1
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Sharma S, Kapoor S, Ansari A, Tyagi AK. The general transcription factors (GTFs) of RNA polymerase II and their roles in plant development and stress responses. Crit Rev Biochem Mol Biol 2024:1-43. [PMID: 39361782 DOI: 10.1080/10409238.2024.2408562] [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: 05/31/2024] [Revised: 09/03/2024] [Accepted: 09/21/2024] [Indexed: 10/05/2024]
Abstract
In eukaryotes, general transcription factors (GTFs) enable recruitment of RNA polymerase II (RNA Pol II) to core promoters to facilitate initiation of transcription. Extensive research in mammals and yeast has unveiled their significance in basal transcription as well as in diverse biological processes. Unlike mammals and yeast, plant GTFs exhibit remarkable degree of variability and flexibility. This is because plant GTFs and GTF subunits are often encoded by multigene families, introducing complexity to transcriptional regulation at both cellular and biological levels. This review provides insights into the general transcription mechanism, GTF composition, and their cellular functions. It further highlights the involvement of RNA Pol II-related GTFs in plant development and stress responses. Studies reveal that GTFs act as important regulators of gene expression in specific developmental processes and help equip plants with resilience against adverse environmental conditions. Their functions may be direct or mediated through their cofactor nature. The versatility of GTFs in controlling gene expression, and thereby influencing specific traits, adds to the intricate complexity inherent in the plant system.
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Affiliation(s)
- Shivam Sharma
- Inter-disciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Sanjay Kapoor
- Inter-disciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, USA
| | - Akhilesh Kumar Tyagi
- Inter-disciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, New Delhi, India
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2
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O’Brien MJ, Schrader JM, Ansari A. TFIIB-Termination Factor Interaction Affects Termination of Transcription on Genome-Wide Scale. Int J Mol Sci 2024; 25:8643. [PMID: 39201330 PMCID: PMC11354755 DOI: 10.3390/ijms25168643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Apart from its well-established role in the initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remain largely unexplored. Using GRO-seq analyses, we compared the terminator readthrough phenotype in the sua7-1 mutant (TFIIBsua7-1) and the isogenic wild type (TFIIBWT) strains. Approximately 74% of genes analyzed exhibited a 2-3-fold increase in readthrough of the poly(A)-termination signal in the TFIIBsua7-1 mutant compared to TFIIBWT cells. To understand the mechanistic basis of TFIIB's role in termination, we performed the mass spectrometry of TFIIB-affinity purified from chromatin and soluble cellular fractions-from TFIIBsua7-1 and TFIIBWT cells. TFIIB purified from the chromatin fraction of TFIIBWT cells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with CF1A and Rat1 complexes in the TFIIBsua7-1 mutant. ChIP assays revealed about a 90% decline in the recruitment of termination factors in the TFIIBsua7-1 mutant compared to wild type cells. The overall conclusion of these results is that TFIIB affects the termination of transcription on a genome-wide scale, and the TFIIB-termination factor interaction plays a crucial role in the process.
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Affiliation(s)
| | | | - Athar Ansari
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, USA; (M.J.O.); (J.M.S.)
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3
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Pessoa J, Carvalho C. Human RNA Polymerase II Segregates from Genes and Nascent RNA and Transcribes in the Presence of DNA-Bound dCas9. Int J Mol Sci 2024; 25:8411. [PMID: 39125980 PMCID: PMC11312690 DOI: 10.3390/ijms25158411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/21/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024] Open
Abstract
RNA polymerase II (Pol II) dysfunction is frequently implied in human disease. Understanding its functional mechanism is essential for designing innovative therapeutic strategies. To visualize its supra-molecular interactions with genes and nascent RNA, we generated a human cell line carrying ~335 consecutive copies of a recombinant β-globin gene. Confocal microscopy showed that Pol II was not homogeneously concentrated around these identical gene copies. Moreover, Pol II signals partially overlapped with the genes and their nascent RNA, revealing extensive compartmentalization. Using a cell line carrying a single copy of the β-globin gene, we also tested if the binding of catalytically dead CRISPR-associated system 9 (dCas9) to different gene regions affected Pol II transcriptional activity. We assessed Pol II localization and nascent RNA levels using chromatin immunoprecipitation and droplet digital reverse transcription PCR, respectively. Some enrichment of transcriptionally paused Pol II accumulated in the promoter region was detected in a strand-specific way of gRNA binding, and there was no decrease in nascent RNA levels. Pol II preserved its transcriptional activity in the presence of DNA-bound dCas9. Our findings contribute further insight into the complex mechanism of mRNA transcription in human cells.
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Affiliation(s)
- João Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal;
- Department of Medical Sciences and Institute of Biomedicine—iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, 1649-028 Lisboa, Portugal;
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4
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O'Brien MJ, Schrader J, Ansari A. Genome-wide analysis of TFIIB's role in termination of transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581640. [PMID: 38915573 PMCID: PMC11195087 DOI: 10.1101/2024.02.22.581640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Apart from its well-established role in initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remains largely unexplored. To determine the prevalence of TFIIB's role in termination, we performed GRO-seq analyses in sua7-1 mutant (TFIIB sua7-1 ) and the isogenic wild type (TFIIB WT ) strains of yeast. Almost a three-fold increase in readthrough of the poly(A)-termination signal was observed in TFIIB sua7-1 mutant compared to the TFIIB WT cells. Of all genes analyzed in this study, nearly 74% genes exhibited a statistically significant increase in terminator readthrough in the mutant. To gain an understanding of the mechanistic basis of TFIIB involvement in termination, we performed mass spectrometry of TFIIB, affinity purified from chromatin and soluble cellular fractions, from TFIIB sua7-1 and TFIIB WT cells. TFIIB purified from the chromatin fraction of TFIIB WT cells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with both CF1A and Rat1 termination complexes in TFIIB sua7-1 mutant. ChIP assay revealed that the recruitment of Pta1 subunit of CPF complex, Rna15 subunit of CF1 complex and Rat1 subunit of Rat1 complex registered nearly 90% decline in the mutant over wild type cells. The overall conclusion of these results is that TFIIB affects termination of transcription on a genome-wide scale, and TFIIB-termination factor interaction may play a crucial role in the process.
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5
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Gulyas L, Glaunsinger BA. The general transcription factor TFIIB is a target for transcriptome control during cellular stress and viral infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575933. [PMID: 38746429 PMCID: PMC11092454 DOI: 10.1101/2024.01.16.575933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Many stressors, including viral infection, induce a widespread suppression of cellular RNA polymerase II (RNAPII) transcription, yet the mechanisms underlying transcriptional repression are not well understood. Here we find that a crucial component of the RNA polymerase II holoenzyme, general transcription factor IIB (TFIIB), is targeted for post-translational turnover by two pathways, each of which contribute to its depletion during stress. Upon DNA damage, translational stress, apoptosis, or replication of the oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV), TFIIB is cleaved by activated caspase-3, leading to preferential downregulation of pro-survival genes. TFIIB is further targeted for rapid proteasome-mediated turnover by the E3 ubiquitin ligase TRIM28. KSHV counteracts proteasome-mediated turnover of TFIIB, thereby preserving a sufficient pool of TFIIB for transcription of viral genes. Thus, TFIIB may be a lynchpin for transcriptional outcomes during stress and a key target for nuclear replicating DNA viruses that rely on host transcriptional machinery. Significance Statement Transcription by RNA polymerase II (RNAPII) synthesizes all cellular protein-coding mRNA. Many cellular stressors and viral infections dampen RNAPII activity, though the processes underlying this are not fully understood. Here we describe a two-pronged degradation strategy by which cells respond to stress by depleting the abundance of the key RNAPII general transcription factor, TFIIB. We further demonstrate that an oncogenic human gammaherpesvirus antagonizes this process, retaining enough TFIIB to support its own robust viral transcription. Thus, modulation of RNAPII machinery plays a crucial role in dictating the outcome of cellular perturbation.
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6
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Kindongo O, Lieb G, Skaggs B, Dusserre Y, Vincenzetti V, Pelet S. Implication of polymerase recycling for nascent transcript quantification by live cell imaging. Yeast 2024; 41:279-294. [PMID: 38389243 DOI: 10.1002/yea.3929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/29/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
Transcription enables the production of RNA from a DNA template. Due to the highly dynamic nature of transcription, live-cell imaging methods play a crucial role in measuring the kinetics of this process. For instance, transcriptional bursts have been visualized using fluorescent phage-coat proteins that associate tightly with messenger RNA (mRNA) stem loops formed on nascent transcripts. To convert the signal emanating from a transcription site into meaningful estimates of transcription dynamics, the influence of various parameters on the measured signal must be evaluated. Here, the effect of gene length on the intensity of the transcription site focus was analyzed. Intuitively, a longer gene can support a larger number of transcribing polymerases, thus leading to an increase in the measured signal. However, measurements of transcription induced by hyper-osmotic stress responsive promoters display independence from gene length. A mathematical model of the stress-induced transcription process suggests that the formation of gene loops that favor the recycling of polymerase from the terminator to the promoter can explain the observed behavior. One experimentally validated prediction from this model is that the amount of mRNA produced from a short gene should be higher than for a long one as the density of active polymerase on the short gene will be increased by polymerase recycling. Our data suggest that this recycling contributes significantly to the expression output from a gene and that polymerase recycling is modulated by the promoter identity and the cellular state.
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Affiliation(s)
- Olivia Kindongo
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Lieb
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Benjamin Skaggs
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Yves Dusserre
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Vincent Vincenzetti
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Serge Pelet
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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Fidler E, Dwyer K, Ansari A. Ssu72: a versatile protein with functions in transcription and beyond. Front Mol Biosci 2024; 11:1332878. [PMID: 38304578 PMCID: PMC10830811 DOI: 10.3389/fmolb.2024.1332878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Eukaryotic transcription is a complex process involving a vast network of protein and RNA factors that influence gene expression. The main player in transcription is the RNA polymerase that synthesizes the RNA from the DNA template. RNA polymerase II (RNAPII) transcribes all protein coding genes and some noncoding RNAs in eukaryotic cells. The polymerase is aided by interacting partners that shuttle it along the gene for initiation, elongation and termination of transcription. One of the many factors that assist RNAPII in transcription of genes is Ssu72. It is a carboxy-terminal-domain (CTD)-phosphatase that plays pleiotropic roles in the transcription cycle. It is essential for cell viability in Saccharomyces cerevisiae, the organism in which it was discovered. The homologues of Ssu72 have been identified in humans, mice, plants, flies, and fungi thereby suggesting the evolutionarily conserved nature of the protein. Recent studies have implicated the factor beyond the confines of transcription in homeostasis and diseases.
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Affiliation(s)
| | | | - Athar Ansari
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
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8
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O'Brien MJ, Ansari A. Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140968. [PMID: 37863410 PMCID: PMC10872477 DOI: 10.1016/j.bbapap.2023.140968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Although TFIIB is widely regarded as an initiation factor, recent reports have implicated it in multiple aspects of eukaryotic transcription. To investigate the broader role of TFIIB in transcription, we performed quantitative proteomic analysis of yeast TFIIB. We purified two different populations of TFIIB; one from soluble cell lysate, which is not engaged in transcription, and the other from the chromatin fraction which yields the transcriptionally active form of the protein. TFIIB purified from the chromatin exhibits several interactions that explain its non-canonical roles in transcription. RNAPII, TFIIF and TFIIH were the only components of the preinitiation complex with a significant presence in chromatin TFIIB. A notable feature was enrichment of all subunits of CF1 and Rat1 3' end processing-termination complexes in chromatin-TFIIB preparation. Subunits of the CPF termination complex were also detected in both chromatin and soluble derived TFIIB preparations. These results may explain the presence of TFIIB at the 3' end of genes during transcription as well as its role in promoter-termination interaction.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America
| | - Athar Ansari
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America.
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9
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Carminati M, Rodríguez-Molina JB, Manav MC, Bellini D, Passmore LA. A direct interaction between CPF and RNA Pol II links RNA 3' end processing to transcription. Mol Cell 2023; 83:4461-4478.e13. [PMID: 38029752 PMCID: PMC10783616 DOI: 10.1016/j.molcel.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Transcription termination by RNA polymerase II (RNA Pol II) is linked to RNA 3' end processing by the cleavage and polyadenylation factor (CPF or CPSF). CPF contains endonuclease, poly(A) polymerase, and protein phosphatase activities, which cleave and polyadenylate pre-mRNAs and dephosphorylate RNA Pol II to control transcription. Exactly how the RNA 3' end processing machinery is coupled to transcription remains unclear. Here, we combine in vitro reconstitution, structural studies, and genome-wide analyses to show that yeast CPF physically and functionally interacts with RNA Pol II. Surprisingly, CPF-mediated dephosphorylation promotes the formation of an RNA Pol II stalk-to-stalk homodimer in vitro. This dimer is compatible with transcription but not with the binding of transcription elongation factors. Disruption of the dimerization interface in cells causes transcription defects, including altered RNA Pol II abundance on protein-coding genes, tRNA genes, and intergenic regions. We hypothesize that RNA Pol II dimerization may provide a mechanistic basis for the allosteric model of transcription termination.
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Affiliation(s)
| | | | - M Cemre Manav
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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10
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Asada R, Hirota K. Multi-Layered Regulations on the Chromatin Architectures: Establishing the Tight and Specific Responses of Fission Yeast fbp1 Gene Transcription. Biomolecules 2022; 12:1642. [PMID: 36358992 PMCID: PMC9687179 DOI: 10.3390/biom12111642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 04/08/2024] Open
Abstract
Transcriptional regulation is pivotal for all living organisms and is required for adequate response to environmental fluctuations and intercellular signaling molecules. For precise regulation of transcription, cells have evolved regulatory systems on the genome architecture, including the chromosome higher-order structure (e.g., chromatin loops), location of transcription factor (TF)-binding sequences, non-coding RNA (ncRNA) transcription, chromatin configuration (e.g., nucleosome positioning and histone modifications), and the topological state of the DNA double helix. To understand how these genome-chromatin architectures and their regulators establish tight and specific responses at the transcription stage, the fission yeast fbp1 gene has been analyzed as a model system for decades. The fission yeast fbp1 gene is tightly repressed in the presence of glucose, and this gene is induced by over three orders of magnitude upon glucose starvation with a cascade of multi-layered regulations on various levels of genome and chromatin architecture. In this review article, we summarize the multi-layered transcriptional regulatory systems revealed by the analysis of the fission yeast fbp1 gene as a model system.
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Affiliation(s)
- Ryuta Asada
- Department of Viticulture and Enology, University of California, Davis, CA 95616, USA
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji 192-0397, Tokyo, Japan
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11
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Terrone S, Valat J, Fontrodona N, Giraud G, Claude JB, Combe E, Lapendry A, Polvèche H, Ameur LB, Duvermy A, Modolo L, Bernard P, Mortreux F, Auboeuf D, Bourgeois C. RNA helicase-dependent gene looping impacts messenger RNA processing. Nucleic Acids Res 2022; 50:9226-9246. [PMID: 36039747 PMCID: PMC9458439 DOI: 10.1093/nar/gkac717] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022] Open
Abstract
DDX5 and DDX17 are DEAD-box RNA helicase paralogs which regulate several aspects of gene expression, especially transcription and splicing, through incompletely understood mechanisms. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed the large impact of these RNA helicases on splicing and revealed a widespread deregulation of 3' end processing. In silico analyses and experiments in cultured cells showed the binding and functional contribution of the genome organizing factor CTCF to chromatin sites at or near a subset of DDX5/DDX17-dependent exons that are characterized by a high GC content and a high density of RNA Polymerase II. We propose the existence of an RNA helicase-dependent relationship between CTCF and the dynamics of transcription across DNA and/or RNA structured regions, that contributes to the processing of internal and terminal exons. Moreover, local DDX5/DDX17-dependent chromatin loops spatially connect RNA helicase-regulated exons with their cognate promoter, and we provide the first direct evidence that de novo gene looping modifies alternative splicing and polyadenylation. Overall our findings uncover the impact of DDX5/DDX17-dependent chromatin folding on pre-messenger RNA processing.
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Affiliation(s)
| | | | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Jean-Baptiste Claude
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Hélène Polvèche
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France,CECS/AFM, I-STEM, 28 rue Henri Desbruères, F-91100, Corbeil-Essonnes, France
| | - Lamya Ben Ameur
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Arnaud Duvermy
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Laurent Modolo
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Pascal Bernard
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Cyril F Bourgeois
- To whom correspondence should be addressed. Tel: +33 47272 8663; Fax: +33 47272 8674;
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12
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Santana JF, Collins GS, Parida M, Luse DS, Price D. Differential dependencies of human RNA polymerase II promoters on TBP, TAF1, TFIIB and XPB. Nucleic Acids Res 2022; 50:9127-9148. [PMID: 35947745 PMCID: PMC9458433 DOI: 10.1093/nar/gkac678] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
The effects of rapid acute depletion of components of RNA polymerase II (Pol II) general transcription factors (GTFs) that are thought to be critical for formation of preinitiation complexes (PICs) and initiation in vitro were quantified in HAP1 cells using precision nuclear run-on sequencing (PRO-Seq). The average dependencies for each factor across >70 000 promoters varied widely even though levels of depletions were similar. Some of the effects could be attributed to the presence or absence of core promoter elements such as the upstream TBP-specificity motif or downstream G-rich sequences, but some dependencies anti-correlated with such sequences. While depletion of TBP had a large effect on most Pol III promoters only a small fraction of Pol II promoters were similarly affected. TFIIB depletion had the largest general effect on Pol II and also correlated with apparent termination defects downstream of genes. Our results demonstrate that promoter activity is combinatorially influenced by recruitment of TFIID and sequence-specific transcription factors. They also suggest that interaction of the preinitiation complex (PIC) with nucleosomes can affect activity and that recruitment of TFIID containing TBP only plays a positive role at a subset of promoters.
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Affiliation(s)
- Juan F Santana
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Geoffrey S Collins
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Mrutyunjaya Parida
- Department of Biochemistry and Molecular Biology, The University of Iowa, Iowa City, IA 52242, USA
| | - Donal S Luse
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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13
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Leidescher S, Ribisel J, Ullrich S, Feodorova Y, Hildebrand E, Galitsyna A, Bultmann S, Link S, Thanisch K, Mulholland C, Dekker J, Leonhardt H, Mirny L, Solovei I. Spatial organization of transcribed eukaryotic genes. Nat Cell Biol 2022; 24:327-339. [PMID: 35177821 DOI: 10.1038/s41556-022-00847-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
Abstract
Despite the well-established role of nuclear organization in the regulation of gene expression, little is known about the reverse: how transcription shapes the spatial organization of the genome. Owing to the small sizes of most previously studied genes and the limited resolution of microscopy, the structure and spatial arrangement of a single transcribed gene are still poorly understood. Here we study several long highly expressed genes and demonstrate that they form open-ended transcription loops with polymerases moving along the loops and carrying nascent RNAs. Transcription loops can span across micrometres, resembling lampbrush loops and polytene puffs. The extension and shape of transcription loops suggest their intrinsic stiffness, which we attribute to decoration with multiple voluminous nascent ribonucleoproteins. Our data contradict the model of transcription factories and suggest that although microscopically resolvable transcription loops are specific for long highly expressed genes, the mechanisms underlying their formation could represent a general aspect of eukaryotic transcription.
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Affiliation(s)
- Susanne Leidescher
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Johannes Ribisel
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Simon Ullrich
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Yana Feodorova
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Department of Medical Biology, Medical University of Plovdiv; Division of Molecular and Regenerative Medicine, Research Institute at Medical University of Plovdiv, Plovdiv, Bulgaria
| | - Erica Hildebrand
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Sebastian Bultmann
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Stephanie Link
- BioMedizinisches Center, Ludwig-Maximilians University Munich, Planegg-Martinsried, Germany
| | - Katharina Thanisch
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.,Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christopher Mulholland
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Heinrich Leonhardt
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany
| | - Leonid Mirny
- Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Irina Solovei
- Department of Biology II, Biozentrum, Ludwig-Maximilians University Munich (LMU), Planegg-Martinsried, Germany.
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14
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Kim HS, Jeon Y, Jang YO, Lee H, Shin Y, Lee CW. Mammalian Ssu72 phosphatase preferentially considers tissue-specific actively transcribed gene expression by regulating RNA Pol II transcription. Theranostics 2022; 12:186-206. [PMID: 34987641 PMCID: PMC8690912 DOI: 10.7150/thno.62274] [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] [Received: 05/03/2021] [Accepted: 10/26/2021] [Indexed: 11/12/2022] Open
Abstract
Reversible phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) is essential for gene expression control. How altering the phosphorylation of the CTD contributes to gene expression in mammalian systems remains poorly understood. Methods: Primary mouse embryonic fibroblasts, hepatocytes, and embryonic stem cells were isolated from conditional Ssu72f/f mice. To knockout the mouse Ssu72 gene, we infected the cells with adenoviruses of incorporated luciferase and Cre recombinase, respectively. RNA sequencing, ChIP sequencing, ChIP assay, immunoblot analyses, qRT-PCR assay, and immunostaining were performed to gain insights into the functional mechanisms of Ssu72 loss in Pol II dynamics. Results: Using primary cells isolated from Ssu72 conditional knockout and transgenic mice, we found that mammalian Ssu72-mediated transcriptional elongation rather than polyadenylation or RNA processing contributed to the transcriptional regulation of various genes. Depletion of Ssu72 resulted in aberrant Pol II pausing and elongation defects. Reduced transcriptional elongation efficiency tended to preferentially affect expression levels of actively transcribed genes in a tissue-specific manner. Furthermore, Ssu72 CTD phosphatase seemed to regulate the phosphorylation levels of CTD Ser2 and Thr4 through accurate modulation of P-TEFb activity and recruitment. Conclusions: Our findings demonstrate that mammalian Ssu72 contributes to the transcription of tissue-specific actively transcribed gene expression by regulating reciprocal phosphorylation of Pol II CTD.
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15
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Beyond the canonical role of TFIIB in eukaryotic transcription. Curr Genet 2021; 68:61-67. [PMID: 34797379 PMCID: PMC8602988 DOI: 10.1007/s00294-021-01223-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/06/2023]
Abstract
The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies demonstrating binding of TFIIB to both the 5’ and 3’ ends of genes in a diverse set of eukaryotes strongly suggested a rather unexpected role of the factor in termination. TFIIB indeed plays a role in termination of transcription. TFIIB occupancy of the 3’ end is possibly due to its interaction with the termination factors residing there. Interaction of the promoter-bound TFIIB with factors occupying the 3’ end of a gene may be the basis of transcription-dependent gene looping. The proximity of the terminator-bound factors with the promoter in a gene loop has the potential to terminate promoter-initiated upstream anti-sense transcription thereby conferring promoter directionality. TFIIB, therefore, is emerging as a factor with pleiotropic roles in the transcription cycle. This could be the reason for preferential targeting of TFIIB by viruses. Further studies are needed to understand the critical role of TFIIB in viral pathogenesis in the context of its newly identified roles in termination, gene looping and promoter directionality.
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16
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Peck Justice SA, McCracken NA, Victorino JF, Qi GD, Wijeratne AB, Mosley AL. Boosting Detection of Low-Abundance Proteins in Thermal Proteome Profiling Experiments by Addition of an Isobaric Trigger Channel to TMT Multiplexes. Anal Chem 2021; 93:7000-7010. [PMID: 33908254 PMCID: PMC8153406 DOI: 10.1021/acs.analchem.1c00012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
The study of low-abundance
proteins is a challenge to discovery-based
proteomics. Mass spectrometry (MS) applications, such as thermal proteome
profiling (TPP), face specific challenges in the detection of the
whole proteome as a consequence of the use of nondenaturing extraction
buffers. TPP is a powerful method for the study of protein thermal
stability, but quantitative accuracy is highly dependent on consistent
detection. Therefore, TPP can be limited in its amenability to study
low-abundance proteins that tend to have stochastic or poor detection
by MS. To address this challenge, we incorporated an affinity-purified
protein complex sample at submolar concentrations as an isobaric trigger
channel into a mutant TPP (mTPP) workflow to provide reproducible
detection and quantitation of the low-abundance subunits of the cleavage
and polyadenylation factor (CPF) complex. The inclusion of an isobaric
protein complex trigger channel increased detection an average of
40× for previously detected subunits and facilitated detection
of CPF subunits that were previously below the limit of detection.
Importantly, these gains in CPF detection did not cause large changes
in melt temperature (Tm) calculations
for other unrelated proteins in the samples, with a high positive
correlation between Tm estimates in samples
with and without isobaric trigger channel addition. Overall, the incorporation
of an affinity-purified protein complex as an isobaric trigger channel
within a tandem mass tag (TMT) multiplex for mTPP experiments is an
effective and reproducible way to gather thermal profiling data on
proteins that are not readily detected using the original TPP or mTPP
protocols.
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Affiliation(s)
- Sarah A Peck Justice
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Neil A McCracken
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - José F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Guihong D Qi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Aruna B Wijeratne
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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17
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Hwang S, Kim MH, Lee CW. Ssu72 Dual-Specific Protein Phosphatase: From Gene to Diseases. Int J Mol Sci 2021; 22:3791. [PMID: 33917542 PMCID: PMC8038829 DOI: 10.3390/ijms22073791] [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: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 12/22/2022] Open
Abstract
More than 70% of eukaryotic proteins are regulated by phosphorylation. However, the mechanism of dephosphorylation that counteracts phosphorylation is less studied. Phosphatases are classified into 104 distinct groups based on substrate-specific features and the sequence homologies in their catalytic domains. Among them, dual-specificity phosphatases (DUSPs) that dephosphorylate both phosphoserine/threonine and phosphotyrosine are important for cellular homeostasis. Ssu72 is a newly studied phosphatase with dual specificity that can dephosphorylate both phosphoserine/threonine and phosphotyrosine. It is important for cell-growth signaling, metabolism, and immune activation. Ssu72 was initially identified as a phosphatase for the Ser5 and Ser7 residues of the C-terminal domain of RNA polymerase II. It prefers the cis configuration of the serine-proline motif within its substrate and regulates Pin1, different from other phosphatases. It has recently been reported that Ssu72 can regulate sister chromatid cohesion and the separation of duplicated chromosomes during the cell cycle. Furthermore, Ssu72 appears to be involved in the regulation of T cell receptor signaling, telomere regulation, and even hepatocyte homeostasis in response to a variety of stress and damage signals. In this review, we aim to summarize various functions of the Ssu72 phosphatase, their implications in diseases, and potential therapeutic indications.
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Affiliation(s)
- Soeun Hwang
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (S.H.); (M.-H.K.)
| | - Min-Hee Kim
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (S.H.); (M.-H.K.)
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Korea; (S.H.); (M.-H.K.)
- SKKU Institute for Convergence, Sungkyunkwan University, Suwon 16419, Korea
- Curogen Technology, Suwon 16419, Korea
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18
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Qiu L, Wang X, Zhuang G, Ouyang X, Huang X. Chromosomal Looping-Based Expression Activation System in Yeast. SMALL METHODS 2021; 5:e2001135. [PMID: 34927829 DOI: 10.1002/smtd.202001135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/04/2021] [Indexed: 06/14/2023]
Abstract
There is growing evidence that 3D genome organization is a universal and significant mechanism of gene expression regulation. Tools to manipulate long-range DNA interactions can advance the accurate control of chromosomal architecture. However, simple eukaryotic systems available to engineer chromosomal looping and gene expression are very limited. This study has developed a tool designated as chromosomal looping-based expression activation system in yeast (CLEASY). Based on a modified yeast chromosome, it consists of conditionally interacting proteins, distal transcriptional regulatory elements, and a reporter gene. Exogenous chemical or light exposure induces the protein interaction, and results in the proximity of distal regulatory elements bound by these interacting proteins, and ultimately activates the reporter gene. In addition to this controllable induction, this system is compatible with the bivalent Cas9 complexes and their guide RNAs, to ensure target specificity and variability. Therefore, CLEASY can be utilized as a simplified eukaryotic model to engineer DNA looping machinery, and potentially serves as a fast platform to investigate looping mechanism and effective molecules.
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Affiliation(s)
- Leilei Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xiaoying Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Gui Zhuang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
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19
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Chromatin modifiers and recombination factors promote a telomere fold-back structure, that is lost during replicative senescence. PLoS Genet 2020; 16:e1008603. [PMID: 33370275 PMCID: PMC7793543 DOI: 10.1371/journal.pgen.1008603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 01/08/2021] [Accepted: 11/03/2020] [Indexed: 12/27/2022] Open
Abstract
Telomeres have the ability to adopt a lariat conformation and hence, engage in long and short distance intra-chromosome interactions. Budding yeast telomeres were proposed to fold back into subtelomeric regions, but a robust assay to quantitatively characterize this structure has been lacking. Therefore, it is not well understood how the interactions between telomeres and non-telomeric regions are established and regulated. We employ a telomere chromosome conformation capture (Telo-3C) approach to directly analyze telomere folding and its maintenance in S. cerevisiae. We identify the histone modifiers Sir2, Sin3 and Set2 as critical regulators for telomere folding, which suggests that a distinct telomeric chromatin environment is a major requirement for the folding of yeast telomeres. We demonstrate that telomeres are not folded when cells enter replicative senescence, which occurs independently of short telomere length. Indeed, Sir2, Sin3 and Set2 protein levels are decreased during senescence and their absence may thereby prevent telomere folding. Additionally, we show that the homologous recombination machinery, including the Rad51 and Rad52 proteins, as well as the checkpoint component Rad53 are essential for establishing the telomere fold-back structure. This study outlines a method to interrogate telomere-subtelomere interactions at a single unmodified yeast telomere. Using this method, we provide insights into how the spatial arrangement of the chromosome end structure is established and demonstrate that telomere folding is compromised throughout replicative senescence.
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20
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Liu C, Zhang W, Xing W. Diverse and conserved roles of the protein Ssu72 in eukaryotes: from yeast to higher organisms. Curr Genet 2020; 67:195-206. [PMID: 33244642 DOI: 10.1007/s00294-020-01132-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 01/21/2023]
Abstract
Gene transcription is a complex biological process that involves a set of factors, enzymes and nucleotides. Ssu72 plays a crucial role in every step of gene transcription. RNA polymerase II (RNAPII) occupies an important position in the synthesis of mRNAs. The largest subunit of RNAPII, Rpb1, harbors its C-terminal domain (CTD), which participates in the initiation, elongation and termination of transcription. The CTD consists of heptad repeats of the consensus motif Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 and is highly conserved among different species. The CTD is flexible in structure and undergoes conformational changes in response to serine phosphorylation and proline isomerization, which are regulated by specific kinases/phosphatases and isomerases, respectively. Ssu72 is a CTD phosphatase with catalytic activity against phosphorylated Ser5 and Ser7. The isomerization of Pro6 affects the binding of Ssu72 to its substrate. Ssu72 can also indirectly change the phosphorylation status of Ser2. In addition, Ssu72 is a member of the 3'-end cleavage and polyadenylation factor (CPF) complex. Together with other CPF components, Ssu72 regulates the 3'-end processing of premature mRNA. Recent studies have revealed other roles of Ssu72, including its roles in balancing phosphate homeostasis and controlling chromosome behaviors, which should be further explored. In conclusion, the protein Ssu72 is an enzyme worthy of attention, not confined to its role in gene transcription.
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Affiliation(s)
- Changfu Liu
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Weihao Zhang
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Wenge Xing
- Department of Interventional Treatment, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.
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21
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Al-Husini N, Medler S, Ansari A. Crosstalk of promoter and terminator during RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194657. [PMID: 33246184 DOI: 10.1016/j.bbagrm.2020.194657] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
The transcription cycle of RNAPII is comprised of three consecutive steps; initiation, elongation and termination. It has been assumed that the initiation and termination steps occur in spatial isolation, essentially as independent events. A growing body of evidence, however, has challenged this dogma. First, factors involved in initiation and termination exhibit both a genetic and a physical interaction during transcription. Second, the initiation and termination factors have been found to occupy both ends of a transcribing gene. Third, physical interaction of initiation and termination factors occupying distal ends of a gene sometime results in the entire terminator region of a genes looping back and contact its cognate promoter, thereby forming a looped gene architecture during transcription. A logical interpretation of these findings is that the initiation and termination steps of transcription do not occur in isolation. There is extensive communication of factors occupying promoter and terminator ends of a gene during transcription cycle. This review entails a discussion of the promoter-terminator crosstalk and its implication in the context of transcription.
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Affiliation(s)
- Nadra Al-Husini
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Scott Medler
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America.
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22
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Gagliardi D, Manavella PA. Short-range regulatory chromatin loops in plants. THE NEW PHYTOLOGIST 2020; 228:466-471. [PMID: 32353900 DOI: 10.1111/nph.16632] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
In all eukaryotic organisms, gene expression correlates with the condensation state of the chromatin. Highly packed genome regions, known as heterochromatins, are associated with repressed loci, whereas euchromatic regions represent a relaxed state of the chromatin actively transcribed. However, even in these active regions, associations between chromatin domains dynamically modify genome topology and alter gene expression. Long-range interaction within and between chromosomes determines chromatin domains that help to coordinate transcriptional events. On the other hand, short-range chromatin interactions emerged as dynamic mechanisms regulating the expression of specific loci. Our current capacity to decipher genome topology at high resolution allowed us to identify numerous cases of short-range regulatory chromatin interactions, which are reviewed in this Insight article.
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Affiliation(s)
- Delfina Gagliardi
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
| | - Pablo A Manavella
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Universidad Nacional del Litoral, 3000, Santa Fe, Argentina
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23
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Tellier M, Maudlin I, Murphy S. Transcription and splicing: A two-way street. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1593. [PMID: 32128990 DOI: 10.1002/wrna.1593] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 12/18/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022]
Abstract
RNA synthesis by RNA polymerase II and RNA processing are closely coupled during the transcription cycle of protein-coding genes. This coupling affords opportunities for quality control and regulation of gene expression and the effects can go in both directions. For example, polymerase speed can affect splice site selection and splicing can increase transcription and affect the chromatin landscape. Here we review the many ways that transcription and splicing influence one another, including how splicing "talks back" to transcription. We will also place the connections between transcription and splicing in the context of other RNA processing events that define the exons that will make up the final mRNA. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Isabella Maudlin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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24
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LaBella ML, Hujber EJ, Moore KA, Rawson RL, Merrill SA, Allaire PD, Ailion M, Hollien J, Bastiani MJ, Jorgensen EM. Casein Kinase 1δ Stabilizes Mature Axons by Inhibiting Transcription Termination of Ankyrin. Dev Cell 2020; 52:88-103.e18. [PMID: 31910362 DOI: 10.1016/j.devcel.2019.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 01/19/2023]
Abstract
After axon outgrowth and synapse formation, the nervous system transitions to a stable architecture. In C. elegans, this transition is marked by the appearance of casein kinase 1δ (CK1δ) in the nucleus. In CK1δ mutants, neurons continue to sprout growth cones into adulthood, leading to a highly ramified nervous system. Nervous system architecture in these mutants is completely restored by suppressor mutations in ten genes involved in transcription termination. CK1δ prevents termination by phosphorylating and inhibiting SSUP-72. SSUP-72 would normally remodel the C-terminal domain of RNA polymerase in anticipation of termination. The antitermination activity of CK1δ establishes the mature state of a neuron by promoting the expression of the long isoform of a single gene, the cytoskeleton protein Ankyrin.
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Affiliation(s)
- Matthew L LaBella
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Edward J Hujber
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Kristin A Moore
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Randi L Rawson
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Sean A Merrill
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Patrick D Allaire
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Julie Hollien
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | | | - Erik M Jorgensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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25
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Calvo O. RNA polymerase II phosphorylation and gene looping: new roles for the Rpb4/7 heterodimer in regulating gene expression. Curr Genet 2020; 66:927-937. [PMID: 32508001 DOI: 10.1007/s00294-020-01084-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/22/2022]
Abstract
In eukaryotes, cellular RNAs are produced by three nuclear RNA polymerases (RNAPI, II, and III), which are multisubunit complexes. They share structural and functional features, although they are specialized in the synthesis of specific RNAs. RNAPII transcribes the vast majority of cellular RNAs, including mRNAs and a large number of noncoding RNAs. The structure of RNAPII is highly conserved in all eukaryotes, consisting of 12 subunits (Rpb1-12) organized into five structural modules, among which the Rpb4 and Rpb7 subunits form the stalk. Early studies suggested an accessory role for Rpb4, because is required for specific gene transcription pathways. Far from this initial hypothesis, it is now well established that the Rpb4/7 heterodimer plays much wider roles in gene expression regulation. It participates in nuclear and cytosolic processes ranging from transcription to translation and mRNA degradation in a cyclical process. For this reason, Rpb4/7 is considered a coordinator of gene expression. New functions have been added to the list of stalk functions during transcription, which will be reviewed herein: first, a role in the maintenance of proper RNAPII phosphorylation levels, and second, a role in the establishment of a looped gene architecture in actively transcribed genes.
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Affiliation(s)
- Olga Calvo
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-USAL, C/ Zacarías González 2, Salamanca, 37007, España.
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26
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Campbell M, Izumiya Y. PAN RNA: transcriptional exhaust from a viral engine. J Biomed Sci 2020; 27:41. [PMID: 32143650 PMCID: PMC7060532 DOI: 10.1186/s12929-020-00637-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV), also designated human herpesvirus 8 (HHV-8), has been linked to Kaposi’s sarcoma, as well as to primary effusion lymphoma (PEL), and a subset of multicentric Castleman’s disease. KSHV genomes are maintained as episomes within infected cells and the virus exhibits a biphasic life cycle consisting of a life-long latent phase during which only a few viral genes are expressed and no viral progeny are produced and a transient lytic reactivation phase, in which a full repertoire of ~ 80 lytic genes are activated in a temporally regulated manner culminating in the release of new virions. Lytic replication is initiated by a single viral protein, K-Rta (ORF50), which activates more than 80 viral genes from multiple resident viral episomes (i.e., viral chromosomes). One of the major targets of K-Rta is a long non-coding nuclear RNA, PAN RNA (polyadenylated nuclear RNA), a lncRNA that accumulates to exceedingly high levels in the nucleus during viral reactivation. K-Rta directly binds to the PAN RNA promoter and robustly activates PAN RNA expression. Although PAN RNA has been known for over 20 years, its role in viral replication is still incompletely understood. In this perspective, we will briefly review the current understanding of PAN RNA and then describe our current working model of this RNA. The model is based on our observations concerning events that occur during KSHV lytic reactivation including (i) a marked accumulation of RNA Pol II at the PAN promoter, (ii) genomic looping emanating from the PAN locus, (iii) interaction of a second viral lytic protein (ORF57) with K-Rta, PAN RNA and RNA Pol II, (iv) the essential requirement for PAN RNA expression in cis for optimal transcriptional execution needed for the entire lytic program, and (v) ORF57 recruitment of RNA Pol II to the PAN genomic locus. Together our results generate a model in which the PAN locus serves as a hub for sequestration/trapping of the cellular transcriptional machinery proximal to viral episomes. Sequestration at the PAN locus facilitates high levels of viral transcription throughout the viral genome during lytic replication. ORF57 acts as a transcription-dependent transactivator at the PAN locus by binding to both Rta and PAN to locally trap RNA Pol II. The resulting accumulation of high levels of nuclear PAN RNA created by this process is an inducible enhancer-derived (eRNA) by-product that litters the infected cell nucleus.
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Affiliation(s)
- Mel Campbell
- Department of Dermatology and UC Davis Comprehensive Cancer Center, University of California Davis School of Medicine, 4645 2nd Avenue Research III Room 3100, Sacramento, CA, 95817, USA.
| | - Yoshihiro Izumiya
- Department of Dermatology and UC Davis Comprehensive Cancer Center, University of California Davis School of Medicine, 4645 2nd Avenue Research III Room 3100, Sacramento, CA, 95817, USA.
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27
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Allepuz-Fuster P, O'Brien MJ, González-Polo N, Pereira B, Dhoondia Z, Ansari A, Calvo O. RNA polymerase II plays an active role in the formation of gene loops through the Rpb4 subunit. Nucleic Acids Res 2019; 47:8975-8987. [PMID: 31304538 PMCID: PMC6753479 DOI: 10.1093/nar/gkz597] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 01/19/2023] Open
Abstract
Gene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in the rpb4Δ mutant. In contrast to the other looping-defective mutants, rpb4Δ cells do not exhibit a transcription termination defect. RPB4 overexpression, however, rescued the transcription termination and gene looping defect of sua7-1, a mutant of TFIIB. Furthermore, RPB4 overexpression rescued the ssu72-2 gene looping defect, while SSU72 overexpression restored the formation of gene loops in rpb4Δ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised in rpb4Δ cells. These results suggest that the TFIIB-Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB-Ssu72 mediated gene looping.
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Affiliation(s)
| | - Michael J O'Brien
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | | | - Bianca Pereira
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | - Zuzer Dhoondia
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | - Athar Ansari
- Department of Biological Science. Wayne State University. Detroit, MI 48202, USA
| | - Olga Calvo
- Instituto de Biología Funcional y Genómica, CSIC-USAL, Salamanca, Spain
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28
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Legrand N, Bretscher CL, Zielke S, Wilke B, Daude M, Fritz B, Diederich WE, Adhikary T. PPARβ/δ recruits NCOR and regulates transcription reinitiation of ANGPTL4. Nucleic Acids Res 2019; 47:9573-9591. [PMID: 31428774 PMCID: PMC6765110 DOI: 10.1093/nar/gkz685] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/20/2019] [Accepted: 07/28/2019] [Indexed: 12/24/2022] Open
Abstract
In the absence of ligands, the nuclear receptor PPARβ/δ recruits the NCOR and SMRT corepressors, which form complexes with HDAC3, to canonical target genes. Agonistic ligands cause dissociation of corepressors and enable enhanced transcription. Vice versa, synthetic inverse agonists augment corepressor recruitment and repression. Both basal repression of the target gene ANGPTL4 and reinforced repression elicited by inverse agonists are partially insensitive to HDAC inhibition. This raises the question how PPARβ/δ represses transcription mechanistically. We show that the PPARβ/δ inverse agonist PT-S264 impairs transcription initiation by decreasing recruitment of activating Mediator subunits, RNA polymerase II, and TFIIB, but not of TFIIA, to the ANGPTL4 promoter. Mass spectrometry identifies NCOR as the main PT-S264-dependent interactor of PPARβ/δ. Reconstitution of knockout cells with PPARβ/δ mutants deficient in basal repression results in diminished recruitment of NCOR, SMRT, and HDAC3 to PPAR target genes, while occupancy by RNA polymerase II is increased. PT-S264 restores binding of NCOR, SMRT, and HDAC3 to the mutants, resulting in reduced polymerase II occupancy. Our findings corroborate deacetylase-dependent and -independent repressive functions of HDAC3-containing complexes, which act in parallel to downregulate transcription.
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Affiliation(s)
- Nathalie Legrand
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Clemens L Bretscher
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Svenja Zielke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Bernhard Wilke
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Michael Daude
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Barbara Fritz
- Centre for Human Genetics, Universitätsklinikum Giessen und Marburg GmbH, Baldingerstrasse, 35043 Marburg, Germany
| | - Wibke E Diederich
- Core Facility Medicinal Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Pharmacy, Institute for Pharmaceutical Chemistry, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Till Adhikary
- Department of Medicine, Institute for Molecular Biology and Tumour Research, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany.,Department of Medicine, Institute for Medical Bioinformatics and Biostatistics, Centre for Tumour Biology and Immunology, Philipps University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
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29
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Chromosome conformation capture that detects novel cis- and trans-interactions in budding yeast. Methods 2019; 170:4-16. [PMID: 31252061 DOI: 10.1016/j.ymeth.2019.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/17/2019] [Accepted: 06/21/2019] [Indexed: 11/22/2022] Open
Abstract
Chromosome Conformation Capture (3C) has emerged as a powerful approach for revealing the conformation and features of three-dimensional (3D) genomic organization. Yet attainment of higher resolution in organisms with compact genomes presents a challenge. Here, we describe modifications in the 3C technique that substantially enhance its resolution and sensitivity when applied to the 3D genome of budding yeast. Keys to our approach include use of a 4 bp cutter, Taq I, for cleaving the genome and quantitative PCR for measuring the frequency of ligation. Most importantly, we normalize the percent digestion at each restriction site to account for variation in accessibility of local chromatin structure under a given physiological condition. This strategy has led to the detection of physical interactions between regulatory elements and gene coding regions as well as intricate, stimulus-specific interchromosomal interactions between activated genes. We provide an algorithm that incorporates these and other modifications and allows quantitative determination of chromatin interaction frequencies in yeast under any physiological condition.
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30
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Functional interaction of human Ssu72 with RNA polymerase II complexes. PLoS One 2019; 14:e0213598. [PMID: 30901332 PMCID: PMC6430399 DOI: 10.1371/journal.pone.0213598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/25/2019] [Indexed: 11/19/2022] Open
Abstract
Phosphorylation of the C-terminal domain (CTD) of the large subunit of human RNA polymerase II (Pol II) is regulated during the transcription cycle by the combined action of specific kinases and phosphatases. Pol II enters into the preinitiation complex (PIC) unphosphorylated, but is quickly phosphorylated by Cdk7 during initiation. How phosphatases alter the pattern and extent of CTD phosphorylation at this early stage of transcription is not clear. We previously demonstrated the functional association of an early-acting, magnesium-independent phosphatase with early elongation complexes. Here we show that Ssu72 is responsible for that activity. We found that the phosphatase enters the transcription cycle during the formation of PICs and that Ssu72 is physically associated with very early elongation complexes. The association of Ssu72 with elongation complexes was stable to extensive washing with up to 200 mM KCl. Interestingly, Ssu72 ceased to function on complexes that contained RNA longer than 28 nt. However, when PICs were washed before initiation, the strict cutoff at 28 nt was lost. This suggests that factor(s) are important for the specific regulation of Ssu72 function during the transition between initiation and pausing. Overall, our results demonstrate when Ssu72 can act on early transcription complexes and suggest that Ssu72 may also function in the PIC prior to initiation.
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31
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Szalaj P, Plewczynski D. Three-dimensional organization and dynamics of the genome. Cell Biol Toxicol 2018; 34:381-404. [PMID: 29568981 PMCID: PMC6133016 DOI: 10.1007/s10565-018-9428-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 03/11/2018] [Indexed: 12/30/2022]
Abstract
Genome is a complex hierarchical structure, and its spatial organization plays an important role in its function. Chromatin loops and topological domains form the basic structural units of this multiscale organization and are essential to orchestrate complex regulatory networks and transcription mechanisms. They also form higher-order structures such as chromosomal compartments and chromosome territories. Each level of this intrinsic architecture is governed by principles and mechanisms that we only start to understand. In this review, we summarize the current view of the genome architecture on the scales ranging from chromatin loops to the whole genome. We describe cell-to-cell variability, links between genome reorganization and various genomic processes, such as chromosome X inactivation and cell differentiation, and the interplay between different experimental techniques.
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Affiliation(s)
- Przemyslaw Szalaj
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland.
- I-BioStat, Hasselt University, Hasselt, Belgium.
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.
| | - Dariusz Plewczynski
- Centre for Innovative Research, Medical University of Bialystok, Białystok, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
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32
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RNA Polymerase II Transcription Attenuation at the Yeast DNA Repair Gene, DEF1, Involves Sen1-Dependent and Polyadenylation Site-Dependent Termination. G3-GENES GENOMES GENETICS 2018; 8:2043-2058. [PMID: 29686108 PMCID: PMC5982831 DOI: 10.1534/g3.118.200072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Termination of RNA Polymerase II (Pol II) activity serves a vital cellular role by separating ubiquitous transcription units and influencing RNA fate and function. In the yeast Saccharomyces cerevisiae, Pol II termination is carried out by cleavage and polyadenylation factor (CPF-CF) and Nrd1-Nab3-Sen1 (NNS) complexes, which operate primarily at mRNA and non-coding RNA genes, respectively. Premature Pol II termination (attenuation) contributes to gene regulation, but there is limited knowledge of its prevalence and biological significance. In particular, it is unclear how much crosstalk occurs between CPF-CF and NNS complexes and how Pol II attenuation is modulated during stress adaptation. In this study, we have identified an attenuator in the DEF1 DNA repair gene, which includes a portion of the 5′-untranslated region (UTR) and upstream open reading frame (ORF). Using a plasmid-based reporter gene system, we conducted a genetic screen of 14 termination mutants and their ability to confer Pol II read-through defects. The DEF1 attenuator behaved as a hybrid terminator, relying heavily on CPF-CF and Sen1 but without Nrd1 and Nab3 involvement. Our genetic selection identified 22 cis-acting point mutations that clustered into four regions, including a polyadenylation site efficiency element that genetically interacts with its cognate binding-protein Hrp1. Outside of the reporter gene context, a DEF1 attenuator mutant increased mRNA and protein expression, exacerbating the toxicity of a constitutively active Def1 protein. Overall, our data support a biologically significant role for transcription attenuation in regulating DEF1 expression, which can be modulated during the DNA damage response.
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33
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Heat Shock Protein Genes Undergo Dynamic Alteration in Their Three-Dimensional Structure and Genome Organization in Response to Thermal Stress. Mol Cell Biol 2017; 37:MCB.00292-17. [PMID: 28970326 DOI: 10.1128/mcb.00292-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/15/2017] [Indexed: 01/11/2023] Open
Abstract
Three-dimensional (3D) chromatin organization is important for proper gene regulation, yet how the genome is remodeled in response to stress is largely unknown. Here, we use a highly sensitive version of chromosome conformation capture in combination with fluorescence microscopy to investigate Heat Shock Protein (HSP) gene conformation and 3D nuclear organization in budding yeast. In response to acute thermal stress, HSP genes undergo intense intragenic folding interactions that go well beyond 5'-3' gene looping previously described for RNA polymerase II genes. These interactions include looping between upstream activation sequence (UAS) and promoter elements, promoter and terminator regions, and regulatory and coding regions (gene "crumpling"). They are also dynamic, being prominent within 60 s, peaking within 2.5 min, and attenuating within 30 min, and correlate with HSP gene transcriptional activity. With similarly striking kinetics, activated HSP genes, both chromosomally linked and unlinked, coalesce into discrete intranuclear foci. Constitutively transcribed genes also loop and crumple yet fail to coalesce. Notably, a missense mutation in transcription factor TFIIB suppresses gene looping, yet neither crumpling nor HSP gene coalescence is affected. An inactivating promoter mutation, in contrast, obviates all three. Our results provide evidence for widespread, transcription-associated gene crumpling and demonstrate the de novo assembly and disassembly of HSP gene foci.
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34
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Bratkowski M, Unarta IC, Zhu L, Shubbar M, Huang X, Liu X. Structural dissection of an interaction between transcription initiation and termination factors implicated in promoter-terminator cross-talk. J Biol Chem 2017; 293:1651-1665. [PMID: 29158257 DOI: 10.1074/jbc.m117.811521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/10/2017] [Indexed: 11/06/2022] Open
Abstract
Functional cross-talk between the promoter and terminator of a gene has long been noted. Promoters and terminators are juxtaposed to form gene loops in several organisms, and gene looping is thought to be involved in transcriptional regulation. The general transcription factor IIB (TFIIB) and the C-terminal domain phosphatase Ssu72, essential factors of the transcription preinitiation complex and the mRNA processing and polyadenylation complex, respectively, are important for gene loop formation. TFIIB and Ssu72 interact both genetically and physically, but the molecular basis of this interaction is not known. Here we present a crystal structure of the core domain of TFIIB in two new conformations that differ in the relative distance and orientation of the two cyclin-like domains. The observed extraordinary conformational plasticity may underlie the binding of TFIIB to multiple transcription factors and promoter DNAs that occurs in distinct stages of transcription, including initiation, reinitiation, and gene looping. We mapped the binding interface of the TFIIB-Ssu72 complex using a series of systematic, structure-guided in vitro binding and site-specific photocross-linking assays. Our results indicate that Ssu72 competes with acidic activators for TFIIB binding and that Ssu72 disrupts an intramolecular TFIIB complex known to impede transcription initiation. We also show that the TFIIB-binding site on Ssu72 overlaps with the binding site of symplekin, a component of the mRNA processing and polyadenylation complex. We propose a hand-off model in which Ssu72 mediates a conformational transition in TFIIB, accounting for the role of Ssu72 in transcription reinitiation, gene looping, and promoter-terminator cross-talk.
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Affiliation(s)
- Matthew Bratkowski
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and.,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
| | - Ilona Christy Unarta
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Lizhe Zhu
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Murtada Shubbar
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and.,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
| | - Xuhui Huang
- the Department of Chemistry and.,Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xin Liu
- From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, and .,the Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390 and
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35
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Asada R, Umeda M, Adachi A, Senmatsu S, Abe T, Iwasaki H, Ohta K, Hoffman CS, Hirota K. Recruitment and delivery of the fission yeast Rst2 transcription factor via a local genome structure counteracts repression by Tup1-family corepressors. Nucleic Acids Res 2017; 45:9361-9371. [PMID: 28934464 PMCID: PMC5766161 DOI: 10.1093/nar/gkx555] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/14/2017] [Indexed: 12/12/2022] Open
Abstract
Transcription factors (TFs) determine the transcription activity of target genes and play a central role in controlling the transcription in response to various environmental stresses. Three dimensional genome structures such as local loops play a fundamental role in the regulation of transcription, although the link between such structures and the regulation of TF binding to cis-regulatory elements remains to be elucidated. Here, we show that during transcriptional activation of the fission yeast fbp1 gene, binding of Rst2 (a critical C2H2 zinc-finger TF) is mediated by a local loop structure. During fbp1 activation, Rst2 is first recruited to upstream-activating sequence 1 (UAS1), then it subsequently binds to UAS2 (a critical cis-regulatory site located approximately 600 base pairs downstream of UAS1) through a loop structure that brings UAS1 and UAS2 into spatially close proximity. Tup11/12 (the Tup-family corepressors) suppress direct binding of Rst2 to UAS2, but this suppression is counteracted by the recruitment of Rst2 at UAS1 and following delivery to UAS2 through a loop structure. These data demonstrate a previously unappreciated mechanism for the recruitment and expansion of TF-DNA interactions within a promoter mediated by local three-dimensional genome structures and for timely TF-binding via counteractive regulation by the Tup-family corepressors.
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Affiliation(s)
- Ryuta Asada
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Miki Umeda
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Akira Adachi
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Satoshi Senmatsu
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Takuya Abe
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Hiroshi Iwasaki
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology M6-11, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan.,Universal Biology Institute, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | | | - Kouji Hirota
- Department of Chemistry, Graduate School of Science and Engineering, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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36
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Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation. Mol Cell Biol 2016; 36:2236-45. [PMID: 27247267 DOI: 10.1128/mcb.00870-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 05/25/2016] [Indexed: 12/12/2022] Open
Abstract
In eukaryotes, the C-terminal domain (CTD) of Rpb1 contains a heptapeptide repeat sequence of (Y1S2P3T4S5P6S7)n that undergoes reversible phosphorylation through the opposing action of kinases and phosphatases. Rtr1 is a conserved protein that colocalizes with RNA polymerase II (RNAPII) and has been shown to be important for the transition from elongation to termination during transcription by removing RNAPII CTD serine 5 phosphorylation (Ser5-P) at a selection of target genes. In this study, we show that Rtr1 is a global regulator of the CTD code with deletion of RTR1 causing genome-wide changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation (H3K36me3). Using chromatin immunoprecipitation and high-resolution microarrays, we show that RTR1 deletion results in global changes in RNAPII Ser5-P levels on genes with different lengths and transcription rates consistent with its role as a CTD phosphatase. Although Ser5-P levels increase, the overall occupancy of RNAPII either decreases or stays the same in the absence of RTR1 Additionally, the loss of Rtr1 in vivo leads to increases in H3K36me3 levels genome-wide, while total histone H3 levels remain relatively constant within coding regions. Overall, these findings suggest that Rtr1 regulates H3K36me3 levels through changes in the number of binding sites for the histone methyltransferase Set2, thereby influencing both the CTD and histone codes.
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37
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Ocampo-Hafalla M, Muñoz S, Samora CP, Uhlmann F. Evidence for cohesin sliding along budding yeast chromosomes. Open Biol 2016; 6:150178. [PMID: 27278645 PMCID: PMC4929932 DOI: 10.1098/rsob.150178] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 05/13/2016] [Indexed: 11/12/2022] Open
Abstract
The ring-shaped cohesin complex is thought to topologically hold sister chromatids together from their synthesis in S phase until chromosome segregation in mitosis. How cohesin stably binds to chromosomes for extended periods, without impeding other chromosomal processes that also require access to the DNA, is poorly understood. Budding yeast cohesin is loaded onto DNA by the Scc2-Scc4 cohesin loader at centromeres and promoters of active genes, from where cohesin translocates to more permanent places of residence at transcription termination sites. Here we show that, at the GAL2 and MET17 loci, pre-existing cohesin is pushed downstream along the DNA in response to transcriptional gene activation, apparently without need for intermittent dissociation or reloading. We observe translocation intermediates and find that the distribution of most chromosomal cohesin is shaped by transcription. Our observations support a model in which cohesin is able to slide laterally along chromosomes while maintaining topological contact with DNA. In this way, stable cohesin binding to DNA and enduring sister chromatid cohesion become compatible with simultaneous underlying chromosomal activities, including but maybe not limited to transcription.
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Affiliation(s)
- Maria Ocampo-Hafalla
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Sofía Muñoz
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Catarina P Samora
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Frank Uhlmann
- The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
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38
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Liu C, Wang C, Wang G, Becker C, Zaidem M, Weigel D. Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution. Genome Res 2016; 26:1057-68. [PMID: 27225844 PMCID: PMC4971768 DOI: 10.1101/gr.204032.116] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022]
Abstract
The three-dimensional packing of the genome plays an important role in regulating gene expression. We have used Hi-C, a genome-wide chromatin conformation capture (3C) method, to analyze Arabidopsis thaliana chromosomes dissected into subkilobase segments, which is required for gene-level resolution in this species with a gene-dense genome. We found that the repressive H3K27me3 histone mark is overrepresented in the promoter regions of genes that are in conformational linkage over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5' and 3' ends of genes, forming local chromatin loops. Such self-loop structures of genes are more likely to occur in more highly expressed genes, although they can also be found in silent genes. Silent genes with local chromatin loops are highly enriched for the histone variant H3.3 at their 5' and 3' ends but depleted of repressive marks such as heterochromatic histone modifications and DNA methylation in flanking regions. Our results suggest that, different from animals, a major theme of genome folding in A. thaliana is the formation of structural units that correspond to gene bodies.
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Affiliation(s)
- Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076 Tübingen, Germany
| | - Congmao Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Institute of Digital Agriculture, Zhejiang Academy of Agriculture Sciences, Hangzhou 310029, China
| | - George Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Maricris Zaidem
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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39
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Agarwal N, Ansari A. Enhancement of Transcription by a Splicing-Competent Intron Is Dependent on Promoter Directionality. PLoS Genet 2016; 12:e1006047. [PMID: 27152651 PMCID: PMC4859611 DOI: 10.1371/journal.pgen.1006047] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/20/2016] [Indexed: 11/23/2022] Open
Abstract
Enhancement of transcription by a splicing-competent intron is an evolutionarily conserved feature among eukaryotes. The molecular mechanism underlying the phenomenon, however, is not entirely clear. Here we show that the intron is an important regulator of promoter directionality. Employing strand-specific transcription run-on (TRO) analysis, we show that the transcription of mRNA is favored over the upstream anti-sense transcripts (uaRNA) initiating from the promoter in the presence of an intron. Mutation of either the 5′ or 3′ splice site resulted in the reversal of promoter directionality, thereby suggesting that it is not merely the 5′ splice site but the entire splicing-competent intron that regulates transcription directionality. ChIP analysis revealed the recruitment of termination factors near the promoter region in the presence of an intron. Removal of intron or the mutation of splice sites adversely affected the promoter localization of termination factors. We have earlier demonstrated that the intron-mediated enhancement of transcription is dependent on gene looping. Here we show that gene looping is crucial for the recruitment of termination factors in the promoter-proximal region of an intron-containing gene. In a looping-defective mutant, despite normal splicing, the promoter occupancy of factors required for poly(A)-dependent termination of transcription was compromised. This was accompanied by a concomitant loss of transcription directionality. On the basis of these results, we propose that the intron-dependent gene looping places the terminator-bound factors in the vicinity of the promoter region for termination of the promoter-initiated upstream antisense transcription, thereby conferring promoter directionality. Eukaryotic genes differ from their prokaryotic counterparts in having intervening non-coding sequences called introns. The precise biological role of introns in eukaryotic systems remains unclear even more than forty years after their initial discovery. One function of intron that has been remarkably conserved during evolution is their ability to enhance the transcription of genes that harbor them. How does the intron regulate transcription, however, is not known. Here we show that the intron enhances gene expression by affecting direction of the promoter-initiated transcription. In the presence of an intron, polymerase tends to transcribe the downstream coding region producing mRNA, while in the absence of a splicing-competent intron polymerase starts transcribing promoter upstream region producing upstream antisense RNA (uaRNA). Intron-mediated promoter directionality was dependent on gene looping, which is the interaction off the promoter and terminator region of a gene in a transcription-dependent manner. We show that the intron-dependent gene looping facilitates the recruitment of termination factors in the promoter-proximal region. The recruited termination factors stop uaRNA synthesis thereby conferring directionality to the promoter-bound polymerase.
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Affiliation(s)
- Neha Agarwal
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
| | - Athar Ansari
- Department of Biological Sciences, Wayne State University, Detroit, Michigan, United States of America
- * E-mail:
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Abstract
InDrosophila, homologous chromosome pairing leads to "transvection," in which the enhancer of a gene can regulate the allelic transcription intrans.Interallelic interactions were also observed in vegetative diploid budding yeast, but their functional significance is unknown. Here, we show that aGAL1reporter can interact with its homologous allele and affect its expression. By ectopically inserting two allelic reporters, one driven by wild-typeGAL1promoter (WTGAL1pr) and the other by a mutant promoter with delayed response to galactose induction, we found that the two reporters physically associate, and the WTGAL1prtriggers synchronized firing of the defective promoter and accelerates its activation without affecting its steady-state expression level. This interaction and the transregulatory effect disappear when the same reporters are located at nonallelic sites. We further demonstrated that the activator Gal4 is essential for the interallelic interaction, and the transregulation requires fully activated WTGAL1prtranscription. The mechanism of this phenomenon was further discussed. Taken together, our data revealed the existence of interallelic gene regulation in yeast, which serves as a starting point for understanding long-distance gene regulation in this genetically tractable system.
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Lamas-Maceiras M, Singh BN, Hampsey M, Freire-Picos MA. Promoter-Terminator Gene Loops Affect Alternative 3'-End Processing in Yeast. J Biol Chem 2016; 291:8960-8. [PMID: 26929407 DOI: 10.1074/jbc.m115.687491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Indexed: 11/06/2022] Open
Abstract
Many eukaryotic genes undergo alternative 3'-end poly(A)-site selection producing transcript isoforms with 3'-UTRs of different lengths and post-transcriptional fates. Gene loops are dynamic structures that juxtapose the 3'-ends of genes with their promoters. Several functions have been attributed to looping, including memory of recent transcriptional activity and polarity of transcription initiation. In this study, we investigated the relationship between gene loops and alternative poly(A)-site. Using the KlCYC1 gene of the yeast Kluyveromyces lactis, which includes a single promoter and two poly(A) sites separated by 394 nucleotides, we demonstrate in two yeast species the formation of alternative gene loops (L1 and L2) that juxtapose the KlCYC1 promoter with either proximal or distal 3'-end processing sites, resulting in the synthesis of short and long forms of KlCYC1 mRNA. Furthermore, synthesis of short and long mRNAs and formation of the L1 and L2 loops are growth phase-dependent. Chromatin immunoprecipitation experiments revealed that the Ssu72 RNA polymerase II carboxyl-terminal domain phosphatase, a critical determinant of looping, peaks in early log phase at the proximal poly(A) site, but as growth phase advances, it extends to the distal site. These results define a cause-and-effect relationship between gene loops and alternative poly(A) site selection that responds to different physiological signals manifested by RNA polymerase II carboxyl-terminal domain phosphorylation status.
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Affiliation(s)
- Mónica Lamas-Maceiras
- From the Departamento de Biología Celular e Molecular, Facultad de Ciencias, Universidade da Coruña, Campus de A Coruña, Rúa da Fraga 10, 15008 A Coruña, Spain and
| | - Badri Nath Singh
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Michael Hampsey
- the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - María A Freire-Picos
- From the Departamento de Biología Celular e Molecular, Facultad de Ciencias, Universidade da Coruña, Campus de A Coruña, Rúa da Fraga 10, 15008 A Coruña, Spain and
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Regulation of miR-200c/141 expression by intergenic DNA-looping and transcriptional read-through. Nat Commun 2016; 7:8959. [PMID: 26725650 PMCID: PMC4727242 DOI: 10.1038/ncomms9959] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/21/2015] [Indexed: 02/07/2023] Open
Abstract
The miR-200 family members have been implicated in stress responses and ovarian tumorigenesis. Here, we find that miR-200c/141 transcription is intimately linked to the transcription of the proximal upstream gene PTPN6 (SHP1) in all physiological conditions tested. PTPN6 and miR-200c/141 are transcriptionally co-regulated by two complementary mechanisms. First, a bypass of the regular PTPN6 polyadenylation signal allows the transcription of the downstream miR-200c/141. Second, the promoters of the PTPN6 and miR-200c/141 transcription units physically interact through a 3-dimensional DNA loop and exhibit similar epigenetic regulation. Our findings highlight that transcription of intergenic miRNAs is a novel outcome of transcriptional read-through and reveal a yet unexplored type of DNA loop associating two closely located promoters. These mechanisms have significant relevance in ovarian cancers and stress response, pathophysiological conditions in which miR-200c/141 exert key functions. The miR-141/200 familly of micro RNAs control oxidative stress and impact on ovarian tumorigenesis. Here the authors show that the transcription of miR-200c/141 is regulated through transcriptional read-through of the upstream gene PTPN6, and DNA looping linking the PTPN6 and miR-200c/141 promoters.
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Mellor J, Woloszczuk R, Howe FS. The Interleaved Genome. Trends Genet 2016; 32:57-71. [DOI: 10.1016/j.tig.2015.10.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 09/29/2015] [Accepted: 10/23/2015] [Indexed: 12/25/2022]
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Rege M, Subramanian V, Zhu C, Hsieh THS, Weiner A, Friedman N, Clauder-Münster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep 2015; 13:1610-22. [PMID: 26586442 PMCID: PMC4662874 DOI: 10.1016/j.celrep.2015.10.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/02/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
The histone variant H2A.Z is a hallmark of nucleosomes flanking promoters of protein-coding genes and is often found in nucleosomes that carry lysine 56-acetylated histone H3 (H3-K56Ac), a mark that promotes replication-independent nucleosome turnover. Here, we find that H3-K56Ac promotes RNA polymerase II occupancy at many protein-coding and noncoding loci, yet neither H3-K56Ac nor H2A.Z has a significant impact on steady-state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on RNA levels are revealed only in the absence of the nuclear RNA exosome. H2A.Z is also necessary for the expression of divergent, promoter-proximal non-coding RNAs (ncRNAs) in mouse embryonic stem cells. Finally, we show that H2A.Z functions with H3-K56Ac to facilitate formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher-order chromatin structures.
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Affiliation(s)
- Mayuri Rege
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vidya Subramanian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chenchen Zhu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Tsung-Han S Hsieh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Assaf Weiner
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | | | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Laurie A Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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45
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Luse DS. The RNA polymerase II preinitiation complex. Through what pathway is the complex assembled? Transcription 2015; 5:e27050. [PMID: 25764109 DOI: 10.4161/trns.27050] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The general transcription factors required for the assembly of the RNA polymerase II preinitiation complex at TATA-dependent promoters are well known. However, recent studies point to two quite distinct pathways for assembly of these components into functional transcription complexes. In this review, the two pathways are compared and potential implications for gene regulatory mechanisms are discussed.
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Affiliation(s)
- Donal S Luse
- a Department of Molecular Genetics; Lerner Research Institute; Cleveland Clinic; Cleveland, OH USA
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Medler S, Ansari A. Gene looping facilitates TFIIH kinase-mediated termination of transcription. Sci Rep 2015; 5:12586. [PMID: 26286112 PMCID: PMC4541409 DOI: 10.1038/srep12586] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 06/08/2015] [Indexed: 12/14/2022] Open
Abstract
TFIIH is a general transcription factor with kinase and helicase activities. The kinase activity resides in the Kin28 subunit of TFIIH. The role of Kin28 kinase in the early steps of transcription is well established. Here we report a novel role of Kin28 in the termination of transcription. We show that RNAPII reads through a termination signal upon kinase inhibition. Furthermore, the recruitment of termination factors towards the 3′ end of a gene was compromised in the kinase mutant, thus confirming the termination defect. A concomitant decrease in crosslinking of termination factors near the 5′ end of genes was also observed in the kinase-defective mutant. Simultaneous presence of termination factors towards both the ends of a gene is indicative of gene looping; while the loss of termination factor occupancy from the distal ends suggest the abolition of a looped gene conformation. Accordingly, CCC analysis revealed that the looped architecture of genes was severely compromised in the Kin28 kinase mutant. In a looping defective sua7-1 mutant, even the enzymatically active Kin28 kinase could not rescue the termination defect. These results strongly suggest a crucial role of Kin28 kinase-dependent gene looping in the termination of transcription in budding yeast.
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Affiliation(s)
- Scott Medler
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall Detroit, MI 48202
| | - Athar Ansari
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall Detroit, MI 48202
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Chen Y, Zhang L, Estarás C, Choi SH, Moreno L, Karn J, Moresco JJ, Yates JR, Jones KA. A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. Genes Dev 2014; 28:2261-75. [PMID: 25319827 PMCID: PMC4201287 DOI: 10.1101/gad.250449.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
HIV-1 Tat stimulates transcription elongation by recruiting the P-TEFb (positive transcription elongation factor-b) (CycT1:CDK9) C-terminal domain (CTD) kinase to the HIV-1 promoter. Here we show that Tat transactivation also requires the Ssu72 CTD Ser5P (S5P)-specific phosphatase, which mediates transcription termination and intragenic looping at eukaryotic genes. Importantly, HIV-1 Tat interacts directly with Ssu72 and strongly stimulates its CTD phosphatase activity. We found that Ssu72 is essential for Tat:P-TEFb-mediated phosphorylation of the S5P-CTD in vitro. Interestingly, Ssu72 also stimulates nascent HIV-1 transcription in a phosphatase-dependent manner in vivo. Chromatin immunoprecipitation (ChIP) experiments reveal that Ssu72, like P-TEFb and AFF4, is recruited by Tat to the integrated HIV-1 proviral promoter in TNF-α signaling 2D10 T cells and leaves the elongation complex prior to the termination site. ChIP-seq (ChIP combined with deep sequencing) and GRO-seq (genome-wide nuclear run-on [GRO] combined with deep sequencing) analysis further reveals that Ssu72 predominantly colocalizes with S5P-RNAPII (RNA polymerase II) at promoters in human embryonic stem cells, with a minor peak in the terminator region. A few genes, like NANOG, also have high Ssu72 at the terminator. Ssu72 is not required for transcription at most cellular genes but has a modest effect on cotranscriptional termination. We conclude that Tat alters the cellular function of Ssu72 to stimulate viral gene expression and facilitate the early S5P-S2P transition at the integrated HIV-1 promoter.
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Affiliation(s)
- Yupeng Chen
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Lirong Zhang
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Conchi Estarás
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Seung H Choi
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Luis Moreno
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - James J Moresco
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John R Yates
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Katherine A Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
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Rosado-Lugo JD, Hampsey M. The Ssu72 phosphatase mediates the RNA polymerase II initiation-elongation transition. J Biol Chem 2014; 289:33916-26. [PMID: 25339178 DOI: 10.1074/jbc.m114.608695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transitions between the different stages of the RNAPII transcription cycle involve the recruitment and exchange of factors, including mRNA capping enzymes, elongation factors, splicing factors, 3'-end-processing complexes, and termination factors. These transitions are coordinated by the dynamic phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNAPII (Rpb1). The CTD is composed of reiterated heptapeptide repeats (Y(1)S(2)P(3)T(4)S(5)P(6)S(7)) that undergo phosphorylation and dephosphorylation as RNAPII transitions through the transcription cycle. An essential phosphatase in this process is Ssu72, which exhibits catalytic specificity for Ser(P)(5) and Ser(P)(7). Ssu72 is unique in that it is specific for Ser(P)(5) in one orientation of the CTD and for Ser(P)(7) when bound in the opposite orientation. Moreover, Ssu72 interacts with components of the initiation machinery and affects start site selection yet is an integral component of the CPF 3'-end-processing complex. Here we provide a comprehensive view of the effects of Ssu72 with respect to its Ser(P)(5) phosphatase activity. We demonstrate that Ssu72 dephosphorylates Ser(P)(5) at the initiation-elongation transition. Furthermore, Ssu72 indirectly affects the levels of Ser(P)(2) during the elongation stage of transcription but does so independent of its catalytic activity.
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Affiliation(s)
- Jesús D Rosado-Lugo
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
| | - Michael Hampsey
- From the Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, New Jersey 08854
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Mayhew D, Mitra RD. Transcription factor regulation and chromosome dynamics during pseudohyphal growth. Mol Biol Cell 2014; 25:2669-76. [PMID: 25009286 PMCID: PMC4148256 DOI: 10.1091/mbc.e14-04-0871] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A multiplexed analysis of the transcriptional regulation of yeast pseudohyphal growth recorded the binding of 28 different transcription factors with barcoded transposons. A core set of target genes is identified, and a process of DNA looping at the FLO11 locus that provides transcriptional memory for expression of the gene is described. Pseudohyphal growth is a developmental pathway seen in some strains of yeast in which cells form multicellular filaments in response to environmental stresses. We used multiplexed transposon “Calling Cards” to record the genome-wide binding patterns of 28 transcription factors (TFs) in nitrogen-starved yeast. We identified TF targets relevant for pseudohyphal growth, producing a detailed map of its regulatory network. Using tools from graph theory, we identified 14 TFs that lie at the center of this network, including Flo8, Mss11, and Mfg1, which bind as a complex. Surprisingly, the DNA-binding preferences for these key TFs were unknown. Using Calling Card data, we predicted the in vivo DNA-binding motif for the Flo8-Mss11-Mfg1 complex and validated it using a reporter assay. We found that this complex binds several important targets, including FLO11, at both their promoter and termination sequences. We demonstrated that this binding pattern is the result of DNA looping, which regulates the transcription of these targets and is stabilized by an interaction with the nuclear pore complex. This looping provides yeast cells with a transcriptional memory, enabling them more rapidly to execute the filamentous growth program when nitrogen starved if they had been previously exposed to this condition.
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Affiliation(s)
- David Mayhew
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108
| | - Robi D Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108
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Grzechnik P, Tan-Wong SM, Proudfoot NJ. Terminate and make a loop: regulation of transcriptional directionality. Trends Biochem Sci 2014; 39:319-27. [PMID: 24928762 PMCID: PMC4085477 DOI: 10.1016/j.tibs.2014.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 04/24/2014] [Accepted: 05/12/2014] [Indexed: 01/28/2023]
Abstract
Transcriptional directionality is controlled by premature transcription termination. Transcriptional directionality is enforced by gene looping. mRNA-specific termination signals and factors are required for gene looping.
Bidirectional promoters are a common feature of many eukaryotic organisms from yeast to humans. RNA Polymerase II that is recruited to this type of promoter can start transcribing in either direction using alternative DNA strands as the template. Such promiscuous transcription can lead to the synthesis of unwanted transcripts that may have negative effects on gene expression. Recent studies have identified transcription termination and gene looping as critical players in the enforcement of promoter directionality. Interestingly, both mechanisms share key components. Here, we focus on recent findings relating to the transcriptional output of bidirectional promoters.
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Affiliation(s)
- Pawel Grzechnik
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sue Mei Tan-Wong
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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