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Jia L, Wang Y, Wang C, Du Z, Zhang S, Wen X, Zhou L, Li H, Chen H, Li D, Zhang S, Li W, Xu W, Hoffman AR, Cui J, Hu JF. Oplr16 serves as a novel chromatin factor to control stem cell fate by modulating pluripotency-specific chromosomal looping and TET2-mediated DNA demethylation. Nucleic Acids Res 2020; 48:3935-3948. [PMID: 32055844 PMCID: PMC7144914 DOI: 10.1093/nar/gkaa097] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/03/2023] Open
Abstract
Formation of a pluripotency-specific chromatin network is a critical event in reprogramming somatic cells into pluripotent status. To characterize the regulatory components in this process, we used ‘chromatin RNA in situ reverse transcription sequencing’ (CRIST-seq) to profile RNA components that interact with the pluripotency master gene Oct4. Using this approach, we identified a novel nuclear lncRNA Oplr16 that was closely involved in the initiation of reprogramming. Oplr16 not only interacted with the Oct4 promoter and regulated its activity, but it was also specifically activated during reprogramming to pluripotency. Active expression of Oplr16 was required for optimal maintenance of pluripotency in embryonic stem cells. Oplr16 was also able to enhance reprogramming of fibroblasts into pluripotent cells. RNA reverse transcription-associated trap sequencing (RAT-seq) indicated that Oplr16 interacted with multiple target genes related to stem cell self-renewal. Of note, Oplr16 utilized its 3′-fragment to recruit the chromatin factor SMC1 to orchestrate pluripotency-specific intrachromosomal looping. After binding to the Oct4 promoter, Oplr16 recruited TET2 to induce DNA demethylation and activate Oct4 in fibroblasts, leading to enhanced reprogramming. These data suggest that Oplr16 may act as a pivotal chromatin factor to control stem cell fate by modulating chromatin architecture and DNA demethylation.
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Affiliation(s)
- Lin Jia
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Yichen Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Cong Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Zhonghua Du
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Shilin Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Xue Wen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Lei Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Hui Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Huiling Chen
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA.,Department of Endocrinology, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Dan Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Songling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Wei Xu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Andrew R Hoffman
- Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Jiuwei Cui
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China
| | - Ji-Fan Hu
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, Stem Cell and Cancer Center, First Hospital, Jilin University, Changchun, Jilin 130061, P.R. China.,Stanford University Medical School, VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
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Lee DP, Tan WLW, Anene-Nzelu CG, Lee CJM, Li PY, Luu TDA, Chan CX, Tiang Z, Ng SL, Huang X, Efthymios M, Autio MI, Jiang J, Fullwood MJ, Prabhakar S, Lieberman Aiden E, Foo RSY. Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response. Circulation 2020; 139:1937-1956. [PMID: 30717603 DOI: 10.1161/circulationaha.118.036726] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND The human genome folds in 3 dimensions to form thousands of chromatin loops inside the nucleus, encasing genes and cis-regulatory elements for accurate gene expression control. Physical tethers of loops are anchored by the DNA-binding protein CTCF and the cohesin ring complex. Because heart failure is characterized by hallmark gene expression changes, it was recently reported that substantial CTCF-related chromatin reorganization underpins the myocardial stress-gene response, paralleled by chromatin domain boundary changes observed in CTCF knockout. METHODS We undertook an independent and orthogonal analysis of chromatin organization with mouse pressure-overload model of myocardial stress (transverse aortic constriction) and cardiomyocyte-specific knockout of Ctcf. We also downloaded published data sets of similar cardiac mouse models and subjected them to independent reanalysis. RESULTS We found that the cardiomyocyte chromatin architecture remains broadly stable in transverse aortic constriction hearts, whereas Ctcf knockout resulted in ≈99% abolition of global chromatin loops. Disease gene expression changes correlated instead with differential histone H3K27-acetylation enrichment at their respective proximal and distal interacting genomic enhancers confined within these static chromatin structures. Moreover, coregulated genes were mapped out as interconnected gene sets on the basis of their multigene 3D interactions. CONCLUSIONS This work reveals a more stable genome-wide chromatin framework than previously described. Myocardial stress-gene transcription responds instead through H3K27-acetylation enhancer enrichment dynamics and gene networks of coregulation. Robust and intact CTCF looping is required for the induction of a rapid and accurate stress response.
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Affiliation(s)
- Dominic Paul Lee
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Wilson Lek Wen Tan
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Chukwuemeka George Anene-Nzelu
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Chang Jie Mick Lee
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Peter Yiqing Li
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Tuan Danh Anh Luu
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Cheryl Xueli Chan
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Zenia Tiang
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Shi Ling Ng
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Xingfan Huang
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (X.H., E.L.A.)
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX (X.H., E.L.A.)
| | - Motakis Efthymios
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Matias I Autio
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Jianming Jiang
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
- Department of Biochemistry, School of Medicine (J.J.), National University of Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute (M.J.F.), National University of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore (M.J.F.)
| | - Shyam Prabhakar
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (X.H., E.L.A.)
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX (X.H., E.L.A.)
| | - Roger Sik-Yin Foo
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
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