1
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Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P. Structural basis of Integrator-dependent RNA polymerase II termination. Nature 2024; 629:219-227. [PMID: 38570683 PMCID: PMC11062913 DOI: 10.1038/s41586-024-07269-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript1, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator-PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10-INTS13-INTS14-INTS15 module that may use its 'sting' to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator-PP2A complex in an inactive closed conformation2 reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements.
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Affiliation(s)
- Isaac Fianu
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Moritz Ochmann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - James L Walshe
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Olexandr Dybkov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Joseph Neos Cruz
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, Bioanalytics Group, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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Soliman SHA, Iwanaszko M, Zheng B, Gold S, Howard BC, Das M, Chakrabarty RP, Chandel NS, Shilatifard A. Transcriptional elongation control of hypoxic response. Proc Natl Acad Sci U S A 2024; 121:e2321502121. [PMID: 38564636 PMCID: PMC11009653 DOI: 10.1073/pnas.2321502121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024] Open
Abstract
The release of paused RNA polymerase II (RNAPII) from promoter-proximal regions is tightly controlled to ensure proper regulation of gene expression. The elongation factor PTEF-b is known to release paused RNAPII via phosphorylation of the RNAPII C-terminal domain by its cyclin-dependent kinase component, CDK9. However, the signal and stress-specific roles of the various RNAPII-associated macromolecular complexes containing PTEF-b/CDK9 are not yet clear. Here, we identify and characterize the CDK9 complex required for transcriptional response to hypoxia. Contrary to previous reports, our data indicate that a CDK9 complex containing BRD4 but not AFF1/4 is essential for this hypoxic stress response. We demonstrate that BRD4 bromodomains (BET) are dispensable for the release of paused RNAPII at hypoxia-activated genes and that BET inhibition by JQ1 is insufficient to impair hypoxic gene response. Mechanistically, we demonstrate that the C-terminal region of BRD4 is required for Polymerase-Associated Factor-1 Complex (PAF1C) recruitment to establish an elongation-competent RNAPII complex at hypoxia-responsive genes. PAF1C disruption using a small-molecule inhibitor (iPAF1C) impairs hypoxia-induced, BRD4-mediated RNAPII release. Together, our results provide insight into potentially targetable mechanisms that control the hypoxia-responsive transcriptional elongation.
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Affiliation(s)
- Shimaa Hassan AbdelAziz Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Bin Zheng
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Sarah Gold
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Benjamin Charles Howard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Madhurima Das
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
| | - Ram Prosad Chakrabarty
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University, Chicago, IL60611
| | - Navdeep S. Chandel
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
- Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University, Chicago, IL60611
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL60611
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Patel A, Dharap A. An Emerging Role for Enhancer RNAs in Brain Disorders. Neuromolecular Med 2024; 26:7. [PMID: 38546891 DOI: 10.1007/s12017-024-08776-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Noncoding DNA undergoes widespread context-dependent transcription to produce noncoding RNAs. In recent decades, tremendous advances in genomics and transcriptomics have revealed important regulatory roles for noncoding DNA elements and the RNAs that they produce. Enhancers are one such element that are well-established drivers of gene expression changes in response to a variety of factors such as external stimuli, cellular responses, developmental cues, and disease states. They are known to act at long distances, interact with multiple target gene loci simultaneously, synergize with other enhancers, and associate with dynamic chromatin architectures to form a complex regulatory network. Recent advances in enhancer biology have revealed that upon activation, enhancers transcribe long noncoding RNAs, known as enhancer RNAs (eRNAs), that have been shown to play important roles in enhancer-mediated gene regulation and chromatin-modifying activities. In the brain, enhancer dysregulation and eRNA transcription has been reported in numerous disorders from acute injuries to chronic neurodegeneration. Because this is an emerging area, a comprehensive understanding of eRNA function has not yet been achieved in brain disorders; however, the findings to date have illuminated a role for eRNAs in activity-driven gene expression and phenotypic outcomes. In this review, we highlight the breadth of the current literature on eRNA biology in brain health and disease and discuss the challenges as well as focus areas and strategies for future in-depth research on eRNAs in brain health and disease.
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Affiliation(s)
- Ankit Patel
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA
| | - Ashutosh Dharap
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA.
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA.
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6
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Gillis A, Berry S. Global control of RNA polymerase II. Biochim Biophys Acta Gene Regul Mech 2024; 1867:195024. [PMID: 38552781 DOI: 10.1016/j.bbagrm.2024.195024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
RNA polymerase II (Pol II) is the multi-protein complex responsible for transcribing all protein-coding messenger RNA (mRNA). Most research on gene regulation is focused on the mechanisms controlling which genes are transcribed when, or on the mechanics of transcription. How global Pol II activity is determined receives comparatively less attention. Here, we follow the life of a Pol II molecule from 'assembly of the complex' to nuclear import, enzymatic activity, and degradation. We focus on how Pol II spends its time in the nucleus, and on the two-way relationship between Pol II abundance and activity in the context of homeostasis and global transcriptional changes.
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Affiliation(s)
- Alexander Gillis
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Scott Berry
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney, Australia; UNSW RNA Institute, University of New South Wales, Sydney, Australia; Department of Molecular Medicine, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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7
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Yu J, Sui F, Gu F, Li W, Yu Z, Wang Q, He S, Wang L, Xu Y. Structural insights into histone exchange by human SRCAP complex. Cell Discov 2024; 10:15. [PMID: 38331872 PMCID: PMC10853557 DOI: 10.1038/s41421-023-00640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 02/10/2024] Open
Abstract
Histone variant H2A.Z is found at promoters and regulates transcription. The ATP-dependent chromatin remodeler SRCAP complex (SRCAP-C) promotes the replacement of canonical histone H2A-H2B dimer with H2A.Z-H2B dimer. Here, we determined structures of human SRCAP-C bound to H2A-containing nucleosome at near-atomic resolution. The SRCAP subunit integrates a 6-subunit actin-related protein (ARP) module and an ATPase-containing motor module. The ATPase-associated ARP module encircles half of the nucleosome along the DNA and may restrain net DNA translocation, a unique feature of SRCAP-C. The motor module adopts distinct nucleosome binding modes in the apo (nucleotide-free), ADP-bound, and ADP-BeFx-bound states, suggesting that ATPase-driven movement destabilizes H2A-H2B by unwrapping the entry DNA and pulls H2A-H2B out of nucleosome through the ZNHIT1 subunit. Structure-guided chromatin immunoprecipitation sequencing analysis confirmed the requirement of H2A-contacting ZNHIT1 in maintaining H2A.Z occupancy on the genome. Our study provides structural insights into the mechanism of H2A-H2A.Z exchange mediated by SRCAP-C.
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Affiliation(s)
- Jiali Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology of China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Fengrui Sui
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Feng Gu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Wanjun Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qianmin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shuang He
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China
| | - Li Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
- Greater Bay Area Institute of Precision Medicine, Fudan University, Nansha District, Guangzhou, Guangdong, China.
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology of China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, China.
- Greater Bay Area Institute of Precision Medicine, Fudan University, Nansha District, Guangzhou, Guangdong, China.
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8
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Wang Z, Zhang Z, Luo S, Zhou T, Zhang J. Power-law behavior of transcriptional bursting regulated by enhancer-promoter communication. Genome Res 2024; 34:106-118. [PMID: 38171575 PMCID: PMC10903953 DOI: 10.1101/gr.278631.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]
Abstract
Revealing how transcriptional bursting kinetics are genomically encoded is challenging because genome structures are stochastic at the organization level and are suggestively linked to gene transcription. To address this challenge, we develop a generic theoretical framework that integrates chromatin dynamics, enhancer-promoter (E-P) communication, and gene-state switching to study transcriptional bursting. The theory predicts that power law can be a general rule to quantitatively describe bursting modulations by E-P spatial communication. Specifically, burst frequency and burst size are up-regulated by E-P communication strength, following power laws with positive exponents. Analysis of the scaling exponents further reveals that burst frequency is preferentially regulated. Bursting kinetics are down-regulated by E-P genomic distance with negative power-law exponents, and this negative modulation desensitizes at large distances. The mutual information between burst frequency (or burst size) and E-P spatial distance further reveals essential characteristics of the information transfer from E-P communication to transcriptional bursting kinetics. These findings, which are in agreement with experimental observations, not only reveal fundamental principles of E-P communication in transcriptional bursting but also are essential for understanding cellular decision-making.
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Affiliation(s)
- Zihao Wang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Zhenquan Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Songhao Luo
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Tianshou Zhou
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Jiajun Zhang
- Guangdong Province Key Laboratory of Computational Science, Sun Yat-sen University, Guangzhou 510275, P.R. China;
- School of Mathematics, Sun Yat-sen University, Guangzhou 510275, P.R. China
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9
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Chen X, Xu Y. Interplay between the transcription preinitiation complex and the +1 nucleosome. Trends Biochem Sci 2024; 49:145-155. [PMID: 38218671 DOI: 10.1016/j.tibs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
Eukaryotic transcription starts with the assembly of a preinitiation complex (PIC) on core promoters. Flanking this region is the +1 nucleosome, the first nucleosome downstream of the core promoter. While this nucleosome is rich in epigenetic marks and plays a key role in transcription regulation, how the +1 nucleosome interacts with the transcription machinery has been a long-standing question. Here, we summarize recent structural and functional studies of the +1 nucleosome in complex with the PIC. We specifically focus on how differently organized promoter-nucleosome templates affect the assembly of the PIC and PIC-Mediator on chromatin and result in distinct transcription initiation.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
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10
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Kaye EG, Basavaraju K, Nelson GM, Zomer HD, Roy D, Joseph II, Rajabi-Toustani R, Qiao H, Adelman K, Reddi PP. RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. Nat Commun 2024; 15:848. [PMID: 38287033 PMCID: PMC10824759 DOI: 10.1038/s41467-024-45177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 01/16/2024] [Indexed: 01/31/2024] Open
Abstract
Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double-strand break (DSB) formation, and disruption of meiotic gene expression and DSB repair in germ cells lacking NELF.
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Affiliation(s)
- Emily G Kaye
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Kavyashree Basavaraju
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Geoffrey M Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Helena D Zomer
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Debarun Roy
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Irene Infancy Joseph
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Reza Rajabi-Toustani
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Huanyu Qiao
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Prabhakara P Reddi
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, IL, 61802, USA.
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11
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Dubiez E, Pellegrini E, Finderup Brask M, Garland W, Foucher AE, Huard K, Heick Jensen T, Cusack S, Kadlec J. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. Cell Rep 2024; 43:113639. [PMID: 38175753 DOI: 10.1016/j.celrep.2023.113639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse "effectors" that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
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Affiliation(s)
- Etienne Dubiez
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Erika Pellegrini
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Maja Finderup Brask
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | | | - Karine Huard
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
| | - Jan Kadlec
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France.
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12
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Maas ZL, Dowell RD. Internal and external normalization of nascent RNA sequencing run-on experiments. BMC Bioinformatics 2024; 25:19. [PMID: 38216877 PMCID: PMC10785432 DOI: 10.1186/s12859-023-05607-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 12/07/2023] [Indexed: 01/14/2024] Open
Abstract
In experiments with significant perturbations to transcription, nascent RNA sequencing protocols are dependent on external spike-ins for reliable normalization. Unlike in RNA-seq, these spike-ins are not standardized and, in many cases, depend on a run-on reaction that is assumed to have constant efficiency across samples. To assess the validity of this assumption, we analyze a large number of published nascent RNA spike-ins to quantify their variability across existing normalization methods. Furthermore, we develop a new biologically-informed Bayesian model to estimate the error in spike-in based normalization estimates, which we term Virtual Spike-In (VSI). We apply this method both to published external spike-ins as well as using reads at the [Formula: see text] end of long genes, building on prior work from Mahat (Mol Cell 62(1):63-78, 2016. https://doi.org/10.1016/j.molcel.2016.02.025 ) and Vihervaara (Nat Commun 8(1):255, 2017. https://doi.org/10.1038/s41467-017-00151-0 ). We find that spike-ins in existing nascent RNA experiments are typically under sequenced, with high variability between samples. Furthermore, we show that these high variability estimates can have significant downstream effects on analysis, complicating biological interpretations of results.
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Affiliation(s)
- Zachary L Maas
- Department of Computer Science, University of Colorado, Boulder, USA
- BioFrontiers Institute, University of Colorado, Boulder, USA
| | - Robin D Dowell
- Department of Computer Science, University of Colorado, Boulder, USA.
- BioFrontiers Institute, University of Colorado, Boulder, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, USA.
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13
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Layden HM, Johnson AE, Hiebert SW. Chemical-genetics refines transcription factor regulatory circuits. Trends Cancer 2024; 10:65-75. [PMID: 37722945 PMCID: PMC10840957 DOI: 10.1016/j.trecan.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/14/2023] [Accepted: 08/25/2023] [Indexed: 09/20/2023]
Abstract
Transcriptional dysregulation is a key step in oncogenesis, but our understanding of transcriptional control has relied on genetic approaches that are slow and allow for compensation. Chemical-genetic approaches have shortened the time frame for the analysis of transcription factors from days or weeks to minutes. These studies show that while DNA-binding proteins bind to thousands of sites, they are directly required to regulate only a small cadre of genes. Moreover, these transcriptional control networks are far more distinct, with much less overlap and interconnectivity than predicted from DNA binding. The identified direct targets can then be used to dissect the mechanism of action of these factors, which could identify ways to therapeutically manipulate these oncogenic transcriptional control networks.
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Affiliation(s)
- Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Anna E Johnson
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37027, USA.
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14
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Ait Said M, Bejjani F, Abdouni A, Ségéral E, Emiliani S. Premature transcription termination complex proteins PCF11 and WDR82 silence HIV-1 expression in latently infected cells. Proc Natl Acad Sci U S A 2023; 120:e2313356120. [PMID: 38015843 DOI: 10.1073/pnas.2313356120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Postintegration transcriptional silencing of HIV-1 leads to the establishment of a pool of latently infected cells. In these cells, mechanisms controlling RNA Polymerase II (RNAPII) pausing and premature transcription termination (PTT) remain to be explored. Here, we found that the cleavage and polyadenylation (CPA) factor PCF11 represses HIV-1 expression independently of the other subunits of the CPA complex or the polyadenylation signal located at the 5' LTR. We show that PCF11 interacts with the RNAPII-binding protein WDR82. Knock-down of PCF11 or WDR82 reactivated HIV-1 expression in latently infected cells. To silence HIV-1 transcription, PCF11 and WDR82 are specifically recruited at the promoter-proximal region of the provirus in an interdependent manner. Codepletion of PCF11 and WDR82 indicated that they act on the same pathway to repress HIV expression. These findings reveal PCF11/WDR82 as a PTT complex silencing HIV-1 expression in latently infected cells.
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Affiliation(s)
- Melissa Ait Said
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Fabienne Bejjani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Ahmed Abdouni
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Emmanuel Ségéral
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
| | - Stéphane Emiliani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris F-75014, France
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15
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Zhao Y, Liu L, Hassett R, Siepel A. Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Res 2023; 51:e106. [PMID: 37889042 PMCID: PMC10681744 DOI: 10.1093/nar/gkad843] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions. Here, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations, we show that this model enables accurate estimation of initiation and pause-escape rates. Furthermore, we show by simulation and analysis of real data that pause-escape is often strongly rate-limiting and that steric hindrance can dramatically reduce initiation rates. Our modeling framework is applicable to a variety of inference problems, and our software for estimation and simulation is freely available.
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Affiliation(s)
- Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Lingjie Liu
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, USA
| | - Rebecca Hassett
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Graduate Program in Genetics, Stony Brook University, Stony Brook, NY, USA
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16
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Morgan MA, Mohammad Parast S, Iwanaszko M, Aoi Y, Yoo D, Dumar ZJ, Howard BC, Helmin KA, Liu Q, Thakur WR, Zeidner JM, Singer BD, Eichler EE, Shilatifard A. ELOA3: A primate-specific RNA polymerase II elongation factor encoded by a tandem repeat gene cluster. Sci Adv 2023; 9:eadj1261. [PMID: 37992162 PMCID: PMC10664989 DOI: 10.1126/sciadv.adj1261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 10/19/2023] [Indexed: 11/24/2023]
Abstract
The biological role of the repetitive DNA sequences in the human genome remains an outstanding question. Recent long-read human genome assemblies have allowed us to identify a function for one of these repetitive regions. We have uncovered a tandem array of conserved primate-specific retrogenes encoding the protein Elongin A3 (ELOA3), a homolog of the RNA polymerase II (RNAPII) elongation factor Elongin A (ELOA). Our genomic analysis shows that the ELOA3 gene cluster is conserved among primates and the number of ELOA3 gene repeats is variable in the human population and across primate species. Moreover, the gene cluster has undergone concerted evolution and homogenization within primates. Our biochemical studies show that ELOA3 functions as a promoter-associated RNAPII pause-release elongation factor with distinct biochemical and functional features from its ancestral homolog, ELOA. We propose that the ELOA3 gene cluster has evolved to fulfil a transcriptional regulatory function unique to the primate lineage that can be targeted to regulate cellular hyperproliferation.
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Affiliation(s)
- Marc A. J. Morgan
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Saeid Mohammad Parast
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yuki Aoi
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
| | - Zachary J. Dumar
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin C. Howard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kathryn A. Helmin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Qianli Liu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - William R. Thakur
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Jacob M. Zeidner
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Benjamin D. Singer
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Simpson Querrey Lung Institute for Translational Science, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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17
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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18
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Pan H, Cheng X, Rodríguez PFG, Zhang X, Chung I, Jin VX, Li W, Hu Y, Li R. An essential signaling function of cytoplasmic NELFB is independent of RNA polymerase II pausing. J Biol Chem 2023; 299:105259. [PMID: 37717699 PMCID: PMC10591015 DOI: 10.1016/j.jbc.2023.105259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/24/2023] [Accepted: 08/30/2023] [Indexed: 09/19/2023] Open
Abstract
The four-subunit negative elongation factor (NELF) complex mediates RNA polymerase II (Pol II) pausing at promoter-proximal regions. Ablation of individual NELF subunits destabilizes the NELF complex and causes cell lethality, leading to the prevailing concept that NELF-mediated Pol II pausing is essential for cell proliferation. Using separation-of-function mutations, we show here that NELFB function in cell proliferation can be uncoupled from that in Pol II pausing. NELFB mutants sequestered in the cytoplasm and deprived of NELF nuclear function still support cell proliferation and part of the NELFB-dependent transcriptome. Mechanistically, cytoplasmic NELFB physically and functionally interacts with prosurvival signaling kinases, most notably phosphatidylinositol-3-kinase/AKT. Ectopic expression of membrane-tethered phosphatidylinositol-3-kinase/AKT partially bypasses the role of NELFB in cell proliferation, but not Pol II occupancy. Together, these data expand the current understanding of the physiological impact of Pol II pausing and underscore the multiplicity of the biological functions of individual NELF subunits.
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Affiliation(s)
- Haihui Pan
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA.
| | - Xiaolong Cheng
- Department of Genomics & Precision Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA; Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Pedro Felipe Gardeazábal Rodríguez
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Xiaowen Zhang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Inhee Chung
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Victor X Jin
- Institute of Health Equity and Cancer Center, The Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Wei Li
- Department of Genomics & Precision Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA; Center for Genetic Medicine Research, Children's National Hospital, Washington, District of Columbia, USA
| | - Yanfen Hu
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA
| | - Rong Li
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, District of Columbia, USA.
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19
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Keller SH, Deng H, Lim B. Regulation of the dynamic RNA Pol II elongation rate in Drosophila embryos. Cell Rep 2023; 42:113225. [PMID: 37837623 PMCID: PMC10842316 DOI: 10.1016/j.celrep.2023.113225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/20/2023] [Accepted: 09/22/2023] [Indexed: 10/16/2023] Open
Abstract
An increasing number of studies have shown the key role that RNA polymerase II (RNA Pol II) elongation plays in gene regulation. We systematically examine how various enhancers, promoters, and gene body composition influence the RNA Pol II elongation rate through a single-cell-resolution live imaging assay. By using reporter constructs containing 5' MS2 and 3' PP7 repeating stem loops, we quantify the rate of RNA Pol II elongation in live Drosophila embryos. We find that promoters and exonic gene lengths have no effect on elongation rate, while enhancers and the presence of long introns may significantly change how quickly RNA Pol II moves across a gene. Furthermore, we observe in multiple constructs that the RNA Pol II elongation rate accelerates after the transcriptional onset of nuclear cycle 14 in Drosophila embryos. Our study provides a single-cell view of various mechanisms that affect the dynamic RNA Pol II elongation rate, ultimately affecting the rate of mRNA production.
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Affiliation(s)
- Samuel H Keller
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hao Deng
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bomyi Lim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
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20
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Xu W, Li X. Regulation of Pol II Pausing during Daily Gene Transcription in Mouse Liver. Biology (Basel) 2023; 12:1107. [PMID: 37626993 PMCID: PMC10452108 DOI: 10.3390/biology12081107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023]
Abstract
Cell autonomous circadian oscillation is present in central and various peripheral tissues. The intrinsic tissue clock and various extrinsic cues drive gene expression rhythms. Transcription regulation is thought to be the main driving force for gene rhythms. However, how transcription rhythms arise remains to be fully characterized due to the fact that transcription is regulated at multiple steps. In particular, Pol II recruitment, pause release, and premature transcription termination are critical regulatory steps that determine the status of Pol II pausing and transcription output near the transcription start site (TSS) of the promoter. Recently, we showed that Pol II pausing exhibits genome-wide changes during daily transcription in mouse liver. In this article, we review historical as well as recent findings on the regulation of transcription rhythms by the circadian clock and other transcription factors, and the potential limitations of those results in explaining rhythmic transcription at the TSS. We then discuss our results on the genome-wide characteristics of daily changes in Pol II pausing, the possible regulatory mechanisms involved, and their relevance to future research on circadian transcription regulation.
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Affiliation(s)
| | - Xiaodong Li
- College of Life Sciences, Wuhan University, Wuhan 430072, China;
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21
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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: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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22
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Garg G, Dienemann C, Farnung L, Schwarz J, Linden A, Urlaub H, Cramer P. Structural insights into human co-transcriptional capping. Mol Cell 2023:S1097-2765(23)00424-0. [PMID: 37369200 DOI: 10.1016/j.molcel.2023.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/22/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Co-transcriptional capping of the nascent pre-mRNA 5' end prevents degradation of RNA polymerase (Pol) II transcripts and suppresses the innate immune response. Here, we provide mechanistic insights into the three major steps of human co-transcriptional pre-mRNA capping based on six different cryoelectron microscopy (cryo-EM) structures. The human mRNA capping enzyme, RNGTT, first docks to the Pol II stalk to position its triphosphatase domain near the RNA exit site. The capping enzyme then moves onto the Pol II surface, and its guanylyltransferase receives the pre-mRNA 5'-diphosphate end. Addition of a GMP moiety can occur when the RNA is ∼22 nt long, sufficient to reach the active site of the guanylyltransferase. For subsequent cap(1) methylation, the methyltransferase CMTR1 binds the Pol II stalk and can receive RNA after it is grown to ∼29 nt in length. The observed rearrangements of capping factors on the Pol II surface may be triggered by the completion of catalytic reaction steps and are accommodated by domain movements in the elongation factor DRB sensitivity-inducing factor (DSIF).
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Affiliation(s)
- Gaurika Garg
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lucas Farnung
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Juliane Schwarz
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Andreas Linden
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry Group, Am Fassberg 11, 37077 Göttingen, Germany; University Medical Center Göttingen, Institute of Clinical Chemistry, Bionalytics Group, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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23
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Weiß E, Hennig T, Graßl P, Djakovic L, Whisnant AW, Jürges CS, Koller F, Kluge M, Erhard F, Dölken L, Friedel CC. HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes. J Virol 2023; 97:e0038123. [PMID: 37093003 PMCID: PMC10231138 DOI: 10.1128/jvi.00381-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) infection exerts a profound shutoff of host gene expression at multiple levels. Recently, HSV-1 infection was reported to also impact promoter-proximal RNA polymerase II (Pol II) pausing, a key step in the eukaryotic transcription cycle, with decreased and increased Pol II pausing observed for activated and repressed genes, respectively. Here, we demonstrate that HSV-1 infection induces more complex alterations in promoter-proximal pausing than previously suspected for the vast majority of cellular genes. While pausing is generally retained, it is shifted to more downstream and less well-positioned sites for most host genes. The downstream shift of Pol II pausing was established between 1.5 and 3 h of infection, remained stable until at least 6 hours postinfection, and was observed in the absence of ICP22. The shift in Pol II pausing does not result from alternative de novo transcription initiation at downstream sites or read-in transcription originating from disruption of transcription termination of upstream genes. The use of downstream secondary pause sites associated with +1 nucleosomes was previously observed upon negative elongation factor (NELF) depletion. However, downstream shifts of Pol II pausing in HSV-1 infection were much more pronounced than observed upon NELF depletion. Thus, our study reveals a novel aspect in which HSV-1 infection fundamentally reshapes host transcriptional processes, providing new insights into the regulation of promoter-proximal Pol II pausing in eukaryotic cells. IMPORTANCE This study provides a genome-wide analysis of changes in promoter-proximal polymerase II (Pol II) pausing on host genes induced by HSV-1 infection. It shows that standard measures of pausing, i.e., pausing indices, do not properly capture the complex and unsuspected alterations in Pol II pausing occurring in HSV-1 infection. Instead of a reduction of pausing with increased elongation, as suggested by pausing index analysis, HSV-1 infection leads to a shift of pausing to downstream and less well-positioned sites than in uninfected cells for the majority of host genes. Thus, HSV-1 infection fundamentally reshapes a key regulatory step at the beginning of the host transcriptional cycle on a genome-wide scale.
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Affiliation(s)
- Elena Weiß
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Pilar Graßl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Christopher S. Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Franziska Koller
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
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DeBerardine M, Booth GT, Versluis PP, Lis JT. The NELF pausing checkpoint mediates the functional divergence of Cdk9. Nat Commun 2023; 14:2762. [PMID: 37179384 PMCID: PMC10182999 DOI: 10.1038/s41467-023-38359-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Promoter-proximal pausing by RNA Pol II is a rate-determining step in gene transcription that is hypothesized to be a prominent point at which regulatory factors act. The pausing factor NELF is known to induce and stabilize pausing, but not all kinds of pausing are NELF-mediated. Here, we find that NELF-depleted Drosophila melanogaster cells functionally recapitulate the NELF-independent pausing we previously observed in fission yeast (which lack NELF). Critically, only NELF-mediated pausing establishes a strict requirement for Cdk9 kinase activity for the release of paused Pol II into productive elongation. Upon inhibition of Cdk9, cells with NELF efficiently shutdown gene transcription, while in NELF-depleted cells, defective, non-productive transcription continues unabated. By introducing a strict checkpoint for Cdk9, the evolution of NELF was likely critical to enable increased regulation of Cdk9 in higher eukaryotes, as Cdk9 availability can be restricted to limit gene transcription without inducing wasteful, non-productive transcription.
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Affiliation(s)
- Michael DeBerardine
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Gregory T Booth
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Kanvas Biosciences, Monmouth Junction, NJ, USA
| | - Philip P Versluis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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25
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Kaye EG, Nelson GM, Zomer HD, Roy D, Joseph II, Adelman K, Reddi PP. RNA polymerase II pausing is essential during spermatogenesis for appropriate gene expression and completion of meiosis. bioRxiv 2023:2023.05.08.539879. [PMID: 37215034 PMCID: PMC10197597 DOI: 10.1101/2023.05.08.539879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Male germ cell development requires precise regulation of gene activity in a cell-type and stage-specific manner, with perturbations in gene expression during spermatogenesis associated with infertility. Here, we use steady-state, nascent and single-cell RNA sequencing strategies to comprehensively characterize gene expression across male germ cell populations, to dissect the mechanisms of gene control and provide new insights towards therapy. We discover a requirement for pausing of RNA Polymerase II (Pol II) at the earliest stages of sperm differentiation to establish the landscape of gene activity across development. Accordingly, genetic knockout of the Pol II pause-inducing factor NELF in immature germ cells blocks differentiation to mature spermatids. Further, we uncover unanticipated roles for Pol II pausing in the regulation of meiosis during spermatogenesis, with the presence of paused Pol II associated with double strand break formation by SPO11, and disruption of SPO11 expression in germ cells lacking NELF.
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Affiliation(s)
- Emily G. Kaye
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Geoffrey M. Nelson
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Helena D. Zomer
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
| | - Debarun Roy
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
| | - Irene Infancy Joseph
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Prabhakara P. Reddi
- Department of Comparative Biosciences, University of Illinois Urbana-Champaign, Urbana, Illinois, 61802, USA
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26
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Ren L, Yang X, Liu J, Wang W, Liu Z, Lin Q, Huang B, Pan J, Mao X. An innovative model based on N7-methylguanosine-related lncRNAs for forecasting prognosis and tumor immune landscape in bladder cancer. Cancer Cell Int 2023; 23:85. [PMID: 37158958 PMCID: PMC10165842 DOI: 10.1186/s12935-023-02933-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND As a novel type of the prevalent post-transcriptional modifications, N7-methylguanosine (m7G) modification is essential in the tumorigenesis, progression, and invasion of many cancers, including bladder cancer (BCa). However, the integrated roles of m7G-related lncRNAs in BCa remain undiscovered. This study aims to develop a prognostic model based on the m7G-related lncRNAs and explore its predictive value of the prognosis and anti-cancer treatment sensitivity. METHODS We obtained RNA-seq data and corresponding clinicopathological information from the TCGA database and collected m7G-related genes from previous studies and GSEA. Based on LASSO and Cox regression analysis, we developed a m7G prognostic model. The Kaplan-Meier (K-M) survival analysis and ROC curves were performed to evaluate the predictive power of the model. Gene set enrichment analysis (GSEA) was conducted to explore the molecular mechanisms behind apparent discrepancies between the low- and high-risk groups. We also investigated immune cell infiltration, TIDE score, TMB, the sensitivity of common chemotherapy drugs, and the response to immunotherapy between the two risk groups. Finally, we validated the expression levels of these ten m7G-related lncRNAs in BCa cell lines by qRT-PCR. RESULTS We developed a m7G prognostic model (risk score) composed of 10 m7G-related lncRNAs that are significantly associated with the OS of BCa patients. The K-M survival curves revealed that the high-risk group patients had significantly worse OS than those in the low-risk group. The Cox regression analysis confirmed that the risk score was a significant independent prognostic factor for BCa patients. We found that the high-risk group had higher the immune scores and immune cell infiltration. Furthermore, the results of the sensitivity of common anti-BCa drugs showed that the high-risk group was more sensitive to neoadjuvant cisplatin-based chemotherapy and anti-PD1 immunotherapy. Finally, qRT-PCR revealed that AC006058.1, AC073133.2, LINC00677, and LINC01338 were significantly downregulated in BCa cell lines, while the expression levels of AC124312.2 and AL158209.1 were significantly upregulated in BCa cell lines compared with normal cell lines. CONCLUSION The m7G prognostic model can be applied to accurately predict the prognosis and provide robust directions for clinicians to develop better individual-based and precise treatment strategies for BCa patients.
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Affiliation(s)
- Lei Ren
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Xu Yang
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Jinwen Liu
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Weifeng Wang
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China
| | - Zixiong Liu
- Department of Urology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Qingyuan Lin
- Department of Urology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, China
| | - Bin Huang
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
| | - Jincheng Pan
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
| | - Xiaopeng Mao
- Department of Urology, The First Affiliated Hospital of Sun Yat-Sen University, Sun Yat-Sen University, No.58 Zhongshan 2nd Road, Guangzhou, 510080, Guangdong, China.
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27
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Escobedo SE, McGovern SE, Jauregui-Lozano JP, Stanhope SC, Anik P, Singhal K, DeBernardis R, Weake VM. Targeted RNAi screen identifies transcriptional mechanisms that prevent premature degeneration of adult photoreceptors. Front Epigenet Epigenom 2023; 1:1187980. [PMID: 37901602 PMCID: PMC10603763 DOI: 10.3389/freae.2023.1187980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Aging is associated with a decline in visual function and increased prevalence of ocular disease, correlating with changes in the transcriptome and epigenome of cells in the eye. Here, we sought to identify the transcriptional mechanisms that are necessary to maintain photoreceptor viability and function during aging. To do this, we performed a targeted photoreceptor-specific RNAi screen in Drosophila to identify transcriptional regulators whose knockdown results in premature, age-dependent retinal degeneration. From an initial set of 155 RNAi lines each targeting a unique gene and spanning a diverse set of transcription factors, chromatin remodelers, and histone modifiers, we identified 18 high-confidence target genes whose decreased expression in adult photoreceptors leads to premature and progressive retinal degeneration. These 18 target genes were enriched for factors involved in the regulation of transcription initiation, pausing, and elongation, suggesting that these processes are essential for maintaining the health of aging photoreceptors. To identify the genes regulated by these factors, we profiled the photoreceptor transcriptome in a subset of lines. Strikingly, two of the 18 target genes, Spt5 and domino, show similar changes in gene expression to those observed in photoreceptors with advanced age. Together, our data suggest that dysregulation of factors involved in transcription initiation and elongation plays a key role in shaping the transcriptome of aging photoreceptors. Further, our findings indicate that the age-dependent changes in gene expression not only correlate but might also contribute to an increased risk of retinal degeneration.
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Affiliation(s)
- Spencer E. Escobedo
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Sarah E. McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | | | - Sarah C. Stanhope
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Paul Anik
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Kratika Singhal
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Ryan DeBernardis
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Vikki M. Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, United States
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28
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Zhang J, Hu Z, Chung HH, Tian Y, Lau KW, Ser Z, Lim YT, Sobota RM, Leong HF, Chen BJ, Yeo CJ, Tan SYX, Kang J, Tan DEK, Sou IF, McClurg UL, Lakshmanan M, Vaiyapuri TS, Raju A, Wong ESM, Tergaonkar V, Rajarethinam R, Pathak E, Tam WL, Tan EY, Tee WW. Dependency of NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis. Nat Commun 2023; 14:2439. [PMID: 37117180 PMCID: PMC10147683 DOI: 10.1038/s41467-023-38132-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/17/2023] [Indexed: 04/30/2023] Open
Abstract
Cancer cells undergo transcriptional reprogramming to drive tumor progression and metastasis. Using cancer cell lines and patient-derived tumor organoids, we demonstrate that loss of the negative elongation factor (NELF) complex inhibits breast cancer development through downregulating epithelial-mesenchymal transition (EMT) and stemness-associated genes. Quantitative multiplexed Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins (qPLEX-RIME) further reveals a significant rewiring of NELF-E-associated chromatin partners as a function of EMT and a co-option of NELF-E with the key EMT transcription factor SLUG. Accordingly, loss of NELF-E leads to impaired SLUG binding on chromatin. Through integrative transcriptomic and genomic analyses, we identify the histone acetyltransferase, KAT2B, as a key functional target of NELF-E-SLUG. Genetic and pharmacological inactivation of KAT2B ameliorate the expression of EMT markers, phenocopying NELF ablation. Elevated expression of NELF-E and KAT2B is associated with poorer prognosis in breast cancer patients, highlighting the clinical relevance of our findings. Taken together, we uncover a crucial role of the NELF-E-SLUG-KAT2B epigenetic axis in breast cancer carcinogenesis.
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Affiliation(s)
- Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Republic of Singapore
| | - Zhenhua Hu
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwa Hwa Chung
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Yun Tian
- Department of Oncology, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, 210004, Nanjing, People's Republic of China
| | - Kah Weng Lau
- Department of Pathology, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Republic of Singapore
| | - Zheng Ser
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Yan Ting Lim
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Radoslaw M Sobota
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Hwei Fen Leong
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Benjamin Jieming Chen
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Clarisse Jingyi Yeo
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Jian Kang
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Dennis Eng Kiat Tan
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Ieng Fong Sou
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Urszula Lucja McClurg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Manikandan Lakshmanan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Thamil Selvan Vaiyapuri
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Anandhkumar Raju
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Esther Sook Miin Wong
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Vinay Tergaonkar
- Department of Pathology, National University Hospital, 5 Lower Kent Ridge Road, Singapore, 119074, Republic of Singapore
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
| | - Ravisankar Rajarethinam
- Advanced Molecular Pathology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
| | - Elina Pathak
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Drive, Genome, Singapore, 138672, Republic of Singapore
| | - Wai Leong Tam
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Drive, Genome, Singapore, 138672, Republic of Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore
| | - Ern Yu Tan
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, 308433, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Republic of Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Lab, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117593, Republic of Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Republic of Singapore.
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29
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Hu S, Peng L, Song A, Ji YX, Cheng J, Wang M, Chen FX. INTAC endonuclease and phosphatase modules differentially regulate transcription by RNA polymerase II. Mol Cell 2023; 83:1588-1604.e5. [PMID: 37080207 DOI: 10.1016/j.molcel.2023.03.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/14/2023] [Accepted: 03/23/2023] [Indexed: 04/22/2023]
Abstract
Gene expression in metazoans is controlled by promoter-proximal pausing of RNA polymerase II, which can undergo productive elongation or promoter-proximal termination. Integrator-PP2A (INTAC) plays a crucial role in determining the fate of paused polymerases, but the underlying mechanisms remain unclear. Here, we establish a rapid degradation system to dissect the functions of INTAC RNA endonuclease and phosphatase modules. We find that both catalytic modules function at most if not all active promoters and enhancers, yet differentially affect polymerase fate. The endonuclease module induces promoter-proximal termination, with its disruption leading to accumulation of elongation-incompetent polymerases and downregulation of highly expressed genes, while elongation-competent polymerases accumulate at lowly expressed genes and non-coding elements, leading to their upregulation. The phosphatase module primarily prevents the release of paused polymerases and limits transcriptional activation, especially for highly paused genes. Thus, both INTAC catalytic modules have unexpectedly general yet distinct roles in dynamic transcriptional control.
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Affiliation(s)
- Shibin Hu
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Linna Peng
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Aixia Song
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu-Xin Ji
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jingdong Cheng
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Mengyun Wang
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, Human Phenome Institute, Shanghai Key Laboratory of Radiation Oncology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China.
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30
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Sen P, Donahue G, Li C, Egervari G, Yang N, Lan Y, Robertson N, Shah PP, Kerkhoven E, Schultz DC, Adams PD, Berger SL. Spurious intragenic transcription is a feature of mammalian cellular senescence and tissue aging. Nat Aging 2023; 3:402-417. [PMID: 37117791 PMCID: PMC10165726 DOI: 10.1038/s43587-023-00384-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 02/22/2023] [Indexed: 04/30/2023]
Abstract
Mammalian aging is characterized by the progressive loss of tissue function and increased risk for disease. Accumulation of senescent cells in aging tissues partly contributes to this decline, and targeted depletion of senescent cells in vivo ameliorates many age-related phenotypes. The fundamental molecular mechanisms responsible for the decline of cellular health and fitness during senescence and aging are largely unknown. In this study, we investigated whether chromatin-mediated loss of transcriptional fidelity, known to contribute to fitness and survival in yeast and worms, also occurs during human cellular senescence and mouse aging. Our findings reveal aberrant transcription initiation inside genes during senescence and aging that co-occurs with changes in the chromatin landscape. Interventions that alter these spurious transcripts have profound consequences on cellular health, primarily affecting intracellular signal transduction pathways. We propose that age-related spurious transcription promotes a noisy transcriptome and degradation of coherent transcriptional networks.
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Affiliation(s)
- Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA.
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Greg Donahue
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine Li
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabor Egervari
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Yemin Lan
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neil Robertson
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Parisha P Shah
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Kerkhoven
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David C Schultz
- High Throughput Screening Core, Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK
| | - Shelley L Berger
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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31
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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. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [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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32
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Abstract
In higher eukaryotes, fine-tuned activation of protein-coding genes and many non-coding RNAs pivots around the regulated activity of RNA polymerase II (Pol II). The Integrator complex is the only Pol II-associated large multiprotein complex that is metazoan specific, and has therefore been understudied for years. Integrator comprises at least 14 subunits, which are grouped into distinct functional modules. The phosphodiesterase activity of the core catalytic module is co-transcriptionally directed against several RNA species, including long non-coding RNAs (lncRNAs), U small nuclear RNAs (U snRNAs), PIWI-interacting RNAs (piRNAs), enhancer RNAs and nascent pre-mRNAs. Processing of non-coding RNAs by Integrator is essential for their biogenesis, and at protein-coding genes, Integrator is a key modulator of Pol II promoter-proximal pausing and transcript elongation. Recent studies have identified an Integrator-specific serine/threonine-protein phosphatase 2A (PP2A) module, which targets Pol II and other components of the basal transcription machinery. In this Review, we discuss how the activity of Integrator regulates transcription, RNA processing, chromatin landscape and DNA repair. We also discuss the diverse roles of Integrator in development and tumorigenesis.
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Cordiner RA, Dou Y, Thomsen R, Bugai A, Granneman S, Heick Jensen T. Temporal-iCLIP captures co-transcriptional RNA-protein interactions. Nat Commun 2023; 14:696. [PMID: 36755023 DOI: 10.1038/s41467-023-36345-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
Dynamic RNA-protein interactions govern the co-transcriptional packaging of RNA polymerase II (RNAPII)-derived transcripts. Yet, our current understanding of this process in vivo primarily stems from steady state analysis. To remedy this, we here conduct temporal-iCLIP (tiCLIP), combining RNAPII transcriptional synchronisation with UV cross-linking of RNA-protein complexes at serial timepoints. We apply tiCLIP to the RNA export adaptor, ALYREF; a component of the Nuclear Exosome Targeting (NEXT) complex, RBM7; and the nuclear cap binding complex (CBC). Regardless of function, all tested factors interact with nascent RNA as it exits RNAPII. Moreover, we demonstrate that the two transesterification steps of pre-mRNA splicing temporally separate ALYREF and RBM7 binding to splicing intermediates, and that exon-exon junction density drives RNA 5'end binding of ALYREF. Finally, we identify underappreciated steps in snoRNA 3'end processing performed by RBM7. Altogether, our data provide a temporal view of RNA-protein interactions during the early phases of transcription.
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34
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Abe K, Schauer T, Torres-Padilla ME. Distinct patterns of RNA polymerase II and transcriptional elongation characterize mammalian genome activation. Cell Rep 2022; 41:111865. [PMID: 36577375 DOI: 10.1016/j.celrep.2022.111865] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 12/28/2022] Open
Abstract
How transcription is regulated as development commences is fundamental to understand how the transcriptionally silent mature gametes are reprogrammed. The embryonic genome is activated for the first time during zygotic genome activation (ZGA). How RNA polymerase II (Pol II) and productive elongation are regulated during this process remains elusive. Here, we generate genome-wide maps of Serine 5 and Serine 2-phosphorylated Pol II during and after ZGA in mouse embryos. We find that both phosphorylated Pol II forms display similar distributions across genes during ZGA, with typical elongation enrichment of Pol II emerging after ZGA. Serine 2-phosphorylated Pol II occurs at genes prior to their activation, suggesting that Serine 2 phosphorylation may prime gene expression. Functional perturbations demonstrate that CDK9 and SPT5 are major ZGA regulators and that SPT5 prevents precocious activation of some genes. Overall, our work sheds molecular insights into transcriptional regulation at the beginning of mammalian development.
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Affiliation(s)
- Kenichiro Abe
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany
| | - Tamas Schauer
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany; Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany; Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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35
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Lu H, Yang M, Zhou Q. Reprogramming transcription after DNA damage: recognition, response, repair, and restart. Trends Cell Biol 2022:S0962-8924(22)00261-6. [PMID: 36513571 DOI: 10.1016/j.tcb.2022.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Genome integrity is constantly challenged by endogenous and exogenous insults that cause DNA damage. To cope with these threats, cells have a surveillance mechanism, known as the DNA damage response (DDR), to repair any lesions. Although transcription has long been implicated in DNA repair, how transcriptional reprogramming is coordinated with the DDR is just beginning to be understood. In this review, we highlight recent advances in elucidating the molecular mechanisms underlying major transcriptional events, including RNA polymerase (Pol) II stalling and transcriptional silencing and recovery, which occur in response to DNA damage. Furthermore, we discuss how such transcriptional adaptation contributes to sensing and eliminating damaged DNA and how it can jeopardize genome integrity when it goes awry.
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Affiliation(s)
- Huasong Lu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Min Yang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qiang Zhou
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong.
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36
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Fong N, Sheridan RM, Ramachandran S, Bentley DL. The pausing zone and control of RNA polymerase II elongation by Spt5: Implications for the pause-release model. Mol Cell 2022; 82:3632-3645.e4. [PMID: 36206739 PMCID: PMC9555879 DOI: 10.1016/j.molcel.2022.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/24/2022] [Accepted: 08/31/2022] [Indexed: 11/07/2022]
Abstract
The pause-release model of transcription proposes that 40-100 bases from the start site RNA Pol II pauses, followed by release into productive elongation. Pause release is facilitated by the PTEFb phosphorylation of the RNA Pol II elongation factor, Spt5. We mapped paused polymerases by eNET-seq and found frequent pausing in zones that extend ∼0.3-3 kb into genes even when PTEFb is inhibited. The fraction of paused polymerases or pausing propensity declines gradually over several kb and not abruptly as predicted for a discrete pause-release event. Spt5 depletion extends pausing zones, suggesting that it promotes the maturation of elongation complexes to a low-pausing state. The expression of mutants after Spt5 depletion showed that phosphomimetic substitutions in the CTR1 domain diminished pausing throughout genes. By contrast, mutants that prevent the phosphorylation of the Spt5 RNA-binding domain strengthened pausing. Thus, distinct Spt5 phospho-isoforms set the balance between pausing and elongation.
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Affiliation(s)
- Nova Fong
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Ryan M Sheridan
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Srinivas Ramachandran
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- RNA Bioscience Initiative, Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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37
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Cortazar MA, Erickson B, Fong N, Pradhan SJ, Ntini E, Bentley DL. Xrn2 substrate mapping identifies torpedo loading sites and extensive premature termination of RNA pol II transcription. Genes Dev 2022; 36:1062-1078. [PMID: 36396340 PMCID: PMC9744234 DOI: 10.1101/gad.350004.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022]
Abstract
The exonuclease torpedo Xrn2 loads onto nascent RNA 5'-PO4 ends and chases down pol II to promote termination downstream from polyA sites. We report that Xrn2 is recruited to preinitiation complexes and "travels" to 3' ends of genes. Mapping of 5'-PO4 ends in nascent RNA identified Xrn2 loading sites stabilized by an active site mutant, Xrn2(D235A). Xrn2 loading sites are approximately two to 20 bases downstream from where CPSF73 cleaves at polyA sites and histone 3' ends. We propose that processing of all mRNA 3' ends comprises cleavage and limited 5'-3' trimming by CPSF73, followed by handoff to Xrn2. A similar handoff occurs at tRNA 3' ends, where cotranscriptional RNase Z cleavage generates novel Xrn2 substrates. Exonuclease-dead Xrn2 increased transcription in 3' flanking regions by inhibiting polyA site-dependent termination. Surprisingly, the mutant Xrn2 also rescued transcription in promoter-proximal regions to the same extent as in 3' flanking regions. eNET-seq revealed Xrn2-mediated degradation of sense and antisense nascent RNA within a few bases of the TSS, where 5'-PO4 ends may be generated by decapping or endonucleolytic cleavage. These results suggest that a major fraction of pol II complexes terminates prematurely close to the start site under normal conditions by an Xrn2-mediated torpedo mechanism.
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Affiliation(s)
- Michael A. Cortazar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Benjamin Erickson
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Sarala J. Pradhan
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Evgenia Ntini
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (FORTH), Heraklion GR-70013, Greece
| | - David L. Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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38
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Aoi Y, Shah AP, Ganesan S, Soliman SHA, Cho BK, Goo YA, Kelleher NL, Shilatifard A. SPT6 functions in transcriptional pause/release via PAF1C recruitment. Mol Cell 2022; 82:3412-3423.e5. [PMID: 35973425 PMCID: PMC9714687 DOI: 10.1016/j.molcel.2022.06.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/11/2022] [Accepted: 06/29/2022] [Indexed: 01/24/2023]
Abstract
It is unclear how various factors functioning in the transcriptional elongation by RNA polymerase II (RNA Pol II) cooperatively regulate pause/release and productive elongation in living cells. Using an acute protein-depletion approach, we report that SPT6 depletion results in the release of paused RNA Pol II into gene bodies through an impaired recruitment of PAF1C. Short genes demonstrate a release with increased mature transcripts, whereas long genes are released but fail to yield mature transcripts, due to a reduced processivity resulting from both SPT6 and PAF1C loss. Unexpectedly, SPT6 depletion causes an association of NELF with the elongating RNA Pol II on gene bodies, without any observed functional significance on transcriptional elongation pattern, arguing against a role for NELF in keeping RNA Pol II in the paused state. Furthermore, SPT6 depletion impairs heat-shock-induced pausing, pointing to a role for SPT6 in regulating RNA Pol II pause/release through PAF1C recruitment.
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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
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sheetal Ganesan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Shimaa H A Soliman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Byoung-Kyu Cho
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Young Ah Goo
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Neil L Kelleher
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, 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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39
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Sanidas I, Lee H, Rumde PH, Boulay G, Morris R, Golczer G, Stanzione M, Hajizadeh S, Zhong J, Ryan MB, Corcoran RB, Drapkin BJ, Rivera MN, Dyson NJ, Lawrence MS. Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression. Mol Cell 2022; 82:3333-3349.e9. [PMID: 35981542 PMCID: PMC9481721 DOI: 10.1016/j.molcel.2022.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/19/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023]
Abstract
The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, c-Jun, and CTCF. While E2F/DP facilitates RB association with promoters, AP-1 recruits RB to enhancers. Although phosphorylation in CDK sites is often portrayed as releasing RB from chromatin, we show that the cell cycle redistributes RB so that it enriches at promoters in G1 and at non-promoter sites in cycling cells. RB-bound promoters include the classic E2F-targets and are similar between lineages, but RB-bound enhancers associate with different categories of genes and vary between cell types. Thus, RB has a well-preserved role controlling E2F in G1, and it targets cell-type-specific enhancers and CTCF sites when cells enter S-phase.
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Affiliation(s)
- Ioannis Sanidas
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Hanjun Lee
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Purva H Rumde
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gaylor Boulay
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Gabriel Golczer
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Marcelo Stanzione
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Soroush Hajizadeh
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Jun Zhong
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Meagan B Ryan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA
| | - Benjamin J Drapkin
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Miguel N Rivera
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA.
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Building 149 13th Street, Charlestown, MA 02129, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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40
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Mazina MY, Kovalenko EV, Evdokimova AA, Erokhin M, Chetverina D, Vorobyeva NE. RNA Polymerase II “Pause” Prepares Promoters for Upcoming Transcription during Drosophila Development. Int J Mol Sci 2022; 23:10662. [PMID: 36142573 PMCID: PMC9503990 DOI: 10.3390/ijms231810662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
According to previous studies, during Drosophila embryogenesis, the recruitment of RNA polymerase II precedes active gene transcription. This work is aimed at exploring whether this mechanism is used during Drosophila metamorphosis. In addition, the composition of the RNA polymerase II “paused” complexes associated with promoters at different developmental stages are described in detail. For this purpose, we performed ChIP-Seq analysis using antibodies for various modifications of RNA polymerase II (total, Pol II CTD Ser5P, and Pol II CTD Ser2P) as well as for subunits of the NELF, DSIF, and PAF complexes and Brd4/Fs(1)h that control transcription elongation. We found that during metamorphosis, similar to mid-embryogenesis, the promoters were bound by RNA polymerase II in the “paused” state, preparing for activation at later stages of development. During mid-embryogenesis, RNA polymerase II in a “pause” state was phosphorylated at Ser5 and Ser2 of Pol II CTD and bound the NELF, DSIF, and PAF complexes, but not Brd4/Fs(1)h. During metamorphosis, the “paused” RNA polymerase II complex included Brd4/Fs(1)h in addition to NELF, DSIF, and PAF. The RNA polymerase II in this complex was phosphorylated at Ser5 of Pol II CTD, but not at Ser2. These results indicate that, during mid-embryogenesis, RNA polymerase II stalls in the “post-pause” state, being phosphorylated at Ser2 of Pol II CTD (after the stage of p-TEFb action). During metamorphosis, the “pause” mechanism is closer to classical promoter-proximal pausing and is characterized by a low level of Pol II CTD Ser2P.
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41
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Li Y, Huang J, Zhu J, Bao L, Wang H, Jiang Y, Tian K, Wang R, Zheng H, Duan W, Lai W, Yi X, Zhu Y, Guo T, Ji X. Targeted protein degradation reveals RNA Pol II heterogeneity and functional diversity. Mol Cell 2022; 82:3943-3959.e11. [PMID: 36113479 DOI: 10.1016/j.molcel.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 10/14/2022]
Abstract
RNA polymerase II (RNA Pol II) subunits are thought to be involved in various transcription-associated processes, but it is unclear whether they play different regulatory roles in modulating gene expression. Here, we performed nascent and mature transcript sequencing after the acute degradation of 12 mammalian RNA Pol II subunits and profiled their genomic binding sites and protein interactomes to dissect their molecular functions. We found that RNA Pol II subunits contribute differently to RNA Pol II cellular localization and transcription processes and preferentially regulate RNA processing (such as RNA splicing and 3' end maturation). Genes sensitive to the depletion of different RNA Pol II subunits tend to be involved in diverse biological functions and show different RNA half-lives. Sequences, associated protein factors, and RNA structures are correlated with RNA Pol II subunit-mediated differential gene expression. These findings collectively suggest that the heterogeneity of RNA Pol II and different genes appear to depend on some of the subunits.
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Affiliation(s)
- Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - WenJia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weifeng Lai
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiao Yi
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yi Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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42
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Bozukova M, Nikopoulou C, Kleinenkuhnen N, Grbavac D, Goetsch K, Tessarz P. Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver. Mol Syst Biol 2022; 18:e11002. [PMID: 36082605 PMCID: PMC9459415 DOI: 10.15252/msb.202211002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes in the level of transcriptional regulation. Here, we used a multi‐omics approach and integrated ATAC‐, RNA‐ and NET‐seq to identify age‐related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility, and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase in transcriptional output. Instead, aging is accompanied by a decrease in promoter‐proximal pausing of RNA polymerase II (Pol II), while initiation of transcription is not decreased as assessed by RNA polymerase mapping using CUT&RUN. Based on the data reported, we propose that these age‐related changes in transcriptional regulation are due to a reduced stability of the pausing complex.
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Affiliation(s)
- Mihaela Bozukova
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Chrysa Nikopoulou
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Niklas Kleinenkuhnen
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.,Faculty of Medicine, Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
| | - Dora Grbavac
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Katrin Goetsch
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Peter Tessarz
- Max Planck Research Group 'Chromatin and Ageing', Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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43
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Abuhashem A, Chivu AG, Zhao Y, Rice EJ, Siepel A, Danko CG, Hadjantonakis AK. RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes Dev 2022; 36:gad.349565.122. [PMID: 35981753 PMCID: PMC9480856 DOI: 10.1101/gad.349565.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/18/2022] [Indexed: 01/03/2023]
Abstract
Promoter-proximal RNA Pol II pausing is a critical step in transcriptional control. Pol II pausing has been predominantly studied in tissue culture systems. While Pol II pausing has been shown to be required for mammalian development, the phenotypic and mechanistic details of this requirement are unknown. Here, we found that loss of Pol II pausing stalls pluripotent state transitions within the epiblast of the early mouse embryo. Using Nelfb -/- mice and a NELFB degron mouse pluripotent stem cell model, we show that embryonic stem cells (ESCs) representing the naïve state of pluripotency successfully initiate a transition program but fail to balance levels of induced and repressed genes and enhancers in the absence of NELF. We found an increase in chromatin-associated NELF during transition from the naïve to later pluripotent states. Overall, our work defines the acute and long-term molecular consequences of NELF loss and reveals a role for Pol II pausing in the pluripotency continuum as a modulator of cell state transitions.
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Affiliation(s)
- Abderhman Abuhashem
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA
| | - Alexandra G Chivu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Yixin Zhao
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, New York 10065, USA
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44
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Vorländer MK, Pacheco-Fiallos B, Plaschka C. Structural basis of mRNA maturation: Time to put it together. Curr Opin Struct Biol 2022; 75:102431. [PMID: 35930970 DOI: 10.1016/j.sbi.2022.102431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 11/27/2022]
Abstract
In eukaryotes, the expression of genetic information begins in the cell nucleus with precursor messenger RNA (pre-mRNA) transcription and processing into mature mRNA. The mRNA is subsequently recognized and packaged by proteins into an mRNA ribonucleoprotein complex (mRNP) and exported to the cytoplasm for translation. Each of the nuclear mRNA maturation steps is carried out by a dedicated molecular machine. Here, we highlight recent structural and mechanistic insights into how these machines function, including the capping enzyme, the spliceosome, the 3'-end processing machinery, and the transcription-export complex. While we increasingly understand individual steps of nuclear gene expression, many questions remain. For example, we are only beginning to reveal how mature mRNAs are recognized and packaged for nuclear export and how mRNA maturation events are coupled to transcription and to each other. Advances in the preparation of recombinant and endogenous protein-nucleic acid complexes, cryo-electron microscopy, and machine learning promise exciting insights into the mechanisms of nuclear gene expression and its spatial organization.
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Affiliation(s)
- Matthias K Vorländer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria. https://twitter.com/@MVorlandr
| | - Belén Pacheco-Fiallos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria. https://twitter.com/@bpachecofiallos
| | - Clemens Plaschka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria.
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45
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Abstract
Cells experiencing proteotoxic stress downregulate the expression of thousands of active genes and upregulate a few stress-response genes. The strategy of downregulating gene expression has conceptual parallels with general lockdown in the global response to the coronavirus disease 2019 (COVID-19) pandemic. The mechanistic details of global transcriptional downregulation of genes, termed stress-induced transcriptional attenuation (SITA), are only beginning to emerge. The reduction in RNA and protein production during stress may spare proteostasis capacity, allowing cells to divert resources to control stress-induced damage. Given the relevance of translational downregulation in a broad variety of diseases, the role of SITA in diseases caused by proteotoxicity should be investigated in future, paving the way for potential novel therapeutics.
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Affiliation(s)
- Ritwick Sawarkar
- Medical Research Council (MRC), University of Cambridge, Cambridge, UK.
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46
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Song A, Chen FX. The pleiotropic roles of SPT5 in transcription. Transcription 2022; 13:53-69. [PMID: 35876486 PMCID: PMC9467590 DOI: 10.1080/21541264.2022.2103366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Initially discovered by genetic screens in budding yeast, SPT5 and its partner SPT4 form a stable complex known as DSIF in metazoa, which plays pleiotropic roles in multiple steps of transcription. SPT5 is the most conserved transcription elongation factor, being found in all three domains of life; however, its structure has evolved to include new domains and associated posttranslational modifications. These gained features have expanded transcriptional functions of SPT5, likely to meet the demand for increasingly complex regulation of transcription in higher organisms. This review discusses the pleiotropic roles of SPT5 in transcription, including RNA polymerase II (Pol II) stabilization, enhancer activation, Pol II pausing and its release, elongation, and termination, with a focus on the most recent progress of SPT5 functions in regulating metazoan transcription.
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Affiliation(s)
- Aixia Song
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
| | - Fei Xavier Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, Province 200032, China
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47
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Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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48
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Wang X, Qi Y, Wang Z, Wang L, Song A, Tao B, Li J, Zhao D, Zhang H, Jin Q, Jiang YZ, Chen FX, Xu Y, Chen X. RPAP2 regulates a transcription initiation checkpoint by inhibiting assembly of pre-initiation complex. Cell Rep 2022; 39:110732. [PMID: 35476980 DOI: 10.1016/j.celrep.2022.110732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/31/2021] [Accepted: 04/02/2022] [Indexed: 11/21/2022] Open
Abstract
RNA polymerase II (Pol II)-mediated transcription in metazoans requires precise regulation. RNA Pol II-associated protein 2 (RPAP2) was previously identified to transport Pol II from cytoplasm to nucleus and dephosphorylates Pol II C-terminal domain (CTD). Here, we show that RPAP2 binds hypo-/hyper-phosphorylated Pol II with undetectable phosphatase activity. The structure of RPAP2-Pol II shows mutually exclusive assembly of RPAP2-Pol II and pre-initiation complex (PIC) due to three steric clashes. RPAP2 prevents and disrupts Pol II-TFIIF interaction and impairs in vitro transcription initiation, suggesting a function in inhibiting PIC assembly. Loss of RPAP2 in cells leads to global accumulation of TFIIF and Pol II at promoters, indicating a critical role of RPAP2 in inhibiting PIC assembly independent of its putative phosphatase activity. Our study indicates that RPAP2 functions as a gatekeeper to inhibit PIC assembly and transcription initiation and suggests a transcription checkpoint.
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49
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Allen BL, Quach K, Jones T, Levandowski CB, Ebmeier CC, Rubin JD, Read T, Dowell RD, Schepartz A, Taatjes DJ. Suppression of p53 response by targeting p53-Mediator binding with a stapled peptide. Cell Rep 2022; 39:110630. [PMID: 35385747 PMCID: PMC9044438 DOI: 10.1016/j.celrep.2022.110630] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 01/24/2022] [Accepted: 03/15/2022] [Indexed: 01/11/2023] Open
Abstract
DNA-binding transcription factors (TFs) remain challenging to target with molecular probes. Many TFs function in part through interaction with Mediator, a 26-subunit complex that controls RNA polymerase II activity genome-wide. We sought to block p53 function by disrupting the p53-Mediator interaction. Through rational design and activity-based screening, we characterize a stapled peptide, with functional mimics of both p53 activation domains, that blocks p53-Mediator binding and selectively inhibits p53-dependent transcription in human cells; importantly, this "bivalent" peptide has negligible impact, genome-wide, on non-p53 target genes. Our proof-of-concept strategy circumvents the TF entirely and targets the TF-Mediator interface instead, with desired functional outcomes (i.e., selective inhibition of p53 activation). Furthermore, these results demonstrate that TF activation domains represent viable starting points for Mediator-targeting molecular probes, as an alternative to large compound libraries. Different TFs bind Mediator through different subunits, suggesting this strategy could be broadly applied to selectively alter gene expression programs.
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Affiliation(s)
- Benjamin L. Allen
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA,These authors contributed equally
| | - Kim Quach
- Department of Chemistry, Yale University, New Haven, CT 06520, USA,These authors contributed equally
| | - Taylor Jones
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA,These authors contributed equally
| | | | | | - Jonathan D. Rubin
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA
| | - Timothy Read
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA,Department of Medicine, Division of Genetics, Brigham & Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Robin D. Dowell
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80303, USA,BioFrontiers Institute, University of Colorado, Boulder, CO 80303, USA
| | - Alanna Schepartz
- Department of Chemistry, Yale University, New Haven, CT 06520, USA,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA,Department of Chemistry, University of California, Berkeley, CA 94720, USA,Correspondence: (A.S.), (D.J.T.)
| | - Dylan J. Taatjes
- Department of Biochemistry, University of Colorado, Boulder, CO 80303, USA,Lead contact,Correspondence: (A.S.), (D.J.T.)
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50
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Nissani N, Ulitsky I. Unique features of transcription termination and initiation at closely spaced tandem human genes. Mol Syst Biol 2022; 18:e10682. [PMID: 35362230 PMCID: PMC8972054 DOI: 10.15252/msb.202110682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 11/09/2022] Open
Abstract
The synthesis of RNA polymerase II (Pol2) products, which include messenger RNAs or long noncoding RNAs, culminates in transcription termination. How the transcriptional termination of a gene impacts the activity of promoters found immediately downstream of it, and which can be subject to potential transcriptional interference, remains largely unknown. We examined in an unbiased manner the features of the intergenic regions between pairs of 'tandem genes'-closely spaced (< 2 kb) human genes found on the same strand. Intergenic regions separating tandem genes are enriched with guanines and are characterized by binding of several proteins, including AGO1 and AGO2 of the RNA interference pathway. Additionally, we found that Pol2 is particularly enriched in this region, and it is lost upon perturbations affecting splicing or transcriptional elongation. Perturbations of genes involved in Pol2 pausing and R loop biology preferentially affect expression of downstream genes in tandem gene pairs. Overall, we find that features associated with Pol2 pausing and accumulation rather than those associated with avoidance of transcriptional interference are the predominant driving force shaping short tandem intergenic regions.
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Affiliation(s)
- Noa Nissani
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Ulitsky
- Departments of Biological Regulation and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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