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Laubscher D, Gryder BE, Sunkel BD, Andresson T, Wachtel M, Das S, Roschitzki B, Wolski W, Wu XS, Chou HC, Song YK, Wang C, Wei JS, Wang M, Wen X, Ngo QA, Marques JG, Vakoc CR, Schäfer BW, Stanton BZ, Khan J. BAF complexes drive proliferation and block myogenic differentiation in fusion-positive rhabdomyosarcoma. Nat Commun 2021; 12:6924. [PMID: 34836971 PMCID: PMC8626462 DOI: 10.1038/s41467-021-27176-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 10/25/2021] [Indexed: 12/12/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric malignancy of skeletal muscle lineage. The aggressive alveolar subtype is characterized by t(2;13) or t(1;13) translocations encoding for PAX3- or PAX7-FOXO1 chimeric transcription factors, respectively, and are referred to as fusion positive RMS (FP-RMS). The fusion gene alters the myogenic program and maintains the proliferative state while blocking terminal differentiation. Here, we investigated the contributions of chromatin regulatory complexes to FP-RMS tumor maintenance. We define the mSWI/SNF functional repertoire in FP-RMS. We find that SMARCA4 (encoding BRG1) is overexpressed in this malignancy compared to skeletal muscle and is essential for cell proliferation. Proteomic studies suggest proximity between PAX3-FOXO1 and BAF complexes, which is further supported by genome-wide binding profiles revealing enhancer colocalization of BAF with core regulatory transcription factors. Further, mSWI/SNF complexes localize to sites of de novo histone acetylation. Phenotypically, interference with mSWI/SNF complex function induces transcriptional activation of the skeletal muscle differentiation program associated with MYCN enhancer invasion at myogenic target genes, which is recapitulated by BRG1 targeting compounds. We conclude that inhibition of BRG1 overcomes the differentiation blockade of FP-RMS cells and may provide a therapeutic strategy for this lethal childhood tumor.
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Affiliation(s)
- Dominik Laubscher
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Berkley E. Gryder
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA ,grid.67105.350000 0001 2164 3847Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH USA
| | - Benjamin D. Sunkel
- grid.240344.50000 0004 0392 3476Nationwide Children’s Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH USA
| | - Thorkell Andresson
- grid.418021.e0000 0004 0535 8394Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Marco Wachtel
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Sudipto Das
- grid.418021.e0000 0004 0535 8394Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Bernd Roschitzki
- grid.7400.30000 0004 1937 0650Functional Genomics Center, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Witold Wolski
- grid.7400.30000 0004 1937 0650Functional Genomics Center, University of Zurich/ETH Zurich, Zurich, Switzerland
| | - Xiaoli S. Wu
- grid.225279.90000 0004 0387 3667Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Hsien-Chao Chou
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Young K. Song
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Chaoyu Wang
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Jun S. Wei
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Meng Wang
- grid.240344.50000 0004 0392 3476Nationwide Children’s Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH USA
| | - Xinyu Wen
- grid.48336.3a0000 0004 1936 8075Genetics Branch, NCI, NIH, Bethesda, MD USA
| | - Quy Ai Ngo
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Joana G. Marques
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Christopher R. Vakoc
- grid.225279.90000 0004 0387 3667Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 USA
| | - Beat W. Schäfer
- grid.412341.10000 0001 0726 4330Department of Oncology and Children’s Research Center, University Children’s Hospital, Zurich, Switzerland
| | - Benjamin Z. Stanton
- grid.240344.50000 0004 0392 3476Nationwide Children’s Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH USA ,grid.261331.40000 0001 2285 7943Department of Biological Chemistry & Pharmacology, The Ohio State University College of Medicine, Columbus, OH USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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2
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Esiso FM, Cunningham D, Lai F, Garcia D, Barrett CB, Thornton K, Sakkas D. The effect of rapid and delayed insemination on reproductive outcome in conventional insemination and intracytoplasmic sperm injection in vitro fertilization cycles. J Assist Reprod Genet 2021; 38:2697-2706. [PMID: 34403017 PMCID: PMC8581094 DOI: 10.1007/s10815-021-02299-7] [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: 04/16/2021] [Accepted: 08/06/2021] [Indexed: 10/20/2022] Open
Abstract
PURPOSE The precise timing of insemination after oocyte retrieval is sometimes challenging. In this study, we have assessed the effect of the variation in insemination timing on reproductive outcome for both conventional insemination (CI) and intracytoplasmic sperm injection (ICSI) cycles. METHODS A single-center retrospective cohort data analysis was performed on 6559 patients (9575 oocyte retrievals) from January 2017 to July 2019. The main outcome measured was live birth rates. Secondary outcomes included fertilization rate per all oocytes retrieved, blastocyst utilization, clinical pregnancy, and miscarriage rates. The time interval between oocyte retrieval and insemination was analyzed in eight categories: 0 (0- < 0.5 h), 1 (0.5- < 1.5 h), 2 (1.5- < 2.5 h), 3 (2.5- < 3.5 h), 4 (3.5- < 4.5), 5 (4.5- < 5.5), 6 (5.5-6.5), and 7 (6.5- < 8 h). The number of retrievals in each group (0-7) was 586, 1594, 1644, 1796, 1836, 1351, 641, and 127 respectively. RESULTS The mean fertilization rate for CI ranged from 54.1 to 64.9% with a significant difference between time categories 0 and 5 (p < 0.001) and 1 and 5 (p < 0.0.001). The mean fertilization rate for ICSI ranged from 52.8 to 67.3% with no significant difference between time categories. Blastocyst rate for CI and ICSI was not significantly different. Miscarriage and clinical pregnancy rates in CI and ICSI were not significantly different. Live birth rates differed significantly (p < 0.05) in CI with time categories 0 and 7 representing the lowest rates, but not in the ICSI group. CONCLUSION If performing CI or ICSI before 1.5 h and > 6.5 h, any detrimental effects are moderate on fertilization but do not affect blastocyst usage and birth rates. TRIAL REGISTRATION Institutional Review Board Approval from the Beth Israel Deaconess Medical Centre [IRB Protocol #: 2015P000122].
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Affiliation(s)
- Fredrick M Esiso
- UPF Barcelona School of Management, Barcelona, Spain
- Boston IVF - Eugin Group, 130 Second Avenue, Waltham, MA, 02451, USA
| | - Donna Cunningham
- Boston IVF - Eugin Group, 130 Second Avenue, Waltham, MA, 02451, USA
| | - FangFang Lai
- Boston IVF - Eugin Group, 130 Second Avenue, Waltham, MA, 02451, USA
| | - Desiree Garcia
- Department of Research and Development, Clínica Eugin, Barcelona, Spain
| | - C Brent Barrett
- Boston IVF - Eugin Group, 130 Second Avenue, Waltham, MA, 02451, USA
| | - Kim Thornton
- Boston IVF - Eugin Group, 130 Second Avenue, Waltham, MA, 02451, USA
| | - Denny Sakkas
- Boston IVF - Eugin Group, 130 Second Avenue, Waltham, MA, 02451, USA.
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3
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Sunkel BD, Wang M, LaHaye S, Kelly BJ, Fitch JR, Barr FG, White P, Stanton BZ. Evidence of pioneer factor activity of an oncogenic fusion transcription factor. iScience 2021; 24:102867. [PMID: 34386729 PMCID: PMC8346656 DOI: 10.1016/j.isci.2021.102867] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 11/29/2022] Open
Abstract
Recent characterizations of pioneer transcription factors provide insights into their structures and patterns of chromatin recognition associated with their roles in cell fate commitment and transformation. Intersecting with these basic science concepts, identification of pioneer factors (PFs) fused together as driver translocations in childhood cancers raises questions of whether these fusions retain the fundamental ability to invade repressed chromatin, consistent with their monomeric PF constituents. This study defines the cellular and chromatin localization of PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a ChIP-seq workflow with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal insights into inactive chromatin localization of PAX3-FOXO1. Taken together, our studies are consistent with pioneer function for a driver oncoprotein in RMS, with repressed chromatin binding and nucleosome-motif targeting. The fusion oncoprotein PAX3-FOXO1 binds to both active and repressed chromatin PAX3-FOXO1-binding sites are adjacent to H3K9me3 domains PAX3-FOXO1 engages partial DNA motifs at early timepoints PAX3-FOXO1 can bind stably to inaccessible chromatin without inducing accessibility
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Affiliation(s)
- Benjamin D Sunkel
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Meng Wang
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA
| | - Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Frederic G Barr
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Benjamin Z Stanton
- Nationwide Children's Hospital, Center for Childhood Cancer and Blood Diseases, Columbus, OH 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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4
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Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nat Commun 2021; 12:1419. [PMID: 33658503 PMCID: PMC7930052 DOI: 10.1038/s41467-021-21707-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 02/09/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetic mechanisms contribute to the initiation and development of cancer, and epigenetic variation promotes dynamic gene expression patterns that facilitate tumor evolution and adaptation. While the NCI-60 panel represents a diverse set of human cancer cell lines that has been used to screen chemical compounds, a comprehensive epigenomic atlas of these cells has been lacking. Here, we report an integrative analysis of 60 human cancer epigenomes, representing a catalog of activating and repressive histone modifications. We identify genome-wide maps of canonical sharp and broad H3K4me3 domains at promoter regions of tumor suppressors, H3K27ac-marked conventional enhancers and super enhancers, and widespread inter-cancer and intra-cancer specific variability in H3K9me3 and H4K20me3-marked heterochromatin domains. Furthermore, we identify features of chromatin states, including chromatin state switching along chromosomes, correlation of histone modification density with genetic mutations, DNA methylation, enrichment of DNA binding motifs in regulatory regions, and gene activity and inactivity. These findings underscore the importance of integrating epigenomic maps with gene expression and genetic variation data to understand the molecular basis of human cancer. Our findings provide a resource for mining epigenomic maps of human cancer cells and for identifying epigenetic therapeutic targets.
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5
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CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation. Proc Natl Acad Sci U S A 2020; 117:22331-22340. [PMID: 32839322 DOI: 10.1073/pnas.1921963117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The chromatin remodeler CHD8 is among the most frequently mutated genes in autism spectrum disorder (ASD). CHD8 has a dosage-sensitive role in ASD, but when and how it becomes critical to human social function is unclear. Here, we conducted genomic analyses of heterozygous and homozygous Chd8 mouse embryonic stem cells and differentiated neural progenitors. We identify dosage-sensitive CHD8 transcriptional targets, sites of regulated accessibility, and an unexpected cooperation with SOX transcription factors. Collectively, our findings reveal that CHD8 negatively regulates expression of neuronal genes to maintain pluripotency and also during differentiation. Thus, CHD8 is essential for both the maintenance of pluripotency and neural differentiation, providing mechanistic insight into its function with potential implications for ASD.
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6
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Symonds AL, Zheng W, Miao T, Wang H, Wang T, Kiome R, Hou X, Li S, Wang P. Egr2 and 3 control inflammation, but maintain homeostasis, of PD-1 high memory phenotype CD4 T cells. Life Sci Alliance 2020; 3:3/9/e202000766. [PMID: 32709717 PMCID: PMC7391068 DOI: 10.26508/lsa.202000766] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 01/13/2023] Open
Abstract
PD-1high memory CD4 T cells are pathogenic in autoimmune disease; here they show their expression of Egr2 is defective in rheumatoid arthritis and Egr2 & 3 control their inflammation and homeostasis. The transcription factors Egr2 and 3 are essential for controlling inflammatory autoimmune responses of memory phenotype (MP) CD4 T cells. However, the mechanism is still unclear. We have now found that the Egr2+ subset (PD-1high MP) of MP CD4 T cells expresses high levels of checkpoint molecules (PD-1 and Lag3) and also markers of effector T cells (CXCR3 and ICAM-1). Egr2/3 are not required for PD-1high MP CD4 cell development but mediate a unique transcriptional programme that effectively controls their inflammatory responses, while promoting homeostatic proliferation and adaptive responses. Egr2 negative PD-1high MP CD4 T cells are impaired in homeostatic proliferation and adaptive responses against viral infection but display inflammatory responses to innate stimulation such as IL-12. PD-1high MP CD4 T cells have recently been implicated in rheumatoid arthritis pathogenesis, and we have now found that Egr2 expression is reduced in PD-1high MP CD4 T cells from patients with active rheumatoid arthritis compared with healthy controls. These findings demonstrate that Egr2/3 control the inflammatory responses of PD-1high MP CD4 T cells and maintain their adaptive immune fitness.
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Affiliation(s)
- Alistair Lj Symonds
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Wei Zheng
- Division of Rheumatology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Tizong Miao
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Haiyu Wang
- Division of Rheumatology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - TieShang Wang
- Division of Rheumatology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Ruth Kiome
- Bioscience, Brunel University, Uxbridge, UK
| | - Xiujuan Hou
- Division of Rheumatology, Dong Fang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Suling Li
- Bioscience, Brunel University, Uxbridge, UK
| | - Ping Wang
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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7
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Gryder BE, Pomella S, Sayers C, Wu XS, Song Y, Chiarella AM, Bagchi S, Chou HC, Sinniah RS, Walton A, Wen X, Rota R, Hathaway NA, Zhao K, Chen J, Vakoc CR, Shern JF, Stanton BZ, Khan J. Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma. Nat Genet 2019; 51:1714-1722. [PMID: 31784732 PMCID: PMC6886578 DOI: 10.1038/s41588-019-0534-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/23/2019] [Indexed: 12/31/2022]
Abstract
Core regulatory transcription factors (CR TFs) orchestrate the placement of super-enhancers (SEs) to activate transcription of cell-identity specifying gene networks, and are critical in promoting cancer. Here, we define the core regulatory circuitry of rhabdomyosarcoma and identify critical CR TF dependencies. These CR TFs build SEs that have the highest levels of histone acetylation, yet paradoxically the same SEs also harbor the greatest amounts of histone deacetylases. We find that hyperacetylation selectively halts CR TF transcription. To investigate the architectural determinants of this phenotype, we used absolute quantification of architecture (AQuA) HiChIP, which revealed erosion of native SE contacts, and aberrant spreading of contacts that involved histone acetylation. Hyperacetylation removes RNA polymerase II (RNA Pol II) from core regulatory genetic elements, and eliminates RNA Pol II but not BRD4 phase condensates. This study identifies an SE-specific requirement for balancing histone modification states to maintain SE architecture and CR TF transcription.
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Affiliation(s)
| | - Silvia Pomella
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù Research Institute, IRCCS, Rome, Italy
| | - Carly Sayers
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Genetics Program, Stony Brook University, Stony Brook, NY, USA
| | - Young Song
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
| | - Anna M Chiarella
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Sukriti Bagchi
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | | | | | | | - Xinyu Wen
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesù Research Institute, IRCCS, Rome, Italy
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Keji Zhao
- Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIBIB, NIH, Bethesda, MD, USA
| | | | - Jack F Shern
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD, USA
| | - Benjamin Z Stanton
- Genetics Branch, NCI, NIH, Bethesda, MD, USA
- The Research Institute at Nationwide, Nationwide Children's Hospital, Columbus, OH, USA
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, MD, USA.
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8
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Lee SK, Xue Y, Shen W, Zhang Y, Joo Y, Ahmad M, Chinen M, Ding Y, Ku WL, De S, Lehrmann E, Becker KG, Lei EP, Zhao K, Zou S, Sharov A, Wang W. Topoisomerase 3β interacts with RNAi machinery to promote heterochromatin formation and transcriptional silencing in Drosophila. Nat Commun 2018; 9:4946. [PMID: 30470739 PMCID: PMC6251927 DOI: 10.1038/s41467-018-07101-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/04/2018] [Indexed: 12/31/2022] Open
Abstract
Topoisomerases solve topological problems during DNA metabolism, but whether they participate in RNA metabolism remains unclear. Top3β represents a family of topoisomerases carrying activities for both DNA and RNA. Here we show that in Drosophila, Top3β interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) containing AGO2, p68 RNA helicase, and FMRP. Top3β and RISC mutants are similarly defective in heterochromatin formation and transcriptional silencing by position-effect variegation assay. Moreover, both Top3β and AGO2 mutants exhibit reduced levels of heterochromatin protein HP1 in heterochromatin. Furthermore, expression of several genes and transposable elements in heterochromatin is increased in the Top3β mutant. Notably, Top3β mutants defective in either RNA binding or catalytic activity are deficient in promoting HP1 recruitment and silencing of transposable elements. Our data suggest that Top3β may act as an RNA topoisomerase in siRNA-guided heterochromatin formation and transcriptional silencing. Topoisomerases solve topological problems during DNA metabolism, but their role in RNA metabolism remains unclear. Here the authors provide evidence that in Drosophila, Topoisomerase 3β interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) to promote heterochromatin formation and transcriptional silencing.
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Affiliation(s)
- Seung Kyu Lee
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yutong Xue
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Weiping Shen
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yongqing Zhang
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Yuyoung Joo
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Muzammil Ahmad
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Madoka Chinen
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive Kidney Diseases, Bethesda, MD, 20892, USA
| | - Yi Ding
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Wai Lim Ku
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Supriyo De
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Elin Lehrmann
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Kevin G Becker
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Elissa P Lei
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive Kidney Diseases, Bethesda, MD, 20892, USA
| | - Keji Zhao
- System Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sige Zou
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Alexei Sharov
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Weidong Wang
- Lab of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA.
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9
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Kurup JT, Kidder BL. Identification of H4K20me3- and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells. J Biol Chem 2018; 293:15120-15135. [PMID: 30115682 DOI: 10.1074/jbc.ra118.004974] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Indexed: 11/06/2022] Open
Abstract
RNA has been shown to interact with various proteins to regulate chromatin dynamics and gene expression. However, it is unknown whether RNAs associate with epigenetic marks such as post-translational modifications of histones, including histone 4 lysine 20 trimethylation (H4K20me3) or trimethylated histone 3 lysine 4 (H3K4me3), to regulate chromatin and gene expression. Here, we used chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) to survey RNAs associated with H4K20me3- and H3K4me3-marked chromatin on a global scale in embryonic stem (ES) cells. We identified thousands of mRNAs and noncoding RNAs that associate with H4K20me3- and H3K4me3-marked chromatin. H4K20me3- and H3K4me3-interacting RNAs are involved in chromatin organization and modification and RNA processing, whereas H4K20me3-only RNAs are involved in cell motility and differentiation, and H3K4me3-only RNAs are involved in metabolic processes and RNA processing. Expression of H3K4me3-associated RNAs is enriched in ES cells, whereas expression of H4K20me3-associated RNAs is enriched in ES cells and differentiated cells. H4K20me3- and H3K4me3-interacting RNAs originate from genes that co-localize with features of active chromatin, including transcriptional machinery and active promoter regions, and the histone modification H3K36me3 in gene body regions. We also found that H4K20me3 and H3K4me3 are associated with distinct gene features including transcripts of greater length and exon number relative to unoccupied transcripts. H4K20me3- and H3K4me3-marked chromatin is also associated with processed RNAs (exon transcripts) relative to unspliced pre-mRNA and ncRNA transcripts. In summary, our results provide evidence that H4K20me3- and H3K4me3-associated RNAs represent a distinct subnetwork of the ES cell transcriptional repertoire.
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Affiliation(s)
- Jiji T Kurup
- From the Department of Oncology and.,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Benjamin L Kidder
- From the Department of Oncology and .,the Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, Michigan 48201
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10
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He R, Kidder BL. Culture of haploid blastocysts in FGF4 favors the derivation of epiblast stem cells with a primed epigenetic and transcriptional landscape. Sci Rep 2018; 8:10775. [PMID: 30018329 PMCID: PMC6050317 DOI: 10.1038/s41598-018-29074-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/05/2018] [Indexed: 01/07/2023] Open
Abstract
Pluripotent stem cells within the inner cell mass and epiblast of mammalian embryos have the capacity to form all lineages in the adult organism, while multipotent trophoblast stem (TS) cells derived from the trophectoderm are capable of differentiating into fetal lineages of the placenta. While mouse embryonic stem (ES) cells and epiblast stem cells (EpiSCs) exhibit distinct expression patterns and utilize distinct external signaling pathways for self-renewal, because mouse EpiSCs resemble human ES cells they are a useful model to investigate mechanisms of human ES cell self-renewal and differentiation. Recent studies have shown that haploid embryos and ES cells can be generated from chemically-activated unfertilized mouse oocytes. However, it is unclear whether EpiSCs or TS cells can be derived from haploid embryos. Here, we describe the derivation of EpiSCs from haploid blastocyst-stage embryos using culture conditions that promote TS cell self-renewal. Maternal (parthenogenetic/gynogenetic) EpiSCs (maEpiSCs) functionally and morphologically resemble conventional EpiSCs. Established maEpiSCs and conventional EpiSCs are diploid and exhibit a normal number of chromosomes. Moreover, global expression analyses and epigenomic profiling revealed that maEpiSCs and conventional EpiSCs exhibit similarly primed transcriptional programs and epigenetic profiles, respectively. Altogether, our results describe a useful experimental model to generate EpiSCs from haploid embryos, provide insight into self-renewal mechanisms of EpiSCs, and suggest that FGF4 is not sufficient to derive TS cells from haploid blastocyst-stage embryos.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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Xu J, Kidder BL. KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation. Biol Open 2018; 7:7/5/bio031245. [PMID: 29748167 PMCID: PMC5992522 DOI: 10.1242/bio.031245] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Trophoblast stem (TS) cells derived from the trophectoderm (TE) of mammalian embryos have the ability to self-renew indefinitely or differentiate into fetal lineages of the placenta. Epigenetic control of gene expression plays an instrumental role in dictating the fate of TS cell self-renewal and differentiation. However, the roles of histone demethylases and activating histone modifications such as methylation of histone 3 lysine 4 (H3K4me3/me2) in regulating TS cell expression programs, and in priming the epigenetic landscape for trophoblast differentiation, are largely unknown. Here, we demonstrate that the H3K4 demethylase, KDM5B, regulates the H3K4 methylome and expression landscapes of TS cells. Depletion of KDM5B resulted in downregulation of TS cell self-renewal genes and upregulation of trophoblast-lineage genes, which was accompanied by altered H3K4 methylation. Moreover, we found that KDM5B resets the H3K4 methylation landscape during differentiation in the absence of the external self-renewal signal, FGF4, by removing H3K4 methylation from promoters of self-renewal genes, and of genes whose expression is enriched in TS cells. Altogether, our data indicate an epigenetic role for KDM5B in regulating H3K4 methylation in TS cells and during trophoblast differentiation. Summary: The histone 3 lysine 4 demethylase KDM5B plays a key role in regulating H3K4 methylation during trophoblast stem cell self-renewal and differentiation. KDM5B regulates the transcriptional profile of TS cells during self-renewal and differentiation, and resets the H3K4 methylation landscape during differentiation by removing H3K4me3 from promoters of self-renewal and TS cell enriched genes.
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Affiliation(s)
- Jian Xu
- Department of Neurology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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12
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Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. Nat Struct Mol Biol 2017; 25:61-72. [PMID: 29323272 PMCID: PMC5909405 DOI: 10.1038/s41594-017-0007-3] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 11/09/2017] [Indexed: 01/03/2023]
Abstract
Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. Unfortunately, the effects of SMARCA4 missense mutations have remained uncertain. Here we show that SMARCA4 cancer missense mutations target conserved ATPase surfaces and disrupt the mechanochemical cycle of remodeling. We find that heterozygous expression of mutants alters the open chromatin landscape at thousands of sites across the genome. Loss of DNA accessibility does not directly overlap with Polycomb accumulation, but is enriched in 'A compartments' at active enhancers, which lose H3K27ac but not H3K4me1. Affected positions include hundreds of sites identified as superenhancers in many tissues. Dominant-negative mutation induces pro-oncogenic expression changes, including increased expression of Myc and its target genes. Together, our data suggest that disruption of enhancer accessibility represents a key source of altered function in disorders with SMARCA4 mutations in a wide variety of tissues.
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13
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He R, Kidder BL. H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells. Nucleic Acids Res 2017; 45:6427-6441. [PMID: 28402433 PMCID: PMC5499819 DOI: 10.1093/nar/gkx251] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/03/2017] [Indexed: 02/04/2023] Open
Abstract
Epigenetic regulation of chromatin plays a critical role in controlling embryonic stem (ES) cell self-renewal and pluripotency. However, the roles of histone demethylases and activating histone modifications such as trimethylated histone 3 lysine 4 (H3K4me3) in transcriptional events such as RNA polymerase II (RNAPII) elongation and alternative splicing are largely unknown. In this study, we show that KDM5B, which demethylates H3K4me3, plays an integral role in regulating RNAPII occupancy, transcriptional initiation and elongation, and alternative splicing events in ES cells. Depletion of KDM5B leads to altered RNAPII promoter occupancy, and decreased RNAPII initiation and elongation rates at active genes and at genes marked with broad H3K4me3 domains. Moreover, our results demonstrate that spreading of H3K4me3 from promoter to gene body regions, which is mediated by depletion of KDM5B, modulates RNAPII elongation rates and RNA splicing in ES cells. We further show that KDM5B is enriched nearby alternatively spliced exons, and depletion of KDM5B leads to altered levels of H3K4 methylation in alternatively spliced exon regions, which is accompanied by differential expression of these alternatively splice exons. Altogether, our data indicate an epigenetic role for KDM5B in regulating RNAPII elongation and alternative splicing, which may support the diverse mRNA repertoire in ES cells.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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He R, Xhabija B, Al-Qanber B, Kidder BL. OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells. Sci Rep 2017; 7:16360. [PMID: 29180818 PMCID: PMC5703885 DOI: 10.1038/s41598-017-16611-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 11/15/2017] [Indexed: 12/29/2022] Open
Abstract
Embryonic stem (ES) cell pluripotency is governed by OCT4-centric transcriptional networks. Conventional ES cells can be derived and maintained in vitro with media containing the cytokine leukemia inhibitory factor (LIF), which propagates the pluripotent state by activating STAT3 signaling, and simultaneous inhibition of glycogen synthase kinase-3 (GSK3) and MAP kinase/ERK kinase signaling. However, it is unclear whether overexpression of OCT4 is sufficient to overcome LIF-dependence. Here, we show that inducible expression of OCT4 (iOCT4) supports long-term LIF-independent self-renewal of ES cells cultured in media containing fetal bovine serum (FBS) and a glycogen synthase kinase-3 (GSK3) inhibitor, and in serum-free media. Global expression analysis revealed that LIF-independent iOCT4 ES cells and control ES cells exhibit similar transcriptional programs relative to epiblast stem cells (EpiSCs) and differentiated cells. Epigenomic profiling also demonstrated similar patterns of histone modifications between LIF-independent iOCT4 and control ES cells. Moreover, LIF-independent iOCT4 ES cells retain the capacity to differentiate in vitro and in vivo upon downregulation of OCT4 expression. These findings indicate that OCT4 expression is sufficient to sustain intrinsic signaling in a LIF-independent manner to promote ES cell pluripotency and self-renewal.
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Affiliation(s)
- Runsheng He
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Besa Xhabija
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Chemistry and Biochemistry, University of Michigan-Flint, Flint, MI, USA
| | - Batool Al-Qanber
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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15
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Smarca4 ATPase mutations disrupt direct eviction of PRC1 from chromatin. Nat Genet 2016; 49:282-288. [PMID: 27941795 DOI: 10.1038/ng.3735] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 11/01/2016] [Indexed: 12/16/2022]
Abstract
Trithorax-group proteins and their mammalian homologs, including those in BAF (mSWI/SNF) complexes, are known to oppose the activity of Polycomb repressive complexes (PRCs). This opposition underlies the tumor-suppressive role of BAF subunits and is expected to contribute to neurodevelopmental disorders. However, the mechanisms underlying opposition to Polycomb silencing are poorly understood. Here we report that recurrent disease-associated mutations in BAF subunits induce genome-wide increases in PRC deposition and activity. We show that point mutations in SMARCA4 (also known as BRG1) mapping to the ATPase domain cause loss of direct binding between BAF and PRC1 that occurs independently of chromatin. Release of this direct interaction is ATP dependent, consistent with a transient eviction mechanism. Using a new chemical-induced proximity assay, we find that BAF directly evicts Polycomb factors within minutes of its occupancy, thereby establishing a new mechanism for the widespread BAF-PRC opposition underlying development and disease.
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