRD4 interacts with UBF and co-localizes to both the rDNA promoter and enhancer regions. Ultimately, BRD4 facilitates rDNA transcription by promoting the enrichment of histone H3 lysine 27 acetylation in the surrounding chromatin. Moreover, we also discovered that early inhibition of BRD4 facilitates cells' transition out of the somatic cell state and activate pluripotent genes. CONCLUSIONS In conclusion, our results demonstrate that early inhibition of BRD4 promotes sequential dynamic expression of rDNA, which improves iPSC reprogramming efficiency.
Collapse
Affiliation(s)
- Zhijing Zhang
- Department of Histology and Embryology, Harbin Medical University, 157 Baojian Street, Nangang DistrictHeilongjiang Province 150086, Harbin, China
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, 31 Mucai Street, Xiangfang DistrictHeilongjiang Province 150030, Harbin, China
| | - Xinglin Hu
- Department of Histology and Embryology, Harbin Medical University, 157 Baojian Street, Nangang DistrictHeilongjiang Province 150086, Harbin, China
| | - Yuchen Sun
- Department of Histology and Embryology, Harbin Medical University, 157 Baojian Street, Nangang DistrictHeilongjiang Province 150086, Harbin, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, 157 Baojian Street, Nangang DistrictHeilongjiang Province 150086, Harbin, China.
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, 31 Mucai Street, Xiangfang DistrictHeilongjiang Province 150030, Harbin, China.
| |
Collapse
|
5
|
Zhang Z, Xu J, Liu J, Wang J, Lei L. SEC: A core hub during cell fate alteration. FASEB J 2024; 38:e23680. [PMID: 38758186 DOI: 10.1096/fj.202400514r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/18/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024]
Abstract
Pol II pause release is a rate-limiting step in gene transcription, influencing various cell fate alterations. Numerous proteins orchestrate Pol II pause release, thereby playing pivotal roles in the intricate process of cellular fate modulation. Super elongation complex (SEC), a large assembly comprising diverse protein components, has garnered attention due to its emerging significance in orchestrating physiological and pathological cellular identity changes by regulating the transcription of crucial genes. Consequently, SEC emerges as a noteworthy functional complex capable of modulating cell fate alterations. Therefore, a comprehensive review is warranted to systematically summarize the core roles of SEC in different types of cell fate alterations. This review focuses on elucidating the current understanding of the structural and functional basis of SEC. Additionally, we discuss the intricate regulatory mechanisms governing SEC in various models of cell fate alteration, encompassing both physiological and pathological contexts. Furthermore, leveraging the existing knowledge of SEC, we propose some insightful directions for future research, aiming to enhance our mechanistic and functional comprehension of SEC within the diverse landscape of cell fate alterations.
Collapse
Affiliation(s)
- Zhijing Zhang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jingyi Xu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jiqiang Liu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang Province, China
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| |
Collapse
|
6
|
Du X, Qin W, Yang C, Dai L, San M, Xia Y, Zhou S, Wang M, Wu S, Zhang S, Zhou H, Li F, He F, Tang J, Chen JY, Zhou Y, Xiao R. RBM22 regulates RNA polymerase II 5' pausing, elongation rate, and termination by coordinating 7SK-P-TEFb complex and SPT5. Genome Biol 2024; 25:102. [PMID: 38641822 PMCID: PMC11027413 DOI: 10.1186/s13059-024-03242-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/09/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Splicing factors are vital for the regulation of RNA splicing, but some have also been implicated in regulating transcription. The underlying molecular mechanisms of their involvement in transcriptional processes remain poorly understood. RESULTS Here, we describe a direct role of splicing factor RBM22 in coordinating multiple steps of RNA Polymerase II (RNAPII) transcription in human cells. The RBM22 protein widely occupies the RNAPII-transcribed gene locus in the nucleus. Loss of RBM22 promotes RNAPII pause release, reduces elongation velocity, and provokes transcriptional readthrough genome-wide, coupled with production of transcripts containing sequences from downstream of the gene. RBM22 preferentially binds to the hyperphosphorylated, transcriptionally engaged RNAPII and coordinates its dynamics by regulating the homeostasis of the 7SK-P-TEFb complex and the association between RNAPII and SPT5 at the chromatin level. CONCLUSIONS Our results uncover the multifaceted role of RBM22 in orchestrating the transcriptional program of RNAPII and provide evidence implicating a splicing factor in both RNAPII elongation kinetics and termination control.
Collapse
Affiliation(s)
- Xian Du
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Wenying Qin
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Chunyu Yang
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Lin Dai
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Mingkui San
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Yingdan Xia
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Siyu Zhou
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Mengyang Wang
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shuang Wu
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Shaorui Zhang
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Huiting Zhou
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Fangshu Li
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Fang He
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, China
| | - Yu Zhou
- TaiKang Center for Life and Medical Sciences, College of Life Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Rui Xiao
- Department of Hematology, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China.
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, China.
| |
Collapse
|
7
|
Ayyamperumal P, Naik HC, Naskar AJ, Bammidi LS, Gayen S. Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming. Life Sci Alliance 2024; 7:e202302337. [PMID: 38320809 PMCID: PMC10847334 DOI: 10.26508/lsa.202302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Two alleles of a gene can be transcribed independently or coordinatedly, which can lead to temporal expression heterogeneity with potentially distinct impacts on cell fate. Here, we profiled genome-wide allelic transcriptional burst kinetics during the reprogramming of MEF to induced pluripotent stem cells. We show that the degree of coordination of allelic bursting differs among genes, and alleles of many reprogramming-related genes burst in a highly coordinated fashion. Notably, we show that the chromatin accessibility of the two alleles of highly coordinated genes is similar, unlike the semi-coordinated or independent genes, suggesting the degree of coordination of allelic bursting is linked to allelic chromatin accessibility. Consistently, we show that many transcription factors have differential binding affinity between alleles of semi-coordinated or independent genes. We show that highly coordinated genes are enriched with chromatin accessibility regulators such as H3K4me3, H3K4me1, H3K36me3, H3K27ac, histone variant H3.3, and BRD4. Finally, we demonstrate that enhancer elements are highly enriched in highly coordinated genes. Our study demonstrates that epigenomic states contribute to coordinated allelic bursting to fine-tune gene expression during induced pluripotent stem cell reprogramming.
Collapse
Affiliation(s)
- Parichitran Ayyamperumal
- Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Hemant Chandru Naik
- Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Amlan Jyoti Naskar
- Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Lakshmi Sowjanya Bammidi
- Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Srimonta Gayen
- Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| |
Collapse
|
8
|
Diaba-Nuhoho P. Plant homeodomain-finger protein 5A: A key player in cancer progression. Biomed Pharmacother 2023; 169:115857. [PMID: 37951028 DOI: 10.1016/j.biopha.2023.115857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/31/2023] [Accepted: 11/05/2023] [Indexed: 11/13/2023] Open
Abstract
PHF5A is a member of the zinc-finger proteins. To advance knowledge on their role in carcinogenesis, data from experimental studies, animal models and clinical studies in different tumorigenesis have been reviewed. Furthermore, PHF5A as an oncogenic function, is frequently high expressed in tumor cells and a potential prognostic marker for different cancers. PHF5A is implicated in the regulation of cancer cell proliferation, invasion, migration and metastasis. Knockdown of PHF5A prevented the invasion and metastasis of tumor cells. Here, the role of PHF5A in different cancers and their possible mechanism in relation to recent literature is reviewed and discussed. There is an open promising perspective to their therapeutic management for different cancer types.
Collapse
Affiliation(s)
- Patrick Diaba-Nuhoho
- Department of Paediatric and Adolescent Medicine, Paediatric Haematology and Oncology, University Hospital Münster, Germany.
| |
Collapse
|
9
|
Lee J, Lee BK, Gross JM. Brd activity regulates Müller glia-dependent retinal regeneration in zebrafish. Glia 2023; 71:2866-2883. [PMID: 37584502 DOI: 10.1002/glia.24457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The zebrafish retina possesses tremendous regenerative potential. Müller glia underlie retinal regeneration through their ability to reprogram and generate multipotent neuronal progenitors that re-differentiate into lost neurons. Many factors required for Müller glia reprogramming and proliferation have been identified; however, we know little about the epigenetic and transcriptional regulation of these genes during regeneration. Here, we determined whether transcriptional regulation by members of the Bromodomain (Brd) family is required for Müller glia-dependent retinal regeneration. Our data demonstrate that three brd genes were expressed in Müller glia upon injury. brd2a and brd2b were expressed in all Müller glia and brd4 was expressed only in reprogramming Müller glia. Utilizing (+)-JQ1, a pharmacological inhibitor of Brd function, we demonstrate that transcriptional regulation by Brds plays a critical role in Müller glia reprogramming and regeneration. (+)-JQ1 treatment prevented cell cycle re-entry of Müller glia and the generation of neurogenic progenitors. Modulating the (+)-JQ1 exposure window, we identified the first 48 h post-injury as the time-period during which Müller glia reprogramming occurs. (+)-JQ1 treatments after 48 h post-injury had no effect on the re-differentiation of UV cones, indicating that Brd function is required only for Müller glia reprogramming and not subsequent specification/differentiation events. Brd inhibition also prevented the expression of reprogramming genes like ascl1a and lepb in Müller glia, but not effector genes like mmp9, nor did it affect microglial recruitment after injury. These results demonstrate that transcriptional regulation by Brds plays a critical role during Müller glia-dependent retinal regeneration in zebrafish.
Collapse
Affiliation(s)
- Jiwoon Lee
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, New York, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
10
|
Dong S, Sun Y, Liu C, Li Y, Yu S, Zhang Q, Xu Y. Stage-specific requirement for m 6A RNA methylation during cardiac differentiation of pluripotent stem cells. Differentiation 2023; 133:77-87. [PMID: 37506593 DOI: 10.1016/j.diff.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
Precise spatiotemporal control of gene expression patterns is critical for normal development. Pluripotent stem cells, including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), with the ability of unlimited self-renewal and differentiation into any cell type, provide a unique tool for understanding the underlying mechanism of development and disease in a dish. N6-methyl-adenosine (m6A) modification is the most extensive internal mRNA modification, which regulates almost all aspects of mRNA metabolism and thus extensively participates in gene expression regulation. However, the role of m6A during cardiogenesis still needs to be fully elucidated. Here, we found that core components of m6A methyltransferase decreased during cardiomyocyte differentiation. Impeding m6A deposition, by either deleting the m6A methyltransferase Mettl3 or overexpressing m6A demethylase alkB homolog 5 (Alkbh5), at early stages of cardiac differentiation of mouse pluripotent stem cells, led to inhibition of cardiac gene activation and retardation of the outgrowth of embryoid bodies, whereas interfering m6A modification at later stages of differentiation had minimal effects. Consistently, stage-specific inhibition of METTL3 with METTL3 inhibitor STM2457 during human ESCs (hESCs) cardiac differentiation demonstrated a similarly pivotal role of METTL3 for the induction of mesodermal cells while dispensable function for later stages. In summary, our study reveals a stage-specific requirement of m6A on the cardiac differentiation of pluripotent stem cells and demonstrates that precise tuning of m6A level is critical for cardiac differentiation.
Collapse
Affiliation(s)
- Shuai Dong
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuetong Sun
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chang Liu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanli Li
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shanshan Yu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qi Zhang
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Cell-gene Therapy Translational Medicine Research Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yan Xu
- Biotherapy Centre, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
11
|
Yasmin IA, Dharmarajan A, Warrier S. iPSC-Derived Glioblastoma Cells Have Enhanced Stemness Wnt/β-Catenin Activity Which Is Negatively Regulated by Wnt Antagonist sFRP4. Cancers (Basel) 2023; 15:3622. [PMID: 37509281 PMCID: PMC10377620 DOI: 10.3390/cancers15143622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Growing evidence indicates that cancer stem cells (CSCs) endow the tumor with stem-like properties. Recently, induced pluripotent stem cells (iPSCs) have gained increased attention because of their easy derivation and availability and their potential to differentiate into any cell type. A CSC model derived from iPSCs of human origin would help understand the driving force of tumor initiation and early progression. We report the efficient generation of feeder-free SSEA4, TRA-1-60 and TRA-1-81 positive iPSCs from amniotic membrane-derived mesenchymal stem cells (AMMSCs), which successfully differentiated into three germ layers. We then developed human iPSC-derived glioblastoma multiforme (GBM) model using conditioned media (CM) from U87MG cell line and CSCs derived from U87MG, which confer iPSCs with GBM and GSC-like phenotypes within five days. Both cell types overexpress MGMT and GLI2, but only GSCs overexpress CD133, CD44, ABCG2 and ABCC2. We also observed overexpression of LEF1 and β-catenin in both cell types. Down-regulation of Wnt antagonist secreted frizzled-related protein 4 (sFRP4) in GBM and GSCs, indicating activation of the Wnt/β-catenin pathway, which could be involved in the conversion of iPSCs to CSCs. From future perspectives, our study will help in the creation of a rapid cell-based platform for understanding the complexity of GBM.
Collapse
Affiliation(s)
- Ishmat Ara Yasmin
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore 560 065, India
| | - Arun Dharmarajan
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai 600 116, India
- School of Human Sciences, Faculty of Life and Physical Sciences, The University of Western Australia, Perth, WA 6009, Australia
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia
| | - Sudha Warrier
- Division of Cancer Stem Cells and Cardiovascular Regeneration, Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore 560 065, India
- Department of Biomedical Sciences, Faculty of Biomedical Sciences and Technology, Sri Ramachandra Institute of Higher Education and Research, Chennai 600 116, India
- Cuor Stem Cellutions Pvt Ltd., Manipal Institute of Regenerative Medicine, Manipal Academy of Higher Education (MAHE), Bangalore 560 065, India
| |
Collapse
|
12
|
Pal S, Biswas D. Promoter-proximal regulation of gene transcription: Key factors involved and emerging role of general transcription factors in assisting productive elongation. Gene 2023:147571. [PMID: 37331491 DOI: 10.1016/j.gene.2023.147571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/20/2023]
Abstract
The pausing of RNA polymerase II (Pol II) at the promoter-proximal sites is a key rate-limiting step in gene expression. Cells have dedicated a specific set of proteins that sequentially establish pause and then release the Pol II from promoter-proximal sites. A well-controlled pausing and subsequent release of Pol II is crucial for thefine tuning of expression of genes including signal-responsive and developmentally-regulated ones. The release of paused Pol II broadly involves its transition from initiation to elongation. In this review article, we will discuss the phenomenon of Pol II pausing, the underlying mechanism, and also the role of different known factors, with an emphasis on general transcription factors, involved in this overall regulation. We will further discuss some recent findings suggesting a possible role (underexplored) of initiation factors in assisting the transition of transcriptionally-engaged paused Pol II into productive elongation.
Collapse
Affiliation(s)
- Sujay Pal
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Debabrata Biswas
- Laboratory of Transcription Biology, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata - 32, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
13
|
Duan W, Yu M, Chen J. BRD4: New Hope in the Battle Against Glioblastoma. Pharmacol Res 2023; 191:106767. [PMID: 37061146 DOI: 10.1016/j.phrs.2023.106767] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
The BET family proteins, comprising BRD2, BRD3 and BRD4, represent epigenetic readers of acetylated histone marks that play pleiotropic roles in the tumorigenesis and growth of multiple human malignancies, including glioblastoma (GBM). A growing body of investigation has proven BET proteins as valuable therapeutic targets for cancer treatment. Recently, several BRD4 inhibitors and degraders have been reported to successfully suppress GBM in preclinical and clinical studies. However, the precise role and mechanism of BRD4 in the pathogenesis of GBM have not been fully elucidated or summarized. This review focuses on summarizing the roles and mechanisms of BRD4 in the context of the initiation and development of GBM. In addition, several BRD4 inhibitors have been evaluated for therapeutic purposes as monotherapy or in combination with chemotherapy, radiotherapy, and immune therapies. Here, we provide a critical appraisal of studies evaluating various BRD4 inhibitors and degraders as novel treatment strategies against GBM.
Collapse
Affiliation(s)
- Weichen Duan
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Miao Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jiajia Chen
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| |
Collapse
|
14
|
Hossain ME, Cevallos RR, Zhang R, Hu K. Attenuating iPSC reprogramming stress with dominant-negative BET peptides. iScience 2023; 26:105889. [PMID: 36691621 PMCID: PMC9860338 DOI: 10.1016/j.isci.2022.105889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/06/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
Generation of induced pluripotent stem cells (iPSCs) is inefficient and stochastic. The underlying causes for these deficiencies are elusive. Here, we showed that the reprogramming factors (OCT4, SOX2, and KLF4, collectively OSK) elicit dramatic reprogramming stress even without the pro-oncogene MYC including massive transcriptional turbulence, massive and random deregulation of stress-response genes, cell cycle impairment, downregulation of mitotic genes, illegitimate reprogramming, and cytotoxicity. The conserved dominant-negative (DN) peptides of the three ubiquitous human bromodomain and extraterminal (BET) proteins enhanced iPSC reprogramming and mitigated all the reprogramming stresses mentioned above. The concept of reprogramming stress developed here affords an alternative avenue to understanding and improving iPSC reprogramming. These DN BET fragments target a similar set of the genes as the BET chemical inhibitors do, indicating a distinct approach to targeting BET proteins.
Collapse
Affiliation(s)
- Md Emon Hossain
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ricardo Raul Cevallos
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ruowen Zhang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kejin Hu
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| |
Collapse
|
15
|
Ji G, Xiao X, Huang M, Wu Q. Jmjd6 regulates ES cell homeostasis and enhances reprogramming efficiency. Heliyon 2022; 8:e09105. [PMID: 35846449 PMCID: PMC9280369 DOI: 10.1016/j.heliyon.2022.e09105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/10/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022] Open
Abstract
Jmjd6 is a conserved nuclear protein which possesses histone arginine demethylation and lysyl hydroxylase activity. Previous studies have revealed that Jmjd6 is essential for cell differentiation and embryo development. However, the role of Jmjd6 in mammalian ES cell identity and reprogramming has been unclear. Here we report that depletion of Jmjd6 not only results in downregulation of pluripotency genes but also is implicated in apoptosis, glycolysis, cell cycle and protein hydroxylation. We also revealed the reduction of BrdU incorporation in Jmjd6 depleted cells. Reprogramming efficiency of MEFs can be enhanced with Jmjd6 overexpression while the efficiency was reduced upon Jmjd6 depletion. Together, these results suggest that Jmjd6 can regulate ES cell homeostasis and enhance somatic cell reprogramming.
Collapse
|
16
|
Li L, Chen K, Wu Y, Xiang G, Liu X. Epigenome-Metabolome-Epigenome signaling cascade in cell biological processes. J Genet Genomics 2021; 49:279-286. [PMID: 34648996 DOI: 10.1016/j.jgg.2021.09.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022]
Abstract
Cell fate determination as a fundamental question in cell biology has been extensively studied at different regulatory levels for many years. However, the mechanisms of multi-level regulation of cell fate determination remain unclear. Recently we have proposed an Epigenome-Metabolome-Epigenome (E-M-E) signaling cascade model to describe the crossover cooperation during mouse somatic cell reprogramming. In this review, we summarize the broad roles of E-M-E signaling cascade in different cell biological processes including cell differentiation and dedifferentiation, cell specialization, cell proliferation and cell pathological processes. Precise E-M-E signaling cascades are critical in these cell biological processes, and it is of worth to explore each step of E-M-E signaling cascade. E-M-E signaling cascade model sheds light on and may open a window to explore the mechanisms of multi-level regulation of cell biological processes.
Collapse
Affiliation(s)
- Linpeng Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Keshi Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yi Wu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ge Xiang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Xingguo Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Medical University; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Guangzhou, 510530, China; Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China.
| |
Collapse
|
17
|
Dey A, Uppal S, Giri J, Misra HS. Emerging roles of bromodomain protein 4 in regulation of stem cell identity. Stem Cells 2021; 39:1615-1624. [PMID: 34520583 DOI: 10.1002/stem.3454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/27/2021] [Indexed: 01/17/2023]
Abstract
Understanding the mechanism of fate decision and lineage commitment is the key step for developing novel stem cell applications in therapeutics. This process is coordinately regulated through systematic epigenetic reprogramming and concomitant changes in the transcriptional landscape of the stem cells. One of the bromo- and extra-terminal domain (BET) family member proteins, bromodomain protein 4 (BRD4), performs the role of epigenetic reader and modulates gene expression by recruiting other transcription factors and directly regulating RNA polymerase II elongation. Controlled gene regulation is the critical step in maintenance of stem cell potency and dysregulation may lead to tumor formation. As a key transcriptional factor and epigenetic regulator, BRD4 contributes to stem cell maintenance in several ways. Being a druggable target, BRD4 is an attractive candidate for exploiting its potential in stem cell therapeutics. Therefore, it is crucial to elucidate how BRD4, through its interplay with pluripotency transcriptional regulators, control lineage commitment in stem cells. Here, we systemically review the role of BRD4 in complex gene regulatory network during three specific states of stem cell transitions: cell differentiation, cell reprogramming and transdifferentiation. A thorough understanding of BRD4 mediated epigenetic regulation in the maintenance of stem cell potency will be helpful to strategically control stem cell fates in regenerative medicine.
Collapse
Affiliation(s)
- Anusree Dey
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Sheetal Uppal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Jayeeta Giri
- TIFR Complex, 605 Raman, Homi Bhabha Road, Navy Nagar, Colaba, Mumbai, India
| | - Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| |
Collapse
|
18
|
Uğurlu-Çimen D, Odluyurt D, Sevinç K, Özkan-Küçük NE, Özçimen B, Demirtaş D, Enüstün E, Aztekin C, Philpott M, Oppermann U, Özlü N, Önder TT. AF10 (MLLT10) prevents somatic cell reprogramming through regulation of DOT1L-mediated H3K79 methylation. Epigenetics Chromatin 2021; 14:32. [PMID: 34215314 PMCID: PMC8254283 DOI: 10.1186/s13072-021-00406-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background The histone H3 lysine 79 (H3K79) methyltransferase DOT1L is a key chromatin-based barrier to somatic cell reprogramming. However, the mechanisms by which DOT1L safeguards cell identity and somatic-specific transcriptional programs remain unknown. Results We employed a proteomic approach using proximity-based labeling to identify DOT1L-interacting proteins and investigated their effects on reprogramming. Among DOT1L interactors, suppression of AF10 (MLLT10) via RNA interference or CRISPR/Cas9, significantly increases reprogramming efficiency. In somatic cells and induced pluripotent stem cells (iPSCs) higher order H3K79 methylation is dependent on AF10 expression. In AF10 knock-out cells, re-expression wild-type AF10, but not a DOT1L binding-impaired mutant, rescues overall H3K79 methylation and reduces reprogramming efficiency. Transcriptomic analyses during reprogramming show that AF10 suppression results in downregulation of fibroblast-specific genes and accelerates the activation of pluripotency-associated genes. Conclusions Our findings establish AF10 as a novel barrier to reprogramming by regulating H3K79 methylation and thereby sheds light on the mechanism by which cell identity is maintained in somatic cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00406-7.
Collapse
Affiliation(s)
| | - Deniz Odluyurt
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Kenan Sevinç
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | | | - Burcu Özçimen
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Deniz Demirtaş
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Eray Enüstün
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | - Can Aztekin
- School of Medicine, Koc University, Istanbul, 34450, Turkey
| | | | - Udo Oppermann
- Botnar Research Centre, University of Oxford, Oxford, UK.,Centre for Medicine Discovery, University of Oxford, Oxford, UK
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
| | - Tamer T Önder
- School of Medicine, Koc University, Istanbul, 34450, Turkey.
| |
Collapse
|
19
|
Ter Huurne M, Stunnenberg HG. G1-phase progression in pluripotent stem cells. Cell Mol Life Sci 2021; 78:4507-4519. [PMID: 33884444 PMCID: PMC8195903 DOI: 10.1007/s00018-021-03797-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/19/2021] [Accepted: 02/19/2021] [Indexed: 11/10/2022]
Abstract
During early embryonic development both the rapid increase in cell number and the expression of genes that control developmental decisions are tightly regulated. Accumulating evidence has indicated that these two seemingly independent processes are mechanistically intertwined. The picture that emerges from studies on the cell cycle of embryonic stem cells is one in which proteins that promote cell cycle progression prevent differentiation and vice versa. Here, we review which transcription factors and signalling pathways play a role in both maintenance of pluripotency as well as cell cycle progression. We will not only describe the mechanism behind their function but also discuss the role of these regulators in different states of mouse pluripotency. Finally, we elaborate on how canonical cell cycle regulators impact on the molecular networks that control the maintenance of pluripotency and lineage specification.
Collapse
Affiliation(s)
- Menno Ter Huurne
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Rd, Parkville, Melbourne, VIC, 3052, Australia
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands.
- Princess Maxima Centre for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
| |
Collapse
|
20
|
Zhang J, Yue W, Zhou Y, Liao M, Chen X, Hua J. Super enhancers-Functional cores under the 3D genome. Cell Prolif 2021; 54:e12970. [PMID: 33336467 PMCID: PMC7848964 DOI: 10.1111/cpr.12970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Complex biochemical reactions take place in the nucleus all the time. Transcription machines must follow the rules. The chromatin state, especially the three-dimensional structure of the genome, plays an important role in gene regulation and expression. The super enhancers are important for defining cell identity in mammalian developmental processes and human diseases. It has been shown that the major components of transcriptional activation complexes are recruited by super enhancer to form phase-separated condensates. We summarize the current knowledge about super enhancer in the 3D genome. Furthermore, a new related transcriptional regulation model from super enhancer is outlined to explain its role in the mammalian cell progress.
Collapse
Affiliation(s)
- Juqing Zhang
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Wei Yue
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Yaqi Zhou
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Mingzhi Liao
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Xingqi Chen
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Jinlian Hua
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| |
Collapse
|
21
|
Arabacı DH, Terzioğlu G, Bayırbaşı B, Önder TT. Going up the hill: chromatin-based barriers to epigenetic reprogramming. FEBS J 2020; 288:4798-4811. [PMID: 33190371 DOI: 10.1111/febs.15628] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/20/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022]
Abstract
The establishment and maintenance of cellular identity are crucial during development and tissue homeostasis. Epigenetic mechanisms based largely on DNA methylation and histone modifications serve to reinforce and safeguard differentiated cell states. Somatic cell nuclear transfer (SCNT) or transcription factors such as Oct4, Sox2, Klf4, c-MYC (OSKM) can erase somatic cell identity and reprogram the cells to a pluripotent state. In doing so, reprogramming must reset the chromatin landscape, silence somatic-specific gene expression programs, and, in their place, activate the pluripotency network. In this viewpoint, we consider the major chromatin-based barriers for reprogramming of somatic cells to pluripotency. Among these, repressive chromatin modifications such as DNA methylation, H3K9 methylation, variant histone deposition, and histone deacetylation generally block the activation of pluripotency genes. In contrast, active transcription-associated chromatin marks such as DOT1L-catalyzed H3K79 methylation, FACT-mediated histone turnover, active enhancer SUMOylation, and EP300/CBP bromodomain-mediated interactions act to maintain somatic-specific gene expression programs. We highlight how genetic or chemical inhibition of both types of barriers can enhance the kinetics and/or efficiency of reprogramming. Understanding the mechanisms by which these barriers function provides insight into how chromatin marks help maintain cell identity.
Collapse
Affiliation(s)
| | | | | | - Tamer T Önder
- School of Medicine, Koç University, Istanbul, Turkey
| |
Collapse
|
22
|
Huang Y, Zhang H, Wang L, Tang C, Qin X, Wu X, Pan M, Tang Y, Yang Z, Babarinde IA, Lin R, Ji G, Lai Y, Xu X, Su J, Wen X, Satoh T, Ahmed T, Malik V, Ward C, Volpe G, Guo L, Chen J, Sun L, Li Y, Huang X, Bao X, Gao F, Liu B, Zheng H, Jauch R, Lai L, Pan G, Chen J, Testa G, Akira S, Hu J, Pei D, Hutchins AP, Esteban MA, Qin B. JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency. Nat Commun 2020; 11:5061. [PMID: 33033262 PMCID: PMC7545202 DOI: 10.1038/s41467-020-18900-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) and transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that the histone H3 lysine 27 trimethylation (H3K27me3) demethylase JMJD3 plays conflicting roles in mouse reprogramming. On one side, JMJD3 induces the pro-senescence factor Ink4a and degrades the pluripotency regulator PHF20 in a reprogramming factor-independent manner. On the other side, JMJD3 is specifically recruited by KLF4 to reduce H3K27me3 at both enhancers and promoters of epithelial and pluripotency genes. JMJD3 also promotes enhancer-promoter looping through the cohesin loading factor NIPBL and ultimately transcriptional elongation. This competition of forces can be shifted towards improved reprogramming by using early passage fibroblasts or boosting JMJD3’s catalytic activity with vitamin C. Our work, thus, establishes a multifaceted role for JMJD3, placing it as a key partner of KLF4 and a scaffold that assists chromatin interactions and activates gene transcription. Previous work suggested that histone demethylase JMJD3 is detrimental to somatic cell reprogramming. Here, the authors show that while JMJD3 has a context-independent detrimental effect on early stages of reprogramming, during late stages it activates epithelial and pluripotency genes together with Klf4.
Collapse
Affiliation(s)
- Yinghua Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Hui Zhang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China
| | - Lulu Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Chuanqing Tang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Xiaogan Qin
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Xinyu Wu
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Meifang Pan
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yujia Tang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Zhongzhou Yang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Isaac A Babarinde
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Runxia Lin
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guanyu Ji
- Science and Technology Department, E-GENE, 518118, Shenzhen, China
| | - Yiwei Lai
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Xueting Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China.,School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China
| | - Jianbin Su
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Xue Wen
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 130061, Changchun, China
| | - Takashi Satoh
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Tanveer Ahmed
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China
| | - Vikas Malik
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Carl Ward
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Giacomo Volpe
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China
| | - Lin Guo
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Jinlong Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Li Sun
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yingying Li
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China
| | - Xiaofen Huang
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China
| | - Xichen Bao
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Fei Gao
- Science and Technology Department, E-GENE, 518118, Shenzhen, China.,Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Baohua Liu
- Health Science Center, Shenzhen University, 518060, Shenzhen, China
| | - Hui Zheng
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Liangxue Lai
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Guangjin Pan
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Jiekai Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China.,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology, Milan, 20139, Italy
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka, 565-0871, Japan
| | - Jifan Hu
- Stem Cell and Cancer Center, First Affiliated Hospital, Jilin University, 130061, Changchun, China
| | - Duanqing Pei
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Miguel A Esteban
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China. .,Laboratory of Integrative Biology, GIBH, CAS, 510530, Guangzhou, China. .,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China. .,Institute for Stem Cells and Regeneration, CAS, 100101, Beijing, China.
| | - Baoming Qin
- Chinese Academy of Sciences (CAS) Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health (GIBH), CAS, 510530, Guangzhou, China. .,Laboratory of Metabolism and Cell Fate, GIBH, CAS, 510530, Guangzhou, China. .,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), 510005, Guangzhou, China. .,Joint School of Life Sciences, GIBH and Guangzhou Medical University, 511436, Guangzhou, China.
| |
Collapse
|
23
|
Zhang M, Lai Y, Krupalnik V, Guo P, Guo X, Zhou J, Xu Y, Yu Z, Liu L, Jiang A, Li W, Abdul MM, Ma G, Li N, Fu X, Lv Y, Jiang M, Tariq M, Kanwal S, Liu H, Xu X, Zhang H, Huang Y, Wang L, Chen S, Babarinde IA, Luo Z, Wang D, Zhou T, Ward C, He M, Ibañez DP, Li Y, Zhou J, Yuan J, Feng Y, Arumugam K, Di Vicino U, Bao X, Wu G, Schambach A, Wang H, Sun H, Gao F, Qin B, Hutchins AP, Doble BW, Hartmann C, Cosma MP, Qin Y, Xu GL, Chen R, Volpe G, Chen L, Hanna JH, Esteban MA. β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus. SCIENCE ADVANCES 2020; 6:eaba1593. [PMID: 32832621 PMCID: PMC7439582 DOI: 10.1126/sciadv.aba1593] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 06/05/2020] [Indexed: 05/12/2023]
Abstract
Mouse embryonic stem cells cultured with MEK (mitogen-activated protein kinase kinase) and GSK3 (glycogen synthase kinase 3) inhibitors (2i) more closely resemble the inner cell mass of preimplantation blastocysts than those cultured with SL [serum/leukemia inhibitory factor (LIF)]. The transcriptional mechanisms governing this pluripotent ground state are unresolved. Release of promoter-proximal paused RNA polymerase II (Pol2) is a multistep process necessary for pluripotency and cell cycle gene transcription in SL. We show that β-catenin, stabilized by GSK3 inhibition in medium with 2i, supplies transcriptional coregulators at pluripotency loci. This selectively strengthens pluripotency loci and renders them addicted to transcription initiation for productive gene body elongation in detriment to Pol2 pause release. By contrast, cell cycle genes are not bound by β-catenin, and proliferation/self-renewal remains tightly controlled by Pol2 pause release under 2i conditions. Our findings explain how pluripotency is reinforced in the ground state and also provide a general model for transcriptional resilience/adaptation upon network perturbation in other contexts.
Collapse
Affiliation(s)
- Meng Zhang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Yiwei Lai
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Pengcheng Guo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Xiangpeng Guo
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Jianguo Zhou
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Yan Xu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhijun Yu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Longqi Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Ao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenjuan Li
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Mazid Md. Abdul
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Gang Ma
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Na Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Xiuling Fu
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuan Lv
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Mengling Jiang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Muqddas Tariq
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Shahzina Kanwal
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Hao Liu
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Xueting Xu
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hui Zhang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yinghua Huang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lulu Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Shuhan Chen
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Isaac A. Babarinde
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Zhiwei Luo
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Guangzhou Medical University, Guangzhou 511436, China
| | - Dongye Wang
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Tiantian Zhou
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Minghui He
- Forevergen Biosciences Center, Guangzhou 510000, China
| | - David P. Ibañez
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Yunpan Li
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Jiajian Zhou
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yayan Feng
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Karthik Arumugam
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Umberto Di Vicino
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Xichen Bao
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Guangming Wu
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
| | - Axel Schambach
- Hannover Medical School, Institute of Experimental Hematology, Hannover 30625, Germany
- Division of Hematology and Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg DK1870C, Denmark
| | - Baoming Qin
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Laboratory of Metabolism and Cell Fate, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Andrew P. Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bradley W. Doble
- Departments of Pediatrics and Child Health and Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0W2, Canada
| | - Christine Hartmann
- Department of Bone and Skeletal Research, Institute of Musculoskeletal Medicine, Medical Faculty of the University of Münster, Münster D-48149, Germany
| | - Maria Pia Cosma
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08003, Spain
| | - Yan Qin
- University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Laboratory of Metabolism and Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Shanghai 200032, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Giacomo Volpe
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
| | - Liang Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Corresponding author. (M.A.E.); (J.H.H.); (L.C.)
| | - Jacob H. Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
- Corresponding author. (M.A.E.); (J.H.H.); (L.C.)
| | - Miguel A. Esteban
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510005, China
- Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 511436, China
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding author. (M.A.E.); (J.H.H.); (L.C.)
| |
Collapse
|
24
|
Bacon CW, Challa A, Hyder U, Shukla A, Borkar AN, Bayo J, Liu J, Wu SY, Chiang CM, Kutateladze TG, D'Orso I. KAP1 Is a Chromatin Reader that Couples Steps of RNA Polymerase II Transcription to Sustain Oncogenic Programs. Mol Cell 2020; 78:1133-1151.e14. [PMID: 32402252 PMCID: PMC7305985 DOI: 10.1016/j.molcel.2020.04.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/25/2020] [Accepted: 04/17/2020] [Indexed: 01/08/2023]
Abstract
Precise control of the RNA polymerase II (RNA Pol II) cycle, including pausing and pause release, maintains transcriptional homeostasis and organismal functions. Despite previous work to understand individual transcription steps, we reveal a mechanism that integrates RNA Pol II cycle transitions. Surprisingly, KAP1/TRIM28 uses a previously uncharacterized chromatin reader cassette to bind hypo-acetylated histone 4 tails at promoters, guaranteeing continuous progression of RNA Pol II entry to and exit from the pause state. Upon chromatin docking, KAP1 first associates with RNA Pol II and then recruits a pathway-specific transcription factor (SMAD2) in response to cognate ligands, enabling gene-selective CDK9-dependent pause release. This coupling mechanism is exploited by tumor cells to aberrantly sustain transcriptional programs commonly dysregulated in cancer patients. The discovery of a factor integrating transcription steps expands the functional repertoire by which chromatin readers operate and provides mechanistic understanding of transcription regulation, offering alternative therapeutic opportunities to target transcriptional dysregulation.
Collapse
Affiliation(s)
- Curtis W Bacon
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Biological Chemistry Graduate Program, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashwini Challa
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Usman Hyder
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ashutosh Shukla
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aditi N Borkar
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Juan Bayo
- Instituto de Investigaciones en Medicina Traslacional, Facultad de Ciencias Biomédicas, CONICET, Universidad Austral, Derqui-Pilar, Buenos Aires 1629, Argentina
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Shwu-Yuan Wu
- Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng-Ming Chiang
- Harold C. Simmons Comprehensive Cancer Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Iván D'Orso
- Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
25
|
Li Y, Song Y, Xu W, Li Q, Wang X, Li K, Wang J, Liu Z, Velychko S, Ye R, Xia Q, Wang L, Guo R, Dong X, Zheng Z, Dai Y, Li H, Yao M, Xue Y, Schöler HR, Sun Q, Yao H. R-loops coordinate with SOX2 in regulating reprogramming to pluripotency. SCIENCE ADVANCES 2020; 6:eaba0777. [PMID: 32704541 PMCID: PMC7360481 DOI: 10.1126/sciadv.aba0777] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/09/2020] [Indexed: 05/06/2023]
Abstract
R-loops modulate genome stability and regulate gene expression, but the functions and the regulatory mechanisms of R-loops in stem cell biology are still unclear. Here, we profiled R-loops during somatic cell reprogramming and found that dynamic changes in R-loops are essential for reprogramming and occurred before changes in gene expression. Disrupting the homeostasis of R-loops by depleting RNaseH1 or catalytic inactivation of RNaseH1 at D209 (RNaseH1D209N) blocks reprogramming. Sox2, but not any other factor in the Yamanaka cocktail, overcomes the inhibitory effects of RNaseH1 activity loss on reprogramming. Sox2 interacts with the reprogramming barrier factor Ddx5 and inhibits the resolvase activity of Ddx5 on R-loops and thus facilitates reprogramming. Furthermore, reprogramming efficiency can be modulated by dCas9-mediated RNaseH1/RNaseH1D209N targeting the specific R-loop regions. Together, these results show that R-loops play important roles in reprogramming and shed light on the regulatory module of Sox2/Ddx5 on R-loops during reprogramming.
Collapse
Affiliation(s)
- Yaoyi Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yawei Song
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Xu
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qin Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xinxiu Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Kuan Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Juehan Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zicong Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Medical Faculty, University of Muenster, Münster 48149, Germany
| | - Rong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Xia
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaotao Dong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhikai Zheng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yushuang Dai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Haojie Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingze Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hans R. Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Medical Faculty, University of Muenster, Münster 48149, Germany
- Medical Faculty, University of Muenster, Domagkstrasse 3, 48149 Muenster, Germany
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Corresponding author. (Q.S.); (H.Y.)
| | - Hongjie Yao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- Guangzhou Regenerative Medicine and Health GuangDong Laboratory (GRMH-GDL), Guangzhou 510005, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding author. (Q.S.); (H.Y.)
| |
Collapse
|
26
|
Negative elongation factor complex enables macrophage inflammatory responses by controlling anti-inflammatory gene expression. Nat Commun 2020; 11:2286. [PMID: 32385332 PMCID: PMC7210294 DOI: 10.1038/s41467-020-16209-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 04/21/2020] [Indexed: 01/06/2023] Open
Abstract
Studies on macrophage gene expression have historically focused on events leading to RNA polymerase II recruitment and transcription initiation, whereas the contribution of post-initiation steps to macrophage activation remains poorly understood. Here, we report that widespread promoter-proximal RNA polymerase II pausing in resting macrophages is marked by co-localization of the negative elongation factor (NELF) complex and facilitated by PU.1. Upon inflammatory stimulation, over 60% of activated transcriptome is regulated by polymerase pause-release and a transient genome-wide NELF dissociation from chromatin, unexpectedly, independent of CDK9, a presumed NELF kinase. Genetic disruption of NELF in macrophages enhanced transcription of AP-1-encoding Fos and Jun and, consequently, AP-1 targets including Il10. Augmented expression of IL-10, a critical anti-inflammatory cytokine, in turn, attenuated production of pro-inflammatory mediators and, ultimately, macrophage-mediated inflammation in vivo. Together, these findings establish a previously unappreciated role of NELF in constraining transcription of inflammation inhibitors thereby enabling inflammatory macrophage activation. Macrophage activation is integral to innate immunity and inflammation, and involves transcriptome remodeling leading to the rapid upregulation of pro- and anti-inflammatory effector genes. Here the authors show that the negative elongation factor (NELF) complex controls the transcription of anti-inflammatory genes through Pol II pause release.
Collapse
|
27
|
Wang Y, Qiu T. Positive transcription elongation factor b and its regulators in development. ALL LIFE 2020. [DOI: 10.1080/21553769.2019.1663277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Yan Wang
- Department of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People’s Republic of China
| | - Tong Qiu
- Department of Pediatrics, West China Second University Hospital, Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, People’s Republic of China
| |
Collapse
|
28
|
DNA methylation directs microRNA biogenesis in mammalian cells. Nat Commun 2019; 10:5657. [PMID: 31827083 PMCID: PMC6906426 DOI: 10.1038/s41467-019-13527-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 10/28/2019] [Indexed: 12/19/2022] Open
Abstract
MicroRNA (miRNA) biogenesis initiates co-transcriptionally, but how the Microprocessor machinery pinpoints the locations of short precursor miRNA sequences within long flanking regions of the transcript is not known. Here we show that miRNA biogenesis depends on DNA methylation. When the regions flanking the miRNA coding sequence are highly methylated, the miRNAs are more highly expressed, have greater sequence conservation, and are more likely to drive cancer-related phenotypes than miRNAs encoded by unmethylated loci. We show that the removal of DNA methylation from miRNA loci leads to their downregulation. Further, we found that MeCP2 binding to methylated miRNA loci halts RNA polymerase II elongation, leading to enhanced processing of the primary miRNA by Drosha. Taken together, our data reveal that DNA methylation directly affects miRNA biogenesis.
Collapse
|
29
|
Vanheer L, Song J, De Geest N, Janiszewski A, Talon I, Provenzano C, Oh T, Chappell J, Pasque V. Tox4 modulates cell fate reprogramming. J Cell Sci 2019; 132:jcs.232223. [PMID: 31519808 PMCID: PMC6826012 DOI: 10.1242/jcs.232223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/06/2019] [Indexed: 01/05/2023] Open
Abstract
Reprogramming to induced pluripotency induces the switch of somatic cell identity to induced pluripotent stem cells (iPSCs). However, the mediators and mechanisms of reprogramming remain largely unclear. To elucidate the mediators and mechanisms of reprogramming, we used a siRNA-mediated knockdown approach for selected candidate genes during the conversion of somatic cells into iPSCs. We identified Tox4 as a novel factor that modulates cell fate through an assay that determined the efficiency of iPSC reprogramming. We found that Tox4 is needed early in reprogramming to efficiently generate early reprogramming intermediates, irrespective of the reprogramming conditions used. Tox4 enables proper exogenous reprogramming factor expression, and the closing and opening of putative somatic and pluripotency enhancers early during reprogramming, respectively. We show that the TOX4 protein assembles into a high molecular form. Moreover, Tox4 is also required for the efficient conversion of fibroblasts towards the neuronal fate, suggesting a broader role of Tox4 in modulating cell fate. Our study reveals Tox4 as a novel transcriptional modulator of cell fate that mediates reprogramming from the somatic state to the pluripotent and neuronal fate.This article has an associated First Person interview with the first author of the paper.
Collapse
Affiliation(s)
- Lotte Vanheer
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Juan Song
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Natalie De Geest
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Adrian Janiszewski
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Irene Talon
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Caterina Provenzano
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Taeho Oh
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Joel Chappell
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| | - Vincent Pasque
- KU Leuven - University of Leuven, Department of Development and Regeneration, Herestraat 49, B-3000 Leuven, Belgium
| |
Collapse
|
30
|
Zhang S, Zhao Y, Heaster TM, Fischer MA, Stengel KR, Zhou X, Ramsey H, Zhou MM, Savona MR, Skala MC, Hiebert SW. BET inhibitors reduce cell size and induce reversible cell cycle arrest in AML. J Cell Biochem 2019; 120:7309-7322. [PMID: 30417424 PMCID: PMC6513713 DOI: 10.1002/jcb.28005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
Inhibitors of the bromodomain and extraterminal domain family (BETi) offer a new approach to treat hematological malignancies, with leukemias containing mixed lineage leukemia rearrangements being especially sensitive due to a reliance on the regulation of transcription elongation. We explored the mechanism of action of BETi in cells expressing the t(8;21), and show that these compounds reduced the size of acute myeloid leukemia cells, triggered a rapid but reversible G0 /G1 arrest, and with time, cause cell death. Meta-analysis of PRO-seq data identified ribosomal genes, which are regulated by MYC, were downregulated within 3 hours of addition of the BETi. This reduction of MYC regulated metabolic genes coincided with the loss of mitochondrial respiration and large reductions in the glycolytic rate. In addition, gene expression analysis showed that transcription of BCL2 was rapidly affected by BETi but this did not cause dramatic increases in cell death. Cell cycle arrest, lowered metabolic activity, and reduced BCL2 levels suggested that a second compound was needed to push these cells over the apoptotic threshold. Indeed, low doses of the BCL2 inhibitor, venetoclax, in combination with the BETi was a potent combination in t(8;21) containing cells. Thus, BET inhibitors that affect MYC and BCL2 expression should be considered for combination therapy with venetoclax.
Collapse
Affiliation(s)
- Susu Zhang
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Tiffany M. Heaster
- Morgridge Institute for Research and the Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Melissa A. Fischer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Kristy R. Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Haley Ramsey
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Michael R. Savona
- Morgridge Institute for Research and the Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706;,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37027
| | - Melissa C. Skala
- Morgridge Institute for Research and the Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706
| | - Scott W. Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232;,Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37027,To whom correspondence should be sent: Department of Biochemistry, 512 Preston Research Building, Vanderbilt University School of Medicine, 2220 Pierce Ave., Nashville Tennessee, 37232, Phone: (615) 936-3582; Fax: (615) 936-1790;
| |
Collapse
|
31
|
He M, Huang TS, Li S, Hong HC, Chen Z, Martin M, Zhou X, Huang HY, Su SH, Zhang J, Wang WT, Kang J, Huang HD, Zhang J, Chien S, Shyy JYJ. Atheroprotective Flow Upregulates ITPR3 (Inositol 1,4,5-Trisphosphate Receptor 3) in Vascular Endothelium via KLF4 (Krüppel-Like Factor 4)-Mediated Histone Modifications. Arterioscler Thromb Vasc Biol 2019; 39:902-914. [PMID: 30917677 PMCID: PMC6536300 DOI: 10.1161/atvbaha.118.312301] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objective- The topographical distribution of atherosclerosis in vasculature underscores the importance of shear stress in regulating endothelium. With a systems approach integrating sequencing data, the current study aims to explore the link between shear stress-regulated master transcription factor and its regulation of endothelial cell (EC) function via epigenetic modifications. Approach and Results- H3K27ac (acetylation of histone 3 lysine 27)-ChIP-seq (chromatin immunoprecipitation followed by high throughput sequencing), ATAC-seq (an assay for transposase-accessible chromatin-sequencing), and RNA-seq (RNA-sequencing) were performed to investigate the genome-wide epigenetic regulations in ECs in response to atheroprotective pulsatile shear stress (PS). In silico prediction revealed that KLF4 binding motifs were enriched in the PS-enhanced H3K27ac regions. By integrating PS- and KLF4-modulated H3K27ac, we identified 18 novel PS-upregulated genes. The promoter regions of these genes showed an overlap between the KLF4-enhanced assay for transposase-accessible chromatin signals and the PS-induced H3K27ac peaks. Experiments using ECs isolated from mouse aorta, lung ECs from EC-KLF4-TG versus EC-KLF4-KO mice, and atorvastatin-treated ECs showed that ITPR3 (inositol 1,4,5-trisphosphate receptor 3) was robustly activated by KLF4 and statins. KLF4 ATAC-qPCR (quantitative polymerase chain reaction) and ChIP-qPCR further demonstrated that a specific locus in the promoter region of the ITPR3 gene was essential for KLF4 binding, H3K27ac enrichment, chromatin accessibility, RNA polymerase II recruitment, and ITPR3 transcriptional activation. Deletion of this KLF4 binding locus in ECs by using CRISPR-Cas9 resulted in blunted calcium influx, reduced expression of endothelial nitric oxide synthase, and diminished nitric oxide bioavailability. Conclusions- These results from a novel multiomics study suggest that KLF4 is crucial for PS-modulated H3K27ac that allow the transcriptional activation of ITPR3. This novel mechanism contributes to the Ca2+-dependent eNOS (endothelial nitric oxide synthase) activation and EC homeostasis.
Collapse
Affiliation(s)
| | | | - Shuai Li
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Hsiao-Chin Hong
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Zhen Chen
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Marcy Martin
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Xin Zhou
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Hsi-Yuan Huang
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Shu-Han Su
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Jiao Zhang
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Wei-Ting Wang
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Jian Kang
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Hsien-Da Huang
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Jin Zhang
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - Shu Chien
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| | - John Y-J. Shyy
- Department of Medicine (M.H., S.L., H.-C.H., Z.C., M.M., H.-Y.H., S.-H.S., Jiao Zhang, W.-T.W., J.K., S.C., J.Y-J.S.), Department of Bioengineering and Institute of Engineering in Medicine (T.-S.H., S.C.), Department of Pharmacology (X.Z., Jin Zhang.), University of California, San Diego, and Institute of Bioinformatics and Systems Biology (H.-C.H., H.-Y.H., H.-D.H.), Department of Biological Science and Technology (W.-T.W.), National Chiao Tung University, Hsin-Chu, Taiwan
| |
Collapse
|
32
|
Nimmakayala RK, Seshacharyulu P, Lakshmanan I, Rachagani S, Chugh S, Karmakar S, Rauth S, Vengoji R, Atri P, Talmon GA, Lele SM, Smith LM, Thapa I, Bastola D, Ouellette MM, Batra SK, Ponnusamy MP. Cigarette Smoke Induces Stem Cell Features of Pancreatic Cancer Cells via PAF1. Gastroenterology 2018; 155:892-908.e6. [PMID: 29864419 PMCID: PMC6120776 DOI: 10.1053/j.gastro.2018.05.041] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 05/08/2018] [Accepted: 05/30/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Cigarette smoking is a major risk factor for pancreatic cancer. Aggressive pancreatic tumors contain cancer cells with stem cell features. We investigated whether cigarette smoke induces stem cell features in pancreatic cancer cells. METHODS KrasG12D; Pdx1-Cre mice were exposed to cigarette smoke or clean air (controls) for up to 20 weeks; pancreata were collected and analyzed by histology, quantitative reverse transcription polymerase chain reaction, and confocal immunofluorescence microscopy. HPNE and Capan1 cells were exposed to cigarette smoke extract (CSE), nicotine and nicotine-derived carcinogens (NNN or NNK), or clean air (controls) for 80 days and evaluated for stem cell markers and features using flow cytometry-based autofluorescence, sphere formation, and immunoblot assays. Proteins were knocked down in cells with small interfering RNAs. We performed RNA sequencing analyses of CSE-exposed cells. We used chromatin immunoprecipitation assays to confirm the binding of FOS-like 1, AP-1 transcription factor subunit (FOSL1) to RNA polymerase II-associated factor (PAF1) promoter. We obtained pancreatic ductal adenocarcinoma (PDAC) and matched nontumor tissues (n = 15) and performed immunohistochemical analyses. RESULTS Chronic exposure of HPNE and Capan1 cells to CSE caused them to increase markers of stem cells, including autofluorescence and sphere formation, compared with control cells. These cells increased expression of ABCG2, SOX9, and PAF1, via cholinergic receptor nicotinic alpha 7 subunit (CHRNA7) signaling to mitogen-activated protein kinase 1 and FOSL1. CSE-exposed pancreatic cells with knockdown of PAF1 did not show stem cell features. Exposure of cells to NNN and NNK led to increased expression of CHRNA7, FOSL1, and PAF1 along with stem cell features. Pancreata from KrasG12D; Pdx1-Cre mice exposed to cigarette smoke had increased levels of PAF1 mRNA and protein, compared with control mice, as well as increased expression of SOX9. Levels of PAF1 and FOSL1 were increased in PDAC tissues, especially those from smokers, compared with nontumor pancreatic tissue. CSE exposure increased expression of PHD-finger protein 5A, a pluripotent transcription factor and its interaction with PAF1. CONCLUSIONS Exposure to cigarette smoke activates stem cell features of pancreatic cells, via CHRNA7 signaling and FOSL1 activation of PAF1 expression. Levels of PAF1 are increased in pancreatic tumors of humans and mice with chronic cigarette smoke exposure.
Collapse
Affiliation(s)
- Rama Krishna Nimmakayala
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Parthasarathy Seshacharyulu
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Satyanarayana Rachagani
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Seema Chugh
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Saswati Karmakar
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Sanchita Rauth
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Raghupathy Vengoji
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA
| | - Geoffrey A. Talmon
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Subodh M. Lele
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Lynette M. Smith
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center, Omaha, NE
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, NE
| | - Dhundy Bastola
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, NE
| | - Michel M. Ouellette
- Department of Internal Medicine, College of Medicine, University of Nebraska medical Center, Omaha, NE
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE,Correspondence: Moorthy P. Ponnusamy and Surinder K. Batra, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5870, U.S.A., Phone: 402-559-1170, Fax: 402-559-6650, (M.P.P) and (S.K.B)
| | - Moorthy P. Ponnusamy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198-5870, USA,Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE,Correspondence: Moorthy P. Ponnusamy and Surinder K. Batra, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, 68198-5870, U.S.A., Phone: 402-559-1170, Fax: 402-559-6650, (M.P.P) and (S.K.B)
| |
Collapse
|
33
|
Apostolou E, Stadtfeld M. Cellular trajectories and molecular mechanisms of iPSC reprogramming. Curr Opin Genet Dev 2018; 52:77-85. [PMID: 29925040 DOI: 10.1016/j.gde.2018.06.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 12/30/2022]
Abstract
The discovery of induced pluripotent stem cells (iPSCs) has solidified the concept of transcription factors as major players in controlling cell identity and provided a tractable tool to study how somatic cell identity can be dismantled and pluripotency established. A number of landmark studies have established hallmarks and roadmaps of iPSC formation by describing relative kinetics of transcriptional, protein and epigenetic changes, including alterations in DNA methylation and histone modifications. Recently, technological advancements such as single-cell analyses, high-resolution genome-wide chromatin assays and more efficient reprogramming systems have been used to challenge and refine our understanding of the reprogramming process. Here, we will outline novel insights into the molecular mechanisms underlying iPSC formation, focusing on how the core reprogramming factors OCT4, KLF4, SOX2 and MYC (OKSM) drive changes in gene expression, chromatin state and 3D genome topology. In addition, we will discuss unexpected consequences of reprogramming factor expression in in vitro and in vivo systems that may point towards new applications of iPSC technology.
Collapse
Affiliation(s)
- Effie Apostolou
- Edward and Sandra Meyer Cancer Center and Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Matthias Stadtfeld
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology and Helen L. and Martin S. Kimmel Center for Biology and Medicine, NYU School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
34
|
Im JH, Hwang SI, Kim JW, Park SJ, Kang KR, You JS, Kim KP, Moon SH, Cha HJ, Chung HM, Schöler HR, Hyun JK, Han DW. Inhibition of BET selectively eliminates undifferentiated pluripotent stem cells. Sci Bull (Beijing) 2018; 63:477-487. [PMID: 36658808 DOI: 10.1016/j.scib.2018.02.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/06/2018] [Accepted: 02/27/2018] [Indexed: 01/21/2023]
Abstract
Embryonic stem cells (ESCs) maintain their cellular identity through the systematic regulation of master transcription factors and chromatin remodeling complexes. Recent work has shown that the unusually large-scale enhancers-namely super-enhancers (SEs), on which BRD4, a member of the bromodomain and extraterminal domain (BET) family is highly enriched-could regulate pluripotency-related transcription factors. Moreover, inhibition of BRD4 binding on SEs has been shown to induce the differentiation of ESCs. However, the underlying mechanism of BRD4 inhibition-mediated stem cell differentiation remains elusive. Here we show that both mouse and human ESCs lose their capacity for self-renewal upon treatment with JQ1, a selective inhibitor of BET family including BRD4, with rapid suppression of pluripotency-associated genes. Notably, a high concentration of JQ1 could selectively eliminate ESCs via apoptosis, without affecting the functionality of differentiated somatic cells from ESCs, suggesting that inhibition of BET may have a beneficial effect on the development of pluripotent stem cell-based cell therapy.
Collapse
Affiliation(s)
- Jung Hyun Im
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Seon In Hwang
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Jong-Wan Kim
- Department of Nanobiomedical Science, Dankook University Graduate School, Cheonan 330714, Republic of Korea
| | - Soon-Jung Park
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Kyu-Ree Kang
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Jueng Soo You
- Department of Biochemistry, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Kee Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Sung-Hwan Moon
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Hyuk-Jin Cha
- Department of Life Sciences, College of Natural Sciences, Sogang University, Seoul 04107, Republic of Korea
| | - Hyung-Min Chung
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Hans R Schöler
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea; Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Jung Keun Hyun
- Department of Nanobiomedical Science, Dankook University Graduate School, Cheonan 330714, Republic of Korea
| | - Dong Wook Han
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea; KU Open-Innovation Center, Institute of Biomedical Science & Technology, Konkuk University, Seoul 05029, Republic of Korea; Department of Advanced Translational Medicine, School of Medicine, Konkuk University, Seoul 05029, Republic of Korea.
| |
Collapse
|
35
|
Ye B, Liu B, Hao L, Zhu X, Yang L, Wang S, Xia P, Du Y, Meng S, Huang G, Qin X, Wang Y, Yan X, Li C, Hao J, Zhu P, He L, Tian Y, Fan Z. Klf4 glutamylation is required for cell reprogramming and early embryonic development in mice. Nat Commun 2018; 9:1261. [PMID: 29593216 PMCID: PMC5871780 DOI: 10.1038/s41467-018-03008-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/10/2018] [Indexed: 12/20/2022] Open
Abstract
Temporal and spatial-specific regulation of pluripotency networks is largely dependent on the precise modifications of core transcription factors. Misregulation of glutamylation is implicated in severe physiological abnormalities. However, how glutamylation regulates cell reprogramming and pluripotency networks remains elusive. Here we show that cytosolic carboxypeptidases 1 (CCP1) or CCP6 deficiency substantially promotes induced pluripotent cell (iPSC) induction and pluripotency of embryonic stem cells (ESCs). Klf4 polyglutamylation at Glu381 by tubulin tyrosine ligase-like 4 (TTLL4) and TTLL1 during cell reprogramming impedes its lysine 48-linked ubiquitination and sustains Klf4 stability. Klf4-E381A knockin mice display impaired blastocyst development and embryonic lethality. Deletion of TTLL4 or TTLL1 abrogates cell reprogramming and early embryogenesis. Thus, Klf4 polyglutamylation plays a critical role in the regulation of cell reprogramming and pluripotency maintenance. Embryonic stem cell pluripotency depends upon precise regulation by a core transcription network. Here the authors show that polyglutamylation mediated stabilization of the transcription factor Klf4 by TTLL1 and TTLL4 promotes reprogramming, pluripotency and preimplantation embryonic development.
Collapse
Affiliation(s)
- Buqing Ye
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Benyu Liu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lu Hao
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhu
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liuliu Yang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pengyan Xia
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shu Meng
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanling Huang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiwen Qin
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanying Wang
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinlong Yan
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chong Li
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Junfeng Hao
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Luyun He
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong Tian
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
36
|
Abstract
Hexim1 acts as a tumor suppressor and is involved in the regulation of innate immunity. It was initially described as a non-coding RNA-dependent regulator of transcription. Here, we detail how 7SK RNA binds to Hexim1 and turns it into an inhibitor of the positive transcription elongation factor (P-TEFb). In addition to its action on P-TEFb, it plays a role in a variety of different mechanisms: it controls the stability of transcription factor components and assists binding of transcription factors to their targets.
Collapse
Affiliation(s)
- Annemieke A Michels
- a IBENS , Ecole Normale Supérieure UMR CNRS 8107, UA INSERM 1024 , 46 rue d'Ulm Paris Cedex France
| | - Olivier Bensaude
- a IBENS , Ecole Normale Supérieure UMR CNRS 8107, UA INSERM 1024 , 46 rue d'Ulm Paris Cedex France
| |
Collapse
|
37
|
Abstract
Several oncogenic factors have been involved in prostate cancer progression. However, therapeutic approaches still focus on suppression of androgen receptor (AR) signaling. In fact, whereas the full-length AR incorporates a ligand-binding domain, which has become a drug target for competitive inhibitors, other transcription factors often do not have tractable binding pockets that aid drug development. Consequently drug development efforts have turned to transcription co-regulators, often chromatin-modifying enzymes or factors that bind to epigenetic modifications to chromatin. Bromodomain (BRD)-containing proteins fall into the latter category and significant progress has been made in developing small molecule inhibitors that target a particular subgroup of BRD-containing proteins known as the Bromodomain and extra-terminal (BET) family proteins. These inhibitors have proven particularly effective in inactivating c-Myc in lymphoma but more recently members of the BET family have also been identified as AR-interacting proteins raising the prospect of using these inhibitors as an alternative strategy for targeting AR-driven cancers. In this review we will provide an overview of BRD-containing proteins and the potential for exploiting them as biomarkers and drug targets in prostate cancer.
Collapse
Affiliation(s)
- Alfonso Urbanucci
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, University of Oslo, Forskningsparken, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
| | - Ian G Mills
- Centre for Molecular Medicine Norway, Nordic European Molecular Biology Laboratory Partnership, University of Oslo, Forskningsparken, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Prostate Cancer UK/Movember Centre of Excellence for Prostate Cancer, Centre for Cancer Research and Cell Biology, Queen's University of Belfast, BT9 7AE Belfast, UK
| |
Collapse
|
38
|
Capturing the interactome of newly transcribed RNA. Nat Methods 2018; 15:213-220. [PMID: 29431736 DOI: 10.1038/nmeth.4595] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/11/2017] [Indexed: 12/18/2022]
Abstract
We combine the labeling of newly transcribed RNAs with 5-ethynyluridine with the characterization of bound proteins. This approach, named capture of the newly transcribed RNA interactome using click chemistry (RICK), systematically captures proteins bound to a wide range of RNAs, including nascent RNAs and traditionally neglected nonpolyadenylated RNAs. RICK has identified mitotic regulators amongst other novel RNA-binding proteins with preferential affinity for nonpolyadenylated RNAs, revealed a link between metabolic enzymes/factors and nascent RNAs, and expanded the known RNA-bound proteome of mouse embryonic stem cells. RICK will facilitate an in-depth interrogation of the total RNA-bound proteome in different cells and systems.
Collapse
|
39
|
Shao Z, Yao C, Khodadadi-Jamayran A, Xu W, Townes TM, Crowley MR, Hu K. Reprogramming by De-bookmarking the Somatic Transcriptional Program through Targeting of BET Bromodomains. Cell Rep 2018; 16:3138-3145. [PMID: 27653680 DOI: 10.1016/j.celrep.2016.08.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/19/2016] [Accepted: 08/18/2016] [Indexed: 01/11/2023] Open
Abstract
One critical event in reprogramming to pluripotency is erasure of the somatic transcriptional program of starting cells. Here, we present the proof of principle of a strategy for reprogramming to pluripotency facilitated by small molecules that interfere with the somatic transcriptional memory. We show that mild chemical targeting of the acetyllysine-binding pockets of the BET bromodomains, the transcriptional bookmarking domains, robustly enhances reprogramming. Furthermore, we show that chemical targeting of the transcriptional bookmarking BET bromodomains downregulates or turns off the expression of somatic genes in both naive and reprogramming fibroblasts. Chemical blocking of the BET bromodomains also results in loss of fibroblast morphology early in reprogramming. We therefore experimentally demonstrate that cell fate conversion can be achieved by chemically targeting the transcriptional bookmarking BET bromodomains responsible for transcriptional memory.
Collapse
Affiliation(s)
- Zhicheng Shao
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Chunping Yao
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA; Department of Radiation Oncology, Shandong Cancer Hospital, Shandong University, Jinan, Shandong 250117, China
| | - Alireza Khodadadi-Jamayran
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Weihua Xu
- Longyan University, Fujian 364012, China
| | - Tim M Townes
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Michael R Crowley
- Howell and Elizabeth Heflin Center for Genomic Science, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA
| | - Kejin Hu
- Stem Cell Institute, Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294-0024, USA.
| |
Collapse
|
40
|
|
41
|
Elagib KE, Lu CH, Mosoyan G, Khalil S, Zasadzińska E, Foltz DR, Balogh P, Gru AA, Fuchs DA, Rimsza LM, Verhoeyen E, Sansó M, Fisher RP, Iancu-Rubin C, Goldfarb AN. Neonatal expression of RNA-binding protein IGF2BP3 regulates the human fetal-adult megakaryocyte transition. J Clin Invest 2017; 127:2365-2377. [PMID: 28481226 DOI: 10.1172/jci88936] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 03/16/2017] [Indexed: 12/31/2022] Open
Abstract
Hematopoietic transitions that accompany fetal development, such as erythroid globin chain switching, play important roles in normal physiology and disease development. In the megakaryocyte lineage, human fetal progenitors do not execute the adult morphogenesis program of enlargement, polyploidization, and proplatelet formation. Although these defects decline with gestational stage, they remain sufficiently severe at birth to predispose newborns to thrombocytopenia. These defects may also contribute to inferior platelet recovery after cord blood stem cell transplantation and may underlie inefficient platelet production by megakaryocytes derived from pluripotent stem cells. In this study, comparison of neonatal versus adult human progenitors has identified a blockade in the specialized positive transcription elongation factor b (P-TEFb) activation mechanism that is known to drive adult megakaryocyte morphogenesis. This blockade resulted from neonatal-specific expression of an oncofetal RNA-binding protein, IGF2BP3, which prevented the destabilization of the nuclear RNA 7SK, a process normally associated with adult megakaryocytic P-TEFb activation. Knockdown of IGF2BP3 sufficed to confer both phenotypic and molecular features of adult-type cells on neonatal megakaryocytes. Pharmacologic inhibition of IGF2BP3 expression via bromodomain and extraterminal domain (BET) inhibition also elicited adult features in neonatal megakaryocytes. These results identify IGF2BP3 as a human ontogenic master switch that restricts megakaryocyte development by modulating a lineage-specific P-TEFb activation mechanism, revealing potential strategies toward enhancing platelet production.
Collapse
Affiliation(s)
- Kamaleldin E Elagib
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Chih-Huan Lu
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Goar Mosoyan
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shadi Khalil
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Ewelina Zasadzińska
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, Virginia, USA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, Virginia, USA.,Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Peter Balogh
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Alejandro A Gru
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Deborah A Fuchs
- Department of Pathology, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona, USA
| | - Els Verhoeyen
- Centre International de Recherche en Infectiologie (CIRI), Team EVIR, Inserm, U1111, Ecole Normale Supériere de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Nice, France
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Camelia Iancu-Rubin
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adam N Goldfarb
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| |
Collapse
|
42
|
LincRNa-p21: function and mechanism in cancer. Med Oncol 2017; 34:98. [PMID: 28425074 DOI: 10.1007/s12032-017-0959-5] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/12/2017] [Indexed: 12/29/2022]
Abstract
In view of the rapid development of gene chips and high-throughput sequencing technology, noncoding RNAs (ncRNas) form a high percentage of the mammalian genome. Two major subgroups of ncRNAs that have been identified are the long ncRNAs (lncRNas) and the microRNAs. A number of studies in the past few years have showed crucial functions for lncRNas in cancer. LincRNa-p21 as a p53-dependent transcriptional target gene and a potential diagnostic marker is involved in proliferation, cell cycle, metabolism and reprogramming. In addition, more researches revealed that lincRNa-p21 is associated with cancer progression and contributed to the treatment and prognosis of cancer. In this review, we briefly summarize the function and molecular mechanisms of lincRNa-p21 in cancer and its regulation for the genes expression .
Collapse
|
43
|
LncBRM initiates YAP1 signalling activation to drive self-renewal of liver cancer stem cells. Nat Commun 2016; 7:13608. [PMID: 27905400 PMCID: PMC5146280 DOI: 10.1038/ncomms13608] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 10/18/2016] [Indexed: 12/15/2022] Open
Abstract
Liver cancer stem cells (CSCs) may contribute to the high rate of recurrence and heterogeneity of hepatocellular carcinoma (HCC). However, the biology of hepatic CSCs remains largely undefined. Through analysis of transcriptome microarray data, we identify a long noncoding RNA (lncRNA) called lncBRM, which is highly expressed in liver CSCs and HCC tumours. LncBRM is required for the self-renewal maintenance of liver CSCs and tumour initiation. In liver CSCs, lncBRM associates with BRM to initiate the BRG1/BRM switch and the BRG1-embedded BAF complex triggers activation of YAP1 signalling. Moreover, expression levels of lncBRM together with YAP1 signalling targets are positively correlated with tumour severity of HCC patients. Therefore, lncBRM and YAP1 signalling may serve as biomarkers for diagnosis and potential drug targets for HCC. Liver cancer stem cells (CSCs) may contribute to the high rate of recurrence of hepatocellular carcinoma. Here, the authors show that the long coding RNA, LcnBRM, regulates the self-renewal of liver CSCs and tumour initiation through binding to BAF complex thereby activating YAP1.
Collapse
|
44
|
Chen J, Pei D. Epigenetic Landmarks During Somatic Reprogramming. IUBMB Life 2016; 68:854-857. [DOI: 10.1002/iub.1577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/08/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Jiekai Chen
- Key Laboratory of Regenerative Biology; South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou 510530 China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou 510530 China
| | - Duanqing Pei
- Key Laboratory of Regenerative Biology; South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou 510530 China
- Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou 510530 China
| |
Collapse
|
45
|
Strikoudis A, Lazaris C, Trimarchi T, Galvao Neto AL, Yang Y, Ntziachristos P, Rothbart S, Buckley S, Dolgalev I, Stadtfeld M, Strahl BD, Dynlacht BD, Tsirigos A, Aifantis I. Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a. Nat Cell Biol 2016; 18:1127-1138. [PMID: 27749823 PMCID: PMC5083132 DOI: 10.1038/ncb3424] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 09/15/2016] [Indexed: 12/12/2022]
Abstract
Pluripotent embryonic stem cells (ESCs) self-renew or differentiate into all tissues of the developing embryo and cell-specification factors are necessary to balance gene expression. Here we delineate the function of the PHD-finger protein 5a (Phf5a) in ESC self-renewal and ascribe its role in regulating pluripotency, cellular reprogramming, and myoblast specification. We demonstrate that Phf5a is essential for maintaining pluripotency, since depleted ESCs exhibit hallmarks of differentiation. Mechanistically, we attribute Phf5a function to the stabilization of the Paf1 transcriptional complex and control of RNA polymerase II elongation on pluripotency loci. Apart from an ESC-specific factor, we demonstrate that Phf5a controls differentiation of adult myoblasts. Our findings suggest a potent mode of regulation by the Phf5a in stem cells, which directs their transcriptional program ultimately regulating maintenance of pluripotency and cellular reprogramming.
Collapse
Affiliation(s)
- Alexandros Strikoudis
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Charalampos Lazaris
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA
| | - Thomas Trimarchi
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Antonio L Galvao Neto
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Ronald O. Perelman Department of Dermatology, NYU School of Medicine, New York, New York 10016, USA
| | - Yan Yang
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA
| | - Panagiotis Ntziachristos
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Scott Rothbart
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599, USA
| | - Shannon Buckley
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Igor Dolgalev
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA.,Genome Technology Center, Office of Collaborative Science, NYU School of Medicine, New York, New York 10016, USA
| | - Matthias Stadtfeld
- Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA.,Department of Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, North Carolina 27599, USA
| | - Brian D Dynlacht
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Center for Health Informatics and Bioinformatics, NYU School of Medicine, New York, New York 10016, USA
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, New York 10016, USA.,Laura &Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, New York 10016, USA.,Helen L. &Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, New York 10016, USA
| |
Collapse
|
46
|
Zhao Y, Liu Q, Acharya P, Stengel KR, Sheng Q, Zhou X, Kwak H, Fischer MA, Bradner JE, Strickland SA, Mohan SR, Savona MR, Venters BJ, Zhou MM, Lis JT, Hiebert SW. High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML. Cell Rep 2016; 16:2003-16. [PMID: 27498870 PMCID: PMC4996374 DOI: 10.1016/j.celrep.2016.07.032] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/17/2015] [Accepted: 07/13/2016] [Indexed: 02/07/2023] Open
Abstract
Bromodomain and extra-terminal domain (BET) family inhibitors offer an approach to treating hematological malignancies. We used precision nuclear run-on transcription sequencing (PRO-seq) to create high-resolution maps of active RNA polymerases across the genome in t(8;21) acute myeloid leukemia (AML), as these polymerases are exceptionally sensitive to BET inhibitors. PRO-seq identified over 1,400 genes showing impaired release of promoter-proximal paused RNA polymerases, including the stem cell factor receptor tyrosine kinase KIT that is mutated in t(8;21) AML. PRO-seq also identified an enhancer 3' to KIT. Chromosome conformation capture confirmed contacts between this enhancer and the KIT promoter, while CRISPRi-mediated repression of this enhancer impaired cell growth. PRO-seq also identified microRNAs, including MIR29C and MIR29B2, that target the anti-apoptotic factor MCL1 and were repressed by BET inhibitors. MCL1 protein was upregulated, and inhibition of BET proteins sensitized t(8:21)-containing cells to MCL1 inhibition, suggesting a potential mechanism of resistance to BET-inhibitor-induced cell death.
Collapse
MESH Headings
- Antineoplastic Agents/pharmacology
- Azepines/pharmacology
- Cell Line, Tumor
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA-Directed RNA Polymerases/genetics
- DNA-Directed RNA Polymerases/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Multigene Family
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Myeloid Cell Leukemia Sequence 1 Protein/metabolism
- Promoter Regions, Genetic
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- Proteins/antagonists & inhibitors
- Proteins/genetics
- Proteins/metabolism
- Proto-Oncogene Proteins c-kit/genetics
- Proto-Oncogene Proteins c-kit/metabolism
- Transcription, Genetic
- Translocation, Genetic
- Triazoles/pharmacology
Collapse
Affiliation(s)
- Yue Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Qi Liu
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Pankaj Acharya
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Quanhu Sheng
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Xiaofan Zhou
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Melissa A Fischer
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Stephen A Strickland
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Sanjay R Mohan
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Michael R Savona
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| |
Collapse
|
47
|
Devaiah BN, Gegonne A, Singer DS. Bromodomain 4: a cellular Swiss army knife. J Leukoc Biol 2016; 100:679-686. [PMID: 27450555 DOI: 10.1189/jlb.2ri0616-250r] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 07/11/2016] [Indexed: 12/19/2022] Open
Abstract
Bromodomain protein 4 (BRD4) is a transcriptional and epigenetic regulator that plays a pivotal role in cancer and inflammatory diseases. BRD4 binds and stays associated with chromatin during mitosis, bookmarking early G1 genes and reactivating transcription after mitotic silencing. BRD4 plays an important role in transcription, both as a passive scaffold via its recruitment of vital transcription factors and as an active kinase that phosphorylates RNA polymerase II, directly and indirectly regulating transcription. Through its HAT activity, BRD4 contributes to the maintenance of chromatin structure and nucleosome clearance. This review summarizes the known functions of BRD4 and proposes a model in which BRD4 actively coordinates chromatin structure and transcription.
Collapse
Affiliation(s)
- Ballachanda N Devaiah
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anne Gegonne
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Dinah S Singer
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
48
|
Compensatory RNA polymerase 2 loading determines the efficacy and transcriptional selectivity of JQ1 in Myc-driven tumors. Leukemia 2016; 31:479-490. [PMID: 27443262 PMCID: PMC5310924 DOI: 10.1038/leu.2016.182] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/18/2016] [Accepted: 06/10/2016] [Indexed: 12/15/2022]
Abstract
Inhibition of bromodomain and extraterminal motif (BET) proteins such as BRD4 bears great promise for cancer treatment and its efficacy has been frequently attributed to Myc downregulation. Here, we use B-cell tumors as a model to address the mechanism of action of JQ1, a widely used BET inhibitor. Although JQ1 led to widespread eviction of BRD4 from chromatin, its effect on gene transcription was limited to a restricted set of genes. This was unlinked to Myc downregulation or its chromatin association. Yet, JQ1-sensitive genes were enriched for Myc and E2F targets, were expressed at high levels, and showed high promoter occupancy by RNAPol2, BRD4, Myc and E2F. Their marked decrease in transcriptional elongation upon JQ1 treatment, indicated that BRD4-dependent promoter clearance was rate limiting for transcription. At JQ1-insensitive genes the drop in transcriptional elongation still occurred, but was compensated by enhanced RNAPol2 recruitment. Similar results were obtained with other inhibitors of transcriptional elongation. Thus, the selective transcriptional effects following JQ1 treatment are linked to the inability of JQ1-sensitive genes to sustain compensatory RNAPol2 recruitment to promoters. These observations highlight the role of BET proteins in supporting transcriptional elongation and rationalize how a general suppression of elongation may selectively affects transcription.
Collapse
|
49
|
Xie Q, Wu Q, Kim L, Miller TE, Liau BB, Mack SC, Yang K, Factor DC, Fang X, Huang Z, Zhou W, Alazem K, Wang X, Bernstein BE, Bao S, Rich JN. RBPJ maintains brain tumor-initiating cells through CDK9-mediated transcriptional elongation. J Clin Invest 2016; 126:2757-72. [PMID: 27322055 DOI: 10.1172/jci86114] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 04/07/2016] [Indexed: 12/26/2022] Open
Abstract
Glioblastomas co-opt stem cell regulatory pathways to maintain brain tumor-initiating cells (BTICs), also known as cancer stem cells. NOTCH signaling has been a molecular target in BTICs, but NOTCH antagonists have demonstrated limited efficacy in clinical trials. Recombining binding protein suppressor of hairless (RBPJ) is considered a central transcriptional mediator of NOTCH activity. Here, we report that pharmacologic NOTCH inhibitors were less effective than targeting RBPJ in suppressing tumor growth. While NOTCH inhibitors decreased canonical NOTCH gene expression, RBPJ regulated a distinct profile of genes critical to BTIC stemness and cell cycle progression. RBPJ was preferentially expressed by BTICs and required for BTIC self-renewal and tumor growth. MYC, a key BTIC regulator, bound the RBPJ promoter and treatment with a bromodomain and extraterminal domain (BET) family bromodomain inhibitor decreased MYC and RBPJ expression. Proteomic studies demonstrated that RBPJ binds CDK9, a component of positive transcription elongation factor b (P-TEFb), to target gene promoters, enhancing transcriptional elongation. Collectively, RBPJ links MYC and transcriptional control through CDK9, providing potential nodes of fragility for therapeutic intervention, potentially distinct from NOTCH.
Collapse
|
50
|
Robinson C, Lowe M, Schwartz A, Kikyo N. Mechanisms and Developmental Roles of Promoter-proximal Pausing of RNA Polymerase II. ACTA ACUST UNITED AC 2016; 6. [PMID: 27158559 PMCID: PMC4855949 DOI: 10.4172/2157-7633.1000330] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
RNA polymerase II (Pol II) temporarily stops transcription after synthesizing 30–50 bases, and resumes elongation only after stimulations by various signaling molecules and developmental cues. This phenomenon, called promoter-proximal pausing, is observed in 10–50% of the entire genes from Drosophila embryos to human cells. Release of paused Pol II is primarily mediated by the activated form of positive transcription elongation factor b (P-TEFb) initially sequestered in the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP) complex. Many proteins and RNAs have been discovered and studied in detail to explain the process of the pausing and release of Pol II in relation to P-TEFb. At the functional level, promoter-proximal pausing regulates genes involved in stimulus-response and development in Drosophila. In mammalian stem cell biology, pausing is important for proliferation and signaling in embryonic stem cells and the formation of induced pluripotent stem cells. Other than this, however, little is known about the biological significance of pausing in mammalian cell differentiation. Further study on pausing mechanisms as well as its functions will contribute to the development of stem cell biology and its clinical applications.
Collapse
Affiliation(s)
- Christine Robinson
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| | - Matthew Lowe
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| | - Amanda Schwartz
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| | - Nobuaki Kikyo
- Stem Cell Institute, Department of Genetics, Cell Biology and Development, University of Minnesota, USA
| |
Collapse
|