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Wang X, Wang L, Zhou L, Chen L, Shi J, Ge J, Tian S, Yang Z, Zhou Y, Yu Q, Jin J, Ding C, Pan Y, Zou D. NUP62 alleviates senescence and promotes the stemness of human dental pulp stem cells via NSD2-dependent epigenetic reprogramming. Int J Oral Sci 2025; 17:34. [PMID: 40246825 PMCID: PMC12006529 DOI: 10.1038/s41368-025-00362-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 03/07/2025] [Accepted: 03/10/2025] [Indexed: 04/19/2025] Open
Abstract
Stem cells play a crucial role in maintaining tissue regenerative capacity and homeostasis. However, mechanisms associated with stem cell senescence require further investigation. In this study, we conducted a proteomic analysis of human dental pulp stem cells (HDPSCs) obtained from individuals of various ages. Our findings showed that the expression of NUP62 was decreased in aged HDPSCs. We discovered that NUP62 alleviated senescence-associated phenotypes and enhanced differentiation potential both in vitro and in vivo. Conversely, the knocking down of NUP62 expression aggravated the senescence-associated phenotypes and impaired the proliferation and migration capacity of HDPSCs. Through RNA-sequence and decoding the epigenomic landscapes remodeled induced by NUP62 overexpression, we found that NUP62 helps alleviate senescence in HDPSCs by enhancing the nuclear transport of the transcription factor E2F1. This, in turn, stimulates the transcription of the epigenetic enzyme NSD2. Finally, the overexpression of NUP62 influences the H3K36me2 and H3K36me3 modifications of anti-aging genes (HMGA1, HMGA2, and SIRT6). Our results demonstrated that NUP62 regulates the fate of HDPSCs via NSD2-dependent epigenetic reprogramming.
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Affiliation(s)
- Xiping Wang
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Li Wang
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Linxi Zhou
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Lu Chen
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiayi Shi
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Jing Ge
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, China
| | - Sha Tian
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Zihan Yang
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Yuqiong Zhou
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, China
| | - Qihao Yu
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China
| | - Jiacheng Jin
- Touro College of Dental Medicine, New York Medical College, New York, USA
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
| | - Yihuai Pan
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China.
- Department of Endodontics, School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China.
| | - Duohong Zou
- School and Hospital of Stomatology, Wenzhou Medical University, Wenzhou, China.
- Department of Oral Surgery, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology and Shanghai Research Institute of Stomatology, Shanghai, China.
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Sun R, Fisher RP. The CDK9-SPT5 Axis in Control of Transcription Elongation by RNAPII. J Mol Biol 2025; 437:168746. [PMID: 39147127 PMCID: PMC11649480 DOI: 10.1016/j.jmb.2024.168746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 08/09/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
The RNA polymerase II (RNAPII) transcription cycle is regulated at every stage by a network of cyclin-dependent protein kinases (CDKs) and protein phosphatases. Progression of RNAPII from initiation to termination is marked by changing patterns of phosphorylation on the highly repetitive carboxy-terminal domain (CTD) of RPB1, its largest subunit, suggesting the existence of a CTD code. In parallel, the conserved transcription elongation factor SPT5, large subunit of the DRB sensitivity-inducing factor (DSIF), undergoes spatiotemporally regulated changes in phosphorylation state that may be directly linked to the transitions between transcription-cycle phases. Here we review insights gained from recent structural, biochemical, and genetic analyses of human SPT5, which suggest that two of its phosphorylated regions perform distinct functions at different points in transcription. Phosphorylation within a flexible, RNA-binding linker promotes release from the promoter-proximal pause-frequently a rate-limiting step in gene expression-whereas modifications in a repetitive carboxy-terminal region are thought to favor processive elongation, and are removed just prior to termination. Phosphorylations in both motifs depend on CDK9, catalytic subunit of positive transcription elongation factor b (P-TEFb); their different timing of accumulation on chromatin and function during the transcription cycle might reflect their removal by different phosphatases, different kinetics of phosphorylation by CDK9, or both. Perturbations of SPT5 regulation have profound impacts on viability and development in model organisms through largely unknown mechanisms, while enzymes that modify SPT5 have emerged as potential therapeutic targets in cancer; elucidating a putative SPT5 code is therefore a high priority.
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Affiliation(s)
- Rui Sun
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA.
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3
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Shipman GA, Padilla R, Horth C, Hu B, Bareke E, Vitorino FN, Gongora JM, Garcia BA, Lu C, Majewski J. Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation. Genome Biol 2024; 25:263. [PMID: 39390582 PMCID: PMC11465688 DOI: 10.1186/s13059-024-03415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear. RESULTS We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. CONCLUSIONS Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
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Affiliation(s)
- Gerry A Shipman
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Reinnier Padilla
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Francisca N Vitorino
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joanna M Gongora
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Benjamin A Garcia
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
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4
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Yustis JC, Devoucoux M, Côté J. The Functional Relationship Between RNA Splicing and the Chromatin Landscape. J Mol Biol 2024; 436:168614. [PMID: 38762032 DOI: 10.1016/j.jmb.2024.168614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/27/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Chromatin is a highly regulated and dynamic structure that has been shown to play an essential role in transcriptional and co-transcriptional regulation. In the context of RNA splicing, early evidence suggested a loose connection between the chromatin landscape and splicing. More recently, it has been shown that splicing occurs in a co-transcriptional manner, meaning that the splicing process occurs in the context of chromatin. Experimental and computational evidence have also shown that chromatin dynamics can influence the splicing process and vice versa. However, much of this evidence provides mainly correlative relationships between chromatin and splicing with just a few concrete examples providing defined molecular mechanisms by which these two processes are functionally related. Nevertheless, it is clear that chromatin and RNA splicing are tightly interconnected to one another. In this review, we highlight the current state of knowledge of the relationship between chromatin and splicing.
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Affiliation(s)
- Juan-Carlos Yustis
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Maëva Devoucoux
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of the CHU de Québec-Université Laval Research Center, Quebec City, Quebec G1R 3S3, Canada.
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5
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Nemsick S, Hansen AS. Molecular models of bidirectional promoter regulation. Curr Opin Struct Biol 2024; 87:102865. [PMID: 38905929 PMCID: PMC11550790 DOI: 10.1016/j.sbi.2024.102865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/30/2024] [Accepted: 05/27/2024] [Indexed: 06/23/2024]
Abstract
Approximately 11% of human genes are transcribed by a bidirectional promoter (BDP), defined as two genes with <1 kb between their transcription start sites. Despite their evolutionary conservation and enrichment for housekeeping genes and oncogenes, the regulatory role of BDPs remains unclear. BDPs have been suggested to facilitate gene coregulation and/or decrease expression noise. This review discusses these potential regulatory functions through the context of six prospective underlying mechanistic models: a single nucleosome free region, shared transcription factor/regulator binding, cooperative negative supercoiling, bimodal histone marks, joint activation by enhancer(s), and RNA-mediated recruitment of regulators. These molecular mechanisms may act independently and/or cooperatively to facilitate the coregulation and/or decreased expression noise predicted of BDPs.
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Affiliation(s)
- Sarah Nemsick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA.
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6
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Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, Verma A, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol Cell 2024; 84:1475-1495.e18. [PMID: 38521065 PMCID: PMC11061666 DOI: 10.1016/j.molcel.2024.02.032] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
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Affiliation(s)
- Prajwal C Boddu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Rahul Roy
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Bárbara De La Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Anne Olazabal-Herrero
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Namrata S Chandhok
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Darren King
- Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Gary M Kupfer
- Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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7
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Nielsen M, Menon G, Zhao Y, Mateo-Bonmati E, Wolff P, Zhou S, Howard M, Dean C. COOLAIR and PRC2 function in parallel to silence FLC during vernalization. Proc Natl Acad Sci U S A 2024; 121:e2311474121. [PMID: 38236739 PMCID: PMC10823242 DOI: 10.1073/pnas.2311474121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Noncoding transcription induces chromatin changes that can mediate environmental responsiveness, but the causes and consequences of these mechanisms are still unclear. Here, we investigate how antisense transcription (termed COOLAIR) interfaces with Polycomb Repressive Complex 2 (PRC2) silencing during winter-induced epigenetic regulation of Arabidopsis FLOWERING LOCUS C (FLC). We use genetic and chromatin analyses on lines ineffective or hyperactive for the antisense pathway in combination with computational modeling to define the mechanisms underlying FLC repression. Our results show that FLC is silenced through pathways that function with different dynamics: a COOLAIR transcription-mediated pathway capable of fast response and in parallel a slow PRC2 switching mechanism that maintains each allele in an epigenetically silenced state. Components of both the COOLAIR and PRC2 pathways are regulated by a common transcriptional regulator (NTL8), which accumulates by reduced dilution due to slow growth at low temperature. The parallel activities of the regulatory steps, and their control by temperature-dependent growth dynamics, create a flexible system for registering widely fluctuating natural temperature conditions that change year on year, and yet ensure robust epigenetic silencing of FLC.
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Affiliation(s)
- Mathias Nielsen
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Govind Menon
- Computational and Systems Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Yusheng Zhao
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Eduardo Mateo-Bonmati
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Philip Wolff
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Shaoli Zhou
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Martin Howard
- Computational and Systems Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
| | - Caroline Dean
- Department of Cell and Developmental Biology, John Innes Centre, NorwichNR4 7UH, United Kingdom
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8
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Che Z, Liu X, Dai Q, Fang K, Guo C, Yue J, Fang H, Xie P, Luo Z, Lin C. Distinct roles of two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA polymerase II transcription elongation. J Mol Cell Biol 2024; 15:mjad049. [PMID: 37528066 PMCID: PMC11113081 DOI: 10.1093/jmcb/mjad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023] Open
Abstract
The super elongation complex (SEC) containing positive transcription elongation factor b plays a critical role in regulating transcription elongation. AFF1 and AFF4, two members of the AF4/FMR2 family, act as central scaffold proteins of SEC and are associated with various human diseases. However, their precise roles in transcriptional control remain unclear. Here, we investigate differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites (TSSs). AFF1 mainly binds upstream of the TSS, while AFF4 is enriched downstream of the TSS. Notably, disruption of AFF4 results in slow elongation and early termination in a subset of AFF4-bound active genes, whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same subset of genes. Additionally, AFF1 knockdown increases AFF4 levels at chromatin, and vice versa. In summary, these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate RNA polymerase II transcription.
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Affiliation(s)
- Zhuanzhuan Che
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Xiaoxu Liu
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Qian Dai
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Ke Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Chenghao Guo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Junjie Yue
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Haitong Fang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
| | - Peng Xie
- School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhuojuan Luo
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
| | - Chengqi Lin
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing 210096, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong 226001, China
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9
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Abrhámová K, Groušlová M, Valentová A, Hao X, Liu B, Převorovský M, Gahura O, Půta F, Sunnerhagen P, Folk P. Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes. RNA Biol 2024; 21:1-17. [PMID: 38711165 PMCID: PMC11085953 DOI: 10.1080/15476286.2024.2348896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 12/13/2023] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of PRP45 (prp45(1-169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Martina Groušlová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Anna Valentová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
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10
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Gill ME, Rohmer A, Erkek-Ozhan S, Liang CY, Chun S, Ozonov EA, Peters AHFM. De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression. Genome Res 2023; 33:2060-2078. [PMID: 38129075 PMCID: PMC10760527 DOI: 10.1101/gr.278060.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/29/2023] [Indexed: 12/23/2023]
Abstract
In mammals, the adult testis is the tissue with the highest diversity in gene expression. Much of that diversity is attributed to germ cells, primarily meiotic spermatocytes and postmeiotic haploid spermatids. Exploiting a newly developed cell purification method, we profiled the transcriptomes of such postmitotic germ cells of mice. We used a de novo transcriptome assembly approach and identified thousands of novel expressed transcripts characterized by features distinct from those of known genes. Novel loci tend to be short in length, monoexonic, and lowly expressed. Most novel genes have arisen recently in evolutionary time and possess low coding potential. Nonetheless, we identify several novel protein-coding genes harboring open reading frames that encode proteins containing matches to conserved protein domains. Analysis of mass-spectrometry data from adult mouse testes confirms protein production from several of these novel genes. We also examine overlap between transcripts and repetitive elements. We find that although distinct families of repeats are expressed with differing temporal dynamics during spermatogenesis, we do not observe a general mode of regulation wherein repeats drive expression of nonrepetitive sequences in a cell type-specific manner. Finally, we observe many fairly long antisense transcripts originating from canonical gene promoters, pointing to pervasive bidirectional promoter activity during spermatogenesis that is distinct and more frequent compared with somatic cells.
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Affiliation(s)
- Mark E Gill
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Alexia Rohmer
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Serap Erkek-Ozhan
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Ching-Yeu Liang
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Sunwoo Chun
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland;
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
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11
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Mori S, Oya S, Takahashi M, Takashima K, Inagaki S, Kakutani T. Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis. EMBO J 2023; 42:e113798. [PMID: 37849386 PMCID: PMC10690457 DOI: 10.15252/embj.2023113798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3-mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is significantly attenuated in the ldl3 mutant, demonstrating the genome-wide impacts of the transcription-driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 demethylation in plants as chromatin records of transcriptional activity, which ensures robust gene control.
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Affiliation(s)
- Shusei Mori
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Satoyo Oya
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | | | | | - Soichi Inagaki
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
- National Institute of GeneticsShizuokaJapan
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12
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Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci 2023; 10:1270285. [PMID: 37877123 PMCID: PMC10591336 DOI: 10.3389/fmolb.2023.1270285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Aging affects nearly all aspects of our cells, from our DNA to our proteins to how our cells handle stress and communicate with each other. Age-related chromatin changes are of particular interest because chromatin can dynamically respond to the cellular and organismal environment, and many modifications at chromatin are reversible. Changes at chromatin occur during aging, and evidence from model organisms suggests that chromatin factors could play a role in modulating the aging process itself, as altering proteins that work at chromatin often affect the lifespan of yeast, worms, flies, and mice. The field of chromatin and aging is rapidly expanding, and high-resolution genomics tools make it possible to survey the chromatin environment or track chromatin factors implicated in longevity with precision that was not previously possible. In this review, we discuss the state of chromatin and aging research. We include examples from yeast, Drosophila, mice, and humans, but we particularly focus on the commonly used aging model, the worm Caenorhabditis elegans, in which there are many examples of chromatin factors that modulate longevity. We include evidence of both age-related changes to chromatin and evidence of specific chromatin factors linked to longevity in core histones, nuclear architecture, chromatin remodeling, and histone modifications.
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Affiliation(s)
| | - Siu Sylvia Lee
- Lee Lab, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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13
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Zukher I, Dujardin G, Sousa-Luís R, Proudfoot NJ. Elongation roadblocks mediated by dCas9 across human genes modulate transcription and nascent RNA processing. Nat Struct Mol Biol 2023; 30:1536-1548. [PMID: 37783853 PMCID: PMC10584677 DOI: 10.1038/s41594-023-01090-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/04/2023] [Indexed: 10/04/2023]
Abstract
Non-cleaving Cas9 (dCas9) is widely employed to manipulate specific gene loci, often with scant regard for unintended transcriptional effects. We demonstrate here that dCas9 mediates precise RNA polymerase II transcriptional pausing followed by transcription termination and potential alternative polyadenylation. By contrast, alternative splicing is unaffected, likely requiring more sustained alteration to elongation speed. The effect on transcription is orientation specific, with pausing only being induced when dCas9-associated guide RNA anneals to the non-template strand. Targeting the template strand induces minimal effects on transcription elongation and thus provides a neutral approach to recruit dCas9-linked effector domains to specific gene regions. In essence, we evaluate molecular effects of targeting dCas9 to mammalian transcription units. In so doing, we also provide new information on elongation by RNA polymerase II and coupled pre-mRNA processing.
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Affiliation(s)
- Inna Zukher
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
| | - Gwendal Dujardin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Rui Sousa-Luís
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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14
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Cortázar MA, Fong N, Bentley DL. Genome-wide Mapping of 5'-monophosphorylated Ends of Mammalian Nascent RNA Transcripts. Bio Protoc 2023; 13:e4828. [PMID: 37753464 PMCID: PMC10518774 DOI: 10.21769/bioprotoc.4828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 09/28/2023] Open
Abstract
In eukaryotic cells, RNA biogenesis generally requires processing of the nascent transcript as it is being synthesized by RNA polymerase. These processing events include endonucleolytic cleavage, exonucleolytic trimming, and splicing of the growing nascent transcript. Endonucleolytic cleavage events that generate an exposed 5'-monophosphorylated (5'-PO4) end on the growing nascent transcript occur in the maturation of rRNAs, tRNAs, and mRNAs. These 5'-PO4 ends can be a target of further processing or be subjected to 5'-3' exonucleolytic digestion that may result in termination of transcription. Here, we describe how to identify 5'-PO4 ends of intermediates in nascent RNA metabolism. We capture these species via metabolic labeling with bromouridine followed by immunoprecipitation and specific ligation of 5'-PO4 RNA ends with the 3'-hydroxyl group of a 5' adaptor (5'-PO4 Bru-Seq) using RNA ligase I. These ligation events are localized at single nucleotide resolution via highthroughput sequencing, which identifies the position of 5'-PO4 groups precisely. This protocol successfully detects the 5'monophosphorylated ends of RNA processing intermediates during production of mature ribosomal, transfer, and micro RNAs. When combined with inhibition of the nuclear 5'-3' exonuclease Xrn2, 5'-PO4 Bru-Seq maps the 5' splice sites of debranched introns and mRNA and tRNA 3' end processing sites cleaved by CPSF73 and RNaseZ, respectively. Key features • Metabolic labeling for brief periods with bromouridine focuses the analysis of 5'-PO4 RNA ends on the population of nascent transcripts that are actively transcribed. • Detects 5'-PO4 RNA ends on nascent transcripts produced by all RNA polymerases. • Detects 5'-PO4 RNA ends at single nucleotide resolution.
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Affiliation(s)
- Michael A. Cortázar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
| | - David L. Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA
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15
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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16
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Henfrey C, Murphy S, Tellier M. Regulation of mature mRNA levels by RNA processing efficiency. NAR Genom Bioinform 2023; 5:lqad059. [PMID: 37305169 PMCID: PMC10251645 DOI: 10.1093/nargab/lqad059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 05/13/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
Transcription and co-transcriptional processes, including pre-mRNA splicing and mRNA cleavage and polyadenylation, regulate the production of mature mRNAs. The carboxyl terminal domain (CTD) of RNA polymerase (pol) II, which comprises 52 repeats of the Tyr1Ser2Pro3Thr4Ser5Pro6Ser7 peptide, is involved in the coordination of transcription with co-transcriptional processes. The pol II CTD is dynamically modified by protein phosphorylation, which regulates recruitment of transcription and co-transcriptional factors. We have investigated whether mature mRNA levels from intron-containing protein-coding genes are related to pol II CTD phosphorylation, RNA stability, and pre-mRNA splicing and mRNA cleavage and polyadenylation efficiency. We find that genes that produce a low level of mature mRNAs are associated with relatively high phosphorylation of the pol II CTD Thr4 residue, poor RNA processing, increased chromatin association of transcripts, and shorter RNA half-life. While these poorly-processed transcripts are degraded by the nuclear RNA exosome, our results indicate that in addition to RNA half-life, chromatin association due to a low RNA processing efficiency also plays an important role in the regulation of mature mRNA levels.
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Affiliation(s)
- Callum Henfrey
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
- Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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17
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Qu J, Betting V, van Iterson R, Kwaschik FM, van Rij RP. Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA biogenesis in mosquitoes. Cell Rep 2023; 42:112257. [PMID: 36930642 DOI: 10.1016/j.celrep.2023.112257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
The piRNA pathway in mosquitoes differs substantially from other model organisms, with an expanded PIWI gene family and functions in antiviral defense. Here, we define core piRNA clusters as genomic loci that show ubiquitous piRNA expression in both somatic and germline tissues. These core piRNA clusters are enriched for non-retroviral endogenous viral elements (nrEVEs) in antisense orientation and depend on key biogenesis factors, Veneno, Tejas, Yb, and Shutdown. Combined transcriptome and chromatin state analyses identify transcriptional readthrough as a conserved mechanism for cluster-derived piRNA biogenesis in the vector mosquitoes Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, and Anopheles gambiae. Comparative analyses between the two Aedes species suggest that piRNA clusters function as traps for nrEVEs, allowing adaptation to environmental challenges such as virus infection. Our systematic transcriptome and chromatin state analyses lay the foundation for studies of gene regulation, genome evolution, and piRNA function in these important vector species.
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Affiliation(s)
- Jieqiong Qu
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Valerie Betting
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Ruben van Iterson
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Florence M Kwaschik
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands.
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18
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Vihervaara A, Versluis P, Lis JT. PRO-IP-seq Tracks Molecular Modifications of Engaged Pol II Complexes at Nucleotide Resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.04.527107. [PMID: 36778434 PMCID: PMC9915724 DOI: 10.1101/2023.02.04.527107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RNA Polymerase II (Pol II) is a multi-subunit complex that undergoes covalent modifications as transcription proceeds through genes and enhancers. Rate-limiting steps of transcription control Pol II recruitment, site and degree of initiation, pausing duration, productive elongation, nascent transcript processing, transcription termination, and Pol II recycling. Here, we developed Precision Run-On coupled to Immuno-Precipitation sequencing (PRO-IP-seq) and tracked phosphorylation of Pol II C-terminal domain (CTD) at nucleotide-resolution. We uncovered precise positional control of Pol II CTD phosphorylation as transcription proceeds from the initiating nucleotide, through early and late promoter-proximal pause, and into productive elongation. Pol II CTD was predominantly unphosphorylated in the early pause-region, whereas serine-2- and serine-5-phosphorylations occurred preferentially in the later pause-region. Serine-7-phosphorylation dominated after the pause-release in a region where Pol II accelerates to its full elongational speed. Interestingly, tracking transcription upon heat-induced reprogramming demonstrated that Pol II with phosphorylated CTD remains paused on heat-repressed genes.
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Affiliation(s)
- Anniina Vihervaara
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Lead contact
| | - Philip Versluis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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19
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Braun TP, Estabrook J, Schonrock Z, Curtiss BM, Darmusey L, Macaraeg J, Enright T, Coblentz C, Callahan R, Yashar W, Taherinasab A, Mohammed H, Coleman DJ, Druker BJ, Demir E, Lusardi TA, Maxson JE. Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors. Leukemia 2023; 37:478-487. [PMID: 36526735 PMCID: PMC9899319 DOI: 10.1038/s41375-022-01792-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
Mutations in the gene Additional Sex-Combs Like 1 (ASXL1) are recurrent in myeloid malignancies as well as the pre-malignant condition clonal hematopoiesis, where they are universally associated with poor prognosis. However, the role of ASXL1 in myeloid lineage maturation is incompletely described. To define the role of ASXL1 in myelopoiesis, we employed single cell RNA sequencing and a murine model of hematopoietic-specific Asxl1 deletion. In granulocyte progenitors, Asxl1 deletion leads to hyperactivation of MYC and a quantitative decrease in neutrophil production. This loss of granulocyte production was not accompanied by significant changes in the landscape of covalent histone modifications. However, Asxl1 deletion results in a decrease in RNAPII promoter-proximal pausing in granulocyte progenitors, indicative of a global increase in productive transcription. These results suggest that ASXL1 inhibits productive transcription in granulocyte progenitors, identifying a new role for this epigenetic regulator in myeloid development.
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Affiliation(s)
- Theodore P. Braun
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Division of Hematology & Medical Oncology, Oregon
Health & Science University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
| | - Joseph Estabrook
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Zachary Schonrock
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Brittany M. Curtiss
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Lucie Darmusey
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Jommel Macaraeg
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Trevor Enright
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Cody Coblentz
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Rowan Callahan
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - William Yashar
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Akram Taherinasab
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Hisham Mohammed
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Daniel J. Coleman
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Division of Hematology & Medical Oncology, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA
| | - Theresa A. Lusardi
- Cancer Early Detection Advanced Research Center, Oregon
Health & Science University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
| | - Julia E. Maxson
- Knight Cancer Institute, Oregon Health & Science
University, Portland, Oregon, 97239, USA.,CORRESPONDENCE: Theodore P. Braun,
Knight Cancer Institute, 3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon,
97239, , Julia E. Maxson, Knight Cancer Institute,
3181 SW Sam Jackson Pk. Rd., KR-HEM, Portland, Oregon, 97239,
, Theresa A. Lusardi, Cancer Early Detection
Advanced Research Center, 3181 SW Sam Jackson Pk. Rd., KR-CEDR, Portland,
Oregon, 97239,
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20
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Wu F, Li X, Looso M, Liu H, Ding D, Günther S, Kuenne C, Liu S, Weissmann N, Boettger T, Atzberger A, Kolahian S, Renz H, Offermanns S, Gärtner U, Potente M, Zhou Y, Yuan X, Braun T. Spurious transcription causing innate immune responses is prevented by 5-hydroxymethylcytosine. Nat Genet 2023; 55:100-111. [PMID: 36539616 PMCID: PMC9839451 DOI: 10.1038/s41588-022-01252-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Generation of functional transcripts requires transcriptional initiation at regular start sites, avoiding production of aberrant and potentially hazardous aberrant RNAs. The mechanisms maintaining transcriptional fidelity and the impact of spurious transcripts on cellular physiology and organ function have not been fully elucidated. Here we show that TET3, which successively oxidizes 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other derivatives, prevents aberrant intragenic entry of RNA polymerase II pSer5 into highly expressed genes of airway smooth muscle cells, assuring faithful transcriptional initiation at canonical start sites. Loss of TET3-dependent 5hmC production in SMCs results in accumulation of spurious transcripts, which stimulate the endosomal nucleic-acid-sensing TLR7/8 signaling pathway, thereby provoking massive inflammation and airway remodeling resembling human bronchial asthma. Furthermore, we found that 5hmC levels are substantially lower in human asthma airways compared with control samples. Suppression of spurious transcription might be important to prevent chronic inflammation in asthma.
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Affiliation(s)
- Fan Wu
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Xiang Li
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hang Liu
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Dong Ding
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Shuya Liu
- grid.418032.c0000 0004 0491 220XDepartment of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany ,grid.13648.380000 0001 2180 3484Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Norbert Weissmann
- grid.440517.3Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany ,grid.8664.c0000 0001 2165 8627Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Thomas Boettger
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ann Atzberger
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Saeed Kolahian
- grid.10253.350000 0004 1936 9756Philipps University of Marburg - Medical Faculty, Center for Tumor- and Immunobiology (ZTI), Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Marburg, Germany
| | - Harald Renz
- grid.10253.350000 0004 1936 9756Philipps University of Marburg - Medical Faculty, Center for Tumor- and Immunobiology (ZTI), Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Marburg, Germany
| | - Stefan Offermanns
- grid.418032.c0000 0004 0491 220XDepartment of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ulrich Gärtner
- Institute for Anatomy und Cell Biology, Giessen, Germany
| | - Michael Potente
- grid.418032.c0000 0004 0491 220XAngiogenesis and Metabolism Laboratory, Max-Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Yonggang Zhou
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Xuejun Yuan
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany. .,Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany.
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21
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Petrova V, Song R, DEEP Consortium, Nordström KJV, Walter J, Wong JJL, Armstrong N, Rasko JEJ, Schmitz U. Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Res 2022; 50:11563-11579. [PMID: 36354002 PMCID: PMC9723627 DOI: 10.1093/nar/gkac994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/05/2022] [Accepted: 10/18/2022] [Indexed: 11/11/2022] Open
Abstract
Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including several cancers. Despite consistent reports demonstrating that intrinsic sequence features can help introns evade splicing, conflicting findings about cell type- or condition-specific IR regulation by trans-regulatory and epigenetic mechanisms demand an unbiased and systematic analysis of IR in a controlled experimental setting. We integrated matched mRNA sequencing (mRNA-Seq), whole-genome bisulfite sequencing (WGBS), nucleosome occupancy methylome sequencing (NOMe-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) data from primary human myeloid and lymphoid cells. Using these multi-omics data and machine learning, we trained two complementary models to determine the role of epigenetic factors in the regulation of IR in cells of the innate immune system. We show that increased chromatin accessibility, as revealed by nucleosome-free regions, contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. This study suggests an important role for chromatin architecture in IR regulation. With an increasing appreciation that pathogenic alterations are linked to RNA processing, our findings may provide useful insights for the development of novel therapeutic approaches that target aberrant splicing.
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Affiliation(s)
- Veronika Petrova
- Computational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | | | - Karl J V Nordström
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Jörn Walter
- Laboratory of EpiGenetics, Saarland University, Campus A2 4, D-66123 Saarbrücken, Germany
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown 2050, Australia,Faculty of Medicine and Health, The University of Sydney, Camperdown 2050, Australia
| | - Nicola J Armstrong
- Mathematics and Statistics, Curtin University, Bentley, WA 6102, Australia
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22
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Deng N, Zhang Y, Ma Z, Lin R, Cheng TH, Tang H, Snyder M, Cohen S. DSIF modulates RNA polymerase II occupancy according to template G + C content. NAR Genom Bioinform 2022; 4:lqac054. [PMID: 35910045 PMCID: PMC9326580 DOI: 10.1093/nargab/lqac054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/03/2022] [Accepted: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
The DSIF complex comprising the Supt4h and Supt5h transcription elongation proteins clamps RNA polymerase II (RNAPII) onto DNA templates, facilitating polymerase processivity. Lowering DSIF components can differentially decrease expression of alleles containing nucleotide repeat expansions, suggesting that RNAPII transit through repeat expansions is dependent on DSIF functions. To globally identify sequence features that affect dependence of the polymerase on DSIF in human cells, we used ultra-deep ChIP-seq analysis and RNA-seq to investigate and quantify the genome-wide effects of Supt4h loss on template occupancy and transcript production. Our results indicate that RNAPII dependence on Supt4h varies according to G + C content. Effects of DSIF knockdown were prominent during transcription of sequences high in G + C but minimal for sequences low in G + C and were particularly evident for G + C-rich segments of long genes. Reanalysis of previously published ChIP-seq data obtained from mouse cells showed similar effects of template G + C composition on Supt5h actions. Our evidence that DSIF dependency varies globally in different template regions according to template sequence composition suggests that G + C content may have a role in the selectivity of Supt4h knockdown and Supt5h knockdown during transcription of gene alleles containing expansions of G + C-rich repeats.
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Affiliation(s)
- Ning Deng
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Yue Zhang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Zhihai Ma
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Richard Lin
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Tzu-Hao Cheng
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University , Taipei 112, Taiwan
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
| | - Stanley N Cohen
- Department of Genetics, Stanford University School of Medicine , Stanford, CA 94305, USA
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23
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Lima ARJ, Silva HGD, Poubel S, Rosón JN, de Lima LPO, Costa-Silva HM, Gonçalves CS, Galante PAF, Holetz F, Motta MCMM, Silber AM, Elias MC, da Cunha JPC. Open chromatin analysis in Trypanosoma cruzi life forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci. Epigenetics Chromatin 2022; 15:22. [PMID: 35650626 PMCID: PMC9158160 DOI: 10.1186/s13072-022-00450-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Genomic organization and gene expression regulation in trypanosomes are remarkable because protein-coding genes are organized into codirectional gene clusters with unrelated functions. Moreover, there is no dedicated promoter for each gene, resulting in polycistronic gene transcription, with posttranscriptional control playing a major role. Nonetheless, these parasites harbor epigenetic modifications at critical regulatory genome features that dynamically change among parasite stages, which are not fully understood. RESULTS Here, we investigated the impact of chromatin changes in a scenario commanded by posttranscriptional control exploring the parasite Trypanosoma cruzi and its differentiation program using FAIRE-seq approach supported by transmission electron microscopy. We identified differences in T. cruzi genome compartments, putative transcriptional start regions, and virulence factors. In addition, we also detected a developmental chromatin regulation at tRNA loci (tDNA), which could be linked to the intense chromatin remodeling and/or the translation regulatory mechanism required for parasite differentiation. We further integrated the open chromatin profile with public transcriptomic and MNase-seq datasets. Strikingly, a positive correlation was observed between active chromatin and steady-state transcription levels. CONCLUSION Taken together, our results indicate that chromatin changes reflect the unusual gene expression regulation of trypanosomes and the differences among parasite developmental stages, even in the context of a lack of canonical transcriptional control of protein-coding genes.
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Affiliation(s)
- Alex Ranieri Jerônimo Lima
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Herbert Guimarães de
Sousa Silva
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil ,grid.411249.b0000 0001 0514 7202Departamento de Microbiologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, Imunologia E Parasitologia, São Paulo, SP Brazil
| | - Saloe Poubel
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Juliana Nunes Rosón
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil ,grid.411249.b0000 0001 0514 7202Departamento de Microbiologia, Universidade Federal de São Paulo, Escola Paulista de Medicina, Imunologia E Parasitologia, São Paulo, SP Brazil
| | - Loyze Paola Oliveira de Lima
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Héllida Marina Costa-Silva
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Camila Silva Gonçalves
- grid.8536.80000 0001 2294 473XLaboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, IBCCF, CCS, UFRJ, Cidade Universitária, Rio de Janeiro, RJ Brazil ,Centro Nacional de Biologia Estrutural E Bioimagem, Rio de Janeiro, RJ Brazil
| | - Pedro A. F. Galante
- grid.413471.40000 0000 9080 8521Centro de Oncologia Molecular, Hospital Sírio Libanês, São Paulo, SP Brazil
| | - Fabiola Holetz
- grid.418068.30000 0001 0723 0931Instituto Carlos Chagas, Fiocruz, Curitiba, PR Brazil
| | - Maria Cristina Machado M. Motta
- grid.8536.80000 0001 2294 473XLaboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal Do Rio de Janeiro, IBCCF, CCS, UFRJ, Cidade Universitária, Rio de Janeiro, RJ Brazil ,Centro Nacional de Biologia Estrutural E Bioimagem, Rio de Janeiro, RJ Brazil
| | - Ariel M. Silber
- grid.11899.380000 0004 1937 0722Universidade de São Paulo, São Paulo, SP Brazil
| | - M. Carolina Elias
- grid.418514.d0000 0001 1702 8585Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP Brazil ,grid.418514.d0000 0001 1702 8585Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil. .,Centro de Toxinas, Resposta Imune E Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil.
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24
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Chan J, Kumar A, Kono H. RNAPII driven post-translational modifications of nucleosomal histones. Trends Genet 2022; 38:1076-1095. [PMID: 35618507 DOI: 10.1016/j.tig.2022.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
Abstract
The current understanding of how specific distributions of histone post-translational modifications (PTMs) are achieved throughout the chromatin remains incomplete. This review focuses on the role of RNA polymerase II (RNAPII) in establishing H2BK120/K123 ubiquitination and H3K4/K36 methylation distribution. The rate of RNAPII transcription is mainly a function of the RNAPII elongation and recruitment rates. Two major mechanisms link RNAPII's transcription rate to the distribution of PTMs. First, the phosphorylation patterns of Ser2P/Ser5P in the C-terminal domain of RNAPII change as a function of time, since the start of elongation, linking them to the elongation rate. Ser2P/Ser5P recruits specific histone PTM enzymes/activators to the nucleosome. Second, multiple rounds of binding and catalysis by the enzymes are required to establish higher methylations (H3K4/36me3). Thus, methylation states are determined by the transcription rate. In summary, the first mechanism determines the location of methylations in the gene, while the second mechanism determines the methylation state.
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Affiliation(s)
- Justin Chan
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
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25
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Park K, Zhong J, Jang JS, Kim J, Kim HJ, Lee JH, Kim J. ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters. Nucleic Acids Res 2022; 50:3835-3851. [PMID: 35325203 PMCID: PMC9023261 DOI: 10.1093/nar/gkac193] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
The human genome encodes large numbers of non-coding RNAs, including divergent antisense transcripts at transcription start sites (TSSs). However, molecular mechanisms by which divergent antisense transcription is regulated have not been detailed. Here, we report a novel ZWC complex composed of ZC3H4, WDR82 and CK2 that suppresses divergent antisense transcription. The ZWC complex preferentially localizes at TSSs of active genes through direct interactions of ZC3H4 and WDR82 subunits with the S5p RNAPII C-terminal domain. ZC3H4 depletion leads to increased divergent antisense transcription, especially at genes that naturally produce divergent antisense transcripts. We further demonstrate that the ZWC complex phosphorylates the previously uncharacterized N-terminal acidic domain of SPT5, a subunit of the transcription-elongation factor DSIF, and that this phosphorylation is responsible for suppressing divergent antisense transcription. Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation.
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Affiliation(s)
- Kihyun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jian Zhong
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hye-Jung Kim
- New Drug Development Center, OSONG Medical Innovation Foundation, Cheongju 28160, South Korea
| | - Jeong-Heon Lee
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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26
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Selvam K, Plummer DA, Mao P, Wyrick JJ. Set2 histone methyltransferase regulates transcription coupled-nucleotide excision repair in yeast. PLoS Genet 2022; 18:e1010085. [PMID: 35263330 PMCID: PMC8936446 DOI: 10.1371/journal.pgen.1010085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/21/2022] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Helix-distorting DNA lesions, including ultraviolet (UV) light-induced damage, are repaired by the global genomic-nucleotide excision repair (GG-NER) and transcription coupled-nucleotide excision repair (TC-NER) pathways. Previous studies have shown that histone post-translational modifications (PTMs) such as histone acetylation and methylation can promote GG-NER in chromatin. Whether histone PTMs also regulate the repair of DNA lesions by the TC-NER pathway in transcribed DNA is unknown. Here, we report that histone H3 K36 methylation (H3K36me) by the Set2 histone methyltransferase in yeast regulates TC-NER. Mutations in Set2 or H3K36 result in UV sensitivity that is epistatic with Rad26, the primary TC-NER factor in yeast, and cause a defect in the repair of UV damage across the yeast genome. We further show that mutations in Set2 or H3K36 in a GG-NER deficient strain (i.e., rad16Δ) partially rescue its UV sensitivity. Our data indicate that deletion of SET2 rescues UV sensitivity in a GG-NER deficient strain by activating cryptic antisense transcription, so that the non-transcribed strand (NTS) of yeast genes is repaired by TC-NER. These findings indicate that Set2 methylation of H3K36 establishes transcriptional asymmetry in repair by promoting canonical TC-NER of the transcribed strand (TS) and suppressing cryptic TC-NER of the NTS.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Dalton A. Plummer
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Peng Mao
- Department of Internal Medicine, Program in Cellular and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States of America
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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27
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Gañez-Zapater A, Mackowiak SD, Guo Y, Tarbier M, Jordán-Pla A, Friedländer MR, Visa N, Östlund Farrants AK. The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA. Mol Genet Genomics 2022; 297:463-484. [PMID: 35187582 PMCID: PMC8960663 DOI: 10.1007/s00438-022-01863-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/23/2022] [Indexed: 11/29/2022]
Abstract
BRG1 and BRM are ATPase core subunits of the human SWI/SNF chromatin remodelling complexes mainly associated with transcriptional initiation. They also have a role in alternative splicing, which has been shown for BRM-containing SWI/SNF complexes at a few genes. Here, we have identified a subset of genes which harbour alternative exons that are affected by SWI/SNF ATPases by expressing the ATPases BRG1 and BRM in C33A cells, a BRG1- and BRM-deficient cell line, and analysed the effect on splicing by RNA sequencing. BRG1- and BRM-affected sub-sets of genes favouring both exon inclusion and exon skipping, with only a minor overlap between the ATPase. Some of the changes in alternative splicing induced by BRG1 and BRM expression did not require the ATPase activity. The BRG1-ATPase independent included exons displayed an exon signature of a high GC content. By investigating three genes with exons affected by the BRG-ATPase-deficient variant, we show that these exons accumulated phosphorylated RNA pol II CTD, both serine 2 and serine 5 phosphorylation, without an enrichment of the RNA polymerase II. The ATPases were recruited to the alternative exons, together with both core and signature subunits of SWI/SNF complexes, and promoted the binding of RNA binding factors to chromatin and RNA at the alternative exons. The interaction with the nascent RNP, however, did not reflect the association to chromatin. The hnRNPL, hnRNPU and SAM68 proteins associated with chromatin in cells expressing BRG1 and BRM wild type, but the binding of hnRNPU to the nascent RNP was excluded. This suggests that SWI/SNF can regulate alternative splicing by interacting with splicing-RNA binding factor and influence their binding to the nascent pre-mRNA particle.
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Affiliation(s)
- Antoni Gañez-Zapater
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Center for Genomic Regulation, 08003, Barcelona, Spain
| | - Sebastian D Mackowiak
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Yuan Guo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencies Biológicas, Valencia University, C/Dr. Moliner, 50, 46100, Burjassot, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 106 91, Stockholm, Sweden
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, The Arrhenius Laboratories F4, 106 91, Stockholm, Sweden.
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28
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De S, Edwards DM, Dwivedi V, Wang J, Varsally W, Dixon HL, Singh AK, Owuamalam PO, Wright MT, Summers RP, Hossain MN, Price EM, Wojewodzic MW, Falciani F, Hodges NJ, Saponaro M, Tanaka K, Azzalin CM, Baumann P, Hebenstreit D, Brogna S. Genome-wide chromosomal association of Upf1 is linked to Pol II transcription in Schizosaccharomyces pombe. Nucleic Acids Res 2021; 50:350-367. [PMID: 34928380 PMCID: PMC8754637 DOI: 10.1093/nar/gkab1249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 11/23/2022] Open
Abstract
Although the RNA helicase Upf1 has hitherto been examined mostly in relation to its cytoplasmic role in nonsense mediated mRNA decay (NMD), here we report high-throughput ChIP data indicating genome-wide association of Upf1 with active genes in Schizosaccharomyces pombe. This association is RNase sensitive, correlates with Pol II transcription and mRNA expression levels. Changes in Pol II occupancy were detected in a Upf1 deficient (upf1Δ) strain, prevalently at genes showing a high Upf1 relative to Pol II association in wild-type. Additionally, an increased Ser2 Pol II signal was detected at all highly transcribed genes examined by ChIP-qPCR. Furthermore, upf1Δ cells are hypersensitive to the transcription elongation inhibitor 6-azauracil. A significant proportion of the genes associated with Upf1 in wild-type conditions are also mis-regulated in upf1Δ. These data envisage that by operating on the nascent transcript, Upf1 might influence Pol II phosphorylation and transcription.
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Affiliation(s)
- Sandip De
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Division of Cellular and Gene Therapies, Tumor Vaccines and Biotechnology Branch, Center for Biologics and Evaluation Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - David M Edwards
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Vibha Dwivedi
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Jianming Wang
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Wazeer Varsally
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Hannah L Dixon
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Anand K Singh
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Interdisciplinary School of Life Sciences, Banaras Hindu University, Varanasi 221005, India
| | - Precious O Owuamalam
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Matthew T Wright
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Reece P Summers
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Md Nazmul Hossain
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Department of Microbial Biotechnology, Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Emily M Price
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Marcin W Wojewodzic
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK.,Department of Environmental Health, Norwegian Institute of Public Health, Oslo, Norway & Department of Research, Cancer Registry of Norway, Oslo University Hospital, Oslo, Norway & Environmental Genomics, School of Biosciences, University of Birmingham, Birmingham, UK
| | - Francesco Falciani
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Nikolas J Hodges
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, University of Birmingham, UK
| | - Kayoko Tanaka
- Department of Molecular and Cell Biology, University of Leicester, UK
| | - Claus M Azzalin
- Instituto de Medicina Molecular João Lobo Antunes (iMM), Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | | | | | - Saverio Brogna
- School of Biosciences and Birmingham Centre of Genome Biology (BCGB), University of Birmingham, UK
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29
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Yu X, Martin PGP, Zhang Y, Trinidad JC, Xu F, Huang J, Thum KE, Li K, Zhao S, Gu Y, Wang X, Michaels SD. The BORDER family of negative transcription elongation factors regulates flowering time in Arabidopsis. Curr Biol 2021; 31:5377-5384.e5. [PMID: 34666004 DOI: 10.1016/j.cub.2021.09.074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/20/2021] [Accepted: 09/27/2021] [Indexed: 11/27/2022]
Abstract
Transcription initiation has long been considered a primary regulatory step in gene expression. Recent work, however, shows that downstream events, such as transcription elongation, can also play important roles.1-3 A well-characterized example from animals is promoter-proximal pausing, where transcriptionally engaged Pol II accumulates 30-50 bp downstream of the transcription start site (TSS) and is thought to enable rapid gene activation.2 Plants do not make widespread use of promoter-proximal pausing; however, in a phenomenon known as 3' pausing, a significant increase in Pol II is observed near the transcript end site (TES) of many genes.4-6 Previous work has shown that 3' pausing is promoted by the BORDER (BDR) family of negative transcription elongation factors. Here we show that BDR proteins play key roles in gene repression. Consistent with BDR proteins acting to slow or pause elongating Pol II, BDR-repressed genes are characterized by high levels of Pol II occupancy, yet low levels of mRNA. The BDR proteins physically interact with FPA,7 one of approximately two dozen genes collectively referred to as the autonomous floral-promotion pathway,8 which are necessary for the repression of the flowering time gene FLOWERING LOCUS C (FLC).9-11 In early-flowering strains, FLC expression is repressed by repressive histone modifications, such as histone H3 lysine 27 trimethylation (H3K27me3), thereby allowing the plants to flower early. These results suggest that the repression of transcription elongation by BDR proteins may allow for the temporary pausing of transcription or facilitate the long-term repression of genes by repressive histone modifications.
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Affiliation(s)
- Xuhong Yu
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.
| | - Pascal G P Martin
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Yixiang Zhang
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
| | - Jonathan C Trinidad
- Department of Chemistry, Indiana University, Bloomington, IN 47405, USA; Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University Bloomington, Bloomington, IN, USA
| | - Feifei Xu
- Institute of Nuclear Agricultural Sciences, Key Laboratory for Nuclear Agricultural Sciences of Zhejiang Province and Ministry of Agriculture and Rural Affairs, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jie Huang
- Center for Genomics and Bioinformatics, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Karen E Thum
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - Ke Li
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA
| | - ShuZhen Zhao
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Yangnan Gu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xingjun Wang
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Scott D Michaels
- Department of Biology, Indiana University, 915 East Third Street, Bloomington, IN 47405, USA.
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Muniz L, Nicolas E, Trouche D. RNA polymerase II speed: a key player in controlling and adapting transcriptome composition. EMBO J 2021; 40:e105740. [PMID: 34254686 PMCID: PMC8327950 DOI: 10.15252/embj.2020105740] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/01/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNA Pol II) speed or elongation rate, i.e., the number of nucleotides synthesized per unit of time, is a major determinant of transcriptome composition. It controls co-transcriptional processes such as splicing, polyadenylation, and transcription termination, thus regulating the production of alternative splice variants, circular RNAs, alternatively polyadenylated transcripts, or read-through transcripts. RNA Pol II speed itself is regulated in response to intra- and extra-cellular stimuli and can in turn affect the transcriptome composition in response to these stimuli. Evidence points to a potentially important role of transcriptome composition modification through RNA Pol II speed regulation for adaptation of cells to a changing environment, thus pointing to a function of RNA Pol II speed regulation in cellular physiology. Analyzing RNA Pol II speed dynamics may therefore be central to fully understand the regulation of physiological processes, such as the development of multicellular organisms. Recent findings also raise the possibility that RNA Pol II speed deregulation can be detrimental and participate in disease progression. Here, we review initial and current approaches to measure RNA Pol II speed, as well as providing an overview of the factors controlling speed and the co-transcriptional processes which are affected. Finally, we discuss the role of RNA Pol II speed regulation in cell physiology.
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Affiliation(s)
- Lisa Muniz
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Estelle Nicolas
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
| | - Didier Trouche
- MCDCentre de Biologie Integrative (CBI)CNRSUPSUniversity of ToulouseToulouseFrance
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31
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The evolutionary acquisition and mode of functions of promoter-associated non-coding RNAs (pancRNAs) for mammalian development. Essays Biochem 2021; 65:697-708. [PMID: 34328174 DOI: 10.1042/ebc20200143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/13/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Increasing evidence has shown that many long non-coding RNAs (lncRNAs) are involved in gene regulation in a variety of ways such as transcriptional, post-transcriptional and epigenetic regulation. Promoter-associated non-coding RNAs (pancRNAs), which are categorized into the most abundant single-copy lncRNA biotype, play vital regulatory roles in finely tuning cellular specification at the epigenomic level. In short, pancRNAs can directly or indirectly regulate downstream genes to participate in the development of organisms in a cell-specific manner. In this review, we will introduce the evolutionarily acquired characteristics of pancRNAs as determined by comparative epigenomics and elaborate on the research progress on pancRNA-involving processes in mammalian embryonic development, including neural differentiation.
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32
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CDK9 keeps RNA polymerase II on track. Cell Mol Life Sci 2021; 78:5543-5567. [PMID: 34146121 PMCID: PMC8257543 DOI: 10.1007/s00018-021-03878-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/26/2021] [Accepted: 06/08/2021] [Indexed: 12/30/2022]
Abstract
Cyclin-dependent kinase 9 (CDK9), the kinase component of positive transcription elongation factor b (P-TEFb), is essential for transcription of most protein-coding genes by RNA polymerase II (RNAPII). By releasing promoter-proximally paused RNAPII into gene bodies, CDK9 controls the entry of RNAPII into productive elongation and is, therefore, critical for efficient synthesis of full-length messenger (m)RNAs. In recent years, new players involved in P-TEFb-dependent processes have been identified and an important function of CDK9 in coordinating elongation with transcription initiation and termination has been unveiled. As the regulatory functions of CDK9 in gene expression continue to expand, a number of human pathologies, including cancers, have been associated with aberrant CDK9 activity, underscoring the need to properly regulate CDK9. Here, I provide an overview of CDK9 function and regulation, with an emphasis on CDK9 dysregulation in human diseases.
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Martónez-Ferníndez V, Navarro F. Rpb5, a subunit shared by eukaryotic RNA polymerases, cooperates with prefoldin-like Bud27/URI. AIMS GENETICS 2021. [DOI: 10.3934/genet.2018.1.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AbstractRpb5 is one of the five common subunits to all eukaryotic RNA polymerases, which is conserved in archaea, but not in bacteria. Among these common subunits, it is the only one that is not interchangeable between yeasts and humans, and accounts for the functional incompatibility of yeast and human subunits. Rpb5 has been proposed to contribute to the gene-specific activation of RNA pol II, notably during the infectious cycle of the hepatitis B virus, and also to participate in general transcription mediated by all eukaryotic RNA pol. The structural analysis of Rpb5 and its interaction with different transcription factors, regulators and DNA, accounts for Rpb5 being necessary to maintain the correct conformation of the shelf module of RNA pol II, which favors the proper organization of the transcription bubble and the clamp closure of the enzyme.In this work we provide details about subunit Rpb5's structure, conservation and the role it plays in transcription regulation by analyzing the different interactions with several factors, as well as its participation in the assembly of the three RNA pols, in cooperation with prefoldin-like Bud27/URI.
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Affiliation(s)
- Veránica Martónez-Ferníndez
- Department of Experimental Biology, Faculty of Experimental Sciences, University of JaÉn, Paraje de las Lagunillas, s/n, 23071, JaÉn, Spain
| | - Francisco Navarro
- Department of Experimental Biology, Faculty of Experimental Sciences, University of JaÉn, Paraje de las Lagunillas, s/n, 23071, JaÉn, Spain
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Saldi T, Riemondy K, Erickson B, Bentley DL. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Mol Cell 2021; 81:1789-1801.e5. [PMID: 33631106 DOI: 10.1016/j.molcel.2021.01.040] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/24/2022]
Abstract
Most RNA processing occurs co-transcriptionally. We interrogated nascent pol II transcripts by chemical and enzymatic probing and determined how the "nascent RNA structureome" relates to splicing, A-I editing and transcription speed. RNA folding within introns and steep structural transitions at splice sites are associated with efficient co-transcriptional splicing. A slow pol II mutant elicits extensive remodeling into more folded conformations with increased A-I editing. Introns that become more structured at their 3' splice sites get co-transcriptionally excised more efficiently. Slow pol II altered folding of intronic Alu elements where cryptic splicing and intron retention are stimulated, an outcome mimicked by UV, which decelerates transcription. Slow transcription also remodeled RNA folding around alternative exons in distinct ways that predict whether skipping or inclusion is favored, even though it occurs post-transcriptionally. Hence, co-transcriptional RNA folding modulates post-transcriptional alternative splicing. In summary, the plasticity of nascent transcripts has widespread effects on RNA processing.
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Affiliation(s)
- Tassa Saldi
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Kent Riemondy
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Benjamin Erickson
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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35
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Hansen AW, Arora P, Khayat MM, Smith LJ, Lewis AM, Rossetti LZ, Jayaseelan J, Cristian I, Haynes D, DiTroia S, Meeks N, Delgado MR, Rosenfeld JA, Pais L, White SM, Meng Q, Pehlivan D, Liu P, Gingras MC, Wangler MF, Muzny DM, Lupski JR, Kaplan CD, Gibbs RA. Germline mutation in POLR2A: a heterogeneous, multi-systemic developmental disorder characterized by transcriptional dysregulation. HGG ADVANCES 2021; 2:100014. [PMID: 33665635 PMCID: PMC7928427 DOI: 10.1016/j.xhgg.2020.100014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/06/2020] [Indexed: 12/23/2022] Open
Abstract
De novo germline variation in POLR2A was recently reported to associate with a neurodevelopmental disorder. We report twelve individuals harboring putatively pathogenic de novo or inherited variants in POLR2A, detail their phenotypes, and map all known variants to the domain structure of POLR2A and crystal structure of RNA polymerase II. Affected individuals were ascertained from a local data lake, pediatric genetics clinic, and an online community of families of affected individuals. These include six affected by de novo missense variants (including one previously reported individual), four clinical laboratory samples affected by missense variation with unknown inheritance-with yeast functional assays further supporting altered function-one affected by a de novo in-frame deletion, and one affected by a C-terminal frameshift variant inherited from a largely asymptomatic mother. Recurrently observed phenotypes include ataxia, joint hypermobility, short stature, skin abnormalities, congenital cardiac abnormalities, immune system abnormalities, hip dysplasia, and short Achilles tendons. We report a significantly higher occurrence of epilepsy (8/12, 66.7%) than previously reported (3/15, 20%) (p value = 0.014196; chi-square test) and a lower occurrence of hypotonia (8/12, 66.7%) than previously reported (14/15, 93.3%) (p value = 0.076309). POLR2A-related developmental disorders likely represent a spectrum of related, multi-systemic developmental disorders, driven by distinct mechanisms, converging at a single locus.
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Affiliation(s)
- Adam W. Hansen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Payal Arora
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Leah J. Smith
- Department of Biochemistry and Biophysics, Texas A&M University, TX, USA
| | - Andrea M. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Linda Z. Rossetti
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joy Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ingrid Cristian
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, USA
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, USA
| | - Stephanie DiTroia
- Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Naomi Meeks
- Departments of Pediatrics and Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mauricio R. Delgado
- Texas Scottish Rite Hospital for Children, Dallas, TX, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Lynn Pais
- Broad Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Susan M. White
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville 3052, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Marie-Claude Gingras
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - James R. Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Craig D. Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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36
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Wang Y, Hou L, Ardehali MB, Kingston RE, Dynlacht BD. Elongin A regulates transcription in vivo through enhanced RNA polymerase processivity. J Biol Chem 2021; 296:100170. [PMID: 33298525 PMCID: PMC7948402 DOI: 10.1074/jbc.ra120.015876] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022] Open
Abstract
Elongin is an RNA polymerase II (RNAPII)-associated factor that has been shown to stimulate transcriptional elongation in vitro. The Elongin complex is thought to be required for transcriptional induction in response to cellular stimuli and to ubiquitinate RNAPII in response to DNA damage. Yet, the impact of the Elongin complex on transcription in vivo has not been well studied. Here, we performed comprehensive studies of the role of Elongin A, the largest subunit of the Elongin complex, on RNAPII transcription genome-wide. Our results suggest that Elongin A localizes to actively transcribed regions and potential enhancers, and the level of recruitment correlated with transcription levels. We also identified a large group of factors involved in transcription as Elongin A-associated factors. In addition, we found that loss of Elongin A leads to dramatically reduced levels of serine2-phosphorylated, but not total, RNAPII, and cells depleted of Elongin A show stronger promoter RNAPII pausing, suggesting that Elongin A may be involved in the release of paused RNAPII. Our RNA-seq studies suggest that loss of Elongin A did not alter global transcription, and unlike prior in vitro studies, we did not observe a dramatic impact on RNAPII elongation rates in our cell-based nascent RNA-seq experiments upon Elongin A depletion. Taken together, our studies provide the first comprehensive analysis of the role of Elongin A in regulating transcription in vivo. Our studies also revealed that unlike prior in vitro findings, depletion of Elongin A has little impact on global transcription profiles and transcription elongation in vivo.
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Affiliation(s)
- Yating Wang
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Liming Hou
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - M Behfar Ardehali
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian D Dynlacht
- Department of Pathology, New York University School of Medicine, New York, New York, USA.
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37
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Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:10241-10258. [PMID: 32941642 PMCID: PMC7544207 DOI: 10.1093/nar/gkaa745] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.
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Affiliation(s)
- Natalia I Reim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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38
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Söderholm S, Cantù C. The WNT/β‐catenin dependent transcription: A tissue‐specific business. WIREs Mech Dis 2020; 13:e1511. [PMID: 33085215 PMCID: PMC9285942 DOI: 10.1002/wsbm.1511] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/11/2022]
Abstract
β‐catenin‐mediated Wnt signaling is an ancient cell‐communication pathway in which β‐catenin drives the expression of certain genes as a consequence of the trigger given by extracellular WNT molecules. The events occurring from signal to transcription are evolutionarily conserved, and their final output orchestrates countless processes during embryonic development and tissue homeostasis. Importantly, a dysfunctional Wnt/β‐catenin pathway causes developmental malformations, and its aberrant activation is the root of several types of cancer. A rich literature describes the multitude of nuclear players that cooperate with β‐catenin to generate a transcriptional program. However, a unified theory of how β‐catenin drives target gene expression is still missing. We will discuss two types of β‐catenin interactors: transcription factors that allow β‐catenin to localize at target regions on the DNA, and transcriptional co‐factors that ultimately activate gene expression. In contrast to the presumed universality of β‐catenin's action, the ensemble of available evidence suggests a view in which β‐catenin drives a complex system of responses in different cells and tissues. A malleable armamentarium of players might interact with β‐catenin in order to activate the right “canonical” targets in each tissue, developmental stage, or disease context. Discovering the mechanism by which each tissue‐specific β‐catenin response is executed will be crucial to comprehend how a seemingly universal pathway fosters a wide spectrum of processes during development and homeostasis. Perhaps more importantly, this could ultimately inform us about which are the tumor‐specific components that need to be targeted to dampen the activity of oncogenic β‐catenin. This article is categorized under:Cancer > Molecular and Cellular Physiology Cancer > Genetics/Genomics/Epigenetics Cancer > Stem Cells and Development
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Affiliation(s)
- Simon Söderholm
- Wallenberg Centre for Molecular Medicine Linköping University Linköping Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Health Science Linköping University Linköping Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine Linköping University Linköping Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Health Science Linköping University Linköping Sweden
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39
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Parua PK, Kalan S, Benjamin B, Sansó M, Fisher RP. Distinct Cdk9-phosphatase switches act at the beginning and end of elongation by RNA polymerase II. Nat Commun 2020; 11:4338. [PMID: 32859893 PMCID: PMC7455706 DOI: 10.1038/s41467-020-18173-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/21/2022] Open
Abstract
Reversible phosphorylation of Pol II and accessory factors helps order the transcription cycle. Here, we define two kinase-phosphatase switches that operate at different points in human transcription. Cdk9/cyclin T1 (P-TEFb) catalyzes inhibitory phosphorylation of PP1 and PP4 complexes that localize to 3′ and 5′ ends of genes, respectively, and have overlapping but distinct specificities for Cdk9-dependent phosphorylations of Spt5, a factor instrumental in promoter-proximal pausing and elongation-rate control. PP1 dephosphorylates an Spt5 carboxy-terminal repeat (CTR), but not Spt5-Ser666, a site between Kyrpides-Ouzounis-Woese (KOW) motifs 4 and 5, whereas PP4 can target both sites. In vivo, Spt5-CTR phosphorylation decreases as transcription complexes pass the cleavage and polyadenylation signal (CPS) and increases upon PP1 depletion, consistent with a PP1 function in termination first uncovered in yeast. Depletion of PP4-complex subunits increases phosphorylation of both Ser666 and the CTR, and promotes redistribution of promoter-proximally paused Pol II into gene bodies. These results suggest that switches comprising Cdk9 and either PP4 or PP1 govern pause release and the elongation-termination transition, respectively. Cdk9 (P-TEFb) and its substrate Spt5 influence events throughout the transcription cycle. Here, the authors define two switches with the potential to regulate promoter-proximal pause release and termination, respectively containing phosphatases PP4 and PP1, which are both inhibited by Cdk9, but have different specificities for sites on Spt5 and occupy opposite ends of genes.
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Affiliation(s)
- Pabitra K Parua
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Sampada Kalan
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Bradley Benjamin
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Miriam Sansó
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Robert P Fisher
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA.
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40
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Geisberg JV, Moqtaderi Z, Struhl K. The transcriptional elongation rate regulates alternative polyadenylation in yeast. eLife 2020; 9:e59810. [PMID: 32845240 PMCID: PMC7532003 DOI: 10.7554/elife.59810] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023] Open
Abstract
Yeast cells undergoing the diauxic response show a striking upstream shift in poly(A) site utilization, with increased use of ORF-proximal poly(A) sites resulting in shorter 3' mRNA isoforms for most genes. This altered poly(A) pattern is extremely similar to that observed in cells containing Pol II derivatives with slow elongation rates. Conversely, cells containing derivatives with fast elongation rates show a subtle downstream shift in poly(A) sites. Polyadenylation patterns of many genes are sensitive to both fast and slow elongation rates, and a global shift of poly(A) utilization is strongly linked to increased purine content of sequences flanking poly(A) sites. Pol II processivity is impaired in diauxic cells, but strains with reduced processivity and normal Pol II elongation rates have normal polyadenylation profiles. Thus, Pol II elongation speed is important for poly(A) site selection and for regulating poly(A) patterns in response to environmental conditions.
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Affiliation(s)
- Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical SchoolBostonUnited States
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41
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Ramani MKV, Escobar EE, Irani S, Mayfield JE, Moreno RY, Butalewicz JP, Cotham VC, Wu H, Tadros M, Brodbelt JS, Zhang YJ. Structural Motifs for CTD Kinase Specificity on RNA Polymerase II during Eukaryotic Transcription. ACS Chem Biol 2020; 15:2259-2272. [PMID: 32568517 DOI: 10.1021/acschembio.0c00474] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The phosphorylation states of RNA polymerase II coordinate the process of eukaryotic transcription by recruitment of transcription regulators. The individual residues of the repetitive heptad of the C-terminal domain (CTD) of the biggest subunit of RNA polymerase II are phosphorylated temporally at different stages of transcription. Intriguingly, despite similar flanking residues, phosphorylation of Ser2 and Ser5 in CTD heptads play dramatically different roles. The mechanism of how the kinases place phosphorylation on the correct serine is not well understood. In this paper, we use biochemical assays, mass spectrometry, molecular modeling, and structural analysis to understand the structural elements determining which serine of the CTD heptad is subject to phosphorylation. We identified three motifs in the activation/P+1 loops differentiating the intrinsic specificity of CTD in various CTD kinases. We characterized the enzyme specificity of the CTD kinases-CDK7 as Ser5-specific, Erk2 with dual specificity for Ser2 and Ser5, and Dyrk1a as a Ser2-specific kinase. We also show that the specificities of kinases are malleable and can be modified by incorporating mutations in their activation/P+1 loops that alter the interactions of the three motifs. Our results provide an important clue to the understanding of post-translational modification of RNA polymerase II temporally during active transcription.
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42
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Jeronimo C, Poitras C, Robert F. Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications. Cell Rep 2020; 28:1206-1218.e8. [PMID: 31365865 DOI: 10.1016/j.celrep.2019.06.097] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/28/2019] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
Genomic DNA is framed by additional layers of information, referred to as the epigenome. Epigenomic marks such as DNA methylation, histone modifications, and histone variants are concentrated on specific genomic sites, where they can both instruct and reflect gene expression. How this information is maintained, notably in the face of transcription, is not completely understood. Specifically, the extent to which modified histones themselves are retained through RNA polymerase II passage is unclear. Here, we show that several histone modifications are mislocalized when the transcription-coupled histone chaperones FACT or Spt6 are disrupted in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates nucleosome loss, which is partially compensated for by the increased activity of non-transcription-coupled histone chaperones. The random incorporation of transcription-evicted modified histones scrambles epigenomic information. Our work highlights the importance of local recycling of modified histones by FACT and Spt6 during transcription in the maintenance of the epigenomic landscape.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, Canada.
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43
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Kaczmarek Michaels K, Mohd Mostafa S, Ruiz Capella J, Moore CL. Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases. Nucleic Acids Res 2020; 48:5407-5425. [PMID: 32356874 PMCID: PMC7261179 DOI: 10.1093/nar/gkaa292] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
Adjusting DNA structure via epigenetic modifications, and altering polyadenylation (pA) sites at which precursor mRNA is cleaved and polyadenylated, allows cells to quickly respond to environmental stress. Since polyadenylation occurs co-transcriptionally, and specific patterns of nucleosome positioning and chromatin modifications correlate with pA site usage, epigenetic factors potentially affect alternative polyadenylation (APA). We report that the histone H3K4 methyltransferase Set1, and the histone H3K36 methyltransferase Set2, control choice of pA site in Saccharomyces cerevisiae, a powerful model for studying evolutionarily conserved eukaryotic processes. Deletion of SET1 or SET2 causes an increase in serine-2 phosphorylation within the C-terminal domain of RNA polymerase II (RNAP II) and in the recruitment of the cleavage/polyadenylation complex, both of which could cause the observed switch in pA site usage. Chemical inhibition of TOR signaling, which causes nutritional stress, results in Set1- and Set2-dependent APA. In addition, Set1 and Set2 decrease efficiency of using single pA sites, and control nucleosome occupancy around pA sites. Overall, our study suggests that the methyltransferases Set1 and Set2 regulate APA induced by nutritional stress, affect the RNAP II C-terminal domain phosphorylation at Ser2, and control recruitment of the 3′ end processing machinery to the vicinity of pA sites.
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Affiliation(s)
- Katarzyna Kaczmarek Michaels
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Salwa Mohd Mostafa
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.,Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Julia Ruiz Capella
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain
| | - Claire L Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.,Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
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44
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Leng X, Thomas Q, Rasmussen SH, Marquardt S. A G(enomic)P(ositioning)S(ystem) for Plant RNAPII Transcription. TRENDS IN PLANT SCIENCE 2020; 25:744-764. [PMID: 32673579 DOI: 10.1016/j.tplants.2020.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/24/2020] [Accepted: 03/10/2020] [Indexed: 06/11/2023]
Abstract
Post-translational modifications (PTMs) of histone residues shape the landscape of gene expression by modulating the dynamic process of RNA polymerase II (RNAPII) transcription. The contribution of particular histone modifications to the definition of distinct RNAPII transcription stages remains poorly characterized in plants. Chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) resolves the genomic distribution of histone modifications. Here, we review histone PTM ChIP-seq data in Arabidopsis thaliana and find support for a Genomic Positioning System (GPS) that guides RNAPII transcription. We review the roles of histone PTM 'readers', 'writers', and 'erasers', with a focus on the regulation of gene expression and biological functions in plants. The distinct functions of RNAPII transcription during the plant transcription cycle may rely, in part, on the characteristic histone PTM profiles that distinguish transcription stages.
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Affiliation(s)
- Xueyuan Leng
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Quentin Thomas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Simon Horskjær Rasmussen
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark
| | - Sebastian Marquardt
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Bülowsvej 34, 1870 Frederiksberg C, Denmark.
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45
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Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Rep 2020; 27:3770-3779.e7. [PMID: 31242411 DOI: 10.1016/j.celrep.2019.05.099] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/22/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
FACT (facilitates chromatin transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II (Pol II) transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including histone H3 lysine 4 (H3K4) and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription. Importantly, we identify a role for FACT in the maintenance of promoter-proximal Pol II pausing, a key step in transcription activation in higher eukaryotes. These findings bring to light a broader role for FACT in the regulation of Pol II transcription.
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Affiliation(s)
- Theophilus T Tettey
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; The Open University, Walton Hall, Milton Keynes, Buckinghamshire MK7 6AA, UK
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Wanqing Shao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Benjamin A Story
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Alex D Chitsazan
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Robert L Glaser
- Wadsworth Center, New York State Department of Health, PO Box 509, Albany, NY 12201, USA
| | - Zach H Goode
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Christopher W Seidel
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Marco Blanchette
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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46
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First Come, First Served: Sui Generis Features of the First Intron. PLANTS 2020; 9:plants9070911. [PMID: 32707681 PMCID: PMC7411622 DOI: 10.3390/plants9070911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.
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47
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Monteuuis G, Wong JJL, Bailey CG, Schmitz U, Rasko JEJ. The changing paradigm of intron retention: regulation, ramifications and recipes. Nucleic Acids Res 2020; 47:11497-11513. [PMID: 31724706 PMCID: PMC7145568 DOI: 10.1093/nar/gkz1068] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Intron retention (IR) is a form of alternative splicing that has long been neglected in mammalian systems although it has been studied for decades in non-mammalian species such as plants, fungi, insects and viruses. It was generally assumed that mis-splicing, leading to the retention of introns, would have no physiological consequence other than reducing gene expression by nonsense-mediated decay. Relatively recent landmark discoveries have highlighted the pivotal role that IR serves in normal and disease-related human biology. Significant technical hurdles have been overcome, thereby enabling the robust detection and quantification of IR. Still, relatively little is known about the cis- and trans-acting modulators controlling this phenomenon. The fate of an intron to be, or not to be, retained in the mature transcript is the direct result of the influence exerted by numerous intrinsic and extrinsic factors at multiple levels of regulation. These factors have altered current biological paradigms and provided unexpected insights into the transcriptional landscape. In this review, we discuss the regulators of IR and methods to identify them. Our focus is primarily on mammals, however, we broaden the scope to non-mammalian organisms in which IR has been shown to be biologically relevant.
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Affiliation(s)
- Geoffray Monteuuis
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Justin J L Wong
- Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, Australia
| | - Charles G Bailey
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Ulf Schmitz
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Computational Biomedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, Australia.,Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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48
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Lyons DE, McMahon S, Ott M. A combinatorial view of old and new RNA polymerase II modifications. Transcription 2020; 11:66-82. [PMID: 32401151 DOI: 10.1080/21541264.2020.1762468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.
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Affiliation(s)
- Danielle E Lyons
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Sarah McMahon
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
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49
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Leng X, Ivanov M, Kindgren P, Malik I, Thieffry A, Brodersen P, Sandelin A, Kaplan CD, Marquardt S. Organismal benefits of transcription speed control at gene boundaries. EMBO Rep 2020; 21:e49315. [PMID: 32103605 PMCID: PMC7132196 DOI: 10.15252/embr.201949315] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
RNA polymerase II (RNAPII) transcription is crucial for gene expression. RNAPII density peaks at gene boundaries, associating these key regions for gene expression control with limited RNAPII movement. The connections between RNAPII transcription speed and gene regulation in multicellular organisms are poorly understood. Here, we directly modulate RNAPII transcription speed by point mutations in the second largest subunit of RNAPII in Arabidopsis thaliana. A RNAPII mutation predicted to decelerate transcription is inviable, while accelerating RNAPII transcription confers phenotypes resembling auto-immunity. Nascent transcription profiling revealed that RNAPII complexes with accelerated transcription clear stalling sites at both gene ends, resulting in read-through transcription. The accelerated transcription mutant NRPB2-Y732F exhibits increased association with 5' splice site (5'SS) intermediates and enhanced splicing efficiency. Our findings highlight potential advantages of RNAPII stalling through local reduction in transcription speed to optimize gene expression for the development of multicellular organisms.
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Affiliation(s)
- Xueyuan Leng
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
| | - Maxim Ivanov
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
| | - Peter Kindgren
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
| | - Indranil Malik
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
- Present address:
Department of NeurologyUniversity of Michigan Medical SchoolAnn ArborMIUSA
| | - Axel Thieffry
- Biotech Research and Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Peter Brodersen
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Albin Sandelin
- Biotech Research and Innovation CentreUniversity of CopenhagenCopenhagenDenmark
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Craig D Kaplan
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Sebastian Marquardt
- Department of Plant and Environmental SciencesCopenhagen Plant Science CentreUniversity of CopenhagenFrederiksbergDenmark
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50
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Hu A, Li J, Tang W, Liu G, Zhang H, Liu C, Chen X. Anthralin Suppresses the Proliferation of Influenza Virus by Inhibiting the Cap-Binding and Endonuclease Activity of Viral RNA Polymerase. Front Microbiol 2020; 11:178. [PMID: 32132985 PMCID: PMC7040080 DOI: 10.3389/fmicb.2020.00178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022] Open
Abstract
Influenza virus RNA-dependent RNA polymerase (vRdRp) does not have capping activity and relies on the capped RNAs produced by the host RNA polymerase II (RNAPII). The viral polymerases process the capped RNAs to produce short capped RNA fragments that are used as primers to initiate the transcription of viral mRNAs. This process, known as cap-snatching, can be targeted by antiviral therapeutics. Here, anthralin was identified as an inhibitor against influenza a virus (IAV) infection by targeting the cap-snatching activity of the viral polymerase. Anthralin, an FDA-approved drug used in the treatment of psoriasis, shows antiviral activity against IAV infection in vitro and in vivo. Importantly, anthralin significantly reduces weight loss, lung injury, and mortality caused by IAV infection in mice. The mechanism of action study revealed that anthralin inhibits the cap-binding function of PB2 subunit and endonuclease activity of PA. As a result, viral mRNA transcription is blocked, leading to the decreases in viral RNA replication and viral protein expression. In conclusion, anthralin has been demonstrated to have the potential of an alternative antiviral against influenza virus infection. Also, targeting the captive pocket structure that includes the N-terminus of PA endonuclease domain and the C-terminal of PB2 cap-binding domain of IAV RdRp may be an excellent strategy for developing anti-influenza drugs.
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Affiliation(s)
- Ao Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Tang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ge Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haiwei Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chunlan Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xulin Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
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