1
|
Chen X, Xu Y. Interplay between the transcription preinitiation complex and the +1 nucleosome. Trends Biochem Sci 2024; 49:145-155. [PMID: 38218671 DOI: 10.1016/j.tibs.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/15/2024]
Abstract
Eukaryotic transcription starts with the assembly of a preinitiation complex (PIC) on core promoters. Flanking this region is the +1 nucleosome, the first nucleosome downstream of the core promoter. While this nucleosome is rich in epigenetic marks and plays a key role in transcription regulation, how the +1 nucleosome interacts with the transcription machinery has been a long-standing question. Here, we summarize recent structural and functional studies of the +1 nucleosome in complex with the PIC. We specifically focus on how differently organized promoter-nucleosome templates affect the assembly of the PIC and PIC-Mediator on chromatin and result in distinct transcription initiation.
Collapse
Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, New Cornerstone Science Laboratory, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.
| |
Collapse
|
2
|
Farnung L. Nucleosomes unwrapped: Structural perspectives on transcription through chromatin. Curr Opin Struct Biol 2023; 82:102690. [PMID: 37633188 DOI: 10.1016/j.sbi.2023.102690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Transcription of most protein-coding genes requires the passage of RNA polymerase II through chromatin. Chromatin with its fundamental unit, the nucleosome, represents a barrier to transcription. How RNA polymerase II and associated factors traverse through nucleosomes and how chromatin architecture is maintained have remained largely enigmatic. Only recently, cryo-EM structures have visualized the transcription process through chromatin. These structures have elucidated how transcription initiation and transcription elongation influence and are influenced by a chromatinized DNA substrate. This review provides a summary of our current structural understanding of transcription through chromatin, highlighting common mechanisms during nucleosomal traversal and novel regulatory mechanisms that have emerged in the last five years.
Collapse
Affiliation(s)
- Lucas Farnung
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
3
|
Weiß E, Hennig T, Graßl P, Djakovic L, Whisnant AW, Jürges CS, Koller F, Kluge M, Erhard F, Dölken L, Friedel CC. HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes. J Virol 2023; 97:e0038123. [PMID: 37093003 PMCID: PMC10231138 DOI: 10.1128/jvi.00381-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
Herpes simplex virus 1 (HSV-1) infection exerts a profound shutoff of host gene expression at multiple levels. Recently, HSV-1 infection was reported to also impact promoter-proximal RNA polymerase II (Pol II) pausing, a key step in the eukaryotic transcription cycle, with decreased and increased Pol II pausing observed for activated and repressed genes, respectively. Here, we demonstrate that HSV-1 infection induces more complex alterations in promoter-proximal pausing than previously suspected for the vast majority of cellular genes. While pausing is generally retained, it is shifted to more downstream and less well-positioned sites for most host genes. The downstream shift of Pol II pausing was established between 1.5 and 3 h of infection, remained stable until at least 6 hours postinfection, and was observed in the absence of ICP22. The shift in Pol II pausing does not result from alternative de novo transcription initiation at downstream sites or read-in transcription originating from disruption of transcription termination of upstream genes. The use of downstream secondary pause sites associated with +1 nucleosomes was previously observed upon negative elongation factor (NELF) depletion. However, downstream shifts of Pol II pausing in HSV-1 infection were much more pronounced than observed upon NELF depletion. Thus, our study reveals a novel aspect in which HSV-1 infection fundamentally reshapes host transcriptional processes, providing new insights into the regulation of promoter-proximal Pol II pausing in eukaryotic cells. IMPORTANCE This study provides a genome-wide analysis of changes in promoter-proximal polymerase II (Pol II) pausing on host genes induced by HSV-1 infection. It shows that standard measures of pausing, i.e., pausing indices, do not properly capture the complex and unsuspected alterations in Pol II pausing occurring in HSV-1 infection. Instead of a reduction of pausing with increased elongation, as suggested by pausing index analysis, HSV-1 infection leads to a shift of pausing to downstream and less well-positioned sites than in uninfected cells for the majority of host genes. Thus, HSV-1 infection fundamentally reshapes a key regulatory step at the beginning of the host transcriptional cycle on a genome-wide scale.
Collapse
Affiliation(s)
- Elena Weiß
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Pilar Graßl
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Christopher S. Jürges
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Franziska Koller
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Michael Kluge
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz-Center for Infection Research (HZI), Würzburg, Germany
| | - Caroline C. Friedel
- Institute of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany
| |
Collapse
|
4
|
Bomber ML, Wang J, Liu Q, Barnett KR, Layden HM, Hodges E, Stengel KR, Hiebert SW. Human SMARCA5 is continuously required to maintain nucleosome spacing. Mol Cell 2023; 83:507-522.e6. [PMID: 36630954 PMCID: PMC9974918 DOI: 10.1016/j.molcel.2022.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023]
Abstract
Genetic models suggested that SMARCA5 was required for DNA-templated events including transcription, DNA replication, and DNA repair. We engineered a degron tag into the endogenous alleles of SMARCA5, a catalytic component of the imitation switch complexes in three different human cell lines to define the effects of rapid degradation of this key regulator. Degradation of SMARCA5 was associated with a rapid increase in global nucleosome repeat length, which may allow greater chromatin compaction. However, there were few changes in nascent transcription within the first 6 h of degradation. Nevertheless, we demonstrated a requirement for SMARCA5 to control nucleosome repeat length at G1/S and during the S phase. SMARCA5 co-localized with CTCF and H2A.Z, and we found a rapid loss of CTCF DNA binding and disruption of nucleosomal phasing around CTCF binding sites. This spatiotemporal analysis indicates that SMARCA5 is continuously required for maintaining nucleosomal spacing.
Collapse
Affiliation(s)
- Monica L Bomber
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kelly R Barnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Hillary M Layden
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
| | - Scott W Hiebert
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
| |
Collapse
|
5
|
Diego-Martin B, Pérez-Alemany J, Candela-Ferre J, Corbalán-Acedo A, Pereyra J, Alabadí D, Jami-Alahmadi Y, Wohlschlegel J, Gallego-Bartolomé J. The TRIPLE PHD FINGERS proteins are required for SWI/SNF complex-mediated +1 nucleosome positioning and transcription start site determination in Arabidopsis. Nucleic Acids Res 2022; 50:10399-10417. [PMID: 36189880 PMCID: PMC9561266 DOI: 10.1093/nar/gkac826] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 11/14/2022] Open
Abstract
Eukaryotes have evolved multiple ATP-dependent chromatin remodelers to shape the nucleosome landscape. We recently uncovered an evolutionarily conserved SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeler complex in plants reminiscent of the mammalian BAF subclass, which specifically incorporates the MINUSCULE (MINU) catalytic subunits and the TRIPLE PHD FINGERS (TPF) signature subunits. Here we report experimental evidence that establishes the functional relevance of TPF proteins for the complex activity. Our results show that depletion of TPF triggers similar pleiotropic phenotypes and molecular defects to those found in minu mutants. Moreover, we report the genomic location of MINU2 and TPF proteins as representative members of this SWI/SNF complex and their impact on nucleosome positioning and transcription. These analyses unravel the binding of the complex to thousands of genes where it modulates the position of the +1 nucleosome. These targets tend to produce 5′-shifted transcripts in the tpf and minu mutants pointing to the participation of the complex in alternative transcription start site usage. Interestingly, there is a remarkable correlation between +1 nucleosome shift and 5′ transcript length change suggesting their functional connection. In summary, this study unravels the function of a plant SWI/SNF complex involved in +1 nucleosome positioning and transcription start site determination.
Collapse
Affiliation(s)
- Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Antonio Corbalán-Acedo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Juan Pereyra
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022, Spain
| |
Collapse
|
6
|
Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes. Nat Commun 2022; 13:2006. [PMID: 35422111 PMCID: PMC9010409 DOI: 10.1038/s41467-022-29739-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/21/2022] [Indexed: 12/29/2022] Open
Abstract
Interactions of the RNA polymerase II (Pol II) preinitiation complex (PIC) and paused early elongation complexes with the first downstream (+1) nucleosome are thought to be functionally important. However, current methods are limited for investigating these relationships, both for cellular chromatin and the human cytomegalovirus (HCMV) genome. Digestion with human DNA fragmentation factor (DFF) before immunoprecipitation (DFF-ChIP) precisely revealed both similarities and major differences in PICs driven by TBP on the host genome in comparison with PICs driven by TBP or the viral-specific, late initiation factor UL87 on the viral genome. Host PICs and paused Pol II complexes are frequently found in contact with the +1 nucleosome and paused Pol II can also be found in a complex involved in the initial invasion of the +1 nucleosome. In contrast, viral transcription complexes have very limited nucleosomal interactions, reflecting a relative lack of chromatinization of transcriptionally active regions of HCMV genomes. Here the authors digested chromatin with DNA fragmentation factor (DFF) prior to chromatin immunoprecipitation (DFF-ChIP) to depict transcription complex interactions with neighboring nucleosomes in cells. Applying this method to human cytomegalovirus (HMCV)-infected cells, they find that the viral genome is underchromatinized, leading to fewer transcription complex interactions with nucleosomes.
Collapse
|
7
|
Cheon Y, Han S, Kim T, Hwang D, Lee D. The chromatin remodeler Ino80 mediates RNAPII pausing site determination. Genome Biol 2021; 22:294. [PMID: 34663418 PMCID: PMC8524862 DOI: 10.1186/s13059-021-02500-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Promoter-proximal pausing of RNA polymerase II (RNAPII) is a critical step for the precise regulation of gene expression. Despite the apparent close relationship between promoter-proximal pausing and nucleosome, the role of chromatin remodeler governing this step has mainly remained elusive. RESULTS Here, we report highly confined RNAPII enrichments downstream of the transcriptional start site in Saccharomyces cerevisiae using PRO-seq experiments. This non-uniform distribution of RNAPII exhibits both similar and different characteristics with promoter-proximal pausing in Schizosaccharomyces pombe and metazoans. Interestingly, we find that Ino80p knockdown causes a significant upstream transition of promoter-proximal RNAPII for a subset of genes, relocating RNAPII from the main pausing site to the alternative pausing site. The proper positioning of RNAPII is largely dependent on nucleosome context. We reveal that the alternative pausing site is closely associated with the + 1 nucleosome, and nucleosome architecture around the main pausing site of these genes is highly phased. In addition, Ino80p knockdown results in an increase in fuzziness and a decrease in stability of the + 1 nucleosome. Furthermore, the loss of INO80 also leads to the shift of promoter-proximal RNAPII toward the alternative pausing site in mouse embryonic stem cells. CONCLUSIONS Based on our collective results, we hypothesize that the highly conserved chromatin remodeler Ino80p is essential in establishing intact RNAPII pausing during early transcription elongation in various organisms, from budding yeast to mouse.
Collapse
Affiliation(s)
- Youngseo Cheon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Sungwook Han
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Taemook Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea
| | - Daehee Hwang
- School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Daeyoup Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, South Korea.
| |
Collapse
|
8
|
Ohguchi H, Park PMC, Wang T, Gryder BE, Ogiya D, Kurata K, Zhang X, Li D, Pei C, Masuda T, Johansson C, Wimalasena VK, Kim Y, Hino S, Usuki S, Kawano Y, Samur MK, Tai YT, Munshi NC, Matsuoka M, Ohtsuki S, Nakao M, Minami T, Lauberth S, Khan J, Oppermann U, Durbin AD, Anderson KC, Hideshima T, Qi J. Lysine Demethylase 5A is Required for MYC Driven Transcription in Multiple Myeloma. Blood Cancer Discov 2021; 2:370-387. [PMID: 34258103 PMCID: PMC8265280 DOI: 10.1158/2643-3230.bcd-20-0108] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 02/22/2021] [Accepted: 03/28/2021] [Indexed: 12/23/2022] Open
Abstract
Lysine demethylase 5A (KDM5A) is a negative regulator of histone H3K4 trimethylation, a histone mark associated with activate gene transcription. We identify that KDM5A interacts with the P-TEFb complex and cooperates with MYC to control MYC targeted genes in multiple myeloma (MM) cells. We develop a cell-permeable and selective KDM5 inhibitor, JQKD82, that increases histone H3K4me3 but paradoxically inhibits downstream MYC-driven transcriptional output in vitro and in vivo. Using genetic ablation together with our inhibitor, we establish that KDM5A supports MYC target gene transcription independent of MYC itself, by supporting TFIIH (CDK7)- and P-TEFb (CDK9)-mediated phosphorylation of RNAPII. These data identify KDM5A as a unique vulnerability in MM functioning through regulation of MYC-target gene transcription, and establish JQKD82 as a tool compound to block KDM5A function as a potential therapeutic strategy for MM.
Collapse
Affiliation(s)
- Hiroto Ohguchi
- Division of Disease Epigenetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan.
| | - Paul M C Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tingjian Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Berkley E Gryder
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Daisuke Ogiya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Keiji Kurata
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Xiaofeng Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Deyao Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Chengkui Pei
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Catrine Johansson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Yong Kim
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Shingo Usuki
- Liaison Laboratory Research Promotion Center, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Yawara Kawano
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, Japan
| | - Mehmet K Samur
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yu-Tzu Tai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Nikhil C Munshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Masao Matsuoka
- Department of Hematology, Rheumatology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Takashi Minami
- Division of Molecular and Vascular Biology, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Shannon Lauberth
- Division of Biological Sciences, University of Califonia, San Diego, La Jolla, California
| | - Javed Khan
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Udo Oppermann
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
- Structural Genomics Consortium, University of Oxford, Headington, United Kingdom; Oxford Centre for Translational Myeloma Research, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Adam D Durbin
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Teru Hideshima
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
9
|
Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
Collapse
Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| |
Collapse
|
10
|
Herrero-Ruiz A, Martínez-García PM, Terrón-Bautista J, Millán-Zambrano G, Lieberman JA, Jimeno-González S, Cortés-Ledesma F. Topoisomerase IIα represses transcription by enforcing promoter-proximal pausing. Cell Rep 2021; 35:108977. [PMID: 33852840 PMCID: PMC8052185 DOI: 10.1016/j.celrep.2021.108977] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 02/05/2021] [Accepted: 03/19/2021] [Indexed: 12/19/2022] Open
Abstract
Accumulation of topological stress in the form of DNA supercoiling is inherent to the advance of RNA polymerase II (Pol II) and needs to be resolved by DNA topoisomerases to sustain productive transcriptional elongation. Topoisomerases are therefore considered positive facilitators of transcription. Here, we show that, in contrast to this general assumption, human topoisomerase IIα (TOP2A) activity at promoters represses transcription of immediate early genes such as c-FOS, maintaining them under basal repressed conditions. Thus, TOP2A inhibition creates a particular topological context that results in rapid release from promoter-proximal pausing and transcriptional upregulation, which mimics the typical bursting behavior of these genes in response to physiological stimulus. We therefore describe the control of promoter-proximal pausing by TOP2A as a layer for the regulation of gene expression, which can act as a molecular switch to rapidly activate transcription, possibly by regulating the accumulation of DNA supercoiling at promoter regions.
Collapse
Affiliation(s)
- Andrés Herrero-Ruiz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain; Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - José Terrón-Bautista
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | - Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain
| | | | - Silvia Jimeno-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain; Departamento de Genética, Universidad de Sevilla, Sevilla 41080, Spain.
| | - Felipe Cortés-Ledesma
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Sevilla 41092, Spain; Topology and DNA Breaks Group, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain.
| |
Collapse
|
11
|
Dollinger R, Gilmour DS. Regulation of Promoter Proximal Pausing of RNA Polymerase II in Metazoans. J Mol Biol 2021; 433:166897. [PMID: 33640324 DOI: 10.1016/j.jmb.2021.166897] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Regulation of transcription is a tightly choreographed process. The establishment of RNA polymerase II promoter proximal pausing soon after transcription initiation and the release of Pol II into productive elongation are key regulatory processes that occur in early elongation. We describe the techniques and tools that have become available for the study of promoter proximal pausing and their utility for future experiments. We then provide an overview of the factors and interactions that govern a multipartite pausing process and address emerging questions surrounding the mechanism of RNA polymerase II's subsequent advancement into the gene body. Finally, we address remaining controversies and future areas of study.
Collapse
Affiliation(s)
- Roberta Dollinger
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 462 North Frear, University Park, PA 16802, USA.
| | - David S Gilmour
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 465A North Frear, University Park, PA 16802, USA.
| |
Collapse
|
12
|
Decker TM. Mechanisms of Transcription Elongation Factor DSIF (Spt4-Spt5). J Mol Biol 2020; 433:166657. [PMID: 32987031 DOI: 10.1016/j.jmb.2020.09.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/16/2020] [Accepted: 09/20/2020] [Indexed: 12/19/2022]
Abstract
The transcription elongation factor Spt5 is conserved from bacteria to humans. In eukaryotes, Spt5 forms a complex with Spt4 and regulates processive transcription elongation. Recent studies on transcription elongation suggest different mechanistic roles in yeast versus mammals. Higher eukaryotes utilize Spt4-Spt5 (DSIF) to regulate promoter-proximal pausing, a transcription-regulatory mechanism that connects initiation to productive elongation. DSIF is a versatile transcription factor and has been implicated in both gene-specific regulation and transcription through nucleosomes. Future studies will further elucidate the role of DSIF in transcriptional dynamics and disentangle its inhibitory and enhancing activities in transcription.
Collapse
Affiliation(s)
- Tim-Michael Decker
- Department of Biochemistry, University of Colorado, 3415 Colorado Ave, Boulder, CO 80303, USA.
| |
Collapse
|
13
|
Luse DS, Parida M, Spector BM, Nilson KA, Price DH. A unified view of the sequence and functional organization of the human RNA polymerase II promoter. Nucleic Acids Res 2020; 48:7767-7785. [PMID: 32597978 PMCID: PMC7641323 DOI: 10.1093/nar/gkaa531] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/31/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location.
Collapse
Affiliation(s)
- Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Benjamin M Spector
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - Kyle A Nilson
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| | - David H Price
- Department of Biochemistry, The University of Iowa, Iowa City, IA 52242, USA
| |
Collapse
|
14
|
Zhao Y, Wang J, Liang F, Liu Y, Wang Q, Zhang H, Jiang M, Zhang Z, Zhao W, Bao Y, Zhang Z, Wu J, Asmann YW, Li R, Xiao J. NucMap: a database of genome-wide nucleosome positioning map across species. Nucleic Acids Res 2020; 47:D163-D169. [PMID: 30335176 PMCID: PMC6323900 DOI: 10.1093/nar/gky980] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/10/2018] [Indexed: 12/16/2022] Open
Abstract
Dynamics of nucleosome positioning affects chromatin state, transcription and all other biological processes occurring on genomic DNA. While MNase-Seq has been used to depict nucleosome positioning map in eukaryote in the past years, nucleosome positioning data is increasing dramatically. To facilitate the usage of published data across studies, we developed a database named nucleosome positioning map (NucMap, http://bigd.big.ac.cn/nucmap). NucMap includes 798 experimental data from 477 samples across 15 species. With a series of functional modules, users can search profile of nucleosome positioning at the promoter region of each gene across all samples and make enrichment analysis on nucleosome positioning data in all genomic regions. Nucleosome browser was built to visualize the profiles of nucleosome positioning. Users can also visualize multiple sources of omics data with the nucleosome browser and make side-by-side comparisons. All processed data in the database are freely available. NucMap is the first comprehensive nucleosome positioning platform and it will serve as an important resource to facilitate the understanding of chromatin regulation.
Collapse
Affiliation(s)
- Yongbing Zhao
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jinyue Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Liang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanxia Liu
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiye Jiang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhewen Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenming Zhao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan W Asmann
- Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Rujiao Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| |
Collapse
|
15
|
Farahani RM, Rezaei-Lotfi S, Hunter N. Genomic competition for noise reduction shaped evolutionary landscape of mir-4673. NPJ Syst Biol Appl 2020; 6:12. [PMID: 32376854 PMCID: PMC7203229 DOI: 10.1038/s41540-020-0131-2] [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: 05/08/2019] [Accepted: 04/09/2020] [Indexed: 12/24/2022] Open
Abstract
The genomic platform that informs evolution of microRNA cascades remains unknown. Here we capitalised on the recent evolutionary trajectory of hominin-specific miRNA-4673, encoded in intron 4 of notch-1, to uncover the identity of one such precursor genomic element and the selective forces acting upon it. The miRNA targets genes that regulate Wnt/β-catenin signalling cascade. Primary sequence of the microRNA and its target region in Wnt modulating genes evolved from homologous signatures mapped to homotypic cis-clusters recognised by TCF3/4 and TFAP2A/B/C families. Integration of homologous TFAP2A/B/C cis-clusters (short range inhibitor of β-catenin) into the transcriptional landscape of Wnt cascade genes can reduce noise in gene expression. Probabilistic adoption of miRNA secondary structure by one such cis-signature in notch-1 reflected selection for superhelical curvature symmetry of precursor DNA to localise a nucleosome that overlapped the latter cis-cluster. By replicating the cis-cluster signature, non-random interactions of the miRNA with key Wnt modulator genes expanded the transcriptional noise buffering capacity via a coherent feed-forward loop mechanism. In consequence, an autonomous transcriptional noise dampener (the cis-cluster/nucleosome) evolved into a post-transcriptional one (the miRNA). The findings suggest a latent potential for remodelling of transcriptional landscape by miRNAs that capitalise on non-random distribution of genomic cis-signatures.
Collapse
Affiliation(s)
- Ramin M Farahani
- IDR/Westmead Institute for Medical Research and Westmead Centre for Oral Health, Sydney, NSW, Australia.
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Saba Rezaei-Lotfi
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research and Westmead Centre for Oral Health, Sydney, NSW, Australia
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| |
Collapse
|
16
|
Oruba A, Saccani S, van Essen D. Role of cell-type specific nucleosome positioning in inducible activation of mammalian promoters. Nat Commun 2020; 11:1075. [PMID: 32103026 PMCID: PMC7044431 DOI: 10.1038/s41467-020-14950-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 02/10/2020] [Indexed: 12/18/2022] Open
Abstract
The organization of nucleosomes across functional genomic elements represents a critical layer of control. Here, we present a strategy for high-resolution nucleosome profiling at selected genomic features, and use this to analyse dynamic nucleosome positioning at inducible and cell-type-specific mammalian promoters. We find that nucleosome patterning at inducible promoters frequently resembles that at active promoters, even before stimulus-driven activation. Accordingly, the nucleosome profile at many inactive inducible promoters is sufficient to predict cell-type-specific responsiveness. Induction of gene expression is generally not associated with major changes to nucleosome patterning, and a subset of inducible promoters can be activated without stable nucleosome depletion from their transcription start sites. These promoters are generally dependent on remodelling enzymes for their inducible activation, and exhibit transient nucleosome depletion only at alleles undergoing transcription initiation. Together, these data reveal how the responsiveness of inducible promoters to activating stimuli is linked to cell-type-specific nucleosome patterning. Nucleosome organisation plays important roles in regulating functional genomic elements. Here, the authors use high-resolution profiling to analyse dynamic nucleosome positioning at inducible and cell-type-specific promoters, providing a global view of chromatin architecture at inducible promoters.
Collapse
Affiliation(s)
- Agata Oruba
- Max Planck Institute for Immunobiology & Epigenetics, Stübeweg 51, Freiburg, D79108, Germany
| | - Simona Saccani
- Max Planck Institute for Immunobiology & Epigenetics, Stübeweg 51, Freiburg, D79108, Germany. .,Institute for Research on Cancer & Aging, Nice (IRCAN), 28 Avenue Valombrose, Nice, 06107, France.
| | - Dominic van Essen
- Max Planck Institute for Immunobiology & Epigenetics, Stübeweg 51, Freiburg, D79108, Germany. .,Institute for Research on Cancer & Aging, Nice (IRCAN), 28 Avenue Valombrose, Nice, 06107, France.
| |
Collapse
|
17
|
Type II DNA Topoisomerases Cause Spontaneous Double-Strand Breaks in Genomic DNA. Genes (Basel) 2019; 10:genes10110868. [PMID: 31671674 PMCID: PMC6895833 DOI: 10.3390/genes10110868] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/31/2022] Open
Abstract
Type II DNA topoisomerase enzymes (TOP2) catalyze topological changes by strand passage reactions. They involve passing one intact double stranded DNA duplex through a transient enzyme-bridged break in another (gated helix) followed by ligation of the break by TOP2. A TOP2 poison, etoposide blocks TOP2 catalysis at the ligation step of the enzyme-bridged break, increasing the number of stable TOP2 cleavage complexes (TOP2ccs). Remarkably, such pathological TOP2ccs are formed during the normal cell cycle as well as in postmitotic cells. Thus, this ‘abortive catalysis’ can be a major source of spontaneously arising DNA double-strand breaks (DSBs). TOP2-mediated DSBs are also formed upon stimulation with physiological concentrations of androgens and estrogens. The frequent occurrence of TOP2-mediated DSBs was previously not appreciated because they are efficiently repaired. This repair is performed in collaboration with BRCA1, BRCA2, MRE11 nuclease, and tyrosyl-DNA phosphodiesterase 2 (TDP2) with nonhomologous end joining (NHEJ) factors. This review first discusses spontaneously arising DSBs caused by the abortive catalysis of TOP2 and then summarizes proteins involved in repairing stalled TOP2ccs and discusses the genotoxicity of the sex hormones.
Collapse
|
18
|
Urekar C, Acharya KK, Chhabra P, Reddi PP. A 50-bp enhancer of the mouse acrosomal vesicle protein 1 gene activates round spermatid-specific transcription in vivo†. Biol Reprod 2019; 101:842-853. [PMID: 31290539 PMCID: PMC6863968 DOI: 10.1093/biolre/ioz115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/04/2019] [Accepted: 07/03/2019] [Indexed: 11/12/2022] Open
Abstract
Enhancers are cis-elements that activate transcription and play critical roles in tissue- and cell type-specific gene expression. During spermatogenesis, genes coding for specialized sperm structures are expressed in a developmental stage- and cell type-specific manner, but the enhancers responsible for their expression have not been identified. Using the mouse acrosomal vesicle protein (Acrv1) gene that codes for the acrosomal protein SP-10 as a model, our previous studies have shown that Acrv1 proximal promoter activates transcription in spermatids; and the goal of the present study was to separate the enhancer responsible. Transgenic mice showed that three copies of the -186/-135 fragment (50 bp enhancer) placed upstream of the Acrv1 core promoter (-91/+28) activated reporter expression in testis but not somatic tissues (n = 4). Immunohistochemistry showed that enhancer activity was restricted to the round spermatids. The Acrv1 enhancer failed to activate transcription in the context of a heterologous core promoter (n = 4), indicating a likely requirement for enhancer-core promoter compatibility. Chromatin accessibility assays showed that the Acrv1 enhancer assumes a nucleosome-free state in male germ cells (but not liver), indicating occupancy by transcription factors. Southwestern assays (SWA) identified specific binding of the enhancer to a testis nuclear protein of 47 kDa (TNP47). TNP47 was predominantly nuclear and becomes abundant during the haploid phase of spermatogenesis. Two-dimensional SWA revealed the isoelectric point of TNP47 to be 5.2. Taken together, this study delineated a 50-bp enhancer of the Acrv1 gene for round spermatid-specific transcription and identified a putative cognate factor. The 50-bp enhancer could become useful for delivery of proteins into spermatids.
Collapse
Affiliation(s)
- Craig Urekar
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Kshitish K Acharya
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Preeti Chhabra
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Prabhakara P Reddi
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana Champaign, Champaign, Illinois, USA
| |
Collapse
|
19
|
Luo D, Kato D, Nogami J, Ohkawa Y, Kurumizaka H, Kono H. MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast. Nucleic Acids Res 2019; 46:7124-7137. [PMID: 29893974 PMCID: PMC6101533 DOI: 10.1093/nar/gky502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/30/2018] [Indexed: 01/06/2023] Open
Abstract
The first nucleosomes in the downstream of transcription starting sites are called +1 nucleosomes, which are expected to be readily unwrapped for DNA transcription. To investigate DNA accessibility in +1 nucleosomes, MNase-seq experiments were carried out with 20 reconstituted +1 nucleosomes of budding yeast. Although MNase has been known for its sequence preference in DNA digestions, we confirmed that this sequence preference is overwhelmed by DNA accessibility by identifying the sequence-driven and accessibility-driven cleavages. Specifically, we find that sequences favoured by MNase at the end regions such as TA dinucleotide are prohibited from cleavage at the internal sites in the early stage of digestion. Nevertheless, sequences less favoured by MNase at the end regions such as AA/TT dinucleotide are predominantly cleaved at the internal sites in the early stage of digestion. Since AA/TT is known as a rigid dinucleotide step resistant to DNA bending, these internal cleavages reflect the local site exposures induced by DNA mechanics. As the DNA entry site of +1 nucleosomes in yeast is found AA/TT-rich, this sequence element may play a role in gene activation by reducing DNA–histone affinities along the direction of DNA transcription.
Collapse
Affiliation(s)
- Di Luo
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| | - Daiki Kato
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Department of Quantum Beam Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto 619-0215, Japan
| |
Collapse
|
20
|
Scheidegger A, Dunn CJ, Samarakkody A, Koney NKK, Perley D, Saha RN, Nechaev S. Genome-wide RNA pol II initiation and pausing in neural progenitors of the rat. BMC Genomics 2019; 20:477. [PMID: 31185909 PMCID: PMC6558777 DOI: 10.1186/s12864-019-5829-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/23/2019] [Indexed: 12/29/2022] Open
Abstract
Background Global RNA sequencing technologies have revealed widespread RNA polymerase II (Pol II) transcription outside of gene promoters. Small 5′-capped RNA sequencing (Start-seq) originally developed for the detection of promoter-proximal Pol II pausing has helped improve annotation of Transcription Start Sites (TSSs) of genes as well as identification of non-genic regulatory elements. However, apart from the most well studied genomes of human and mouse, mammalian transcription has not been profiled with sufficiently high precision. Results We prepared and sequenced Start-seq libraries from rat (Rattus norgevicus) primary neural progenitor cells. Over 48 million uniquely mappable reads from two independent biological replicates allowed us to define the TSSs of 7365 known genes in the rn6 genome, reannotating 2503 TSSs by more than 5 base pairs, characterize promoter-associated antisense transcription, and profile Pol II pausing. By combining TSS data with polyA-selected RNA sequencing, we also identified thousands of potential new genes producing stable RNA as well as non-genic transcripts representing possible regulatory elements. Conclusions Our study has produced the first Start-seq dataset for the rat. Apart from profiling transcription initiation, our data reaffirm the prevalence of Pol II pausing across the rat genome and indicate conservation of pausing mechanisms across metazoan genomes. We suggest that pausing location, at least in mammals, is constrained by a distance from initiation of transcription, whether it occurs at or outside of a gene promoter. Abundant antisense transcription initiation around protein coding genes indicates that Pol II recruited to the vicinity of a promoter is distributed to available start sites of transcription at either DNA strand. Transcriptome profiling of neural progenitors presented here will facilitate further studies of other rat cell types as well as other organisms. Electronic supplementary material The online version of this article (10.1186/s12864-019-5829-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Adam Scheidegger
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.,Present address: Omega Therapeutics, Cambridge, MA, 02139, USA
| | - Carissa J Dunn
- Molecular and Cell Biology Department, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Ann Samarakkody
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.,Present address: Department of Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Nii Koney-Kwaku Koney
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Danielle Perley
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA
| | - Ramendra N Saha
- Molecular and Cell Biology Department, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, 58202, USA.
| |
Collapse
|
21
|
Taylor R, Long J, Yoon JW, Childs R, Sylvestersen KB, Nielsen ML, Leong KF, Iannaccone S, Walterhouse DO, Robbins DJ, Iannaccone P. Regulation of GLI1 by cis DNA elements and epigenetic marks. DNA Repair (Amst) 2019; 79:10-21. [PMID: 31085420 PMCID: PMC6570425 DOI: 10.1016/j.dnarep.2019.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022]
Abstract
GLI1 is one of three transcription factors (GLI1, GLI2 and GLI3) that mediate the Hedgehog signal transduction pathway and play important roles in normal development. GLI1 and GLI2 form a positive-feedback loop and function as human oncogenes. The mouse and human GLI1 genes have untranslated 5′ exons and large introns 5′ of the translational start. Here we show that Sonic Hedgehog (SHH) stimulates occupancy in the introns by H3K27ac, H3K4me3 and the histone reader protein BRD4. H3K27ac and H3K4me3 occupancy is not significantly changed by removing BRD4 from the human intron and transcription start site (TSS) region. We identified six GLI binding sites (GBS) in the first intron of the human GLI1 gene that are in regions of high sequence conservation among mammals. GLI1 and GLI2 bind all of the GBS in vitro. Elimination of GBS1 and 4 attenuates transcriptional activation by GLI1. Elimination of GBS1, 2, and 4 attenuates transcriptional activation by GLI2. Eliminating all sites essentially eliminates reporter gene activation. Further, GLI1 binds the histone variant H2A.Z. These results suggest that GLI1 and GLI2 can regulate GLI1 expression through protein-protein interactions involving complexes of transcription factors, histone variants, and reader proteins in the regulatory intron of the GLI1 gene. GLI1 acting in trans on the GLI1 intron provides a mechanism for GLI1 positive feedback and auto-regulation. Understanding the combinatorial protein landscape in this locus will be important to interrupting the GLI positive feedback loop and providing new therapeutic approaches to cancers associated with GLI1 overexpression.
Collapse
Affiliation(s)
- Robert Taylor
- Developmental Biology Program, Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, USA
| | - Jun Long
- The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, USA
| | - Joon Won Yoon
- Developmental Biology Program, Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, USA
| | - Ronnie Childs
- Developmental Biology Program, Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, USA
| | | | | | - King-Fu Leong
- Developmental Biology Program, Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, USA
| | - Stephen Iannaccone
- Developmental Biology Program, Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, USA
| | - David O Walterhouse
- Developmental Biology Program, Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, USA
| | - David J Robbins
- The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, USA.
| | - Philip Iannaccone
- Developmental Biology Program, Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital, Northwestern University Feinberg School of Medicine, USA.
| |
Collapse
|
22
|
Law CT, Wei L, Tsang FHC, Chan CYK, Xu IMJ, Lai RKH, Ho DWH, Lee JMF, Wong CCL, Ng IOL, Wong CM. HELLS Regulates Chromatin Remodeling and Epigenetic Silencing of Multiple Tumor Suppressor Genes in Human Hepatocellular Carcinoma. Hepatology 2019; 69:2013-2030. [PMID: 30516846 DOI: 10.1002/hep.30414] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/29/2018] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third most lethal cancer worldwide. Increasing evidence shows that epigenetic alterations play an important role in human carcinogenesis. Deregulation of DNA methylation and histone modifications have recently been characterized in HCC, but the significance of chromatin remodeling in liver carcinogenesis remains to be explored. In this study, by systematically analyzing the expression of chromatin remodeling genes in human HCCs, we found that helicase, lymphoid-specific (HELLS), an SWI2/SNF2 chromatin remodeling enzyme, was remarkably overexpressed in HCC. Overexpression of HELLS correlated with more aggressive clinicopathological features and poorer patient prognosis compared to patients with lower HELLS expression. We further showed that up-regulation of HELLS in HCC was conferred by hyperactivation of transcription factor specificity protein 1 (SP1). To investigate the functions of HELLS in HCC, we generated both gain-of-function and loss-of-function models by the CRISPR activation system, lentiviral short hairpin RNA, and the CRISPR/Cas9 genome editing system. We demonstrated that overexpression of HELLS augmented HCC cell proliferation and migration. In contrast, depletion of HELLS reduced HCC growth and metastasis both in vitro and in vivo. Moreover, inactivation of HELLS led to metabolic reprogramming and reversed the Warburg effect in HCC cells. Mechanistically, by integrating analysis of RNA sequencing and micrococcal nuclease sequencing, we revealed that overexpression of HELLS increased nucleosome occupancy, which obstructed the accessibility of enhancers and hindered formation of the nucleosome-free region (NFR) at the transcription start site. Though this mechanism, up-regulation of HELLS mediated epigenetic silencing of multiple tumor suppressor genes including E-cadherin, FBP1, IGFBP3, XAF1 and CREB3L3 in HCC. Conclusion: Our data reveal that HELLS is a key epigenetic driver of HCC; by altering the nucleosome occupancy at the NFR and enhancer, HELLS epigenetically suppresses multiple tumor suppressor genes to promote HCC progression.
Collapse
MESH Headings
- Animals
- Antigens, CD/metabolism
- Cadherins/metabolism
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/etiology
- Cell Line, Tumor
- Chromatin Assembly and Disassembly
- DNA Helicases/genetics
- DNA Helicases/metabolism
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Humans
- Liver Neoplasms, Experimental/enzymology
- Liver Neoplasms, Experimental/etiology
- Mice, Knockout
- Mice, Nude
- Neoplasm Metastasis
- Nucleosomes/metabolism
- Sp1 Transcription Factor/metabolism
Collapse
Affiliation(s)
- Cheuk-Ting Law
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Lai Wei
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
- The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - Felice Ho-Ching Tsang
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
- The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - Cerise Yuen-Ki Chan
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Iris Ming-Jing Xu
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Robin Kit-Ho Lai
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Joyce Man-Fong Lee
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Carmen Chak-Lui Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Chun-Ming Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
- The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| |
Collapse
|
23
|
Shao W, Alcantara SGM, Zeitlinger J. Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing. eLife 2019; 8:41461. [PMID: 31021316 PMCID: PMC6483594 DOI: 10.7554/elife.41461] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 04/04/2019] [Indexed: 12/11/2022] Open
Abstract
RNA polymerase II (Pol II) pausing is a general regulatory step in transcription, yet the stability of paused Pol II varies widely between genes. Although paused Pol II stability correlates with core promoter elements, the contribution of individual sequences remains unclear, in part because no rapid assay is available for measuring the changes in Pol II pausing as a result of altered promoter sequences. Here, we overcome this hurdle by showing that ChIP-nexus captures the endogenous Pol II pausing on transfected plasmids. Using this reporter-ChIP-nexus assay in Drosophila cells, we show that the pausing stability is influenced by downstream promoter sequences, but that the strongest contribution to Pol II pausing comes from the initiator sequence, in which a single nucleotide, a G at the +2 position, is critical for stable Pol II pausing. These results establish reporter-ChIP-nexus as a valuable tool to analyze Pol II pausing.
Collapse
Affiliation(s)
- Wanqing Shao
- Stowers Institute for Medical Research, Kansas City, United States
| | | | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, United States.,Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, United States
| |
Collapse
|
24
|
Jeronimo C, Robert F. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription. Trends Cell Biol 2017; 27:765-783. [DOI: 10.1016/j.tcb.2017.07.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/15/2022]
|
25
|
García A, González S, Antequera F. Nucleosomal organization and DNA base composition patterns. Nucleus 2017. [PMID: 28635365 PMCID: PMC5703254 DOI: 10.1080/19491034.2017.1337611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Nucleosomes are the basic units of chromatin. They compact the genome inside the nucleus and regulate the access of proteins to DNA. In the yeast genome, most nucleosomes occupy well-defined positions, which are maintained under many different physiological situations and genetic backgrounds. Although several short sequence elements have been described that favor or reduce the affinity between histones and DNA, the extent to which the DNA sequence affects nucleosome positioning in the genomic context remains unclear. Recent analyses indicate that the base composition pattern of mononucleosomal DNA differs among species, and that the same sequence elements have a different impact on nucleosome positioning in different genomes despite the high level of phylogenetic conservation of histones. These studies have also shown that the DNA sequence contributes to nucleosome positioning to the point that it is possible to design synthetic DNA molecules capable of generating regular and species-specific nucleosomal patterns in vivo.
Collapse
Affiliation(s)
- Alicia García
- a Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca , Salamanca , Spain
| | - Sara González
- a Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca , Salamanca , Spain
| | - Francisco Antequera
- a Instituto de Biología Funcional y Genómica, Consejo Superior de Investigaciones Científicas (CSIC)/Universidad de Salamanca , Salamanca , Spain
| |
Collapse
|
26
|
Histone Hypervariants H2A.Z.1 and H2A.Z.2 Play Independent and Context-Specific Roles in Neuronal Activity-Induced Transcription of Arc/Arg3.1 and Other Immediate Early Genes. eNeuro 2017; 4:eN-NWR-0040-17. [PMID: 28856239 PMCID: PMC5569379 DOI: 10.1523/eneuro.0040-17.2017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 12/21/2022] Open
Abstract
The histone variant H2A.Z is an essential and conserved regulator of eukaryotic gene transcription. However, the exact role of this histone in the transcriptional process remains perplexing. In vertebrates, H2A.Z has two hypervariants, H2A.Z.1 and H2A.Z.2, that have almost identical sequences except for three amino acid residues. Due to such similarity, functional specificity of these hypervariants in neurobiological processes, if any, remain largely unknown. In this study with dissociated rat cortical neurons, we asked if H2A.Z hypervariants have distinct functions in regulating basal and activity-induced gene transcription. Hypervariant-specific RNAi and microarray analyses revealed that H2A.Z.1 and H2A.Z.2 regulate basal expression of largely nonoverlapping gene sets, including genes that code for several synaptic proteins. In response to neuronal activity, rapid transcription of our model gene Arc is impaired by depletion of H2A.Z.2, but not H2A.Z.1. This impairment is partially rescued by codepletion of the H2A.Z chaperone, ANP32E. In contrast, under a different context (after 48 h of tetrodotoxin, TTX), rapid transcription of Arc is impaired by depletion of either hypervariant. Such context-dependent roles of H2A.Z hypervariants, as revealed by our multiplexed gene expression assays, are also evident with several other immediate early genes, where regulatory roles of these hypervariants vary from gene to gene under different conditions. Together, our data suggest that H2A.Z hypervariants have context-specific roles that complement each other to mediate activity-induced neuronal gene transcription.
Collapse
|
27
|
Helbo AS, Lay FD, Jones PA, Liang G, Grønbæk K. Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters. Sci Rep 2017; 7:41947. [PMID: 28176797 PMCID: PMC5296907 DOI: 10.1038/srep41947] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/03/2017] [Indexed: 12/20/2022] Open
Abstract
Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.
Collapse
Affiliation(s)
- Alexandra Søgaard Helbo
- Department of Hematology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Fides D Lay
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA
| | - Peter A Jones
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA.,Van Andel Research Institute, Grand Rapids, 49503, USA
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2100, Denmark
| |
Collapse
|
28
|
Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A. Using RNA as Molecular Code for Programming Cellular Function. ACS Synth Biol 2016; 5:795-809. [PMID: 26999422 DOI: 10.1021/acssynbio.5b00297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
Collapse
Affiliation(s)
- Manish Kushwaha
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - William Rostain
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| | - Satya Prakash
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - John N. Duncan
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| |
Collapse
|
29
|
McKnight RA, Yost CC, Zinkhan EK, Fu Q, Callaway CW, Fung CM. Intrauterine growth restriction inhibits expression of eukaryotic elongation factor 2 kinase, a regulator of protein translation. Physiol Genomics 2016; 48:616-25. [PMID: 27317589 DOI: 10.1152/physiolgenomics.00045.2016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/14/2016] [Indexed: 11/22/2022] Open
Abstract
Nutrient deprivation suppresses protein synthesis by blocking peptide elongation. Transcriptional upregulation and activation of eukaryotic elongation factor 2 kinase (eEF2K) blocks peptide elongation by phosphorylating eukaryotic elongation factor 2. Previous studies examining placentas from intrauterine growth restricted (IUGR) newborn infants show decreased eEF2K expression and activity despite chronic nutrient deprivation. However, the effect of IUGR on hepatic eEF2K expression in the fetus is unknown. We, therefore, examined the transcriptional regulation of hepatic eEF2K gene expression in a Sprague-Dawley rat model of IUGR. We found decreased hepatic eEF2K mRNA and protein levels in IUGR offspring at birth compared with control, consistent with previous placental observations. Furthermore, the CpG island within the eEF2K promoter demonstrated increased methylation at a critical USF 1/2 transcription factor binding site. In vitro methylation of this binding site caused near complete loss of eEF2K promoter activity, designating this promoter as methylation sensitive. The eEF2K promotor in IUGR offspring also lost the protective histone covalent modifications associated with unmethylated CGIs. In addition, the +1 nucleosome was displaced 3' and RNA polymerase loading was reduced at the IUGR eEF2K promoter. Our findings provide evidence to explain why IUGR-induced chronic nutrient deprivation does not result in the upregulation of eEF2K gene transcription.
Collapse
Affiliation(s)
- Robert A McKnight
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Christian C Yost
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Erin K Zinkhan
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Qi Fu
- Division of Neonatology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Christopher W Callaway
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| | - Camille M Fung
- Division of Neonatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah; and
| |
Collapse
|
30
|
Vos SM, Pöllmann D, Caizzi L, Hofmann KB, Rombaut P, Zimniak T, Herzog F, Cramer P. Architecture and RNA binding of the human negative elongation factor. eLife 2016; 5. [PMID: 27282391 PMCID: PMC4940160 DOI: 10.7554/elife.14981] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/09/2016] [Indexed: 11/30/2022] Open
Abstract
Transcription regulation in metazoans often involves promoter-proximal pausing of RNA polymerase (Pol) II, which requires the 4-subunit negative elongation factor (NELF). Here we discern the functional architecture of human NELF through X-ray crystallography, protein crosslinking, biochemical assays, and RNA crosslinking in cells. We identify a NELF core subcomplex formed by conserved regions in subunits NELF-A and NELF-C, and resolve its crystal structure. The NELF-AC subcomplex binds single-stranded nucleic acids in vitro, and NELF-C associates with RNA in vivo. A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo. These results reveal the three-dimensional architecture and three RNA-binding faces of NELF. DOI:http://dx.doi.org/10.7554/eLife.14981.001
Collapse
Affiliation(s)
- Seychelle M Vos
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - David Pöllmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Katharina B Hofmann
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Pascaline Rombaut
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tomasz Zimniak
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Franz Herzog
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| |
Collapse
|
31
|
Jimeno-González S, Reyes JC. Chromatin structure and pre-mRNA processing work together. Transcription 2016; 7:63-8. [PMID: 27028548 PMCID: PMC4984687 DOI: 10.1080/21541264.2016.1168507] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022] Open
Abstract
Chromatin is the natural context for transcription elongation. However, the elongating RNA polymerase II (RNAPII) is forced to pause by the positioned nucleosomes present in gene bodies. Here, we briefly discuss the current results suggesting that those pauses could serve as a mechanism to coordinate transcription elongation with pre-mRNA processing. Further, histone post-translational modifications have been found to regulate the recruitment of factors involved in pre-mRNA processing. This view highlights the important regulatory role of the chromatin context in the whole process of the mature mRNA synthesis.
Collapse
Affiliation(s)
- Silvia Jimeno-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| | - José C. Reyes
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC), Seville, Spain
| |
Collapse
|
32
|
Prado F, Jimeno-González S, Reyes JC. Histone availability as a strategy to control gene expression. RNA Biol 2016; 14:281-286. [PMID: 27211514 DOI: 10.1080/15476286.2016.1189071] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Histone proteins are main structural components of the chromatin and major determinants of gene regulation. Expression of canonical histone genes is strictly controlled during the cell cycle in order to couple DNA replication with histone deposition. Indeed, reductions in the levels of canonical histones or defects in chromatin assembly cause genetic instability. Early data from yeast demonstrated that severe histone depletion also causes strong gene expression changes. We have recently reported that a moderated depletion of canonical histones in human cells leads to an open chromatin configuration, which in turn increases RNA polymerase II elongation rates and causes pre-mRNA splicing defects. Interestingly, some of the observed defects accompany the scheduled histone depletion that is associated with several senescence and aging processes. Thus, our comparison of induced and naturally-occurring histone depletion processes suggests that a programmed reduction of the level of canonical histones might be a strategy to control gene expression during specific physiological processes.
Collapse
Affiliation(s)
- Félix Prado
- a Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC) , Seville , Spain
| | - Silvia Jimeno-González
- a Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC) , Seville , Spain
| | - José C Reyes
- a Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), Consejo Superior de Investigaciones Científicas (CSIC) , Seville , Spain
| |
Collapse
|
33
|
Bunch H. Role of genome guardian proteins in transcriptional elongation. FEBS Lett 2016; 590:1064-75. [PMID: 27010360 DOI: 10.1002/1873-3468.12152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
Abstract
Maintaining genomic integrity is vital for cell survival and homeostasis. Mutations in critical genes in germ-line and somatic cells are often implicated with the onset or progression of diseases. DNA repair enzymes thus take important roles as guardians of the genome in the cell. Besides the known function to repair DNA damage, recent findings indicate that DNA repair enzymes regulate the transcription of protein-coding and noncoding RNA genes. In particular, a novel role of DNA damage response signaling has been identified in the regulation of transcriptional elongation. Topoisomerases-mediated DNA breaks appear important for the regulation. In this review, recent findings of these DNA break- and repair-associated enzymes in transcription and potential roles of transcriptional activation-coupled DNA breaks are discussed.
Collapse
Affiliation(s)
- Heeyoun Bunch
- Department of Genetics and Complex Diseases, Harvard School of Public Health, Boston, MA, USA
| |
Collapse
|
34
|
Parmar JJ, Das D, Padinhateeri R. Theoretical estimates of exposure timescales of protein binding sites on DNA regulated by nucleosome kinetics. Nucleic Acids Res 2016; 44:1630-41. [PMID: 26553807 PMCID: PMC4770213 DOI: 10.1093/nar/gkv1153] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 09/29/2015] [Accepted: 10/19/2015] [Indexed: 12/14/2022] Open
Abstract
It is being increasingly realized that nucleosome organization on DNA crucially regulates DNA-protein interactions and the resulting gene expression. While the spatial character of the nucleosome positioning on DNA has been experimentally and theoretically studied extensively, the temporal character is poorly understood. Accounting for ATPase activity and DNA-sequence effects on nucleosome kinetics, we develop a theoretical method to estimate the time of continuous exposure of binding sites of non-histone proteins (e.g. transcription factors and TATA binding proteins) along any genome. Applying the method to Saccharomyces cerevisiae, we show that the exposure timescales are determined by cooperative dynamics of multiple nucleosomes, and their behavior is often different from expectations based on static nucleosome occupancy. Examining exposure times in the promoters of GAL1 and PHO5, we show that our theoretical predictions are consistent with known experiments. We apply our method genome-wide and discover huge gene-to-gene variability of mean exposure times of TATA boxes and patches adjacent to TSS (+1 nucleosome region); the resulting timescale distributions have non-exponential tails.
Collapse
Affiliation(s)
- Jyotsana J Parmar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dibyendu Das
- Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| |
Collapse
|
35
|
Liu H, Wang P, Liu L, Min Z, Luo K, Wan Y. Nucleosome alterations caused by mutations at modifiable histone residues in Saccharomyces cerevisiae. Sci Rep 2015; 5:15583. [PMID: 26498326 PMCID: PMC4620441 DOI: 10.1038/srep15583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 09/28/2015] [Indexed: 01/13/2023] Open
Abstract
Nucleosome organization exhibits dynamic properties depending on the cell state and environment. Histone proteins, fundamental components of nucleosomes, are subject to chemical modifications on particular residues. We examined the effect of substituting modifiable residues of four core histones with the non-modifiable residue alanine on nucleosome dynamics. We mapped the genome-wide nucleosomes in 22 histone mutants of Saccharomyces cerevisiae and compared the nucleosome alterations relative to the wild-type strain. Our results indicated that different types of histone mutation resulted in different phenotypes and a distinct reorganization of nucleosomes. Nucleosome occupancy was altered at telomeres, but not at centromeres. The first nucleosomes upstream (−1) and downstream (+1) of the transcription start site (TSS) were more dynamic than other nucleosomes. Mutations in histones affected the nucleosome array downstream of the TSS. Highly expressed genes, such as ribosome genes and genes involved in glycolysis, showed increased nucleosome occupancy in many types of histone mutant. In particular, the H3K56A mutant exhibited a high percentage of dynamic genomic regions, decreased nucleosome occupancy at telomeres, increased occupancy at the +1 and −1 nucleosomes, and a slow growth phenotype under stress conditions. Our findings provide insight into the influence of histone mutations on nucleosome dynamics.
Collapse
Affiliation(s)
- Hongde Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Pingyan Wang
- Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Lingjie Liu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Zhu Min
- Institute of Life Sciences, Southeast University, Nanjing 210096, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kun Luo
- Department of Neurosurgery, Xinjiang Evidence-Based Medicine Research Institute, First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Yakun Wan
- Institute of Life Sciences, Southeast University, Nanjing 210096, China.,Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| |
Collapse
|
36
|
Scheidegger A, Nechaev S. RNA polymerase II pausing as a context-dependent reader of the genome. Biochem Cell Biol 2015; 94:82-92. [PMID: 26555214 DOI: 10.1139/bcb-2015-0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The RNA polymerase II (Pol II) transcribes all mRNA genes in eukaryotes and is among the most highly regulated enzymes in the cell. The classic model of mRNA gene regulation involves recruitment of the RNA polymerase to gene promoters in response to environmental signals. Higher eukaryotes have an additional ability to generate multiple cell types. This extra level of regulation enables each cell to interpret the same genome by committing to one of the many possible transcription programs and executing it in a precise and robust manner. Whereas multiple mechanisms are implicated in cell type-specific transcriptional regulation, how one genome can give rise to distinct transcriptional programs and what mechanisms activate and maintain the appropriate program in each cell remains unclear. This review focuses on the process of promoter-proximal Pol II pausing during early transcription elongation as a key step in context-dependent interpretation of the metazoan genome. We highlight aspects of promoter-proximal Pol II pausing, including its interplay with epigenetic mechanisms, that may enable cell type-specific regulation, and emphasize some of the pertinent questions that remain unanswered and open for investigation.
Collapse
Affiliation(s)
- Adam Scheidegger
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| | - Sergei Nechaev
- Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA.,Department of Basic Sciences, University of North Dakota School of Medicine, Grand Forks, ND 58201, USA
| |
Collapse
|
37
|
Chromatin, DNA structure and alternative splicing. FEBS Lett 2015; 589:3370-8. [PMID: 26296319 DOI: 10.1016/j.febslet.2015.08.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/31/2015] [Accepted: 08/04/2015] [Indexed: 02/07/2023]
Abstract
Coupling of transcription and alternative splicing via regulation of the transcriptional elongation rate is a well-studied phenomenon. Template features that act as roadblocks for the progression of RNA polymerase II comprise histone modifications and variants, DNA-interacting proteins and chromatin compaction. These may affect alternative splicing decisions by inducing pauses or decreasing elongation rate that change the time-window for splicing regulatory sequences to be recognized. Herein we discuss the evidence supporting the influence of template structural modifications on transcription and splicing, and provide insights about possible roles of non-B DNA conformations on the regulation of alternative splicing.
Collapse
|