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Estell C, West S. ZC3H4/Restrictor Exerts a Stranglehold on Pervasive Transcription. J Mol Biol 2024:168707. [PMID: 39002716 DOI: 10.1016/j.jmb.2024.168707] [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: 05/14/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
The regulation of transcription by RNA polymerase II (RNAPII) underpins all cellular processes and is perturbed in thousands of diseases. In humans, RNAPII transcribes ∼20000 protein-coding genes and engages in apparently futile non-coding transcription at thousands of other sites. Despite being so ubiquitous, this transcription is usually attenuated soon after initiation and the resulting products are immediately degraded by the nuclear exosome. We and others have recently described a new complex, "Restrictor", which appears to control such unproductive transcription. Underpinned by the RNA binding protein, ZC3H4, Restrictor curtails unproductive/pervasive transcription genome-wide. Here, we discuss these recent discoveries and speculate on some of the many unknowns regarding Restrictor function and mechanism.
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Affiliation(s)
- Chris Estell
- The Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
| | - Steven West
- The Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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2
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Eaton JD, Board J, Davidson L, Estell C, West S. Human promoter directionality is determined by transcriptional initiation and the opposing activities of INTS11 and CDK9. eLife 2024; 13:RP92764. [PMID: 38976490 PMCID: PMC11230626 DOI: 10.7554/elife.92764] [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] [Indexed: 07/10/2024] Open
Abstract
RNA polymerase II (RNAPII) transcription initiates bidirectionally at many human protein-coding genes. Sense transcription usually dominates and leads to messenger RNA production, whereas antisense transcription rapidly terminates. The basis for this directionality is not fully understood. Here, we show that sense transcriptional initiation is more efficient than in the antisense direction, which establishes initial promoter directionality. After transcription begins, the opposing functions of the endonucleolytic subunit of Integrator, INTS11, and cyclin-dependent kinase 9 (CDK9) maintain directionality. Specifically, INTS11 terminates antisense transcription, whereas sense transcription is protected from INTS11-dependent attenuation by CDK9 activity. Strikingly, INTS11 attenuates transcription in both directions upon CDK9 inhibition, and the engineered recruitment of CDK9 desensitises transcription to INTS11. Therefore, the preferential initiation of sense transcription and the opposing activities of CDK9 and INTS11 explain mammalian promoter directionality.
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Affiliation(s)
- Joshua D Eaton
- The Living Systems Institute, University of ExeterExeterUnited Kingdom
| | - Jessica Board
- The Living Systems Institute, University of ExeterExeterUnited Kingdom
| | - Lee Davidson
- The Living Systems Institute, University of ExeterExeterUnited Kingdom
| | - Chris Estell
- The Living Systems Institute, University of ExeterExeterUnited Kingdom
| | - Steven West
- The Living Systems Institute, University of ExeterExeterUnited Kingdom
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3
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Gualdrini F, Rizzieri S, Polletti S, Pileri F, Zhan Y, Cuomo A, Natoli G. An integrative epigenome-based strategy for unbiased functional profiling of clinical kinase inhibitors. Mol Syst Biol 2024; 20:626-650. [PMID: 38724853 PMCID: PMC11148061 DOI: 10.1038/s44320-024-00040-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 06/05/2024] Open
Abstract
More than 500 kinases are implicated in the control of most cellular process in mammals, and deregulation of their activity is linked to cancer and inflammatory disorders. 80 clinical kinase inhibitors (CKIs) have been approved for clinical use and hundreds are in various stages of development. However, CKIs inhibit other kinases in addition to the intended target(s), causing both enhanced clinical effects and undesired side effects that are only partially predictable based on in vitro selectivity profiling. Here, we report an integrative approach grounded on the use of chromatin modifications as unbiased, information-rich readouts of the functional effects of CKIs on macrophage activation. This approach exceeded the performance of transcriptome-based approaches and allowed us to identify similarities and differences among CKIs with identical intended targets, to recognize novel CKI specificities and to pinpoint CKIs that may be repurposed to control inflammation, thus supporting the utility of this strategy to improve selection and use of CKIs in clinical settings.
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Affiliation(s)
- Francesco Gualdrini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy.
| | - Stefano Rizzieri
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Francesco Pileri
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Yinxiu Zhan
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milano, 20139, Italy.
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4
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Russo M, Gualdrini F, Vallelonga V, Prosperini E, Noberini R, Pedretti S, Borriero C, Di Chiaro P, Polletti S, Imperato G, Marenda M, Ghirardi C, Bedin F, Cuomo A, Rodighiero S, Bonaldi T, Mitro N, Ghisletti S, Natoli G. Acetyl-CoA production by Mediator-bound 2-ketoacid dehydrogenases boosts de novo histone acetylation and is regulated by nitric oxide. Mol Cell 2024; 84:967-980.e10. [PMID: 38242130 PMCID: PMC7615796 DOI: 10.1016/j.molcel.2023.12.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
Abstract
Histone-modifying enzymes depend on the availability of cofactors, with acetyl-coenzyme A (CoA) being required for histone acetyltransferase (HAT) activity. The discovery that mitochondrial acyl-CoA-producing enzymes translocate to the nucleus suggests that high concentrations of locally synthesized metabolites may impact acylation of histones and other nuclear substrates, thereby controlling gene expression. Here, we show that 2-ketoacid dehydrogenases are stably associated with the Mediator complex, thus providing a local supply of acetyl-CoA and increasing the generation of hyper-acetylated histone tails. Nitric oxide (NO), which is produced in large amounts in lipopolysaccharide-stimulated macrophages, inhibited the activity of Mediator-associated 2-ketoacid dehydrogenases. Elevation of NO levels and the disruption of Mediator complex integrity both affected de novo histone acetylation within a shared set of genomic regions. Our findings indicate that the local supply of acetyl-CoA generated by 2-ketoacid dehydrogenases bound to Mediator is required to maximize acetylation of histone tails at sites of elevated HAT activity.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Francesco Gualdrini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Veronica Vallelonga
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Pierluigi Di Chiaro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Gabriele Imperato
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Chiara Ghirardi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; Department of Hematology and Hematology-Oncology (DIPO), Università degli Studi di Milano, Milano 20122, Italy
| | - Nico Mitro
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy; DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milano 20133, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan 20139, Italy.
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5
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Russo M, Piccolo V, Polizzese D, Prosperini E, Borriero C, Polletti S, Bedin F, Marenda M, Michieletto D, Mandana GM, Rodighiero S, Cuomo A, Natoli G. Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription. Genes Dev 2023; 37:1017-1040. [PMID: 38092518 PMCID: PMC10760643 DOI: 10.1101/gad.351057.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]
Abstract
Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements. The Restrictor complex, composed of the Pol II-interacting protein WDR82 and the RNA-binding protein ZC3H4, suppresses processive transcription at thousands of extragenic sites in mammalian genomes. Restrictor-driven termination does not involve nascent RNA cleavage, and its interplay with other termination machineries is unclear. Here we show that efficient termination at Restrictor-controlled extragenic transcription units involves the recruitment of the protein phosphatase 1 (PP1) regulatory subunit PNUTS, a negative regulator of the SPT5 elongation factor, and Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent and phosphatase-dependent termination of noncoding RNAs in yeast. PNUTS and Symplekin act synergistically with, but independently from, Restrictor to dampen processive extragenic transcription. Moreover, the presence of limiting nuclear levels of Symplekin imposes a competition for its recruitment among multiple transcription termination machineries, resulting in mutual regulatory interactions. Hence, by synergizing with Restrictor, Symplekin and PNUTS enable efficient termination of processive, long-range extragenic transcription.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Danilo Polizzese
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Gaurav Madappa Mandana
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy;
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6
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Ait Said M, Bejjani F, Abdouni A, Ségéral E, Emiliani S. Premature transcription termination complex proteins PCF11 and WDR82 silence HIV-1 expression in latently infected cells. Proc Natl Acad Sci U S A 2023; 120:e2313356120. [PMID: 38015843 PMCID: PMC10710072 DOI: 10.1073/pnas.2313356120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Postintegration transcriptional silencing of HIV-1 leads to the establishment of a pool of latently infected cells. In these cells, mechanisms controlling RNA Polymerase II (RNAPII) pausing and premature transcription termination (PTT) remain to be explored. Here, we found that the cleavage and polyadenylation (CPA) factor PCF11 represses HIV-1 expression independently of the other subunits of the CPA complex or the polyadenylation signal located at the 5' LTR. We show that PCF11 interacts with the RNAPII-binding protein WDR82. Knock-down of PCF11 or WDR82 reactivated HIV-1 expression in latently infected cells. To silence HIV-1 transcription, PCF11 and WDR82 are specifically recruited at the promoter-proximal region of the provirus in an interdependent manner. Codepletion of PCF11 and WDR82 indicated that they act on the same pathway to repress HIV expression. These findings reveal PCF11/WDR82 as a PTT complex silencing HIV-1 expression in latently infected cells.
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Affiliation(s)
- Melissa Ait Said
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Fabienne Bejjani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Ahmed Abdouni
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Emmanuel Ségéral
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Stéphane Emiliani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
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7
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Polák P, Garland W, Rathore O, Schmid M, Salerno-Kochan A, Jakobsen L, Gockert M, Gerlach P, Silla T, Andersen JS, Conti E, Jensen TH. Dual agonistic and antagonistic roles of ZC3H18 provide for co-activation of distinct nuclear RNA decay pathways. Cell Rep 2023; 42:113325. [PMID: 37889751 PMCID: PMC10720265 DOI: 10.1016/j.celrep.2023.113325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/19/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The RNA exosome is a versatile ribonuclease. In the nucleoplasm of mammalian cells, it is assisted by its adaptors the nuclear exosome targeting (NEXT) complex and the poly(A) exosome targeting (PAXT) connection. Via its association with the ARS2 and ZC3H18 proteins, NEXT/exosome is recruited to capped and short unadenylated transcripts. Conversely, PAXT/exosome is considered to target longer and adenylated substrates via their poly(A) tails. Here, mutational analysis of the core PAXT component ZFC3H1 uncovers a separate branch of the PAXT pathway, which targets short adenylated RNAs and relies on a direct ARS2-ZFC3H1 interaction. We further demonstrate that similar acidic-rich short linear motifs of ZFC3H1 and ZC3H18 compete for a common ARS2 epitope. Consequently, while promoting NEXT function, ZC3H18 antagonizes PAXT activity. We suggest that this organization of RNA decay complexes provides co-activation of NEXT and PAXT at loci with abundant production of short exosome substrates.
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Affiliation(s)
- Patrik Polák
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Om Rathore
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark
| | - Maria Gockert
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Piotr Gerlach
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Toomas Silla
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, Martinsried/Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark.
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8
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Ntini E, Budach S, Vang Ørom UA, Marsico A. Genome-wide measurement of RNA dissociation from chromatin classifies transcripts by their dynamics and reveals rapid dissociation of enhancer lncRNAs. Cell Syst 2023; 14:906-922.e6. [PMID: 37857083 DOI: 10.1016/j.cels.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 05/24/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) are involved in gene expression regulation in cis. Although enriched in the cell chromatin fraction, to what degree this defines their regulatory potential remains unclear. Furthermore, the factors underlying lncRNA chromatin tethering, as well as the molecular basis of efficient lncRNA chromatin dissociation and its impact on enhancer activity and target gene expression, remain to be resolved. Here, we developed chrTT-seq, which combines the pulse-chase metabolic labeling of nascent RNA with chromatin fractionation and transient transcriptome sequencing to follow nascent RNA transcripts from their transcription on chromatin to release and allows the quantification of dissociation dynamics. By incorporating genomic, transcriptomic, and epigenetic metrics, as well as RNA-binding protein propensities, in machine learning models, we identify features that define transcript groups of different chromatin dissociation dynamics. Notably, lncRNAs transcribed from enhancers display reduced chromatin retention, suggesting that, in addition to splicing, their chromatin dissociation may shape enhancer activity.
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Affiliation(s)
- Evgenia Ntini
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Institute of Molecular Biology and Biotechnology, IMBB-FORTH, 70013 Heraklio, Greece.
| | - Stefan Budach
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany
| | - Ulf A Vang Ørom
- Aarhus University, Department of Molecular Biology and Genetics, 8000 Aarhus, Denmark
| | - Annalisa Marsico
- Max-Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Freie Universität Berlin, 14195 Berlin, Germany; Computational Health Center, Helmholtz Center Munich, Munich, Germany.
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9
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van der Laan L, Rooney K, Haghshenas S, Silva A, McConkey H, Relator R, Levy MA, Valenzuela I, Trujillano L, Lasa-Aranzasti A, Campos B, Castells N, Verberne EA, Maas S, Alders M, Mannens MMAM, van Haelst MM, Sadikovic B, Henneman P. Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature. Int J Mol Sci 2023; 24:14240. [PMID: 37762546 PMCID: PMC10531903 DOI: 10.3390/ijms241814240] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
JARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved in the regulation of histone methyltransferase complexes. JARID2 plays a role in the epigenetic machinery, and the associated syndrome has an identified DNA methylation episignature derived from sequence variants and intragenic deletions involving JARID2. For this study, our aim was to determine whether patients with larger deletions spanning beyond JARID2 present a similar DNA methylation episignature and to define the critical region involved in aberrant DNA methylation in 6p22-p24 microdeletions. We examined the DNA methylation profiles of peripheral blood from 56 control subjects, 13 patients with (likely) pathogenic JARID2 variants or patients carrying copy number variants, and three patients with JARID2 VUS variants. The analysis showed a distinct and strong differentiation between patients with (likely) pathogenic variants, both sequence and copy number, and controls. Using the identified episignature, we developed a binary model to classify patients with the JARID2-neurodevelopmental syndrome. DNA methylation analysis indicated that JARID2 is the driver gene for aberrant DNA methylation observed in 6p22-p24 microdeletions. In addition, we performed analysis of functional correlation of the JARID2 genome-wide methylation profile with the DNA methylation profiles of 56 additional neurodevelopmental disorders. To conclude, we refined the critical region for the presence of the JARID2 episignature in 6p22-p24 microdeletions and provide insight into the functional changes in the epigenome observed when regulation by JARID2 is lost.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Irene Valenzuela
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Laura Trujillano
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Berta Campos
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Neus Castells
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Eline A. Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Saskia Maas
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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10
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Estell C, Davidson L, Eaton JD, Kimura H, Gold VAM, West S. A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription. Mol Cell 2023:S1097-2765(23)00385-4. [PMID: 37329883 DOI: 10.1016/j.molcel.2023.05.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The transcriptional termination of unstable non-coding RNAs (ncRNAs) is poorly understood compared to coding transcripts. We recently identified ZC3H4-WDR82 ("restrictor") as restricting human ncRNA transcription, but how it does this is unknown. Here, we show that ZC3H4 additionally associates with ARS2 and the nuclear exosome targeting complex. The domains of ZC3H4 that contact ARS2 and WDR82 are required for ncRNA restriction, suggesting their presence in a functional complex. Consistently, ZC3H4, WDR82, and ARS2 co-transcriptionally control an overlapping population of ncRNAs. ZC3H4 is proximal to the negative elongation factor, PNUTS, which we show enables restrictor function and is required to terminate the transcription of all major RNA polymerase II transcript classes. In contrast to short ncRNAs, longer protein-coding transcription is supported by U1 snRNA, which shields transcripts from restrictor and PNUTS at hundreds of genes. These data provide important insights into the mechanism and control of transcription by restrictor and PNUTS.
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Affiliation(s)
- Chris Estell
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Lee Davidson
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Joshua D Eaton
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Hiroshi Kimura
- Cell Biology Centre, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Steven West
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom.
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11
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Rouvière JO, Salerno-Kochan A, Lykke-Andersen S, Garland W, Dou Y, Rathore O, Molska EŠ, Wu G, Schmid M, Bugai A, Jakobsen L, Žumer K, Cramer P, Andersen JS, Conti E, Jensen TH. ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts. Mol Cell 2023:S1097-2765(23)00384-2. [PMID: 37329882 DOI: 10.1016/j.molcel.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The RNA-binding ARS2 protein is centrally involved in both early RNA polymerase II (RNAPII) transcription termination and transcript decay. Despite its essential nature, the mechanisms by which ARS2 enacts these functions have remained unclear. Here, we show that a conserved basic domain of ARS2 binds a corresponding acidic-rich, short linear motif (SLiM) in the transcription restriction factor ZC3H4. This interaction recruits ZC3H4 to chromatin to elicit RNAPII termination, independent of other early termination pathways defined by the cleavage and polyadenylation (CPA) and Integrator (INT) complexes. We find that ZC3H4, in turn, forms a direct connection to the nuclear exosome targeting (NEXT) complex, hereby facilitating rapid degradation of the nascent RNA. Hence, ARS2 instructs the coupled transcription termination and degradation of the transcript onto which it is bound. This contrasts with ARS2 function at CPA-instructed termination sites where the protein exclusively partakes in RNA suppression via post-transcriptional decay.
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Affiliation(s)
- Jérôme O Rouvière
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | - Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Yuhui Dou
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Om Rathore
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Ewa Šmidová Molska
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Guifen Wu
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Andrii Bugai
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Kristina Žumer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark.
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12
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Spencley AL, Bar S, Swigut T, Flynn RA, Lee CH, Chen LF, Bassik MC, Wysocka J. Co-transcriptional genome surveillance by HUSH is coupled to termination machinery. Mol Cell 2023; 83:1623-1639.e8. [PMID: 37164018 PMCID: PMC10915761 DOI: 10.1016/j.molcel.2023.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or absence of H3K9me3. These classes are further distinguished by their transposon content and differential response to the loss of HUSH. A de novo genomic rearrangement at the Sox2 locus induces a switch from H3K9me3-independent to H3K9me3-associated HUSH targeting, resulting in silencing. We further demonstrate that HUSH interacts with the termination factor WDR82 and-via its component MPP8-with nascent RNA. HUSH accumulates at sites of high RNAPII occupancy including long exons and transcription termination sites in a manner dependent on WDR82 and CPSF. Together, our results uncover the functional diversity of HUSH targets and show that this vertebrate-specific complex exploits evolutionarily ancient transcription termination machinery for co-transcriptional chromatin targeting and genome surveillance.
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Affiliation(s)
- Andrew L Spencley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Shiran Bar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Cameron H Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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13
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Zhang W, Liu Y, Luo Y, Shu X, Pu C, Zhang B, Feng P, Xiong A, Kong Q. New insights into the role of long non-coding RNAs in osteoporosis. Eur J Pharmacol 2023; 950:175753. [PMID: 37119958 DOI: 10.1016/j.ejphar.2023.175753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/12/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023]
Abstract
Osteoporosis is a common disease in elderly individuals, and osteoporosis can easily lead to bone and hip fractures that seriously endanger the health of elderly individuals. At present, the treatment of osteoporosis is mainly anti-osteoporosis drugs, but there are side effects associated with anti-osteoporosis drugs. Therefore, it is very important to develop early diagnostic indicators and new therapeutic drugs for the prevention and treatment of osteoporosis. Long noncoding RNAs (lncRNAs), noncoding RNAs longer than 200 nucleotides, can be used as diagnostic markers for osteoporosis, and lncRNAs play an important role in the progression of osteoporosis. Many studies have shown that lncRNAs can be the target of osteoporosis. Therefore, herein, the role of lncRNAs in osteoporosis is summarized, aiming to provide some information for the prevention and treatment of osteoporosis.
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Affiliation(s)
- Weifei Zhang
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuheng Liu
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuanrui Luo
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiang Shu
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital.C.T.), Sichuan University, Chengdu, 610041, China
| | - Congmin Pu
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital.C.T.), Sichuan University, Chengdu, 610041, China
| | - Bin Zhang
- Department of Orthopedics, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital.C.T.), Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Pin Feng
- Department of Orthopedics, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital.C.T.), Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ao Xiong
- Department of Bone and Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
| | - Qingquan Kong
- Department of Orthopedics, Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Department of Orthopedics, Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital.C.T.), Orthopedic Research Institute, West China Hospital, Sichuan University, Chengdu, 610041, China.
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14
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Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. A CpG island-encoded mechanism protects genes from premature transcription termination. Nat Commun 2023; 14:726. [PMID: 36759609 PMCID: PMC9911701 DOI: 10.1038/s41467-023-36236-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
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Affiliation(s)
- Amy L Hughes
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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15
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Rodríguez-Molina JB, West S, Passmore LA. Knowing when to stop: Transcription termination on protein-coding genes by eukaryotic RNAPII. Mol Cell 2023; 83:404-415. [PMID: 36634677 PMCID: PMC7614299 DOI: 10.1016/j.molcel.2022.12.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Gene expression is controlled in a dynamic and regulated manner to allow for the consistent and steady expression of some proteins as well as the rapidly changing production of other proteins. Transcription initiation has been a major focus of study because it is highly regulated. However, termination of transcription also plays an important role in controlling gene expression. Transcription termination on protein-coding genes is intimately linked with 3' end cleavage and polyadenylation of transcripts, and it generally results in the production of a mature mRNA that is exported from the nucleus. Termination on many non-coding genes can also result in the production of a mature transcript. Termination is dynamically regulated-premature termination and transcription readthrough occur in response to a number of cellular signals, and these can have varied consequences on gene expression. Here, we review eukaryotic transcription termination by RNA polymerase II (RNAPII), focusing on protein-coding genes.
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Affiliation(s)
| | - Steven West
- The Living Systems Institute, University of Exeter, Exeter, UK.
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16
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Funk L, Su KC, Ly J, Feldman D, Singh A, Moodie B, Blainey PC, Cheeseman IM. The phenotypic landscape of essential human genes. Cell 2022; 185:4634-4653.e22. [PMID: 36347254 PMCID: PMC10482496 DOI: 10.1016/j.cell.2022.10.017] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/01/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
Understanding the basis for cellular growth, proliferation, and function requires determining the roles of essential genes in diverse cellular processes, including visualizing their contributions to cellular organization and morphology. Here, we combined pooled CRISPR-Cas9-based functional screening of 5,072 fitness-conferring genes in human HeLa cells with microscopy-based imaging of DNA, the DNA damage response, actin, and microtubules. Analysis of >31 million individual cells identified measurable phenotypes for >90% of gene knockouts, implicating gene targets in specific cellular processes. Clustering of phenotypic similarities based on hundreds of quantitative parameters further revealed co-functional genes across diverse cellular activities, providing predictions for gene functions and associations. By conducting pooled live-cell screening of ∼450,000 cell division events for 239 genes, we additionally identified diverse genes with functional contributions to chromosome segregation. Our work establishes a resource detailing the consequences of disrupting core cellular processes that represents the functional landscape of essential human genes.
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Affiliation(s)
- Luke Funk
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Harvard-MIT Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kuan-Chung Su
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jimmy Ly
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - David Feldman
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Brittania Moodie
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, 415 Main St., Cambridge, MA 02142, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA.
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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17
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Cortazar MA, Erickson B, Fong N, Pradhan SJ, Ntini E, Bentley DL. Xrn2 substrate mapping identifies torpedo loading sites and extensive premature termination of RNA pol II transcription. Genes Dev 2022; 36:1062-1078. [PMID: 36396340 PMCID: PMC9744234 DOI: 10.1101/gad.350004.122] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022]
Abstract
The exonuclease torpedo Xrn2 loads onto nascent RNA 5'-PO4 ends and chases down pol II to promote termination downstream from polyA sites. We report that Xrn2 is recruited to preinitiation complexes and "travels" to 3' ends of genes. Mapping of 5'-PO4 ends in nascent RNA identified Xrn2 loading sites stabilized by an active site mutant, Xrn2(D235A). Xrn2 loading sites are approximately two to 20 bases downstream from where CPSF73 cleaves at polyA sites and histone 3' ends. We propose that processing of all mRNA 3' ends comprises cleavage and limited 5'-3' trimming by CPSF73, followed by handoff to Xrn2. A similar handoff occurs at tRNA 3' ends, where cotranscriptional RNase Z cleavage generates novel Xrn2 substrates. Exonuclease-dead Xrn2 increased transcription in 3' flanking regions by inhibiting polyA site-dependent termination. Surprisingly, the mutant Xrn2 also rescued transcription in promoter-proximal regions to the same extent as in 3' flanking regions. eNET-seq revealed Xrn2-mediated degradation of sense and antisense nascent RNA within a few bases of the TSS, where 5'-PO4 ends may be generated by decapping or endonucleolytic cleavage. These results suggest that a major fraction of pol II complexes terminates prematurely close to the start site under normal conditions by an Xrn2-mediated torpedo mechanism.
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Affiliation(s)
- Michael A. Cortazar
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Benjamin Erickson
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Sarala J. Pradhan
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Evgenia Ntini
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology–Hellas (FORTH), Heraklion GR-70013, Greece
| | - David L. Bentley
- Department of Biochemistry and Molecular Genetics, RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
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18
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Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential. Nat Struct Mol Biol 2022; 29:613-620. [PMID: 35681023 DOI: 10.1038/s41594-022-00785-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 04/28/2022] [Indexed: 01/07/2023]
Abstract
Precise regulation of transcription by RNA polymerase II (RNAPII) is critical for organismal growth and development. However, what determines whether an engaged RNAPII will synthesize a full-length transcript or terminate prematurely is poorly understood. Notably, RNAPII is far more susceptible to termination when transcribing non-coding RNAs than when synthesizing protein-coding mRNAs, but the mechanisms underlying this are unclear. To investigate the impact of transcribed sequence on elongation potential, we developed a method to screen the effects of thousands of INtegrated Sequences on Expression of RNA and Translation using high-throughput sequencing (INSERT-seq). We found that higher AT content in non-coding RNAs, rather than specific sequence motifs, drives RNAPII termination. Further, we demonstrate that 5' splice sites autonomously stimulate processive transcription, even in the absence of polyadenylation signals. Our results reveal a potent role for the transcribed sequence in dictating gene output and demonstrate the power of INSERT-seq toward illuminating these contributions.
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19
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Park K, Zhong J, Jang JS, Kim J, Kim HJ, Lee JH, Kim J. ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters. Nucleic Acids Res 2022; 50:3835-3851. [PMID: 35325203 PMCID: PMC9023261 DOI: 10.1093/nar/gkac193] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
The human genome encodes large numbers of non-coding RNAs, including divergent antisense transcripts at transcription start sites (TSSs). However, molecular mechanisms by which divergent antisense transcription is regulated have not been detailed. Here, we report a novel ZWC complex composed of ZC3H4, WDR82 and CK2 that suppresses divergent antisense transcription. The ZWC complex preferentially localizes at TSSs of active genes through direct interactions of ZC3H4 and WDR82 subunits with the S5p RNAPII C-terminal domain. ZC3H4 depletion leads to increased divergent antisense transcription, especially at genes that naturally produce divergent antisense transcripts. We further demonstrate that the ZWC complex phosphorylates the previously uncharacterized N-terminal acidic domain of SPT5, a subunit of the transcription-elongation factor DSIF, and that this phosphorylation is responsible for suppressing divergent antisense transcription. Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation.
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Affiliation(s)
- Kihyun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jian Zhong
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hye-Jung Kim
- New Drug Development Center, OSONG Medical Innovation Foundation, Cheongju 28160, South Korea
| | - Jeong-Heon Lee
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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20
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Gualdrini F, Polletti S, Simonatto M, Prosperini E, Pileri F, Natoli G. H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats. Genes Dev 2022; 36:414-432. [PMID: 35361678 PMCID: PMC9067402 DOI: 10.1101/gad.349282.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/16/2022] [Indexed: 12/23/2022]
Abstract
Here, Gualdrini et al. found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. Their findings suggest a role for H3K9me3 in restraining genomic distribution and activity of CTCF, influencing chromatin organization and gene regulation. Six methyltransferases divide labor in establishing genomic profiles of histone H3 lysine 9 methylation (H3K9me), an epigenomic modification controlling constitutive heterochromatin, gene repression, and silencing of retroelements. Among them, SETDB1 is recruited to active chromatin domains to silence the expression of endogenous retroviruses. In the context of experiments aimed at determining the impact of SETDB1 on stimulus-inducible gene expression in macrophages, we found that loss of H3K9me3 caused by SETDB1 depletion was associated with increased recruitment of CTCF to >1600 DNA binding motifs contained within SINE B2 repeats, a previously unidentified target of SETDB1-mediated repression. CTCF is an essential regulator of chromatin folding that restrains DNA looping by cohesin, thus creating boundaries among adjacent topological domains. Increased CTCF binding to SINE B2 repeats enhanced insulation at hundreds of sites and increased loop formation within topological domains containing lipopolysaccharide-inducible genes, which correlated with their impaired regulation in response to stimulation. These data indicate a role of H3K9me3 in restraining genomic distribution and activity of CTCF, with an impact on chromatin organization and gene regulation.
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Affiliation(s)
- Francesco Gualdrini
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Sara Polletti
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Marta Simonatto
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Elena Prosperini
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Francesco Pileri
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
| | - Gioacchino Natoli
- European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan 20139, Italy
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21
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Control of non-productive RNA polymerase II transcription via its early termination in metazoans. Biochem Soc Trans 2022; 50:283-295. [PMID: 35166324 DOI: 10.1042/bst20201140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Transcription establishes the universal first step of gene expression where RNA is produced by a DNA-dependent RNA polymerase. The most versatile of eukaryotic RNA polymerases, RNA polymerase II (Pol II), transcribes a broad range of DNA including protein-coding and a variety of non-coding transcription units. Although Pol II can be configured as a durable enzyme capable of transcribing hundreds of kilobases, there is reliable evidence of widespread abortive Pol II transcription termination shortly after initiation, which is often followed by rapid degradation of the associated RNA. The molecular details underlying this phenomenon are still vague but likely reflect the action of quality control mechanisms on the early Pol II complex. Here, we summarize current knowledge of how and when such promoter-proximal quality control is asserted on metazoan Pol II.
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22
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Sergeeva OV, Shcherbinina EY, Shomron N, Zatsepin TS. Modulation of RNA Splicing by Oligonucleotides: Mechanisms of Action and Therapeutic Implications. Nucleic Acid Ther 2022; 32:123-138. [PMID: 35166605 DOI: 10.1089/nat.2021.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Dysregulation of RNA splicing causes many diseases and disorders. Several therapeutic approaches have been developed to correct aberrant alternative splicing events for the treatment of cancers and hereditary diseases, including gene therapy and redirecting splicing, using small molecules or splice switching oligonucleotides (SSO). Significant advances in the chemistry and pharmacology of nucleic acid have led to the development of clinically approved SSO drugs for the treatment of spinal muscular dystrophy and Duchenne muscular dystrophy (DMD). In this review, we discuss the mechanisms of SSO action with emphasis on "less common" approaches to modulate alternative splicing, including bipartite and bifunctional SSO, oligonucleotide decoys for splice factors and SSO-mediated mRNA degradation via AS-NMD and NGD pathways. We briefly discuss the current progress and future perspectives of SSO therapy for rare and ultrarare diseases.
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Affiliation(s)
- Olga V Sergeeva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Timofei S Zatsepin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Department of Chemistry, Moscow State University, Moscow, Russia
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23
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Xu S, Xie J, Zhou Y, Liu H, Wang Y, Li Z. Integrated Analysis of RNA Binding Protein-Related lncRNA Prognostic Signature for Breast Cancer Patients. Genes (Basel) 2022; 13:genes13020345. [PMID: 35205391 PMCID: PMC8872055 DOI: 10.3390/genes13020345] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 12/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been well known for their multiple functions in the tumorigenesis, development, and prognosis of breast cancer (BC). Mechanistically, their production, function, or stability can be regulated by RNA binding proteins (RBPs), which were also involved in the carcinogenesis and progression of BC. However, the roles and clinical implications of RBP-related lncRNAs in BC remain largely unknown. Therefore, we herein aim to construct a prognostic signature with RBP-relevant lncRNAs for the prognostic evaluation of BC patients. Firstly, based on the RNA sequencing data of female BC patients from The Cancer Genome Atlas (TCGA) database, we screened out 377 differentially expressed lncRNAs related to RBPs. The univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were then performed to establish a prognostic signature composed of 12-RBP-related lncRNAs. Furthermore, we divided the BC patients into high- and low-risk groups by the prognostic signature and found the overall survival (OS) of patients in the high-risk group was significantly shorter than that of the low-risk group. Moreover, the 12-lncRNA signature exhibited independence in evaluating the prognosis of BC patients. Additionally, a functional enrichment analysis revealed that the prognostic signature was associated with some cancer-relevant pathways, including cell cycle and immunity. In summary, our 12-lncRNA signature may provide a theoretical reference for the prognostic evaluation or clinical treatment of BC patients.
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Affiliation(s)
- Shaohua Xu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha 410082, China; (S.X.); (J.X.); (Y.Z.); (H.L.)
| | - Jiahui Xie
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha 410082, China; (S.X.); (J.X.); (Y.Z.); (H.L.)
| | - Yanjie Zhou
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha 410082, China; (S.X.); (J.X.); (Y.Z.); (H.L.)
| | - Hui Liu
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha 410082, China; (S.X.); (J.X.); (Y.Z.); (H.L.)
| | - Yirong Wang
- Bioinformatics Center, College of Biology, Hunan University, Changsha 410082, China
- Correspondence: (Y.W.); (Z.L.)
| | - Zhaoyong Li
- Hunan Provincial Key Laboratory of Medical Virology, Institute of Pathogen Biology and Immunology, College of Biology, Hunan University, Changsha 410082, China; (S.X.); (J.X.); (Y.Z.); (H.L.)
- Research Institute of Hunan University in Chongqing, Chongqing 401120, China
- Correspondence: (Y.W.); (Z.L.)
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24
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Nojima T, Proudfoot NJ. Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics. Nat Rev Mol Cell Biol 2022; 23:389-406. [DOI: 10.1038/s41580-021-00447-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
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25
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A broad analysis of splicing regulation in yeast using a large library of synthetic introns. PLoS Genet 2021; 17:e1009805. [PMID: 34570750 PMCID: PMC8496845 DOI: 10.1371/journal.pgen.1009805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/07/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
RNA splicing is a key process in eukaryotic gene expression, in which an intron is spliced out of a pre-mRNA molecule to eventually produce a mature mRNA. Most intron-containing genes are constitutively spliced, hence efficient splicing of an intron is crucial for efficient regulation of gene expression. Here we use a large synthetic oligo library of ~20,000 variants to explore how different intronic sequence features affect splicing efficiency and mRNA expression levels in S. cerevisiae. Introns are defined by three functional sites, the 5’ donor site, the branch site, and the 3’ acceptor site. Using a combinatorial design of synthetic introns, we demonstrate how non-consensus splice site sequences in each of these sites affect splicing efficiency. We then show that S. cerevisiae splicing machinery tends to select alternative 3’ splice sites downstream of the original site, and we suggest that this tendency created a selective pressure, leading to the avoidance of cryptic splice site motifs near introns’ 3’ ends. We further use natural intronic sequences from other yeast species, whose splicing machineries have diverged to various extents, to show how intron architectures in the various species have been adapted to the organism’s splicing machinery. We suggest that the observed tendency for cryptic splicing is a result of a loss of a specific splicing factor, U2AF1. Lastly, we show that synthetic sequences containing two introns give rise to alternative RNA isoforms in S. cerevisiae, demonstrating that merely a synthetic fusion of two introns might be suffice to facilitate alternative splicing in yeast. Our study reveals novel mechanisms by which introns are shaped in evolution to allow cells to regulate their transcriptome. In addition, it provides a valuable resource to study the regulation of constitutive and alternative splicing in a model organism. RNA splicing is a process in which parts of a new pre-mRNA are spliced out of the mRNA molecule to produce eventually a mature mRNA. Those RNA segments that are spliced out are termed introns, and they are found in most genes in eukaryotic organisms. Hence regulation of this process has a major role in the control of gene expression. The budding yeast S. cerevisiae is a popular model organism for eukaryotic cell biology, but in terms of splicing it differs, as it has only few intron-containing genes. Nevertheless, this species has been used to study basic principles of splicing regulation based on its ~300 introns. Here we used the technology of a large synthetic genetic library to introduce many new intron-containing genes to the yeast genome, to explore splicing regulation at a wider scope than was possible so far. Reassuringly, our results confirm known regulatory mechanisms, and further expand our understanding of splicing regulation, specifically how the yeast splicing machinery interacts with the end of introns, and how through evolution introns have evolved to avoid unwanted misidentifications of this end. We further demonstrate the potential of the yeast splicing machinery to alternatively splice a two-intron gene, which is common in other eukaryotes but rare in yeast. Our work presents a first-of-its-kind resource for the systematic study of splicing in live cells.
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26
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Transcription and chromatin-based surveillance mechanism controls suppression of cryptic antisense transcription. Cell Rep 2021; 36:109671. [PMID: 34496258 PMCID: PMC8441049 DOI: 10.1016/j.celrep.2021.109671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/26/2020] [Accepted: 08/13/2021] [Indexed: 12/25/2022] Open
Abstract
Phosphorylation of the RNA polymerase II C-terminal domain Y1S2P3T4S5P6S7 consensus sequence coordinates key events during transcription, and its deregulation leads to defects in transcription and RNA processing. Here, we report that the histone deacetylase activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of antisense transcription when RNA polymerase II phosphorylation is dysregulated due to the loss of Ssu72 phosphatase. Interestingly, although single Hos2 and Set3 mutants have little effect, loss of Hos2 or Set3 combined with ssu72Δ results in a synergistic increase in antisense transcription globally and correlates with elevated sensitivity to genotoxic agents. We demonstrate a key role for the Ssu72/Hos2/Set3 mechanism in the suppression of cryptic antisense transcription at the 3' end of convergent genes that are most susceptible to these defects, ensuring the fidelity of gene expression within dense genomes of simple eukaryotes.
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27
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Estell C, Davidson L, Steketee PC, Monier A, West S. ZC3H4 restricts non-coding transcription in human cells. eLife 2021; 10:67305. [PMID: 33913806 PMCID: PMC8137146 DOI: 10.7554/elife.67305] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene transcriptional termination factors, we identified ZC3H4. Its depletion causes upregulation and extension of hundreds of unstable transcripts, particularly antisense RNAs and those transcribed from so-called super-enhancers. These loci are occupied by ZC3H4, suggesting that it directly functions in their transcription. Consistently, engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the exosome. ZC3H4 is predominantly metazoan –interesting when considering its impact on enhancer RNAs that are less prominent in single-celled organisms. Finally, ZC3H4 loss causes a substantial reduction in cell proliferation, highlighting its overall importance. In summary, we identify ZC3H4 as playing an important role in restricting non-coding transcription in multicellular organisms.
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Affiliation(s)
- Chris Estell
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Lee Davidson
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Pieter C Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Monier
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Steven West
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
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28
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Gil N, Ulitsky I. Inefficient splicing curbs noncoding RNA transcription. Nat Struct Mol Biol 2021; 28:327-328. [PMID: 33767453 DOI: 10.1038/s41594-021-00582-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Noa Gil
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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