1
|
Low BH, Kaliskar KK, Perna S, Lee B. Cross-cellular analysis of chromatin accessibility markers H3K4me3 and DNase in the context of detecting cell-identity genes: An "all-or-nothing" approach. J Bioinform Comput Biol 2025; 23:2540002. [PMID: 40169369 DOI: 10.1142/s0219720025400025] [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] [Indexed: 04/03/2025]
Abstract
Cell identity is often associated to a subset of highly-expressed genes that define the cell processes, as opposed to essential genes that are always active. Cell-specific genes may be defined in opposition to essential genes, or via experimental means. Detection of said cell-specific genes is often a primary goal in the study of novel biosamples. Chromatin accessibility markers (such as DNase and H3K4me3) help identify actively transcribed genes, but data can be difficult to come by for entirely novel biosamples. In this study, we investigate the possibility of associating the cell-specificity status of genes with chromatin accessibility markers from different cell lines, and we suggest that the number of cell lines in which a gene is found to be marked by DNase/H3K4me3 is predictive of the essentiality status itself. We define a measure called the Cross-cellular Chromatin Openness (CCO) level, and show that it is associated with the essentiality status using two differentiation experiments. We then compare the CCO-level predictive power to existing scRNA-Seq and bulk RNA-Seq methods, showing it has good concordance when applicable.
Collapse
Affiliation(s)
- Boon How Low
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 50 Nanyang Drive, Singapore 639798, Singapore
| | - Kaushal Krishna Kaliskar
- Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Drive, Singapore 639798, Singapore
| | - Stefano Perna
- Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Drive, Singapore 639798, Singapore
| | - Bernett Lee
- Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Drive, Singapore 639798, Singapore
| |
Collapse
|
2
|
Nijsure MP, Tobin B, Jones DL, Lang A, Hallström G, Baitner M, Tanner GI, Moharrer Y, Panebianco CJ, Seidl EG, Dyment NA, Szeto GL, Wood L, Boerckel JD. YAP regulates periosteal expansion in fracture repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.23.630086. [PMID: 39764016 PMCID: PMC11703278 DOI: 10.1101/2024.12.23.630086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2025]
Abstract
Bone fracture repair initiates by periosteal expansion. The periosteum is typically quiescent, but upon fracture, periosteal cells proliferate and contribute to bone fracture repair. The expansion of the periosteum is regulated by gene transcription; however, the molecular mechanisms behind periosteal expansion are unclear. Here, we show that Yes-Associated Protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) mediate periosteal expansion and periosteal cell proliferation. Bone fracture increases the number of YAP-expressing periosteal cells, and deletion of YAP and TAZ from Osterix (Osx) expressing cells impairs early periosteal expansion. Mechanistically, YAP regulates both 'cell-intrinsic' and 'cell-extrinsic' factors that allow for periosteal expansion. Specifically, we identified Bone Morphogenetic Protein 4 (BMP4) as a cell extrinsic factor regulated by YAP, that rescues the impairment of periosteal expansion upon YAP/TAZ deletion. Together, these data establish YAP mediated transcriptional mechanisms that induce periosteal expansion in the early stages of fracture repair and provide new putative targets for therapeutic interventions.
Collapse
Affiliation(s)
- Madhura P Nijsure
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brendan Tobin
- School of Chemical and Biomolecular Engineering, Georgia Tech College of Engineering, Atlanta, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, USA
| | - Dakota L Jones
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Annemarie Lang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Grey Hallström
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Miriam Baitner
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabrielle I Tanner
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yasaman Moharrer
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Mechanical Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher J Panebianco
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth G Seidl
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nathaniel A Dyment
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory L Szeto
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, USA
| | - Levi Wood
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Tech College of Engineering, Atlanta, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, USA
| | - Joel D Boerckel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Department of Orthopedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
3
|
Prat A, Muñoz D, Lizarraga A, Seifert-Gorzycki J, Sanchez-Vazquez E, Johnson P, Mazzulla PHS, de Miguel N. Chromatin accessibility and gene expression in the parasite Trichomonas vaginalis. RESEARCH SQUARE 2024:rs.3.rs-5455511. [PMID: 39764130 PMCID: PMC11702783 DOI: 10.21203/rs.3.rs-5455511/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
Abstract
Trichomonas vaginalis, the most common non-viral sexually transmitted parasite, causes more than 270 million infections annually. The infection's outcome varies greatly depending on different factors that include variation in human immune responses, the vaginal microbiome, and the inherent virulence of the strain. Although the pathogenicity of the different strains depends, at least partially, on differential gene expression of virulence genes; the regulatory mechanisms governing this transcriptional control remain incompletely understood. While many studies have reported a positive correlation between gene expression and chromatin accessibility in other cells, this relationship has not been analyzed in T. vaginalis. To address these questions, we selected two contrasting T. vaginalis strains based on their interactions with host cells: B7268 strain, a highly adherent one and resistant to metronidazole, and NYH209 strain, a poorly adherent one and sensitive to metronidazole. Next, we combined the assay for transposase-accessible chromatin using sequencing (ATAC-seq) with RNA sequencing (RNA-seq), to delve into the relationship between chromatin accessibility and gene expression in these distinct T. vaginalis strains. Our findings demonstrate a correlation between chromatin accessibility and gene expression across both strains. Moreover, we found that chromatin accessibility plays a pivotal role in modulating mRNA expression levels of several established genes linked to parasite pathogenesis and drug resistance. We also identified several open chromatin peaks residing at intergenic regions, revealing possible distal regulatory elements that may control gene expression. These results highlight the importance of chromatin accessibility in modulating gene expression in the parasite T. vaginalis, with possible consequences in pathogenesis and/or drug treatment.
Collapse
Affiliation(s)
- Agustina Prat
- Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM
| | - Daniela Muñoz
- Instituto Tecnológico Chascomús (INTECH), CONICET-UNSAM
| | | | | | | | | | | | | |
Collapse
|
4
|
Liu C, Ao N, Liang Y, Ma T, Wang Q, Wang Z, Wu F, Zhang Z, Fang Y, Wang M, Pan Y, Fu J. Analysis of cis-regulatory changes underlying phenotype divergence shaped by domestication in pigs. Front Genet 2024; 15:1421859. [PMID: 39582787 PMCID: PMC11581869 DOI: 10.3389/fgene.2024.1421859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 10/07/2024] [Indexed: 11/26/2024] Open
Abstract
Background Cis-regulatory elements (CREs) are regions of DNA that regulate the expression of nearby genes. Changes in these elements can lead to phenotypic variations and adaptations in different populations. However, the regulatory dynamics underlying the local adaptation of traits remain poorly understood in Chinese and Western pigs. By comparing the chromatin accessibility profiles of skeletal muscle, liver, and fat between these two pig populations, we aimed to identify key regulatory elements that could explain phenotypic differences observed between the two groups. Results Our results revealed that the genome-wide chromatin accessibility profiles were largely similar at a qualitative level within tissues. However, we also identified local regions that exhibited quantitative differences, most of which occurred in liver tissue. Interestingly, we found that most of the increased chromatin accessibility in the livers of Chinese pigs was associated with tissue-specific openness. Furthermore, we observed a positive correlation between the ATAC-seq signal at the transcript start site (TSS) and the expression levels of nearby genes. Motif enrichment analysis revealed NR2F1 as a key regulator in Chinese pigs. Differentially expressed genes (DEGs) in Chinese pigs showed enrichment for NR2F1 response targets. One of the genes regulated by NR2F1 in Chinese pigs, NPC1, harbored a high alternative allelic frequency in the intron region. Conclusion Overall, our study provides valuable insights into the regulatory dynamics underlying phenotypic variation in pigs. By elucidating the role of CREs in driving phenotypic variation, we can better understand the genetic basis of complex traits and potentially identify targets for genetic improvement in livestock breeding programs.
Collapse
Affiliation(s)
- Chunpeng Liu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Na Ao
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yuwen Liang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Tingting Ma
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Qishan Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Fen Wu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenyang Zhang
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yifei Fang
- Department of Animal Science, Cornell University, Ithaca, NY, United States
| | - Minghui Wang
- Center for Life Science Ventures, Cornell University, Ithaca, NY, United States
| | - Yuchun Pan
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Fu
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
- Innovative Institute of Animal Healthy Breeding, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| |
Collapse
|
5
|
Ocampo D, Damon LJ, Sanford L, Holtzen SE, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of p53 to DNA. Life Sci Alliance 2024; 7:e202402638. [PMID: 38969365 PMCID: PMC11231577 DOI: 10.26508/lsa.202402638] [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: 02/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
Zn2+ is an essential metal required by approximately 850 human transcription factors. How these proteins acquire their essential Zn2+ cofactor and whether they are sensitive to changes in the labile Zn2+ pool in cells remain open questions. Using ATAC-seq to profile regions of accessible chromatin coupled with transcription factor enrichment analysis, we examined how increases and decreases in the labile zinc pool affect chromatin accessibility and transcription factor enrichment. We found 685 transcription factor motifs were differentially enriched, corresponding to 507 unique transcription factors. The pattern of perturbation and the types of transcription factors were notably different at promoters versus intergenic regions, with zinc-finger transcription factors strongly enriched in intergenic regions in elevated Zn2+ To test whether ATAC-seq and transcription factor enrichment analysis predictions correlate with changes in transcription factor binding, we used ChIP-qPCR to profile six p53 binding sites. We found that for five of the six targets, p53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc alter chromatin accessibility and transcription factor binding to DNA.
Collapse
Affiliation(s)
- Daniel Ocampo
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Leah J Damon
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Lynn Sanford
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Samuel E Holtzen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Taylor Jones
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Mary A Allen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| |
Collapse
|
6
|
Wu C, Huang J. Enhancer selectivity across cell types delineates three functionally distinct enhancer-promoter regulation patterns. BMC Genomics 2024; 25:483. [PMID: 38750461 PMCID: PMC11097474 DOI: 10.1186/s12864-024-10408-w] [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: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Multiple enhancers co-regulating the same gene is prevalent and plays a crucial role during development and disease. However, how multiple enhancers coordinate the same gene expression across various cell types remains largely unexplored at genome scale. RESULTS We develop a computational approach that enables the quantitative assessment of enhancer specificity and selectivity across diverse cell types, leveraging enhancer-promoter (E-P) interactions data. We observe two well-known gene regulation patterns controlled by enhancer clusters, which regulate the same gene either in a limited number of cell types (Specific pattern, Spe) or in the majority of cell types (Conserved pattern, Con), both of which are enriched for super-enhancers (SEs). We identify a previously overlooked pattern (Variable pattern, Var) that multiple enhancers link to the same gene, but rarely coexist in the same cell type. These three patterns control the genes associating with distinct biological function and exhibit unique epigenetic features. Specifically, we discover a subset of Var patterns contains Shared enhancers with stable enhancer-promoter interactions in the majority of cell types, which might contribute to maintaining gene expression by recruiting abundant CTCF. CONCLUSIONS Together, our findings reveal three distinct E-P regulation patterns across different cell types, providing insights into deciphering the complexity of gene transcriptional regulation.
Collapse
Affiliation(s)
- Chengyi Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, Fujian, China.
| |
Collapse
|
7
|
van Dijk AD, Hoff FW, Qiu Y, Hubner SE, Go RL, Ruvolo VR, Leonti AR, Gerbing RB, Gamis AS, Aplenc R, Kolb EA, Alonzo TA, Meshinchi S, de Bont ESJM, Horton TM, Kornblau SM. Chromatin Profiles Are Prognostic of Clinical Response to Bortezomib-Containing Chemotherapy in Pediatric Acute Myeloid Leukemia: Results from the COG AAML1031 Trial. Cancers (Basel) 2024; 16:1448. [PMID: 38672531 PMCID: PMC11048007 DOI: 10.3390/cancers16081448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The addition of the proteasome inhibitor bortezomib to standard chemotherapy did not improve survival in pediatric acute myeloid leukemia (AML) when all patients were analyzed as a group in the Children's Oncology Group phase 3 trial AAML1031 (NCT01371981). Proteasome inhibition influences the chromatin landscape and proteostasis, and we hypothesized that baseline proteomic analysis of histone- and chromatin-modifying enzymes (HMEs) would identify AML subgroups that benefitted from bortezomib addition. A proteomic profile of 483 patients treated with AAML1031 chemotherapy was generated using a reverse-phase protein array. A relatively high expression of 16 HME was associated with lower EFS and higher 3-year relapse risk after AML standard treatment compared to low expressions (52% vs. 29%, p = 0.005). The high-HME profile correlated with more transposase-accessible chromatin, as demonstrated via ATAC-sequencing, and the bortezomib addition improved the 3-year overall survival compared with standard therapy (62% vs. 75%, p = 0.033). These data suggest that there are pediatric AML populations that respond well to bortezomib-containing chemotherapy.
Collapse
Affiliation(s)
- Anneke D. van Dijk
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.W.H.)
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Fieke W. Hoff
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.W.H.)
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Yihua Qiu
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Stefan E. Hubner
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Robin L. Go
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Vivian R. Ruvolo
- Department of Molecular Therapy and Hematology, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| | - Amanda R. Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Alan S. Gamis
- Department of Hematology-Oncology, Children’s Mercy Hospitals and Clinics, Kansas City, MO 64108, USA
| | - Richard Aplenc
- Division of Pediatric Oncology and Stem Cell Transplant, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Edward A. Kolb
- Nemours Center for Cancer and Blood Disorders, Alfred I. DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Todd A. Alonzo
- COG Statistics and Data Center, Monrovia, CA 91016, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90007, USA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eveline S. J. M. de Bont
- Division of Pediatric Oncology and Hematology, Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (F.W.H.)
| | - Terzah M. Horton
- Texas Children’s Cancer and Hematology Centers, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven M. Kornblau
- Department of Leukemia, M.D. Anderson Cancer Center, The University of Texas, Houston, TX 78712, USA
| |
Collapse
|
8
|
Reeves GA, Singh PP, Brunet A. Chromatin Accessibility Profiling and Data Analysis Using ATAC-seq in Nothobranchius furzeri. Cold Spring Harb Protoc 2024; 2024:107747. [PMID: 37100469 DOI: 10.1101/pdb.prot107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
The state of genome-wide chromatin accessibility in cells, tissues, or organisms can be investigated with a technique called assay for transposase-accessible chromatin using sequencing (ATAC-seq). ATAC-seq is a powerful approach for profiling the epigenomic landscape of cells using very low input materials. Analysis of chromatin accessibility data allows for prediction of gene expression and identification of regulatory elements such as potential enhancers and specific transcription-factor binding sites. Here, we describe an optimized ATAC-seq protocol for the preparation of isolated nuclei and subsequent next-generation sequencing from whole embryos and tissues of the African turquoise killifish (Nothobranchius furzeri). Importantly, we provide an overview of a pipeline for processing and analyzing ATAC-seq data from killifish.
Collapse
Affiliation(s)
- G Adam Reeves
- Department of Genetics, Stanford University, Stanford University, Stanford, California 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford University, Stanford, California 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford University, Stanford, California 94305, USA
- Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, California 94305, USA
| |
Collapse
|
9
|
Damon LJ, Ocampo D, Sanford L, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567954. [PMID: 38045276 PMCID: PMC10690171 DOI: 10.1101/2023.11.20.567954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Zinc (Zn2+) is an essential metal required by approximately 2500 proteins. Nearly half of these proteins act on DNA, including > 850 human transcription factors, polymerases, DNA damage response factors, and proteins involved in chromatin architecture. How these proteins acquire their essential Zn2+ cofactor and whether they are sensitive to changes in the labile Zn2+ pool in cells remain open questions. Here, we examine how changes in the labile Zn2+ pool affect chromatin accessibility and transcription factor binding to DNA. We observed both increases and decreases in accessibility in different chromatin regions via ATAC-seq upon treating MCF10A cells with elevated Zn2+ or the Zn2+-specific chelator tris(2-pyridylmethyl)amine (TPA). Transcription factor enrichment analysis was used to correlate changes in chromatin accessibility with transcription factor motifs, revealing 477 transcription factor motifs that were differentially enriched upon Zn2+ perturbation. 186 of these transcription factor motifs were enriched in Zn2+ and depleted in TPA, and the majority correspond to Zn2+ finger transcription factors. We selected TP53 as a candidate to examine how changes in motif enrichment correlate with changes in transcription factor occupancy by ChIP-qPCR. Using publicly available ChIP-seq and nascent transcription datasets, we narrowed the 50,000+ ATAC-seq peaks to 2164 TP53 targets and subsequently selected 6 high-probability TP53 binding sites for testing. ChIP-qPCR revealed that for 5 of the 6 targets, TP53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc directly alter chromatin accessibility and transcription factor binding to DNA.
Collapse
Affiliation(s)
- Leah J. Damon
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Daniel Ocampo
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Lynn Sanford
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Taylor Jones
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Mary A. Allen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Robin D. Dowell
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| |
Collapse
|
10
|
Anderson AG, Rogers BB, Loupe JM, Rodriguez-Nunez I, Roberts SC, White LM, Brazell JN, Bunney WE, Bunney BG, Watson SJ, Cochran JN, Myers RM, Rizzardi LF. Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer's disease-specific cis-regulatory elements. CELL GENOMICS 2023; 3:100263. [PMID: 36950385 PMCID: PMC10025452 DOI: 10.1016/j.xgen.2023.100263] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/06/2022] [Accepted: 01/12/2023] [Indexed: 02/05/2023]
Abstract
Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer's disease (AD) and unaffected controls have been well documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq plus snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell type-specific transposase accessible regions enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as candidate transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respectively. Microglia links were globally enriched for heritability of AD risk and previously identified active regulatory regions.
Collapse
Affiliation(s)
| | - Brianne B. Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jacob M. Loupe
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Lauren M. White
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - William E. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Blynn G. Bunney
- Department of Psychiatry and Human Behavior, College of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stanley J. Watson
- Mental Health Research Institute, University of Michigan, Ann Arbor, MI, USA
| | | | | | | |
Collapse
|
11
|
Mekapogu M, Kwon OK, Song HY, Jung JA. Towards the Improvement of Ornamental Attributes in Chrysanthemum: Recent Progress in Biotechnological Advances. Int J Mol Sci 2022; 23:ijms232012284. [PMID: 36293140 PMCID: PMC9603847 DOI: 10.3390/ijms232012284] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
Incessant development and introduction of novel cultivars with improved floral attributes are vital in the dynamic ornamental industry. Chrysanthemum (Chrysanthemum morifolium) is a highly favored ornamental plant, ranking second globally in the cut flower trade, after rose. Development of new chrysanthemum cultivars with improved and innovative modifications in ornamental attributes, including floral color, shape, plant architecture, flowering time, enhanced shelf life, and biotic and abiotic stress tolerance, is a major goal in chrysanthemum breeding. Despite being an economically important ornamental plant, the application of conventional and molecular breeding approaches to various key traits of chrysanthemum is hindered owing to its genomic complexity, heterozygosity, and limited gene pool availability. Although classical breeding of chrysanthemum has resulted in the development of several hundreds of cultivars with various morphological variations, the genetic and transcriptional control of various important ornamental traits remains unclear. The coveted blue colored flowers of chrysanthemums cannot be achieved through conventional breeding and mutation breeding due to technical limitations. However, blue-hued flower has been developed by genetic engineering, and transgenic molecular breeding has been successfully employed, leading to substantial progress in improving various traits. The recent availability of whole-genome sequences of chrysanthemum offers a platform to extensively employ MAS to identify a large number of markers for QTL mapping, and GWAS to dissect the genetic control of complex traits. The combination of NGS, multi-omic platforms, and genome editing technologies has provided a tremendous scope to decipher the molecular and regulatory mechanisms. However, the application and integration of these technologies remain inadequate for chrysanthemum. This review, therefore, details the significance of floral attributes, describes the efforts of recent advancements, and highlights the possibilities for future application towards the improvement of crucial ornamental traits in the globally popular chrysanthemum plant.
Collapse
|
12
|
Kiani K, Sanford EM, Goyal Y, Raj A. Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations. Mol Syst Biol 2022; 18:e10979. [PMID: 36069349 PMCID: PMC9450098 DOI: 10.15252/msb.202210979] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
A major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor-binding events. In concert with RNA-sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short-duration treatments with specific perturbations. Here, we used tandem, bulk ATAC-seq, and RNA-seq measurements from MCF-7 breast carcinoma cells to systematically evaluate the concordance between changes in accessibility and changes in expression in response to retinoic acid and TGF-β. We found two classes of genes whose expression showed a significant change: those that showed some changes in the accessibility of nearby chromatin, and those that showed virtually no change despite strong changes in expression. The peaks associated with genes in the former group had lower baseline accessibility prior to exposure to signal. Focusing the analysis specifically on peaks with motifs for transcription factors associated with retinoic acid and TGF-β signaling did not reduce the lack of correspondence. Analysis of paired chromatin accessibility and gene expression data from distinct paths along the hematopoietic differentiation trajectory showed a much stronger correspondence, suggesting that the multifactorial biological processes associated with differentiation may lead to changes in chromatin accessibility that reflect rather than driving altered transcriptional status. Together, these results show many gene expression changes can happen independently of changes in the accessibility of local chromatin in the context of a single-factor perturbation.
Collapse
Affiliation(s)
- Karun Kiani
- Genetics and Epigenetics, Cell and Molecular Biology Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Eric M Sanford
- Genomics and Computational Biology Graduate Group, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Yogesh Goyal
- Department of Bioengineering, School of Engineering and Applied SciencesUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Cell and Developmental Biology, Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
- Center for Synthetic BiologyNorthwestern UniversityChicagoIllinoisUSA
| | - Arjun Raj
- Department of Bioengineering, School of Engineering and Applied SciencesUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
- Department of Genetics, Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| |
Collapse
|
13
|
Wu J, Huang Q, Li Q, Gu Y, Zhan Y, Wang T, Chen J, Zeng Z, Lv Y, Zhao J, Xia J, Xie J. Increased Methyl-CpG-Binding Domain Protein 2 Promotes Cigarette Smoke-Induced Pulmonary Hypertension. Front Oncol 2022; 12:879793. [PMID: 35785161 PMCID: PMC9243313 DOI: 10.3389/fonc.2022.879793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Pulmonary hypertension (PH) is a chronic vascular proliferative disorder. While cigarette smoke (CS) plays a vital part in PH related to chronic obstructive pulmonary disease (COPD). Methyl-CpG-Binding Domain Protein 2 (MBD2) has been linked to multiple proliferative diseases. However, the specific mechanisms of MBD2 in CS-induced PH remain to be elucidated. Herein, the differential expression of MBD2 was tested between the controls and the PH patients’ pulmonary arteries, CS-exposed rat models’ pulmonary arteries, and primary human pulmonary artery smooth muscle cells (HPASMCs) following cigarette smoke extract (CSE) stimulation. As a result, PH patients and CS-induced rats and HPASMCs showed an increase in MBD2 protein expression compared with the controls. Then, MBD2 silencing was used to investigate the function of MBD2 on CSE-induced HPASMCs’ proliferation, migration, and cell cycle progression. As a consequence, CSE could induce HPASMCs’ increased proliferation and migration, and cell cycle transition, which were suppressed by MBD2 interference. Furthermore, RNA-seq, ChIP-qPCR, and MassARRAY were conducted to find out the downstream mechanisms of MBD2 for CS-induced pulmonary vascular remodeling. Subsequently, RNA-seq revealed MBD2 might affect the transcription of BMP2 gene, which furtherly altered the expression of BMP2 protein. ChIP-qPCR demonstrated MBD2 could bind BMP2’s promotor. MassARRAY indicated that MBD2 itself could not directly affect DNA methylation. In sum, our results indicate that increased MBD2 expression promotes CS-induced pulmonary vascular remodeling. The fundamental mechanisms may be that MBD2 can bind BMP2’s promoter and downregulate its expression. Thus, MBD2 may promote the occurrence of the CS-induced PH.
Collapse
Affiliation(s)
- Jixing Wu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Huang
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinghai Li
- Department of Respiratory and Critical Care Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, China
| | - Yiya Gu
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Zhan
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Wang
- Department of Respiratory Disease, Thoracic Disease Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinkun Chen
- Department of Science, Western University, London, ON, Canada
| | - Zhilin Zeng
- Department and Institute of Infectious Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongman Lv
- Health Management Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianping Zhao
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Xia
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jungang Xie, ; Jie Xia,
| | - Jungang Xie
- Department of Respiratory and Critical Care Medicine, National Clinical Research Center of Respiratory Disease, Key Laboratory of Pulmonary Diseases of Health Ministry, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Jungang Xie, ; Jie Xia,
| |
Collapse
|
14
|
Liu T, Tang J, Li X, Lin Y, Yang Y, Ma K, Hui Z, Ma H, Qin Y, Lei H, Yang Y. The Key Network of mRNAs and miRNAs Regulated by HIF1A in Hypoxic Hepatocellular Carcinoma Cells. Front Genet 2022; 13:857507. [PMID: 35774500 PMCID: PMC9237512 DOI: 10.3389/fgene.2022.857507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/03/2022] [Indexed: 01/17/2023] Open
Abstract
Purpose: Hypoxia plays an essential role in the progression of hepatocellular carcinoma (HCC), whereas hypoxia inducible factor-1 (HIF-1) is the key transcription factor allowing HCC to survive hypoxia. The aim of this study was to define the essential mRNAs and miRNAs regulated by HIF1A and dissect their functions, interactions, and tumor-infiltrating immune cells in HCC. Methods: A human HCC cell line HepG2 was used as a cell model of HCC. The CRISPR/Cas9 system was used to knock out HIF1A in HepG2 cells, and RNA sequencing was utilized to characterize differentially expressed mRNAs and miRNAs in the HIF1A-knockout HepG2 cells; the identified candidates were then analyzed by GO annotation and KEGG pathway enrichment to study their function and establish a PPI network. Quantitative (q) PCR was used to verify if there were significant differences in the expression of mRNAs, and the association of the selected mRNAs expression with immune cell infiltration levels was further analyzed using The Cancer Genome Atlas (TCGA) pan-cancer data. Results: Using RNA-sequencing, we discovered that there were 1535 mRNAs differentially expressed (adjusted p < 0.05, |fold change|>1.5) in the HIF1A-knockout HepG2 cells, among which there were 644 mRNAs upregulated and 891 mRNAs downregulated. GO annotation and KEGG pathway enrichment showed that these mRNAs were involved in glycolysis/gluconeogenesis, PI3K-Akt signaling pathways, and HIF-1 signaling pathways. In addition, we found that there were 309 miRNAs differentially expressed (adjusted p < 0.05, |fold change|>1.5) in the HIF1A-knockout HepG2 cells, of which there were 213 miRNAs upregulated and 96 miRNAs downregulated. Our further analyses uncovered that these miRNA putative targets were involved in the hippo signaling pathway, axon guidance, and tight junction. Moreover, the construction and analysis of the PPI network showed that OASL, IL6, and TAF1 were recognized as hub genes with the highest connectivity degrees. Importantly, in the HIF1A-knockout HepG2 cells, our qRT-PCR data confirmed the selected mRNA changes revealed by RNA-sequencing, and with TCGA pan-cancer data, we revealed that the expressional levels of these three genes, LUM, SCOC, and CCL2, were associated with immune cell infiltration levels. Conclusion: The identified potential key network of mRNAs and miRNAs regulated by HIF1A in the HCC cells suggests a key role of HIF1A in the tumorigenesis of HCC.
Collapse
Affiliation(s)
- Tong Liu
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Jing Tang
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Xiaoyu Li
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Yuan Lin
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Yuma Yang
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Kai Ma
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Zhaoyuan Hui
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Hong Ma
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Yanyan Qin
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| | - Hetian Lei
- Shenzhen Eye Hospital, Shenzhen Eye Institute, Jinan University, Shenzhen, China
| | - Yanhui Yang
- Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, The School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
| |
Collapse
|
15
|
Zhang Z, Lin L, Chen H, Ye W, Dong S, Zheng X, Wang Y. ATAC-Seq Reveals the Landscape of Open Chromatin and cis-Regulatory Elements in the Phytophthora sojae Genome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:301-310. [PMID: 35037783 DOI: 10.1094/mpmi-11-21-0291-ta] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nucleosome-free open chromatin often harbors transcription factor (TF)-binding sites that are associated with active cis-regulatory elements. However, analysis of open chromatin regions has rarely been applied to oomycete or fungal plant pathogens. In this study, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify open chromatin and cis-regulatory elements in Phytophthora sojae at the mycelial stage. We identified 10,389 peaks representing nucleosome-free regions (NFRs). The peaks were enriched in gene-promoter regions and associated with 40% of P. sojae genes; transcription levels were higher for genes with multiple peaks than genes with a single peak and were higher for genes with a single peak than genes without peak. Chromatin accessibility was positively correlated with gene transcription level. Through motif discovery based on NFR peaks in core promoter regions, 25 candidate cis-regulatory motifs with evidence of TF-binding footprints were identified. These motifs exhibited various preferences for location in the promoter region and associations with the transcription level of their target genes, which included some putative pathogenicity-related genes. As the first study revealing the landscape of open chromatin and the correlation between chromatin accessibility and gene transcription level in oomycetes, the results provide a technical reference and data resources for future studies on the regulatory mechanisms of gene transcription.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Zhichao Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Long Lin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Han Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
- Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), Nanjing, Jiangsu 210095, China
| |
Collapse
|
16
|
Nair VD, Vasoya M, Nair V, Smith GR, Pincas H, Ge Y, Douglas CM, Esser KA, Sealfon SC. Differential analysis of chromatin accessibility and gene expression profiles identifies cis-regulatory elements in rat adipose and muscle. Genomics 2021; 113:3827-3841. [PMID: 34547403 DOI: 10.1016/j.ygeno.2021.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023]
Abstract
Chromatin accessibility is a key factor influencing gene expression. We optimized the Omni-ATAC-seq protocol and used it together with RNA-seq to investigate cis-regulatory elements in rat white adipose and skeletal muscle, two tissues with contrasting metabolic functions. While promoter accessibility correlated with RNA expression, integration of the two datasets identified tissue-specific differentially accessible regions (DARs) that predominantly localized in intergenic and intron regions. DARs were mapped to differentially expressed (DE) genes enriched in distinct biological processes in each tissue. Randomly selected DE genes were validated by qPCR. Top enriched motifs in DARs predicted binding sites for transcription factors (TFs) showing tissue-specific up-regulation. The correlation between differential chromatin accessibility at a given TF binding motif and differential expression of target genes further supported the functional relevance of that motif. Our study identified cis-regulatory regions that likely play a major role in the regulation of tissue-specific gene expression in adipose and muscle.
Collapse
Affiliation(s)
- Venugopalan D Nair
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Mital Vasoya
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vishnu Nair
- Department of Computer Sciences, Columbia University, New York, NY 10027, USA
| | - Gregory R Smith
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hanna Pincas
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yongchao Ge
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Collin M Douglas
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Karyn A Esser
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32610, USA
| | - Stuart C Sealfon
- Department of Neurology, Center for Advanced Research on Diagnostic Assays, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
17
|
A long noncoding RNA, LncMyoD, modulates chromatin accessibility to regulate muscle stem cell myogenic lineage progression. Proc Natl Acad Sci U S A 2020; 117:32464-32475. [PMID: 33293420 PMCID: PMC7768704 DOI: 10.1073/pnas.2005868117] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic regulations control the accessibility of transcription factors to their target regions. Modulation of chromatin accessibility determines which transcripts to be expressed and therefore, defines cell identity. Chromatin modulation during cell fate determination involves a complex regulatory network, yet the comprehensive view remains to be explored. Here, we provide a global view of chromatin accessibility during muscle stem cell activation. We identified a long noncoding RNA (lncRNA), LncMyoD, which regulates lineage determination and progression through modulating chromatin accessibility. Functional analysis showed that loss of LncMyoD strongly impairs reprogramming of fibroblasts into myogenic lineage and causes defects in muscle stem cell differentiation. Our findings provide an epigenetic mechanism for the regulation of muscle stem cell myogenic lineage progression by an lncRNA. Epigenetics regulation plays a critical role in determining cell identity by controlling the accessibility of lineage-specific regulatory regions. In muscle stem cells, epigenetic mechanisms of how chromatin accessibility is modulated during cell fate determination are not fully understood. Here, we identified a long noncoding RNA, LncMyoD, that functions as a chromatin modulator for myogenic lineage determination and progression. The depletion of LncMyoD in muscle stem cells led to the down-regulation of myogenic genes and defects in myogenic differentiation. LncMyoD exclusively binds with MyoD and not with other myogenic regulatory factors and promotes transactivation of target genes. The mechanistic study revealed that loss of LncMyoD prevents the establishment of a permissive chromatin environment at myogenic E-box–containing regions, therefore restricting the binding of MyoD. Furthermore, the depletion of LncMyoD strongly impairs the reprogramming of fibroblasts into the myogenic lineage. Taken together, our study shows that LncMyoD associates with MyoD and promotes myogenic gene expression through modulating MyoD accessibility to chromatin, thereby regulating myogenic lineage determination and progression.
Collapse
|
18
|
Bunina D, Abazova N, Diaz N, Noh KM, Krijgsveld J, Zaugg JB. Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Syst 2020; 10:480-494.e8. [PMID: 32553182 PMCID: PMC7322528 DOI: 10.1016/j.cels.2020.05.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 03/19/2020] [Accepted: 05/15/2020] [Indexed: 02/08/2023]
Abstract
Cellular differentiation requires dramatic changes in chromatin organization, transcriptional regulation, and protein production. To understand the regulatory connections between these processes, we generated proteomic, transcriptomic, and chromatin accessibility data during differentiation of mouse embryonic stem cells (ESCs) into postmitotic neurons and found extensive associations between different molecular layers within and across differentiation time points. We observed that SOX2, as a regulator of pluripotency and neuronal genes, redistributes from pluripotency enhancers to neuronal promoters during differentiation, likely driven by changes in its protein interaction network. We identified ATRX as a major SOX2 partner in neurons, whose co-localization correlated with an increase in active enhancer marks and increased expression of nearby genes, which we experimentally confirmed for three loci. Collectively, our data provide key insights into the regulatory transformation of SOX2 during neuronal differentiation, and we highlight the significance of multi-omic approaches in understanding gene regulation in complex systems. Complex interplay of RNA, protein, and chromatin during neuronal differentiation Multi-omic profiling reveals divergent roles of SOX2 in stem cells and neurons SOX2 on-chromatin interaction network changes from pluripotent to neuronal factors ATRX interacts with SOX2 in neurons and co-binds highly expressed neuronal genes
Collapse
Affiliation(s)
- Daria Bunina
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Nade Abazova
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Nichole Diaz
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
| | - Jeroen Krijgsveld
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Heidelberg University, Medical Faculty Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
| |
Collapse
|
19
|
Murphy DP, Hughes AEO, Lawrence KA, Myers CA, Corbo JC. Cis-regulatory basis of sister cell type divergence in the vertebrate retina. eLife 2019; 8:e48216. [PMID: 31633482 PMCID: PMC6802965 DOI: 10.7554/elife.48216] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 09/19/2019] [Indexed: 12/27/2022] Open
Abstract
Multicellular organisms evolved via repeated functional divergence of transcriptionally related sister cell types, but the mechanisms underlying sister cell type divergence are not well understood. Here, we study a canonical pair of sister cell types, retinal photoreceptors and bipolar cells, to identify the key cis-regulatory features that distinguish them. By comparing open chromatin maps and transcriptomic profiles, we found that while photoreceptor and bipolar cells have divergent transcriptomes, they share remarkably similar cis-regulatory grammars, marked by enrichment of K50 homeodomain binding sites. However, cell class-specific enhancers are distinguished by enrichment of E-box motifs in bipolar cells, and Q50 homeodomain motifs in photoreceptors. We show that converting K50 motifs to Q50 motifs represses reporter expression in bipolar cells, while photoreceptor expression is maintained. These findings suggest that partitioning of Q50 motifs within cell type-specific cis-regulatory elements was a critical step in the evolutionary divergence of the bipolar transcriptome from that of photoreceptors.
Collapse
Affiliation(s)
- Daniel P Murphy
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Andrew EO Hughes
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Karen A Lawrence
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Connie A Myers
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| | - Joseph C Corbo
- Department of Pathology and ImmunologyWashington University School of MedicineSt. LouisUnited States
| |
Collapse
|
20
|
miR-26a promotes hepatocellular carcinoma invasion and metastasis by inhibiting PTEN and inhibits cell growth by repressing EZH2. J Transl Med 2019; 99:1484-1500. [PMID: 31201367 DOI: 10.1038/s41374-019-0270-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/23/2019] [Accepted: 04/28/2019] [Indexed: 12/13/2022] Open
Abstract
A previous study revealed that therapeutic miR-26a delivery suppresses tumorigenesis in a murine liver cancer model, whereas we found that forced miR-26a expression increased hepatocellular carcinoma (HCC) cell migration and invasion, which prompted us to characterize the causes and mechanisms underlying enhanced invasion due to ectopic miR-26a expression. Gain-of-function and loss-of-function experiments demonstrated that miR-26a promoted migration and invasion of BEL-7402 and HepG2 cells in vitro and positively modulated matrix metalloproteinase (MMP)-1, MMP-2, MMP-9, and MMP-10 expression. In addition, exogenous miR-26a expression significantly enhanced the metastatic ability of HepG2 cells in vivo. miR-26a negatively regulated in vitro proliferation of HCC cells, and miR-26a overexpression suppressed HepG2 cell tumor growth in nude mice. Further studies revealed that miR-26a inhibited cell growth by repressing the methyltransferase EZH2 and promoted cell migration and invasion by inhibiting the phosphatase PTEN. Furthermore, PTEN expression negatively correlated with miR-26a expression in HCC specimens from patients with and without metastasis. Thus, our findings suggest for the first time that miR-26a promotes invasion/metastasis by inhibiting PTEN and inhibits cell proliferation by repressing EZH2 in HCC. More importantly, our data also suggest caution if miR-26a is used as a target for cancer therapy in the future.
Collapse
|
21
|
Chen Y, Chen A. Unveiling the gene regulatory landscape in diseases through the identification of DNase I-hypersensitive sites. Biomed Rep 2019; 11:87-97. [PMID: 31423302 PMCID: PMC6684942 DOI: 10.3892/br.2019.1233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/03/2019] [Indexed: 01/18/2023] Open
Abstract
DNase I-hypersensitive sites (DHSs) serve key roles in the regulation of gene transcription as markers of cis-regulatory elements (CREs). Recent advances in next-generation sequencing have enabled the genome-wide location and annotation of DHSs in a variety of cells. Numerous studies have confirmed that DHSs are involved in several processes in cell fate decision and development. DHSs have also been indicated in cancer and inherited diseases as driver distal regulatory elements. Here, the definition of DHSs is reviewed, in addition to high-throughput methods of DHS identification. Furthermore, the function of DHSs in gene expression is probed. The roles of DHSs in disease occurrence are also reviewed and discussed. Concomitant advances in the identification of essential roles of DHSs will assist in disclosing the underlying molecular mechanisms, supplementing gene transcription and enlarging the molecular basis of DHS-related bioprocesses, phenotypes, distinct traits and diseases.
Collapse
Affiliation(s)
- Ying Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| | - Ailing Chen
- Central Laboratory, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, Jiangsu 214002, P.R. China
| |
Collapse
|
22
|
Starks RR, Biswas A, Jain A, Tuteja G. Combined analysis of dissimilar promoter accessibility and gene expression profiles identifies tissue-specific genes and actively repressed networks. Epigenetics Chromatin 2019; 12:16. [PMID: 30795793 PMCID: PMC6385419 DOI: 10.1186/s13072-019-0260-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 02/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The assay for transposase-accessible chromatin (ATAC-seq) is a powerful method to examine chromatin accessibility. While many studies have reported a positive correlation between gene expression and promoter accessibility, few have investigated the genes that deviate from this trend. In this study, we aimed to understand the relationship between gene expression and promoter accessibility in multiple cell types while also identifying gene regulatory networks in the placenta, an understudied organ that is critical for a successful pregnancy. RESULTS We started by assaying the open chromatin landscape in the mid-gestation placenta, when the fetal vasculature has started developing. After incorporating transcriptomic data generated in the placenta at the same time point, we grouped genes based on their expression levels and ATAC-seq promoter coverage. We found that the genes with the strongest correlation (high expression and high coverage) are likely involved in housekeeping functions, whereas tissue-specific genes were highly expressed and had only medium-low coverage. We also predicted that genes with medium-low expression and high promoter coverage were actively repressed. Within this group, we extracted a protein-protein interaction network enriched for neuronal functions, likely preventing the cells from adopting a neuronal fate. We further confirmed that a repressive histone mark is bound to the promoters of genes in this network. Finally, we ran our pipeline using ATAC-seq and RNA-seq data generated in ten additional cell types. We again found that genes with the strongest correlation are enriched for housekeeping functions and that genes with medium-low promoter coverage and high expression are more likely to be tissue-specific. These results demonstrate that only two data types, both of which require relatively low starting material to generate and are becoming more commonly available, can be integrated to understand multiple aspects of gene regulation. CONCLUSIONS Within the placenta, we identified an active placenta-specific gene network as well as a repressed neuronal network. Beyond the placenta, we demonstrate that ATAC-seq data and RNA-seq data can be integrated to identify tissue-specific genes and actively repressed gene networks in multiple cell types.
Collapse
Affiliation(s)
- Rebekah R. Starks
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011 USA
| | - Anilisa Biswas
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Molecular, Cellular, and Developmental Biology, Iowa State University, Ames, IA 50011 USA
| | - Ashish Jain
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011 USA
| | - Geetu Tuteja
- Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
- Bioinformatics and Computational Biology, Iowa State University, Ames, IA 50011 USA
- Molecular, Cellular, and Developmental Biology, Iowa State University, Ames, IA 50011 USA
| |
Collapse
|
23
|
Ampuja M, Kallioniemi A. Transcription factors-Intricate players of the bone morphogenetic protein signaling pathway. Genes Chromosomes Cancer 2017; 57:3-11. [DOI: 10.1002/gcc.22502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022] Open
Affiliation(s)
- M. Ampuja
- BioMediTech Institute and Faculty of Medicine and Life Sciences; University of Tampere; Tampere Finland
| | - Anne Kallioniemi
- BioMediTech Institute and Faculty of Medicine and Life Sciences; University of Tampere; Tampere Finland
- Fimlab Laboratories; Tampere Finland
| |
Collapse
|