1
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Jia T, Liu C, Guo P, Xu Y, Wang W, Liu X, Wang S, Zhang X, Guo H. FOXA1 regulates ribosomal RNA transcription in prostate cancer. Prostate 2024; 84:967-976. [PMID: 38632701 DOI: 10.1002/pros.24714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Ribosome biogenesis is excessively activated in tumor cells, yet it is little known whether oncogenic transcription factors (TFs) are involved in the ribosomal RNA (rRNA) transactivation. METHODS Nucleolar proteomics data and large-scale immunofluorescence were re-analyzed to jointly identify the proteins localized at nucleolus. RNA-Seq data of five prostate cancer (PCa) cohorts were combined and integrated with multi-dimensional data to define the upregulated nucleolar TFs in PCa tissues. Then, ChIP-Seq data of PCa cell lines and two PCa clinical cohorts were re-analyzed to reveal the TF binding patterns at ribosomal DNA (rDNA) repeats. The TF binding at rDNA was validated by ChIP-qPCR. The effect of the TF on rRNA transcription was determined by rDNA luciferase reporter, nascent RNA synthesis, and global protein translation assays. RESULTS In this study, we reveal the role of oncogenic TF FOXA1 in regulating rRNA transcription within nucleolar organization regions. By analyzing human TFs in prostate cancer clinical datasets and nucleolar proteomics data, we identified that FOXA1 is partially localized in the nucleolus and correlated with global protein translation. Our extensive FOXA1 ChIP-Seq analysis provides robust evidence of FOXA1 binding across rDNA repeats in prostate cancer cell lines, primary tumors, and castration-resistant variants. Notably, FOXA1 occupancy at rDNA repeats correlates with histone modifications associated with active transcription, namely H3K27ac and H3K4me3. Reducing FOXA1 expression results in decreased transactivation at rDNA, subsequently diminishing global protein synthesis. CONCLUSIONS Our results suggest FOXA1 regulates aberrant ribosome biogenesis downstream of oncogenic signaling in prostate cancer.
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Affiliation(s)
- Tianwei Jia
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Chenxu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Ping Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Yaning Xu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Wenzheng Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Song Wang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Xianglin Zhang
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
| | - Haiyang Guo
- Department of Clinical Laboratory, the Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Shandong Engineering & Technology Research Center for Tumor Marker Detection, Jinan, Shandong, China
- Shandong Provincial Clinical Medicine Research Center for Clinical Laboratory, Jinan, Shandong, China
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2
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Yang Y, Li S, Luo L. Responses of organ precursors to correct and incorrect inductive signals. Trends Cell Biol 2024; 34:484-495. [PMID: 37739814 DOI: 10.1016/j.tcb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
During embryonic development, the inductive molecules produced by local origins normally arrive at their target tissues in a nondirectional, diffusion manner. The target organ precursor cells must correctly interpret these inductive signals to ensure proper specification/differentiation, which is dependent on two prerequisites: (i) obtaining cell-intrinsic competence; and (ii) receiving correct inductive signals while resisting incorrect ones. Gain of intrinsic competence could avoid a large number of misinductions because the incompetent cells are nonresponsive to inductive signals. However, in cases of different precursor cells with similar competence and located in close proximity, resistance to incorrect inductive signals is essential for accurate determination of cell fate. Here we outline the mechanisms of how organ precursors respond to correct and incorrect inductive signals.
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Affiliation(s)
- Yun Yang
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Shuang Li
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Lingfei Luo
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China; School of Life Sciences, Fudan University, Shanghai, China.
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3
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Shiraishi R, Cancila G, Kumegawa K, Torrejon J, Basili I, Bernardi F, Silva PBGD, Wang W, Chapman O, Yang L, Jami M, Nishitani K, Arai Y, Xiao Z, Yu H, Lo Re V, Marsaud V, Talbot J, Lombard B, Loew D, Jingu M, Okonechnikov K, Sone M, Motohashi N, Aoki Y, Pfister SM, Chavez L, Hoshino M, Maruyama R, Ayrault O, Kawauchi D. Cancer-specific epigenome identifies oncogenic hijacking by nuclear factor I family proteins for medulloblastoma progression. Dev Cell 2024:S1534-5807(24)00330-7. [PMID: 38834071 DOI: 10.1016/j.devcel.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/01/2024] [Accepted: 05/10/2024] [Indexed: 06/06/2024]
Abstract
Normal cells coordinate proliferation and differentiation by precise tuning of gene expression based on the dynamic shifts of the epigenome throughout the developmental timeline. Although non-mutational epigenetic reprogramming is an emerging hallmark of cancer, the epigenomic shifts that occur during the transition from normal to malignant cells remain elusive. Here, we capture the epigenomic changes that occur during tumorigenesis in a prototypic embryonal brain tumor, medulloblastoma. By comparing the epigenomes of the different stages of transforming cells in mice, we identify nuclear factor I family of transcription factors, known to be cell fate determinants in development, as oncogenic regulators in the epigenomes of precancerous and cancerous cells. Furthermore, genetic and pharmacological inhibition of NFIB validated a crucial role of this transcription factor by disrupting the cancer epigenome in medulloblastoma. Thus, this study exemplifies how epigenomic changes contribute to tumorigenesis via non-mutational mechanisms involving developmental transcription factors.
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Affiliation(s)
- Ryo Shiraishi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Gabriele Cancila
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Kohei Kumegawa
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Jacob Torrejon
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Irene Basili
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Flavia Bernardi
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Patricia Benites Goncalves da Silva
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Wanchen Wang
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Owen Chapman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Liying Yang
- Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Maki Jami
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Kayo Nishitani
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Yukimi Arai
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Zhize Xiao
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Hua Yu
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Valentina Lo Re
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Véronique Marsaud
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Julie Talbot
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France
| | - Bérangère Lombard
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, Paris 75005, France
| | - Damarys Loew
- Institut Curie, PSL Research University, CurieCoreTech Mass Spectrometry Proteomics, Paris 75005, France
| | - Maho Jingu
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan; Department of Biomolecular Science, Graduate School of Science, Toho University, Chiba 274-8510, Japan
| | - Konstantin Okonechnikov
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Masaki Sone
- Department of Biomolecular Science, Graduate School of Science, Toho University, Chiba 274-8510, Japan
| | - Norio Motohashi
- Department of Molecular Therapy, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ) and Heidelberg University Hospital, Heidelberg 69120, Germany
| | - Lukas Chavez
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan
| | - Reo Maruyama
- Cancer Cell Diversity Project, NEXT-Ganken Program, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan; Project for Cancer Epigenomics, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan.
| | - Olivier Ayrault
- Institut Curie, PSL Research University, CNRS UMR, INSERM, Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay 91400, France.
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan.
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4
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Wang L, Yi S, Cui X, Guo Z, Wang M, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Yang G, Chen J, Gao R. Chromatin landscape instructs precise transcription factor regulome during embryonic lineage specification. Cell Rep 2024; 43:114136. [PMID: 38643480 DOI: 10.1016/j.celrep.2024.114136] [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: 11/29/2023] [Revised: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
Embryos, originating from fertilized eggs, undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Chromatin regulators, including transcription factors (TFs), play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass and trophectoderm of blastocysts, prompting inquiry into Tfap2c's function in post-lineage establishment. In this study, we delineate the dynamics of TFAP2C during the mouse peri-implantation stage and elucidate its collaboration with the key lineage regulators CDX2 and NANOG. Importantly, we propose that de novo formation of H3K9me3 in the extraembryonic ectoderm during implantation antagonizes TFAP2C binding to crucial developmental genes, thereby maintaining its lineage identity. Together, these results highlight the plasticity of the chromatin environment in designating the genomic binding of highly adaptable lineage-specific TFs and regulating embryonic cell fates.
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Affiliation(s)
- Liping Wang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Guang Yang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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5
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Moyung K, Li Y, Hartemink AJ, MacAlpine DM. Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595391. [PMID: 38826400 PMCID: PMC11142231 DOI: 10.1101/2024.05.24.595391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Epigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy throughout the genome. Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely unexplored on a comprehensive scale. We address this by employing a factor-agnostic, reverse-genetics approach that uses MNase-seq to capture genome-wide TF and nucleosome occupancies in response to the individual deletion of 201 transcriptional regulators in Saccharomyces cerevisiae, thereby assaying nearly one million mutant-gene interactions. We develop a principled approach to identify and quantify chromatin changes genome-wide, observing differences in TF and nucleosome occupancy that recapitulate well-established pathways identified by gene expression data. We also discover distinct chromatin signatures associated with the up- and downregulation of genes, and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity and leverage these features to reconstruct chromatin-based transcriptional regulatory networks. Overall, these results illustrate the power of an approach combining genetic perturbation with high-resolution epigenomic profiling; the latter enables a close examination of the interplay between TFs and nucleosomes genome-wide, providing a deeper, more mechanistic understanding of the complex relationship between chromatin organization and transcription.
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Affiliation(s)
- Kevin Moyung
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
| | - Yulong Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
- Department of Computer Science, Duke University, Durham, NC 27708
| | - Alexander J. Hartemink
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Computer Science, Duke University, Durham, NC 27708
| | - David M. MacAlpine
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710
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6
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He Z, Wang Z, Lu Z, Gao C, Wang Y. An electrophoretic mobility shift assay using the protein isolated from host plants. PLANT METHODS 2024; 20:68. [PMID: 38735938 PMCID: PMC11089672 DOI: 10.1186/s13007-024-01201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 05/01/2024] [Indexed: 05/14/2024]
Abstract
BACKGROUND The electrophoretic mobility shift assay (EMSA) is a common technology to detect DNA-protein interactions. However, in most cases, the protein used in EMSA is obtained via prokaryotic expression, and rarely from plants. At the same time, the proteins expressed from prokaryotic systems usually cannot fold naturally and have no post translationally modification, which may affect the binding of proteins to DNA. RESULTS Here, we develop a technique to quickly isolate proteins of interest from host plants and then analyze them using fluorescent EMSA. This technology system is called: protein from plants fluorescent EMSA method (PPF-EMSA). In PPF-EMSA, a special transient transformation method is employed to transiently deliver genes into the plant, enabling efficient synthesis the encoded proteins. Then, the target protein is isolated using immunoprecipitation, and the DNA probes were labeled with cyanine 3 (Cy3). Both fluorescent EMSA and super-shift fluorescent EMSA can be performed using the proteins from plants. Three kinds of plants, Betula platyphylla, Populus. davidiana×P. bolleana and Arabidopsis thaliana, are used in this study. The proteins isolated from plants are in a natural state, can fold naturally and are posttranslationally modified, enabling true binding to their cognate DNAs. CONCLUSION As transient transformation can be performed quickly and not depended on whether stable transformation is available or not, we believe this method will have a wide application, enabling isolation of proteins from host plant conveniently.
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Affiliation(s)
- Zihang He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhangguo Lu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China.
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7
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Torshizi Esfahani A, Mohammadpour S, Jalali P, Yaghoobi A, Karimpour R, Torkamani S, Pardakhtchi A, Salehi Z, Nazemalhosseini-Mojarad E. Differential expression of angiogenesis-related genes 'VEGF' and 'angiopoietin-1' in metastatic and EMAST-positive colorectal cancer patients. Sci Rep 2024; 14:10539. [PMID: 38719941 PMCID: PMC11079037 DOI: 10.1038/s41598-024-61000-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Abnormal angiogenesis leads to tumor progression and metastasis in colorectal cancer (CRC). This study aimed to elucidate the association between angiogenesis-related genes, including VEGF-A, ANGPT-1, and ANGPT-2 with both metastatic and microsatellite alterations at selected tetranucleotide repeats (EMAST) subtypes of CRC. We conducted a thorough assessment of the ANGPT-1, ANGPT-2, and VEGF-A gene expression utilizing publicly available RNA sequencing and microarray datasets. Then, the experimental validation was performed in 122 CRC patients, considering their disease metastasis and EMAST+/- profile by using reverse transcription polymerase chain reaction (RT-PCR). Subsequently, a competing endogenous RNA (ceRNA) network associated with these angiogenesis-related genes was constructed and analyzed. The expression level of VEGF-A and ANGPT-2 genes were significantly higher in tumor tissues as compared with normal adjacent tissues (P-value < 0.001). Nevertheless, ANGPT-1 had a significantly lower expression in tumor samples than in normal colon tissue (P-value < 0.01). We identified a significantly increased VEGF-A (P-value = 0.002) and decreased ANGPT-1 (P-value = 0.04) expression in EMAST+ colorectal tumors. Regarding metastasis, a significantly increased VEGF-A and ANGPT-2 expression (P-value = 0.001) and decreased ANGPT-1 expression (P-value < 0.05) were established in metastatic CRC patients. Remarkably, co-expression analysis also showed a strong correlation between ANGPT-2 and VEGF-A gene expressions. The ceRNA network was constructed by ANGPT-1, ANGPT-2, VEGF-A, and experimentally validated miRNAs (hsa-miR-190a-3p, hsa-miR-374c-5p, hsa-miR-452-5p, and hsa-miR-889-3p), lncRNAs (AFAP1-AS1, KCNQ1OT1 and MALAT1), and TFs (Sp1, E2F1, and STAT3). Network analysis revealed that colorectal cancer is amongst the 82 significant pathways. We demonstrated a significant differential expression of VEGF-A and ANGPT-1 in colorectal cancer patients exhibiting the EMAST+ phenotype. This finding provides novel insights into the molecular pathogenesis of colorectal cancer, specifically in EMAST subtypes. Yet, the generalization of in silico findings to EMAST+ colorectal cancer warrants future experimental investigations. In the end, this study proposes that the EMAST biomarker could serve as an additional perspective on CMS4 biology which is well-defined by activated angiogenesis and worse overall survival.
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Affiliation(s)
- Amir Torshizi Esfahani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mohammadpour
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Yaghoobi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Raana Karimpour
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Soha Torkamani
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Pardakhtchi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands.
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8
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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Muñoz Gomez M, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. Cell Stem Cell 2024:S1934-5909(24)00142-5. [PMID: 38733993 DOI: 10.1016/j.stem.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.
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Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Gu
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Allen W Lynch
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Swarnabh Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Muñoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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9
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Hoffmann MH, Kirchner H, Krönke G, Riemekasten G, Bonelli M. Inflammatory tissue priming: novel insights and therapeutic opportunities for inflammatory rheumatic diseases. Ann Rheum Dis 2024:ard-2023-224092. [PMID: 38702177 DOI: 10.1136/ard-2023-224092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Due to optimised treatment strategies and the availability of new therapies during the last decades, formerly devastating chronic inflammatory diseases such as rheumatoid arthritis or systemic sclerosis (SSc) have become less menacing. However, in many patients, even state-of-the-art treatment cannot induce remission. Moreover, the risk for flares strongly increases once anti-inflammatory therapy is tapered or withdrawn, suggesting that underlying pathological processes remain active even in the absence of overt inflammation. It has become evident that tissues have the ability to remember past encounters with pathogens, wounds and other irritants, and to react more strongly and/or persistently to the next occurrence. This priming of the tissue bears a paramount role in defence from microbes, but on the other hand drives inflammatory pathologies (the Dr Jekyll and Mr Hyde aspect of tissue adaptation). Emerging evidence suggests that long-lived tissue-resident cells, such as fibroblasts, macrophages, long-lived plasma cells and tissue-resident memory T cells, determine inflammatory tissue priming in an interplay with infiltrating immune cells of lymphoid and myeloid origin, and with systemically acting factors such as cytokines, extracellular vesicles and antibodies. Here, we review the current state of science on inflammatory tissue priming, focusing on tissue-resident and tissue-occupying cells in arthritis and SSc, and reflect on the most promising treatment options targeting the maladapted tissue response during these diseases.
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Affiliation(s)
| | - Henriette Kirchner
- Institute for Human Genetics, Epigenetics and Metabolism Lab, University of Lübeck, Lübeck, Germany
| | - Gerhard Krönke
- Department of Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Michael Bonelli
- Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Vienna, Austria
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10
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Miyazawa K, Itoh Y, Fu H, Miyazono K. Receptor-activated transcription factors and beyond: multiple modes of Smad2/3-dependent transmission of TGF-β signaling. J Biol Chem 2024; 300:107256. [PMID: 38569937 PMCID: PMC11063908 DOI: 10.1016/j.jbc.2024.107256] [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: 01/19/2024] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Transforming growth factor β (TGF-β) is a pleiotropic cytokine that is widely distributed throughout the body. Its receptor proteins, TGF-β type I and type II receptors, are also ubiquitously expressed. Therefore, the regulation of various signaling outputs in a context-dependent manner is a critical issue in this field. Smad proteins were originally identified as signal-activated transcription factors similar to signal transducer and activator of transcription proteins. Smads are activated by serine phosphorylation mediated by intrinsic receptor dual specificity kinases of the TGF-β family, indicating that Smads are receptor-restricted effector molecules downstream of ligands of the TGF-β family. Smad proteins have other functions in addition to transcriptional regulation, including post-transcriptional regulation of micro-RNA processing, pre-mRNA splicing, and m6A methylation. Recent technical advances have identified a novel landscape of Smad-dependent signal transduction, including regulation of mitochondrial function without involving regulation of gene expression. Therefore, Smad proteins are receptor-activated transcription factors and also act as intracellular signaling modulators with multiple modes of function. In this review, we discuss the role of Smad proteins as receptor-activated transcription factors and beyond. We also describe the functional differences between Smad2 and Smad3, two receptor-activated Smad proteins downstream of TGF-β, activin, myostatin, growth and differentiation factor (GDF) 11, and Nodal.
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Affiliation(s)
- Keiji Miyazawa
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan.
| | - Yuka Itoh
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hao Fu
- Department of Biochemistry, Graduate School of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Kohei Miyazono
- Department of Applied Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Laboratory for Cancer Invasion and Metastasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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11
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Saotome M, Poduval D, Grimm SA, Nagornyuk A, Gunarathna S, Shimbo T, Wade P, Takaku M. Genomic transcription factor binding site selection is edited by the chromatin remodeling factor CHD4. Nucleic Acids Res 2024; 52:3607-3622. [PMID: 38281186 PMCID: PMC11039999 DOI: 10.1093/nar/gkae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/30/2024] Open
Abstract
Biologically precise enhancer licensing by lineage-determining transcription factors enables activation of transcripts appropriate to biological demand and prevents deleterious gene activation. This essential process is challenged by the millions of matches to most transcription factor binding motifs present in many eukaryotic genomes, leading to questions about how transcription factors achieve the exquisite specificity required. The importance of chromatin remodeling factors to enhancer activation is highlighted by their frequent mutation in developmental disorders and in cancer. Here, we determine the roles of CHD4 in enhancer licensing and maintenance in breast cancer cells and during cellular reprogramming. In unchallenged basal breast cancer cells, CHD4 modulates chromatin accessibility. Its depletion leads to redistribution of transcription factors to previously unoccupied sites. During cellular reprogramming induced by the pioneer factor GATA3, CHD4 activity is necessary to prevent inappropriate chromatin opening. Mechanistically, CHD4 promotes nucleosome positioning over GATA3 binding motifs to compete with transcription factor-DNA interaction. We propose that CHD4 acts as a chromatin proof-reading enzyme that prevents unnecessary gene expression by editing chromatin binding activities of transcription factors.
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Affiliation(s)
- Mika Saotome
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Deepak B Poduval
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sara A Grimm
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Aerica Nagornyuk
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Sakuntha Gunarathna
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
| | - Takashi Shimbo
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Motoki Takaku
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND 58202, USA
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12
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Wu K, Dhillon N, Bajor A, Abrahamsson S, Kamakaka RT. Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration. Cell Rep 2024; 43:113983. [PMID: 38517895 PMCID: PMC11141299 DOI: 10.1016/j.celrep.2024.113983] [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: 08/24/2023] [Revised: 12/25/2023] [Accepted: 03/06/2024] [Indexed: 03/24/2024] Open
Abstract
Transcriptional silencing in Saccharomyces cerevisiae involves the generation of a chromatin state that stably represses transcription. Using multiple reporter assays, a diverse set of upstream activating sequence enhancers and core promoters were investigated for their susceptibility to silencing. We show that heterochromatin stably silences only weak and stress-induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements, and the partial repression of these elements did not result in bistable expression states. Permutation analysis of enhancers and promoters indicates that both elements are targets of repression. Chromatin remodelers help specific regulatory elements to resist repression, most probably by altering nucleosome mobility and changing transcription burst duration. The strong enhancers/promoters can be repressed if silencer-bound Sir1 is increased. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating-type gene regulatory elements but not strong housekeeping gene regulatory sequences.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Namrita Dhillon
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Sara Abrahamsson
- Electrical Engineering Department, Baskin School of Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Rohinton T Kamakaka
- Department of MCD Biology, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
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13
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Xue G, Zhang X, Li W, Zhang L, Zhang Z, Zhou X, Zhang D, Zhang L, Li Z. A logic-incorporated gene regulatory network deciphers principles in cell fate decisions. eLife 2024; 12:RP88742. [PMID: 38652107 PMCID: PMC11037919 DOI: 10.7554/elife.88742] [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] [Indexed: 04/25/2024] Open
Abstract
Organisms utilize gene regulatory networks (GRN) to make fate decisions, but the regulatory mechanisms of transcription factors (TF) in GRNs are exceedingly intricate. A longstanding question in this field is how these tangled interactions synergistically contribute to decision-making procedures. To comprehensively understand the role of regulatory logic in cell fate decisions, we constructed a logic-incorporated GRN model and examined its behavior under two distinct driving forces (noise-driven and signal-driven). Under the noise-driven mode, we distilled the relationship among fate bias, regulatory logic, and noise profile. Under the signal-driven mode, we bridged regulatory logic and progression-accuracy trade-off, and uncovered distinctive trajectories of reprogramming influenced by logic motifs. In differentiation, we characterized a special logic-dependent priming stage by the solution landscape. Finally, we applied our findings to decipher three biological instances: hematopoiesis, embryogenesis, and trans-differentiation. Orthogonal to the classical analysis of expression profile, we harnessed noise patterns to construct the GRN corresponding to fate transition. Our work presents a generalizable framework for top-down fate-decision studies and a practical approach to the taxonomy of cell fate decisions.
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Affiliation(s)
- Gang Xue
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Xiaoyi Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Wanqi Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Lu Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Zongxu Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Xiaolin Zhou
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Di Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Lei Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- Beijing International Center for Mathematical Research, Center for Machine Learning Research, Peking UniversityBeijingChina
| | - Zhiyuan Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
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14
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Lian T, Guan R, Zhou BR, Bai Y. Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα. Nat Struct Mol Biol 2024; 31:633-643. [PMID: 38267599 DOI: 10.1038/s41594-023-01189-z] [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: 10/30/2022] [Accepted: 11/23/2023] [Indexed: 01/26/2024]
Abstract
Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remains elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp of entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome.
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Affiliation(s)
- Tengfei Lian
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Ruifang Guan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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15
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Yoon I, Kim U, Song Y, Park T, Lee DS. 3C methods in cancer research: recent advances and future prospects. Exp Mol Med 2024; 56:788-798. [PMID: 38658701 PMCID: PMC11059347 DOI: 10.1038/s12276-024-01236-9] [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: 12/17/2023] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
In recent years, Hi-C technology has revolutionized cancer research by elucidating the mystery of three-dimensional chromatin organization and its role in gene regulation. This paper explored the impact of Hi-C advancements on cancer research by delving into high-resolution techniques, such as chromatin loops, structural variants, haplotype phasing, and extrachromosomal DNA (ecDNA). Distant regulatory elements interact with their target genes through chromatin loops. Structural variants contribute to the development and progression of cancer. Haplotype phasing is crucial for understanding allele-specific genomic rearrangements and somatic clonal evolution in cancer. The role of ecDNA in driving oncogene amplification and drug resistance in cancer cells has also been revealed. These innovations offer a deeper understanding of cancer biology and the potential for personalized therapies. Despite these advancements, challenges, such as the accurate mapping of repetitive sequences and precise identification of structural variants, persist. Integrating Hi-C with multiomics data is key to overcoming these challenges and comprehensively understanding complex cancer genomes. Thus, Hi-C is a powerful tool for guiding precision medicine in cancer research and treatment.
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Affiliation(s)
- Insoo Yoon
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Uijin Kim
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Yousuk Song
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Taesoo Park
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea
| | - Dong-Sung Lee
- Department of Life Science, University of Seoul, Seoul, 02504, Republic of Korea.
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16
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Chen Y, Guo P, Dong Z. The role of histone acetylation in transcriptional regulation and seed development. PLANT PHYSIOLOGY 2024; 194:1962-1979. [PMID: 37979164 DOI: 10.1093/plphys/kiad614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/09/2023] [Accepted: 10/29/2023] [Indexed: 11/20/2023]
Abstract
Histone acetylation is highly conserved across eukaryotes and has been linked to gene activation since its discovery nearly 60 years ago. Over the past decades, histone acetylation has been evidenced to play crucial roles in plant development and response to various environmental cues. Emerging data indicate that histone acetylation is one of the defining features of "open chromatin," while the role of histone acetylation in transcription remains controversial. In this review, we briefly describe the discovery of histone acetylation, the mechanism of histone acetylation regulating transcription in yeast and mammals, and summarize the research progress of plant histone acetylation. Furthermore, we also emphasize the effect of histone acetylation on seed development and its potential use in plant breeding. A comprehensive knowledge of histone acetylation might provide new and more flexible research perspectives to enhance crop yield and stress resistance.
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Affiliation(s)
- Yan Chen
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Peiguo Guo
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhicheng Dong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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17
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Cheng YJ, Wang JW, Ye R. Histone dynamics responding to internal and external cues underlying plant development. PLANT PHYSIOLOGY 2024; 194:1980-1997. [PMID: 38124490 DOI: 10.1093/plphys/kiad676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Plants necessitate a refined coordination of growth and development to effectively respond to external triggers for survival and successful reproduction. This intricate harmonization of plant developmental processes and adaptability hinges on significant alterations within their epigenetic landscapes. In this review, we first delve into recent strides made in comprehending underpinning the dynamics of histones, driven by both internal and external cues. We encapsulate the prevailing working models through which cis/trans elements navigate the acquisition and removal of histone modifications, as well as the substitution of histone variants. As we look ahead, we anticipate that delving deeper into the dynamics of epigenetic regulation at the level of individual cells or specific cell types will significantly enrich our comprehension of how plant development unfolds under the influence of internal and external cues. Such exploration holds the potential to provide unprecedented resolution in understanding the orchestration of plant growth and development.
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Affiliation(s)
- Ying-Juan Cheng
- College of Horticulture, Nanjing Agriculture University, Nanjing 210095, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- New Cornerstone Science Laboratory, Shanghai 200032, China
| | - Ruiqiang Ye
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai 200032, China
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18
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Won SJ, Zhang Y, Reinhardt CJ, MacRae NS, DeMeester KE, Njomen E, Hargis LM, Remsberg JR, Melillo B, Cravatt BF, Erb MA. Redirecting the pioneering function of FOXA1 with covalent small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586158. [PMID: 38562719 PMCID: PMC10983899 DOI: 10.1101/2024.03.21.586158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pioneer transcription factors (TFs) exhibit a specialized ability to bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report the chemical proteomic discovery of electrophilic small molecules that stereoselectively and site-specifically bind the pioneer TF, FOXA1, at a cysteine (C258) within the forkhead DNA-binding domain. We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the covalent ligands relax the canonical DNA binding preference of FOXA1 by strengthening interactions with suboptimal ancillary sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.
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19
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Patra P, Gao YQ. Structural and dynamical aspect of DNA motif sequence specific binding of AP-1 transcription factor. J Chem Phys 2024; 160:115103. [PMID: 38506297 DOI: 10.1063/5.0196508] [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: 01/07/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Activator protein-1 (AP-1) comprises one of the largest and most evolutionary conserved families of ubiquitous eukaryotic transcription factors that act as a pioneer factor. Diversity in DNA binding interaction of AP-1 through a conserved basic-zipper (bZIP) domain directs in-depth understanding of how AP-1 achieves its DNA binding selectivity and consequently gene regulation specificity. Here, we address the structural and dynamical aspects of the DNA target recognition process of AP-1 using microsecond-long atomistic simulations based on the structure of the human AP-1 FosB/JunD bZIP-DNA complex. Our results show the unique role of DNA shape features in selective base specific interactions, characteristic ion population, and solvation properties of DNA grooves to form the motif sequence specific AP-1-DNA complex. The TpG step at the two terminals of the AP-1 site plays an important role in the structural adjustment of DNA by modifying the helical twist in the AP-1 bound state. We addressed the role of intrinsic motion of the bZIP domain in terms of opening and closing gripper motions of DNA binding helices, in target site recognition and binding of AP-1 factors. Our observations suggest that binding to the cognate motif in DNA is mainly accompanied with the precise adjustment of closing gripper motion of DNA binding helices of the bZIP domain.
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Affiliation(s)
- Piya Patra
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
| | - Yi Qin Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, 518107 Shenzhen, China
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
- Biomedical Pioneering Innovation Center, Peking University, 100871 Beijing, China
- Changping Laboratory, Beijing 102200, China
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20
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Tsanov KM, Barriga FM, Ho YJ, Alonso-Curbelo D, Livshits G, Koche RP, Baslan T, Simon J, Tian S, Wuest AN, Luan W, Wilkinson JE, Masilionis I, Dimitrova N, Iacobuzio-Donahue CA, Chaligné R, Pe’er D, Massagué J, Lowe SW. Metastatic site influences driver gene function in pancreatic cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.17.585402. [PMID: 38562717 PMCID: PMC10983983 DOI: 10.1101/2024.03.17.585402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Driver gene mutations can increase the metastatic potential of the primary tumor1-3, but their role in sustaining tumor growth at metastatic sites is poorly understood. A paradigm of such mutations is inactivation of SMAD4 - a transcriptional effector of TGFβ signaling - which is a hallmark of multiple gastrointestinal malignancies4,5. SMAD4 inactivation mediates TGFβ's remarkable anti- to pro-tumorigenic switch during cancer progression and can thus influence both tumor initiation and metastasis6-14. To determine whether metastatic tumors remain dependent on SMAD4 inactivation, we developed a mouse model of pancreatic ductal adenocarcinoma (PDAC) that enables Smad4 depletion in the pre-malignant pancreas and subsequent Smad4 reactivation in established metastases. As expected, Smad4 inactivation facilitated the formation of primary tumors that eventually colonized the liver and lungs. By contrast, Smad4 reactivation in metastatic disease had strikingly opposite effects depending on the tumor's organ of residence: suppression of liver metastases and promotion of lung metastases. Integrative multiomic analysis revealed organ-specific differences in the tumor cells' epigenomic state, whereby the liver and lungs harbored chromatin programs respectively dominated by the KLF and RUNX developmental transcription factors, with Klf4 depletion being sufficient to reverse Smad4's tumor-suppressive activity in liver metastases. Our results show how epigenetic states favored by the organ of residence can influence the function of driver genes in metastatic tumors. This organ-specific gene-chromatin interplay invites consideration of anatomical site in the interpretation of tumor genetics, with implications for the therapeutic targeting of metastatic disease.
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Affiliation(s)
- Kaloyan M. Tsanov
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco M. Barriga
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Yu-Jui Ho
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Direna Alonso-Curbelo
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Geulah Livshits
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timour Baslan
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Biomedical Sciences, School of Veterinary Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Janelle Simon
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sha Tian
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra N. Wuest
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Luan
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John E. Wilkinson
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Ignas Masilionis
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nevenka Dimitrova
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A. Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligné
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Pe’er
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Joan Massagué
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W. Lowe
- Cancer Biology & Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
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21
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Lorzadeh A, Ye G, Sharma S, Jadhav U. DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.11.579850. [PMID: 38405700 PMCID: PMC10888781 DOI: 10.1101/2024.02.11.579850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. In turn, DNA and chromatin modifications direct the genomic binding of TFs. However, how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci is still not well understood. Here we show that Cdx2 - a pioneer TF that binds distinct targets in developing versus adult intestinal epithelial cells - has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic and fetal Cdx2 target loci and the specifically methylated state of the CpG during development allows selective Cdx2 binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds its canonical motif without a CpG. This differential Cdx2 binding allows for corecruitment of Ctcf and Hnf4, facilitating the establishment of intestinal superenhancers during development and enhancers mediating adult homeostatic functions, respectively. Induced gain of DNA methylation in the adult mouse epithelium or cultured cells causes ectopic recruitment of Cdx2 to the developmental target loci and facilitates cobinding of the partner TFs. Together, our results demonstrate that the differential CpG motif requirements for Cdx2 binding to developmental versus adult target sites allow it to navigate different DNA methylation profiles and activate cell type-specific genes at appropriate times.
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Affiliation(s)
- Alireza Lorzadeh
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - George Ye
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - Sweta Sharma
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
| | - Unmesh Jadhav
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USC
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22
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Gibson TJ, Larson ED, Harrison MM. Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function. Nat Struct Mol Biol 2024; 31:548-558. [PMID: 38365978 DOI: 10.1038/s41594-024-01231-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Chromatin is a barrier to the binding of many transcription factors. By contrast, pioneer factors access nucleosomal targets and promote chromatin opening. Despite binding to target motifs in closed chromatin, many pioneer factors display cell-type-specific binding and activity. The mechanisms governing pioneer factor occupancy and the relationship between chromatin occupancy and opening remain unclear. We studied three Drosophila transcription factors with distinct DNA-binding domains and biological functions: Zelda, Grainy head and Twist. We demonstrated that the level of chromatin occupancy is a key determinant of pioneering activity. Multiple factors regulate occupancy, including motif content, local chromatin and protein concentration. Regions outside the DNA-binding domain are required for binding and chromatin opening. Our results show that pioneering activity is not a binary feature intrinsic to a protein but occurs on a spectrum and is regulated by a variety of protein-intrinsic and cell-type-specific features.
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Affiliation(s)
- Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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23
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Katsuda T, Sussman JH, Ito K, Katznelson A, Yuan S, Takenaka N, Li J, Merrell AJ, Cure H, Li Q, Rasool RU, Asangani IA, Zaret KS, Stanger BZ. Cellular reprogramming in vivo initiated by SOX4 pioneer factor activity. Nat Commun 2024; 15:1761. [PMID: 38409161 PMCID: PMC10897393 DOI: 10.1038/s41467-024-45939-z] [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: 08/27/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Tissue damage elicits cell fate switching through a process called metaplasia, but how the starting cell fate is silenced and the new cell fate is activated has not been investigated in animals. In cell culture, pioneer transcription factors mediate "reprogramming" by opening new chromatin sites for expression that can attract transcription factors from the starting cell's enhancers. Here we report that SOX4 is sufficient to initiate hepatobiliary metaplasia in the adult mouse liver, closely mimicking metaplasia initiated by toxic damage to the liver. In lineage-traced cells, we assessed the timing of SOX4-mediated opening of enhancer chromatin versus enhancer decommissioning. Initially, SOX4 directly binds to and closes hepatocyte regulatory sequences via an overlapping motif with HNF4A, a hepatocyte master regulatory transcription factor. Subsequently, SOX4 exerts pioneer factor activity to open biliary regulatory sequences. The results delineate a hierarchy by which gene networks become reprogrammed under physiological conditions, providing deeper insight into the basis for cell fate transitions in animals.
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Affiliation(s)
- Takeshi Katsuda
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Jonathan H Sussman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenji Ito
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Katznelson
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Salina Yuan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Naomi Takenaka
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jinyang Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Allyson J Merrell
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Hector Cure
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Qinglan Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Reyaz Ur Rasool
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Irfan A Asangani
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
| | - Ben Z Stanger
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
- The Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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24
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Mitchell DG, Edgar A, Mateu JR, Ryan JF, Martindale MQ. The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor. Commun Biol 2024; 7:203. [PMID: 38374160 PMCID: PMC10876535 DOI: 10.1038/s42003-024-05901-7] [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: 06/29/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024] Open
Abstract
Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response.
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Affiliation(s)
- Dorothy G Mitchell
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Júlia Ramon Mateu
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
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25
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [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: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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26
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Maytum A, Edginton-White B, Keane P, Cockerill PN, Cazier JB, Bonifer C. Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification. Life Sci Alliance 2024; 7:e202302363. [PMID: 37989524 PMCID: PMC10663361 DOI: 10.26508/lsa.202302363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023] Open
Abstract
Tissue-specific gene regulation during development involves the interplay between transcription factors and epigenetic regulators binding to enhancer and promoter elements. The pattern of active enhancers defines the cellular differentiation state. However, developmental gene activation involves a previous step called chromatin priming which is not fully understood. We recently developed a genome-wide functional assay that allowed us to functionally identify enhancer elements integrated in chromatin regulating five stages spanning the in vitro differentiation of embryonic stem cells to blood. We also measured global chromatin accessibility, histone modifications, and transcription factor binding. The integration of these data identified and characterised cis-regulatory elements which become activated before the onset of gene expression, some of which are primed in a signalling-dependent fashion. Deletion of such a priming element leads to a delay in the up-regulation of its associated gene in development. Our work uncovers the details of a complex network of regulatory interactions with the dynamics of early chromatin opening being at the heart of dynamic tissue-specific gene expression control.
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Affiliation(s)
- Alexander Maytum
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Benjamin Edginton-White
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Peter Keane
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Peter N Cockerill
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jean-Baptiste Cazier
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Constanze Bonifer
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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27
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Peng Y, Song W, Teif VB, Ovcharenko I, Landsman D, Panchenko AR. Detection of new pioneer transcription factors as cell-type-specific nucleosome binders. eLife 2024; 12:RP88936. [PMID: 38293962 PMCID: PMC10945518 DOI: 10.7554/elife.88936] [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] [Indexed: 02/01/2024] Open
Abstract
Wrapping of DNA into nucleosomes restricts accessibility to DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, initiate local chromatin opening, and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding, and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq, and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2, and HeLa-S3 cell lines. Last, we systematically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.
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Affiliation(s)
- Yunhui Peng
- Institute of Biophysics and Department of Physics, Central China Normal UniversityWuhanChina
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Wei Song
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe ParkColchesterUnited Kingdom
| | - Ivan Ovcharenko
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - David Landsman
- National Library of Medicine, National Institutes of HealthBethesdaUnited States
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen’s UniversityKingstonCanada
- Department of Biology and Molecular Sciences, Queen’s UniversityKingstonCanada
- School of Computing, Queen’s UniversityKingstonCanada
- Ontario Institute of Cancer ResearchTorontoCanada
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28
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Thakur A, Park K, Cullum R, Fuglerud BM, Khoshnoodi M, Drissler S, Stephan TL, Lotto J, Kim D, Gonzalez FJ, Hoodless PA. HNF4A guides the MLL4 complex to establish and maintain H3K4me1 at gene regulatory elements. Commun Biol 2024; 7:144. [PMID: 38297077 PMCID: PMC10830483 DOI: 10.1038/s42003-024-05835-0] [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: 03/25/2022] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Hepatocyte nuclear factor 4A (HNF4A/NR2a1), a transcriptional regulator of hepatocyte identity, controls genes that are crucial for liver functions, primarily through binding to enhancers. In mammalian cells, active and primed enhancers are marked by monomethylation of histone 3 (H3) at lysine 4 (K4) (H3K4me1) in a cell type-specific manner. How this modification is established and maintained at enhancers in connection with transcription factors (TFs) remains unknown. Using analysis of genome-wide histone modifications, TF binding, chromatin accessibility and gene expression, we show that HNF4A is essential for an active chromatin state. Using HNF4A loss and gain of function experiments in vivo and in cell lines in vitro, we show that HNF4A affects H3K4me1, H3K27ac and chromatin accessibility, highlighting its contribution to the establishment and maintenance of a transcriptionally permissive epigenetic state. Mechanistically, HNF4A interacts with the mixed-lineage leukaemia 4 (MLL4) complex facilitating recruitment to HNF4A-bound regions. Our findings indicate that HNF4A enriches H3K4me1, H3K27ac and establishes chromatin opening at transcriptional regulatory regions.
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Affiliation(s)
- Avinash Thakur
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Kwangjin Park
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
| | - Bettina M Fuglerud
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | | | - Sibyl Drissler
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Tabea L Stephan
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Jeremy Lotto
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Donghwan Kim
- Center of Cancer Research, National Cancer Institute, Bethesda, 2089, USA
| | - Frank J Gonzalez
- Center of Cancer Research, National Cancer Institute, Bethesda, 2089, USA
| | - Pamela A Hoodless
- Terry Fox Laboratory, BC Cancer, Vancouver, V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, V6T 1Z4, Canada.
- Cell and Developmental Biology Program, University of British Columbia, Vancouver, V6T 1Z4, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, V6T 1Z4, Canada.
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29
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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Gomez MM, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574746. [PMID: 38260422 PMCID: PMC10802488 DOI: 10.1101/2024.01.09.574746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Enteroendocrine cells (EECs), which secrete serotonin (enterochromaffin cells, EC) or a dominant peptide hormone, serve vital physiologic functions. As with any adult human lineage, the basis for terminal cell diversity remains obscure. We replicated human EEC differentiation in vitro , mapped transcriptional and chromatin dynamics that culminate in discrete cell types, and studied abundant EEC precursors expressing selected transcription factors (TFs) and gene programs. Before expressing the pre-terminal factor NEUROD1, non-replicating precursors oscillated between epigenetically similar but transcriptionally distinct ASCL1 + and HES6 hi cell states. Loss of either factor substantially accelerated EEC differentiation and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and hormone-producing cell features. Expressed late in EEC differentiation, the latter TFs mainly bind cis -elements that are accessible in undifferentiated stem cells and tailor the subsequent expression of TF combinations that specify EEC types. Thus, TF oscillations retard EEC maturation to enable accurate EEC diversification.
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30
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Brahma S, Henikoff S. The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes. Nat Genet 2024; 56:100-111. [PMID: 38049663 PMCID: PMC10786724 DOI: 10.1038/s41588-023-01603-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 10/30/2023] [Indexed: 12/06/2023]
Abstract
Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent nucleosome remodeling, which is carried out by complexes such as Brahma-associated factor (BAF). However, the mechanistic links between transcription, nucleosome remodeling and chromatin accessibility are unclear. Here, we used a chemical-genetic approach coupled with time-resolved chromatin profiling to dissect the interplay between RNA Polymerase II (RNAPII), BAF and DNA-sequence-specific transcription factors in mouse embryonic stem cells. We show that BAF dynamically unwraps and evicts nucleosomes at accessible chromatin regions, while RNAPII promoter-proximal pausing stabilizes BAF chromatin occupancy and enhances ATP-dependent nucleosome eviction by BAF. We find that although RNAPII and BAF dynamically probe both transcriptionally active and Polycomb-repressed genomic regions, pluripotency transcription factor chromatin binding confers locus specificity for productive chromatin remodeling and nucleosome eviction by BAF. Our study suggests a paradigm for how functional synergy between dynamically acting chromatin factors regulates locus-specific nucleosome organization and chromatin accessibility.
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Affiliation(s)
- Sandipan Brahma
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Department of Genetics, Cell Biology & Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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31
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Wang P, Wen X, Li H, Lang P, Li S, Lei Y, Shu H, Gao L, Zhao D, Zeng J. Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON. Nat Commun 2023; 14:8459. [PMID: 38123534 PMCID: PMC10733330 DOI: 10.1038/s41467-023-44103-3] [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: 02/07/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Single-cell technologies enable the dynamic analyses of cell fate mapping. However, capturing the gene regulatory relationships and identifying the driver factors that control cell fate decisions are still challenging. We present CEFCON, a network-based framework that first uses a graph neural network with attention mechanism to infer a cell-lineage-specific gene regulatory network (GRN) from single-cell RNA-sequencing data, and then models cell fate dynamics through network control theory to identify driver regulators and the associated gene modules, revealing their critical biological processes related to cell states. Extensive benchmarking tests consistently demonstrated the superiority of CEFCON in GRN construction, driver regulator identification, and gene module identification over baseline methods. When applied to the mouse hematopoietic stem cell differentiation data, CEFCON successfully identified driver regulators for three developmental lineages, which offered useful insights into their differentiation from a network control perspective. Overall, CEFCON provides a valuable tool for studying the underlying mechanisms of cell fate decisions from single-cell RNA-seq data.
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Affiliation(s)
- Peizhuo Wang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Xiao Wen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, 100101, Beijing, China
| | - Han Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Peng Lang
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Shuya Li
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China
| | - Yipin Lei
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Hantao Shu
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China
| | - Lin Gao
- School of Computer Science and Technology, Xidian University, 710071, Xi'an, Shaanxi Province, China
| | - Dan Zhao
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
| | - Jianyang Zeng
- Institute for Interdisciplinary Information Sciences, Tsinghua University, 100084, Beijing, China.
- School of Engineering, Westlake University, 310030, Hangzhou, Zhejiang Province, China.
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32
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Rampersaud A, Connerney J, Waxman DJ. Plasma growth hormone pulses induce male-biased pulsatile chromatin opening and epigenetic regulation in adult mouse liver. eLife 2023; 12:RP91367. [PMID: 38091606 PMCID: PMC10721219 DOI: 10.7554/elife.91367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Sex differences in plasma growth hormone (GH) profiles, pulsatile in males and persistent in females, regulate sex differences in hepatic STAT5 activation linked to sex differences in gene expression and liver disease susceptibility, but little is understood about the fundamental underlying, GH pattern-dependent regulatory mechanisms. Here, DNase-I hypersensitivity site (DHS) analysis of liver chromatin accessibility in a cohort of 18 individual male mice established that the endogenous male rhythm of plasma GH pulse-stimulated liver STAT5 activation induces dynamic, repeated cycles of chromatin opening and closing at several thousand liver DHS and comprises a novel mechanism conferring male bias to liver chromatin accessibility. Strikingly, a single physiological replacement dose of GH given to hypophysectomized male mice restored, within 30 min, liver STAT5 activity and chromatin accessibility at 83% of the dynamic, pituitary hormone-dependent male-biased DHS. Sex-dependent transcription factor binding patterns and chromatin state analysis identified key genomic and epigenetic features distinguishing this dynamic, STAT5-driven mechanism of male-biased chromatin opening from a second GH-dependent mechanism operative at static male-biased DHS, which are constitutively open in male liver. Dynamic but not static male-biased DHS adopt a bivalent-like epigenetic state in female liver, as do static female-biased DHS in male liver, albeit using distinct repressive histone marks in each sex, namely, H3K9me3 at male-biased DHS in female liver and H3K27me3 at female-biased DHS in male liver. Moreover, sex-biased H3K36me3 marks are uniquely enriched at static sex-biased DHS, which may serve to keep these sex-dependent hepatocyte enhancers free of H3K27me3 repressive marks and thus constitutively open. Pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is thus one of two distinct GH-determined mechanisms for establishing widespread sex differences in hepatic chromatin accessibility and epigenetic regulation, both closely linked to sex-biased gene transcription and the sexual dimorphism of liver function.
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Affiliation(s)
- Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston UniversityBostonUnited States
| | - Jeannette Connerney
- Department of Biology and Bioinformatics Program, Boston UniversityBostonUnited States
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston UniversityBostonUnited States
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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Ishida H, Matsumoto A, Tanaka H, Okuda A, Morishima K, Wade PA, Kurumizaka H, Sugiyama M, Kono H. Structural and Dynamic Changes of Nucleosome upon GATA3 Binding. J Mol Biol 2023; 435:168308. [PMID: 37805066 PMCID: PMC10843466 DOI: 10.1016/j.jmb.2023.168308] [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: 08/03/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023]
Abstract
Pioneer factors, which can directly bind to nucleosomes, have been considered to change chromatin conformations. However, the binding impact on the nucleosome is little known. Here, we show how the pioneer factor GATA3 binds to nucleosomal DNA and affects the conformation and dynamics of nucleosomes by using a combination of SAXS, molecular modeling, and molecular dynamics simulations. Our structural models, consistent with the SAXS data, indicate that only one of the two DNA binding domains, N- and C-fingers, of GATA3 binds to an end of the DNA in solution. Our MD simulations further showed that the other unbound end of the DNA increases the fluctuation and enhances the DNA dissociation from the histone core when the N-finger binds to a DNA end, a site near the entry or exit of the nucleosome. However, this was not true for the binding of the C-finger that binds to a location about 15 base pairs distant from the DNA end. In this case, DNA dissociation occurred on the bound end. Taken together, we suggest that the N-finger and C-finger bindings of GATA3 commonly enhance DNA dissociation at one of the two DNA ends (the bound end for the C-finger binding and the unbound end for the N-finger binding), leading to triggering a conformational change in the chromatin.
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Affiliation(s)
- Hisashi Ishida
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan
| | - Atsushi Matsumoto
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan
| | - Hiroki Tanaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan; Present address: Department of Structural Virology, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Aya Okuda
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Ken Morishima
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Paul A Wade
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, 2-1010 Asashironishi, Kumatori, Sennan-gun, Osaka, 590-0494, Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, Institutes for Quantum Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba city, Chiba 263-8555, Japan; Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan.
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Bulyk ML, Drouin J, Harrison MM, Taipale J, Zaret KS. Pioneer factors - key regulators of chromatin and gene expression. Nat Rev Genet 2023; 24:809-815. [PMID: 37740118 DOI: 10.1038/s41576-023-00648-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2023] [Indexed: 09/24/2023]
Affiliation(s)
- Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal (IRCM), Montreal, Quebec, Canada.
- Département de Biochimie, Université de Montréal, Montreal, Quebec, Canada.
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Jussi Taipale
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Applied Tumour Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Peng Y, Song W, Teif VB, Ovcharenko I, Landsman D, Panchenko AR. Detection of new pioneer transcription factors as cell-type specific nucleosome binders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540098. [PMID: 37425841 PMCID: PMC10327179 DOI: 10.1101/2023.05.10.540098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Wrapping of DNA into nucleosomes restricts accessibility to the DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, may initiate local chromatin opening and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2 and HeLa cell lines. Lastly, we systemically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.
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Affiliation(s)
- Yunhui Peng
- current address: Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wei Song
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Vladimir B. Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK
| | - Ivan Ovcharenko
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David Landsman
- National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anna R. Panchenko
- Department of Pathology and Molecular Medicine, Queen’s University, ON, Canada
- Department of Biology and Molecular Sciences, Queen’s University, ON, Canada
- School of Computing, Queen’s University, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
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37
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Lee SW, Frankston CM, Kim J. Epigenome editing in cancer: Advances and challenges for potential therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:191-230. [PMID: 38359969 DOI: 10.1016/bs.ircmb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cancers are diseases caused by genetic and non-genetic environmental factors. Epigenetic alterations, some attributed to non-genetic factors, can lead to cancer development. Epigenetic changes can occur in tumor suppressors or oncogenes, or they may contribute to global cell state changes, making cells abnormal. Recent advances in gene editing technology show potential for cancer treatment. Herein, we will discuss our current knowledge of epigenetic alterations occurring in cancer and epigenetic editing technologies that can be applied to developing therapeutic options.
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Affiliation(s)
- Seung-Won Lee
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Connor Mitchell Frankston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Biomedical Engineering Graduate Program, Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Jungsun Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States; Cancer Biology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States.
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38
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Rampersaud A, Connerney J, Waxman DJ. Plasma Growth Hormone Pulses Induce Male-biased Pulsatile Chromatin Opening and Epigenetic Regulation in Adult Mouse Liver. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554153. [PMID: 37662275 PMCID: PMC10473588 DOI: 10.1101/2023.08.21.554153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Sex-differences in plasma growth hormone (GH) profiles, pulsatile in males and persistent in females, regulate sex differences in hepatic STAT5 activation linked to sex differences in gene expression and liver disease susceptibility, but little is understood about the fundamental underlying, GH pattern-dependent regulatory mechanisms. Here, DNase hypersensitivity site (DHS) analysis of liver chromatin accessibility in a cohort of 18 individual male mice established that the endogenous male rhythm of plasma GH pulse-stimulated liver STAT5 activation induces dynamic, repeated cycles of chromatin opening and closing at several thousand liver DHS and comprises a novel mechanism conferring male bias to liver chromatin accessibility. Strikingly, a single physiological replacement dose of GH given to hypophysectomized male mice restored, within 30 min, liver STAT5 activity and chromatin accessibility at 83% of the pituitary hormone-dependent dynamic male-biased DHS. Sex-dependent transcription factor binding patterns and chromatin state analysis identified key genomic and epigenetic features distinguishing this dynamic, STAT5-driven mechanism of male-biased chromatin opening from a second GH-dependent mechanism operative at static male-biased DHS, which are constitutively open in male liver. Dynamic but not static male-biased DHS adopt a bivalent-like epigenetic state in female liver, as do static female-biased DHS in male liver, albeit using distinct repressive histone marks in each sex, namely, H3K27me3 at female-biased DHS in male liver, and H3K9me3 at male-biased DHS in female liver. Moreover, sex-biased H3K36me3 marks are uniquely enriched at static sex-biased DHS, which may serve to keep these sex-dependent hepatocyte enhancers free of H3K27me3 repressive marks and thus constitutively open. Pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is thus one of two distinct GH-determined mechanisms for establishing widespread sex differences in hepatic chromatin accessibility and epigenetic regulation, both closely linked to sex-biased gene transcription and the sexual dimorphism of liver function.
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Affiliation(s)
- Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215 USA
| | - Jeannette Connerney
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215 USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215 USA
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Katsarou A, Trasanidis N, Ponnusamy K, Kostopoulos IV, Alvarez-Benayas J, Papaleonidopoulou F, Keren K, Sabbattini PMR, Feldhahn N, Papaioannou M, Hatjiharissi E, Sudbery IM, Chaidos A, Caputo VS, Karadimitris A. MAF functions as a pioneer transcription factor that initiates and sustains myelomagenesis. Blood Adv 2023; 7:6395-6410. [PMID: 37224458 PMCID: PMC10598502 DOI: 10.1182/bloodadvances.2023009772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/17/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Deregulated expression of lineage-affiliated transcription factors (TFs) is a major mechanism of oncogenesis. However, how the deregulation of nonlineage affiliated TF affects chromatin to initiate oncogenic transcriptional programs is not well-known. To address this, we studied the chromatin effects imposed by oncogenic MAF as the cancer-initiating driver in the plasma cell cancer multiple myeloma. We found that the ectopically expressed MAF endows myeloma plasma cells with migratory and proliferative transcriptional potential. This potential is regulated by the activation of enhancers and superenhancers, previously inactive in healthy B cells and plasma cells, and the cooperation of MAF with the plasma cell-defining TF IRF4. Forced ectopic MAF expression confirms the de novo ability of oncogenic MAF to convert transcriptionally inert chromatin to active chromatin with the features of superenhancers, leading to the activation of the MAF-specific oncogenic transcriptome and the acquisition of cancer-related cellular phenotypes such as CCR1-dependent cell migration. These findings establish oncogenic MAF as a pioneer transcription factor that can initiate as well as sustain oncogenic transcriptomes and cancer phenotypes. However, despite its pioneer function, myeloma cells remain MAF-dependent, thus validating oncogenic MAF as a therapeutic target that would be able to circumvent the challenges of subsequent genetic diversification driving disease relapse and drug resistance.
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Affiliation(s)
- Alexia Katsarou
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Nikolaos Trasanidis
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Kanagaraju Ponnusamy
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Ioannis V. Kostopoulos
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Jaime Alvarez-Benayas
- Department of the Higher School of Computer Science, Nebrija ARIES Research Group, Universidad Antonio de Nebrija, Madrid, Spain
| | - Foteini Papaleonidopoulou
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Keren Keren
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Pierangela M. R. Sabbattini
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
| | - Niklas Feldhahn
- Centre for Haematology, Imperial College London, London, United Kingdom
| | - Maria Papaioannou
- Division of Haematology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Evdoxia Hatjiharissi
- Division of Haematology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ian M. Sudbery
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Aristeidis Chaidos
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
| | - Valentina S. Caputo
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Cancer Biology and Therapy laboratory, School of Applied Science, London South Bank University, London, United Kingdom
| | - Anastasios Karadimitris
- Department of Immunology and Inflammation, Hugh & Josseline Langmuir Centre for Myeloma Research, Centre for Haematology, Imperial College London, London, United Kingdom
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare National Health Service Trust, London, United Kingdom
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Xu C, Kleinschmidt H, Yang J, Leith E, Johnson J, Tan S, Mahony S, Bai L. Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566246. [PMID: 37986839 PMCID: PMC10659273 DOI: 10.1101/2023.11.08.566246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Despite the unique ability of pioneer transcription factors (PFs) to target nucleosomal sites in closed chromatin, they only bind a small fraction of their genomic motifs. The underlying mechanism of this selectivity is not well understood. Here, we design a high-throughput assay called ChIP-ISO to systematically dissect sequence features affecting the binding specificity of a classic PF, FOXA1. Combining ChIP-ISO with in vitro and neural network analyses, we find that 1) FOXA1 binding is strongly affected by co-binding TFs AP-1 and CEBPB, 2) FOXA1 and AP-1 show binding cooperativity in vitro, 3) FOXA1's binding is determined more by local sequences than chromatin context, including eu-/heterochromatin, and 4) AP-1 is partially responsible for differential binding of FOXA1 in different cell types. Our study presents a framework for elucidating genetic rules underlying PF binding specificity and reveals a mechanism for context-specific regulation of its binding.
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Affiliation(s)
- Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Holly Kleinschmidt
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jianyu Yang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Erik Leith
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jenna Johnson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Song Tan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
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Zhou JL, de Guglielmo G, Ho AJ, Kallupi M, Pokhrel N, Li HR, Chitre AS, Munro D, Mohammadi P, Carrette LLG, George O, Palmer AA, McVicker G, Telese F. Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition. Nat Neurosci 2023; 26:1868-1879. [PMID: 37798411 PMCID: PMC10620093 DOI: 10.1038/s41593-023-01452-y] [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: 09/03/2022] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The amygdala processes positive and negative valence and contributes to addiction, but the cell-type-specific gene regulatory programs involved are unknown. We generated an atlas of single-nucleus gene expression and chromatin accessibility in the amygdala of outbred rats with high and low cocaine addiction-like behaviors following prolonged abstinence. Differentially expressed genes between the high and low groups were enriched for energy metabolism across cell types. Rats with high addiction index (AI) showed increased relapse-like behaviors and GABAergic transmission in the amygdala. Both phenotypes were reversed by pharmacological inhibition of the glyoxalase 1 enzyme, which metabolizes methylglyoxal-a GABAA receptor agonist produced by glycolysis. Differences in chromatin accessibility between high and low AI rats implicated pioneer transcription factors in the basic helix-loop-helix, FOX, SOX and activator protein 1 families. We observed opposite regulation of chromatin accessibility across many cell types. Most notably, excitatory neurons had greater accessibility in high AI rats and inhibitory neurons had greater accessibility in low AI rats.
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Affiliation(s)
- Jessica L Zhou
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | - Aaron J Ho
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Marsida Kallupi
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Narayan Pokhrel
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Hai-Ri Li
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Munro
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Pejman Mohammadi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Olivier George
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Graham McVicker
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Francesca Telese
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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42
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Malik S, Roeder RG. Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators. Nat Rev Genet 2023; 24:767-782. [PMID: 37532915 PMCID: PMC11088444 DOI: 10.1038/s41576-023-00630-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/04/2023]
Abstract
The RNA polymerase II (Pol II) pre-initiation complex (PIC) is a critical node in eukaryotic transcription regulation, and its formation is the major rate-limiting step in transcriptional activation. Diverse cellular signals borne by transcriptional activators converge on this large, multiprotein assembly and are transduced via intermediary factors termed coactivators. Cryogenic electron microscopy, multi-omics and single-molecule approaches have recently offered unprecedented insights into both the structure and cellular functions of the PIC and two key PIC-associated coactivators, Mediator and TFIID. Here, we review advances in our understanding of how Mediator and TFIID interact with activators and affect PIC formation and function. We also discuss how their functions are influenced by their chromatin environment and selected cofactors. We consider how, through its multifarious interactions and functionalities, a Mediator-containing and TFIID-containing PIC can yield an integrated signal processing system with the flexibility to determine the unique temporal and spatial expression pattern of a given gene.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA
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43
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Morozov VM, Riva A, Sarwar S, Kim WJ, Li J, Zhou L, Licht J, Daaka Y, Ishov A. HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers. Nucleic Acids Res 2023; 51:10194-10217. [PMID: 37638746 PMCID: PMC10602887 DOI: 10.1093/nar/gkad700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/21/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Incorporation of histone variant H3.3 comprises active territories of chromatin. Exploring the function of H3.3 in prostate cancer (PC), we found that knockout (KO) of H3.3 chaperone HIRA suppresses PC growth in vitro and in xenograft settings, deregulates androgen-induced gene expression and alters androgen receptor (AR) binding within enhancers of target genes. H3.3 affects transcription in multiple ways, including activation of p300 by phosphorylated H3.3 at Ser-31 (H3.3S31Ph), which results in H3K27 acetylation (H3K27Ac) at enhancers. In turn, H3K27Ac recruits bromodomain protein BRD4 for enhancer-promoter interaction and transcription activation. We observed that HIRA KO reduces H3.3 incorporation, diminishes H3.3S31Ph and H3K27Ac, modifies recruitment of BRD4. These results suggest that H3.3-enriched enhancer chromatin serves as a platform for H3K27Ac-mediated BRD4 recruitment, which interacts with and retains AR at enhancers, resulting in transcription reprogramming. In addition, HIRA KO deregulates glucocorticoid- (GR) driven transcription of genes co-regulated by AR and GR, suggesting a common H3.3/HIRA-dependent mechanism of nuclear receptors function. Expression of HIRA complex proteins is increased in PC compared with normal prostate tissue, especially in high-risk PC groups, and is associated with a negative prognosis. Collectively, our results demonstrate function of HIRA-dependent H3.3 pathway in regulation of nuclear receptors activity.
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Affiliation(s)
- Viacheslav M Morozov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Sadia Sarwar
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Wan-Ju Kim
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jianping Li
- Division of Hematology/Oncology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Lei Zhou
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Yehia Daaka
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
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44
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Neugebauer E, Bastidas-Quintero AM, Weidl D, Full F. Pioneer factors in viral infection. Front Immunol 2023; 14:1286617. [PMID: 37876935 PMCID: PMC10591220 DOI: 10.3389/fimmu.2023.1286617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
Pioneer factors are transcription factors sharing the fascinating ability to bind to compact chromatin and thereby alter its transcriptional fate. Most pioneer factors are known for their importance during embryonic development, for instance, in inducing zygotic genome activation or cell fate decision. Some pioneer factors are actively induced or downregulated by viral infection. With this, viruses are capable to modulate different signaling pathways resulting for example in MHC-receptor up/downregulation which contributes to viral immune evasion. In this article, we review the current state of research on how different viruses (Herpesviruses, Papillomaviruses and Hepatitis B virus) use pioneer factors for their viral replication and persistence in the host, as well as for the development of viral cancer.
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Affiliation(s)
- Eva Neugebauer
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- German Consulting Laboratory for Herpes-Simplex Virus (HSV) and Varizellla-Zoster Virus (VZV), Medical Center, University of Freiburg, Freiburg, Germany
| | - Aura M. Bastidas-Quintero
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Consulting Laboratory for Herpes-Simplex Virus (HSV) and Varizellla-Zoster Virus (VZV), Medical Center, University of Freiburg, Freiburg, Germany
| | - Daniel Weidl
- Institute for Clinical and Molecular Virology, University Hospital Erlangen, Erlangen, Germany
| | - Florian Full
- Institute of Virology, University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- German Consulting Laboratory for Herpes-Simplex Virus (HSV) and Varizellla-Zoster Virus (VZV), Medical Center, University of Freiburg, Freiburg, Germany
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45
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Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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46
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Wu K, Dhillon N, Bajor A, Abrahamson S, Kamakaka RT. Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561072. [PMID: 37873261 PMCID: PMC10592971 DOI: 10.1101/2023.10.05.561072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The interplay between nucleosomes and transcription factors leads to programs of gene expression. Transcriptional silencing involves the generation of a chromatin state that represses transcription and is faithfully propagated through DNA replication and cell division. Using multiple reporter assays, including directly visualizing transcription in single cells, we investigated a diverse set of UAS enhancers and core promoters for their susceptibility to heterochromatic gene silencing. These results show that heterochromatin only stably silences weak and stress induced regulatory elements but is unable to stably repress housekeeping gene regulatory elements and the partial repression did not result in bistable expression states. Permutation analysis of different UAS enhancers and core promoters indicate that both elements function together to determine the susceptibility of regulatory sequences to repression. Specific histone modifiers and chromatin remodellers function in an enhancer specific manner to aid these elements to resist repression suggesting that Sir proteins likely function in part by reducing nucleosome mobility. We also show that the strong housekeeping regulatory elements can be repressed if silencer bound Sir1 is increased, suggesting that Sir1 is a limiting component in silencing. Together, our data suggest that the heterochromatic locus has been optimized to stably silence the weak mating type gene regulatory elements but not strong housekeeping gene regulatory sequences which could help explain why these genes are often found at the boundaries of silenced domains.
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Affiliation(s)
- Kenneth Wu
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Namrita Dhillon
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Antone Bajor
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Sara Abrahamson
- Electrical Engineering Department, Baskin School of Engineering, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
| | - Rohinton T. Kamakaka
- Department of MCD Biology, 1156 High Street, University of California, Santa Cruz, CA 95064 USA
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47
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Arenas-Mena C, Akin S. Widespread priming of transcriptional regulatory elements by incipient accessibility or RNA polymerase II pause in early embryos of the sea urchin Strongylocentrotus purpuratus. Genetics 2023; 225:iyad145. [PMID: 37551428 PMCID: PMC10789315 DOI: 10.1093/genetics/iyad145] [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: 05/17/2023] [Revised: 05/17/2023] [Accepted: 07/25/2023] [Indexed: 08/09/2023] Open
Abstract
Transcriptional regulatory elements (TREs) are the primary nodes that control developmental gene regulatory networks. In embryo stages, larvae, and adult differentiated red spherule cells of the sea urchin Strongylocentrotus purpuratus, transcriptionally engaged TREs are detected by Precision Run-On Sequencing (PRO-seq), which maps genome-wide at base pair resolution the location of paused or elongating RNA polymerase II (Pol II). In parallel, TRE accessibility is estimated by the Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq). Our analysis identifies surprisingly early and widespread TRE accessibility in 4-cell cleavage embryos that is not necessarily followed by concurrent or subsequent transcription. TRE transcriptional differences identified by PRO-seq provide more contrast among embryonic stages than ATAC-seq accessibility differences, in agreement with the apparent excess of accessible but inactive TREs during embryogenesis. Global TRE accessibility reaches a maximum around the 20-hour late blastula stage, which coincides with the consolidation of major embryo regionalizations and peak histone variant H2A.Z expression. A transcriptional potency model based on labile nucleosome TRE occupancy driven by DNA sequences and the prevalence of histone variants is proposed in order to explain the basal accessibility of transcriptionally inactive TREs during embryogenesis. However, our results would not reconcile well with labile nucleosome models based on simple A/T sequence enrichment. In addition, a large number of distal TREs become transcriptionally disengaged during developmental progression, in support of an early Pol II paused model for developmental gene regulation that eventually resolves in transcriptional activation or silencing. Thus, developmental potency in early embryos may be facilitated by incipient accessibility and transcriptional pause at TREs.
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Affiliation(s)
- Cesar Arenas-Mena
- Department of Biology, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY, 10314, USA
- PhD Programs in Biology and Biochemistry at the City University of New York (CUNY), Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA
| | - Serhat Akin
- Department of Biology, College of Staten Island, City University of New York (CUNY), 2800 Victory Boulevard, Staten Island, NY, 10314, USA
- PhD Program in Biology at the City University of New York (CUNY), Graduate Center, 365 Fifth Avenue, New York, NY, 10016, USA
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48
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Harrison MM, Marsh AJ, Rushlow CA. Setting the stage for development: the maternal-to-zygotic transition in Drosophila. Genetics 2023; 225:iyad142. [PMID: 37616526 PMCID: PMC10550319 DOI: 10.1093/genetics/iyad142] [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: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/26/2023] Open
Abstract
The zygote has a daunting task ahead of itself; it must develop from a single cell (fertilized egg) into a fully functioning adult with a multitude of different cell types. In the beginning, the zygote has help from its mother, in the form of gene products deposited into the egg, but eventually, it must rely on its own resources to proceed through development. The transfer of developmental control from the mother to the embryo is called the maternal-to-zygotic transition (MZT). All animals undergo this transition, which is defined by two main processes-the degradation of maternal RNAs and the synthesis of new RNAs from the zygote's own genome. Here, we review the regulation of the MZT in Drosophila, but given the broad conservation of this essential process, much of the regulation is shared among metazoans.
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Affiliation(s)
- Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706USA
| | - Audrey J Marsh
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706USA
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49
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Bondra ER, Rine J. Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2023; 120:e2304343120. [PMID: 37769255 PMCID: PMC10556627 DOI: 10.1073/pnas.2304343120] [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: 03/17/2023] [Accepted: 08/04/2023] [Indexed: 09/30/2023] Open
Abstract
In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Repressor Activator Protein (Rap1), and Sir proteins. Despite an understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high-resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bidirectional HMLα promoter, bound its recognition sequence in silenced chromatin, and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HMLα in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the role of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HMLα when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability.
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Affiliation(s)
- Eliana R. Bondra
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
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50
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Smits JGA, Cunha DL, Amini M, Bertolin M, Laberthonnière C, Qu J, Owen N, Latta L, Seitz B, Roux LN, Stachon T, Ferrari S, Moosajee M, Aberdam D, Szentmary N, van Heeringen SJ, Zhou H. Identification of the regulatory circuit governing corneal epithelial fate determination and disease. PLoS Biol 2023; 21:e3002336. [PMID: 37856539 PMCID: PMC10586658 DOI: 10.1371/journal.pbio.3002336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/14/2023] [Indexed: 10/21/2023] Open
Abstract
The transparent corneal epithelium in the eye is maintained through the homeostasis regulated by limbal stem cells (LSCs), while the nontransparent epidermis relies on epidermal keratinocytes for renewal. Despite their cellular similarities, the precise cell fates of these two types of epithelial stem cells, which give rise to functionally distinct epithelia, remain unknown. We performed a multi-omics analysis of human LSCs from the cornea and keratinocytes from the epidermis and characterized their molecular signatures, highlighting their similarities and differences. Through gene regulatory network analyses, we identified shared and cell type-specific transcription factors (TFs) that define specific cell fates and established their regulatory hierarchy. Single-cell RNA-seq (scRNA-seq) analyses of the cornea and the epidermis confirmed these shared and cell type-specific TFs. Notably, the shared and LSC-specific TFs can cooperatively target genes associated with corneal opacity. Importantly, we discovered that FOSL2, a direct PAX6 target gene, is a novel candidate associated with corneal opacity, and it regulates genes implicated in corneal diseases. By characterizing molecular signatures, our study unveils the regulatory circuitry governing the LSC fate and its association with corneal opacity.
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Affiliation(s)
- Jos G. A. Smits
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Dulce Lima Cunha
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Maryam Amini
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | | | - Camille Laberthonnière
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Jieqiong Qu
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Nicholas Owen
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
| | - Lorenz Latta
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
- Department of Ophthalmology, Saarland University Medical Center, UKS, Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, UKS, Homburg, Germany
| | | | - Tanja Stachon
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | | | - Mariya Moosajee
- Development, Ageing and Disease, UCL Institute of Ophthalmology, London, United Kingdom
- Department of Genetics, Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
| | - Daniel Aberdam
- INSERM U976, Paris, France
- Université de Paris, INSERM U1138, Centre des Cordeliers, Paris, France
| | - Nora Szentmary
- Dr. Rolf M. Schwiete Center for Limbal Stem Cell and Aniridia Research, Saarland University, Homburg/Saar, Germany
| | - Simon J. van Heeringen
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Huiqing Zhou
- Faculty of Science, Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
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