1
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Gao D, Li C, Liu SY, Xu TT, Lin XT, Tan YP, Gao FM, Yi LT, Zhang JV, Ma JY, Meng TG, Yeung WSB, Liu K, Ou XH, Su RB, Sun QY. P300 regulates histone crotonylation and preimplantation embryo development. Nat Commun 2024; 15:6418. [PMID: 39080296 PMCID: PMC11289097 DOI: 10.1038/s41467-024-50731-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 07/19/2024] [Indexed: 08/02/2024] Open
Abstract
Histone lysine crotonylation, an evolutionarily conserved modification differing from acetylation, exerts pivotal control over diverse biological processes. Among these are gene transcriptional regulation, spermatogenesis, and cell cycle processes. However, the dynamic changes and functions of histone crotonylation in preimplantation embryonic development in mammals remain unclear. Here, we show that the transcription coactivator P300 functions as a writer of histone crotonylation during embryonic development. Depletion of P300 results in significant developmental defects and dysregulation of the transcriptome of embryos. Importantly, we demonstrate that P300 catalyzes the crotonylation of histone, directly stimulating transcription and regulating gene expression, thereby ensuring successful progression of embryo development up to the blastocyst stage. Moreover, the modification of histone H3 lysine 18 crotonylation (H3K18cr) is primarily localized to active promoter regions. This modification serves as a distinctive epigenetic indicator of crucial transcriptional regulators, facilitating the activation of gene transcription. Together, our results propose a model wherein P300-mediated histone crotonylation plays a crucial role in regulating the fate of embryonic development.
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Affiliation(s)
- Di Gao
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, 518053, Shenzhen, China
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Chao Li
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Shao-Yuan Liu
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Teng-Teng Xu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Xiao-Ting Lin
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Yong-Peng Tan
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Fu-Min Gao
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Li-Tao Yi
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Jian V Zhang
- Center for Energy Metabolism and Reproduction, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Jun-Yu Ma
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - Tie-Gang Meng
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China
| | - William S B Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, 518053, Shenzhen, China
| | - Kui Liu
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, 518053, Shenzhen, China
| | - Xiang-Hong Ou
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China.
| | - Rui-Bao Su
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China.
| | - Qing-Yuan Sun
- Guangzhou Key Laboratory of Metabolic Diseases and Reproductive Health, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, 510317, Guangzhou, China.
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2
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Ren L, Ma W, Wang Y. Predicting RNA polymerase II transcriptional elongation pausing and associated histone code. Brief Bioinform 2024; 25:bbae246. [PMID: 38783706 PMCID: PMC11116834 DOI: 10.1093/bib/bbae246] [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: 01/22/2024] [Revised: 04/12/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
RNA Polymerase II (Pol II) transcriptional elongation pausing is an integral part of the dynamic regulation of gene transcription in the genome of metazoans. It plays a pivotal role in many vital biological processes and disease progression. However, experimentally measuring genome-wide Pol II pausing is technically challenging and the precise governing mechanism underlying this process is not fully understood. Here, we develop RP3 (RNA Polymerase II Pausing Prediction), a network regularized logistic regression machine learning method, to predict Pol II pausing events by integrating genome sequence, histone modification, gene expression, chromatin accessibility, and protein-protein interaction data. RP3 can accurately predict Pol II pausing in diverse cellular contexts and unveil the transcription factors that are associated with the Pol II pausing machinery. Furthermore, we utilize a forward feature selection framework to systematically identify the combination of histone modification signals associated with Pol II pausing. RP3 is freely available at https://github.com/AMSSwanglab/RP3.
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Affiliation(s)
- Lixin Ren
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Wanbiao Ma
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, 55 Zhongguancun East Road, Haidian District, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Wuhua District, Kunming 650223, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 1 Xiangshan Zhi Nong, West Lake District, Hangzhou 330106, China
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3
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Santana JF, Spector BM, Suarez G, Luse D, Price D. NELF focuses sites of initiation and maintains promoter architecture. Nucleic Acids Res 2024; 52:2977-2994. [PMID: 38197272 PMCID: PMC11014283 DOI: 10.1093/nar/gkad1253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
Many factors control the elongation phase of transcription by RNA polymerase II (Pol II), a process that plays an essential role in regulating gene expression. We utilized cells expressing degradation tagged subunits of NELFB, PAF1 and RTF1 to probe the effects of depletion of the factors on nascent transcripts using PRO-Seq and on chromatin architecture using DFF-ChIP. Although NELF is involved in promoter proximal pausing, depletion of NELFB had only a minimal effect on the level of paused transcripts and almost no effect on control of productive elongation. Instead, NELF depletion increased the utilization of downstream transcription start sites and caused a dramatic, genome-wide loss of H3K4me3 marked nucleosomes. Depletion of PAF1 and RTF1 both had major effects on productive transcript elongation in gene bodies and also caused initiation site changes like those seen with NELFB depletion. Our study confirmed that the first nucleosome encountered during initiation and early elongation is highly positioned with respect to the major TSS. In contrast, the positions of H3K4me3 marked nucleosomes in promoter regions are heterogeneous and are influenced by transcription. We propose a model defining NELF function and a general role of the H3K4me3 modification in blocking transcription initiation.
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Affiliation(s)
- Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Benjamin M Spector
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Gustavo A Suarez
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - David H Price
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
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4
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Su BG, Vos SM. Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing. Mol Cell 2024; 84:1243-1256.e5. [PMID: 38401543 PMCID: PMC10997474 DOI: 10.1016/j.molcel.2024.01.023] [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: 10/11/2023] [Revised: 12/17/2023] [Accepted: 01/25/2024] [Indexed: 02/26/2024]
Abstract
Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II.
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Affiliation(s)
- Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, USA
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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5
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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6
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Bisia AM, Costello I, Xypolita ME, Harland LTG, Kurbel PJ, Bikoff EK, Robertson EJ. A degron-based approach to manipulate Eomes functions in the context of the developing mouse embryo. Proc Natl Acad Sci U S A 2023; 120:e2311946120. [PMID: 37871215 PMCID: PMC10622880 DOI: 10.1073/pnas.2311946120] [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: 07/13/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
The T-box transcription factor Eomesodermin (Eomes), also known as Tbr2, plays essential roles in the early mouse embryo. Loss-of-function mutant embryos arrest at implantation due to Eomes requirements in the trophectoderm cell lineage. Slightly later, expression in the visceral endoderm promotes anterior visceral endoderm formation and anterior-posterior axis specification. Early induction in the epiblast beginning at day 6 is necessary for nascent mesoderm to undergo epithelial to mesenchymal transition (EMT). Eomes acts in a temporally and spatially restricted manner to sequentially specify the yolk sac haemogenic endothelium, cardiac mesoderm, definitive endoderm, and axial mesoderm progenitors during gastrulation. Little is known about the underlying molecular mechanisms governing Eomes actions during the formation of these distinct progenitor cell populations. Here, we introduced a degron-tag and mCherry reporter sequence into the Eomes locus. Our experiments analyzing homozygously tagged embryonic stem cells and embryos demonstrate that the degron-tagged Eomes protein is fully functional. dTAG (degradation fusion tag) treatment in vitro results in rapid protein degradation and recapitulates the Eomes-null phenotype. However in utero administration of dTAG resulted in variable and lineage-specific degradation, likely reflecting diverse cell type-specific Eomes expression dynamics. Finally, we demonstrate that Eomes protein rapidly recovers following dTAG wash-out in vitro. The ability to temporally manipulate Eomes protein expression in combination with cell marking by the mCherry-reporter offers a powerful tool for dissecting Eomes-dependent functional roles in these diverse cell types in the early embryo.
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Affiliation(s)
- Alexandra M. Bisia
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Ita Costello
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Maria-Eleni Xypolita
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Luke T. G. Harland
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Philipp J. Kurbel
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Elizabeth K. Bikoff
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Elizabeth J. Robertson
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
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7
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Martell DJ, Merens HE, Caulier A, Fiorini C, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NBA, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. Dev Cell 2023; 58:2112-2127.e4. [PMID: 37586368 PMCID: PMC10615711 DOI: 10.1016/j.devcel.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/23/2023] [Accepted: 07/25/2023] [Indexed: 08/18/2023]
Abstract
Controlled release of promoter-proximal paused RNA polymerase II (RNA Pol II) is crucial for gene regulation. However, studying RNA Pol II pausing is challenging, as pause-release factors are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H, which encodes SPT5, in individuals with β-thalassemia. During erythropoiesis in healthy human cells, cell cycle genes were highly paused as cells transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, RNA Pol II pause release was globally disrupted, and as cells began transitioning from progenitors to precursors, differentiation was delayed, accompanied by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, identifying a role for RNA Pol II pausing in temporally coordinating the cell cycle and erythroid differentiation.
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Affiliation(s)
- Danya J Martell
- Department of Genetics, Harvard University, Boston, MA, USA; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hope E Merens
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Karine Choquet
- Department of Genetics, Harvard University, Boston, MA, USA
| | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi B A Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK; Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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8
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Barshad G, Lewis JJ, Chivu AG, Abuhashem A, Krietenstein N, Rice EJ, Ma Y, Wang Z, Rando OJ, Hadjantonakis AK, Danko CG. RNA polymerase II dynamics shape enhancer-promoter interactions. Nat Genet 2023; 55:1370-1380. [PMID: 37430091 DOI: 10.1038/s41588-023-01442-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 06/09/2023] [Indexed: 07/12/2023]
Abstract
How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we investigated enhancer-promoter communication by integrating data from nucleosome-resolution genomic contact maps, nascent transcription and perturbations affecting either RNA polymerase II (Pol II) dynamics or the activity of thousands of candidate enhancers. Integration of new Micro-C experiments with published CRISPRi data demonstrated that enhancers spend more time in close proximity to their target promoters in functional enhancer-promoter pairs compared to nonfunctional pairs, which can be attributed in part to factors unrelated to genomic position. Manipulation of the transcription cycle demonstrated a key role for Pol II in enhancer-promoter interactions. Notably, promoter-proximal paused Pol II itself partially stabilized interactions. We propose an updated model in which elements of transcriptional dynamics shape the duration or frequency of interactions to facilitate enhancer-promoter communication.
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Affiliation(s)
- Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York City, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York City, NY, USA
| | - Nils Krietenstein
- The Novo Nordisk Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yitian Ma
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Dalian, China
| | - Zhong Wang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Dalian, China
| | - Oliver J Rando
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York City, NY, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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9
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Chivu AG, Abuhashem A, Barshad G, Rice EJ, Leger MM, Vill AC, Wong W, Brady R, Smith JJ, Wikramanayake AH, Arenas-Mena C, Brito IL, Ruiz-Trillo I, Hadjantonakis AK, Lis JT, Lewis JJ, Danko CG. Evolution of promoter-proximal pausing enabled a new layer of transcription control. RESEARCH SQUARE 2023:rs.3.rs-2679520. [PMID: 36993251 PMCID: PMC10055653 DOI: 10.21203/rs.3.rs-2679520/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Promoter-proximal pausing of RNA polymerase II (Pol II) is a key regulatory step during transcription. Despite the central role of pausing in gene regulation, we do not understand the evolutionary processes that led to the emergence of Pol II pausing or its transition to a rate-limiting step actively controlled by transcription factors. Here we analyzed transcription in species across the tree of life. We found that unicellular eukaryotes display a slow acceleration of Pol II near transcription start sites. This proto-paused-like state transitioned to a longer, focused pause in derived metazoans which coincided with the evolution of new subunits in the NELF and 7SK complexes. Depletion of NELF reverts the mammalian focal pause to a proto-pause-like state and compromises transcriptional activation for a set of heat shock genes. Collectively, this work details the evolutionary history of Pol II pausing and sheds light on how new transcriptional regulatory mechanisms evolve.
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Affiliation(s)
- Alexandra G. Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, NY 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, NY 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, NY 10065, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Edward J. Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michelle M. Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, 08003, Spain
| | - Albert C. Vill
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Wilfred Wong
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Tri-Institutional training Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - Rebecca Brady
- Department of Biology, Ithaca College, Ithaca NY 14850, USA
| | - Jeramiah J. Smith
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | | | - César Arenas-Mena
- Department of Biology at the College of Staten Island and PhD Programs in Biology and Biochemistry at The Graduate Center, The City University of New York (CUNY), Staten Island, NY 10314, USA
| | - Ilana L. Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14850, USA
| | - Iñaki Ruiz-Trillo
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, 08003, Spain
- ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain., Barcelona, 08003, Spain
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, NY 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, NY 10065, USA
| | - John T. Lis
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - James J. Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Genetics and Biochemistry, Clemson University, 105 Collings St, Clemson, SC 29634
| | - Charles G. Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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Martell DJ, Merens HE, Fiorini C, Caulier A, Ulirsch JC, Ietswaart R, Choquet K, Graziadei G, Brancaleoni V, Cappellini MD, Scott C, Roberts N, Proven M, Roy NB, Babbs C, Higgs DR, Sankaran VG, Churchman LS. RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.03.23286760. [PMID: 36945604 PMCID: PMC10029049 DOI: 10.1101/2023.03.03.23286760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The controlled release of promoter-proximal paused RNA polymerase II (Pol II) into productive elongation is a major step in gene regulation. However, functional analysis of Pol II pausing is difficult because factors that regulate pause release are almost all essential. In this study, we identified heterozygous loss-of-function mutations in SUPT5H , which encodes SPT5, in individuals with β-thalassemia unlinked to HBB mutations. During erythropoiesis in healthy human cells, cell cycle genes were highly paused at the transition from progenitors to precursors. When the pathogenic mutations were recapitulated by SUPT5H editing, Pol II pause release was globally disrupted, and the transition from progenitors to precursors was delayed, marked by a transient lag in erythroid-specific gene expression and cell cycle kinetics. Despite this delay, cells terminally differentiate, and cell cycle phase distributions normalize. Therefore, hindering pause release perturbs proliferation and differentiation dynamics at a key transition during erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.
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Affiliation(s)
- Danya J Martell
- Harvard University, Department of Genetics, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Hope E Merens
- Harvard University, Department of Genetics, Boston, MA
| | - Claudia Fiorini
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Alexis Caulier
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | - Jacob C Ulirsch
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
| | | | | | - Giovanna Graziadei
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Valentina Brancaleoni
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community, University of Milan, IRCCS Ca'Granda Foundation Maggiore Policlinico Hospital, Milan, Italy
| | - Caroline Scott
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Nigel Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Melanie Proven
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Noémi Ba Roy
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre and BRC/NHS Translational Molecular Diagnostics Centre, John Radcliffe Hospital, Oxford, UK
- Department of Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of MIT and Harvard, Cambridge, MA
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