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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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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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Dean DM, Deitcher DL, Paster CO, Xu M, Loehlin DW. "A fly appeared": sable, a classic Drosophila mutation, maps to Yippee, a gene affecting body color, wings, and bristles. G3 (BETHESDA, MD.) 2022; 12:jkac058. [PMID: 35266526 PMCID: PMC9073688 DOI: 10.1093/g3journal/jkac058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022]
Abstract
Insect body color is an easily assessed and visually engaging trait that is informative on a broad range of topics including speciation, biomaterial science, and ecdysis. Mutants of the fruit fly Drosophila melanogaster have been an integral part of body color research for more than a century. As a result of this long tenure, backlogs of body color mutations have remained unmapped to their genes, all while their strains have been dutifully maintained, used for recombination mapping, and part of genetics education. Stemming from a lesson plan in our undergraduate genetics class, we have mapped sable1, a dark body mutation originally described by Morgan and Bridges, to Yippee, a gene encoding a predicted member of the E3 ubiquitin ligase complex. Deficiency/duplication mapping, genetic rescue, DNA and cDNA sequencing, RT-qPCR, and 2 new CRISPR alleles indicated that sable1 is a hypomorphic Yippee mutation due to an mdg4 element insertion in the Yippee 5'-UTR. Further analysis revealed additional Yippee mutant phenotypes including curved wings, ectopic/missing bristles, delayed development, and failed adult emergence. RNAi of Yippee in the ectoderm phenocopied sable body color and most other Yippee phenotypes. Although Yippee remains functionally uncharacterized, the results presented here suggest possible connections between melanin biosynthesis, copper homeostasis, and Notch/Delta signaling; in addition, they provide insight into past studies of sable cell nonautonomy and of the genetic modifier suppressor of sable.
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Affiliation(s)
- Derek M Dean
- Department of Biology, Williams College, Williamstown, MA 01267, USA
| | - David L Deitcher
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Caleigh O Paster
- Department of Biology, Williams College, Williamstown, MA 01267, USA
| | - Manting Xu
- Department of Biology, Williams College, Williamstown, MA 01267, USA
| | - David W Loehlin
- Department of Biology, Williams College, Williamstown, MA 01267, USA
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Abstract
The RNA exosome is a ribonucleolytic multiprotein complex that is conserved and essential in all eukaryotes. Although we tend to speak of "the" exosome complex, it should be more correctly viewed as several different subtypes that share a common core. Subtypes of the exosome complex are present in the cytoplasm, the nucleus and the nucleolus of all eukaryotic cells, and carry out the 3'-5' processing and/or degradation of a wide range of RNA substrates.Because the substrate specificity of the exosome complex is determined by cofactors, the system is highly adaptable, and different organisms have adjusted the machinery to their specific needs. Here, we present an overview of exosome complexes and their cofactors that have been described in different eukaryotes.
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Affiliation(s)
- Cornelia Kilchert
- Institut für Biochemie, Justus-Liebig-Universität Gießen, Gießen, Germany.
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Brewer-Jensen P, Wilson CB, Abernethy J, Mollison L, Card S, Searles LL. Suppressor of sable [Su(s)] and Wdr82 down-regulate RNA from heat-shock-inducible repetitive elements by a mechanism that involves transcription termination. RNA (NEW YORK, N.Y.) 2016; 22:139-54. [PMID: 26577379 PMCID: PMC4691828 DOI: 10.1261/rna.048819.114] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/23/2015] [Indexed: 05/26/2023]
Abstract
Although RNA polymerase II (Pol II) productively transcribes very long genes in vivo, transcription through extragenic sequences often terminates in the promoter-proximal region and the nascent RNA is degraded. Mechanisms that induce early termination and RNA degradation are not well understood in multicellular organisms. Here, we present evidence that the suppressor of sable [su(s)] regulatory pathway of Drosophila melanogaster plays a role in this process. We previously showed that Su(s) promotes exosome-mediated degradation of transcripts from endogenous repeated elements at an Hsp70 locus (Hsp70-αβ elements). In this report, we identify Wdr82 as a component of this process and show that it works with Su(s) to inhibit Pol II elongation through Hsp70-αβ elements. Furthermore, we show that the unstable transcripts produced during this process are polyadenylated at heterogeneous sites that lack canonical polyadenylation signals. We define two distinct regions that mediate this regulation. These results indicate that the Su(s) pathway promotes RNA degradation and transcription termination through a novel mechanism.
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Affiliation(s)
- Paul Brewer-Jensen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Carrie B Wilson
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - John Abernethy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Lonna Mollison
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Samantha Card
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
| | - Lillie L Searles
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3280, USA
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Abstract
Eukaryotic mRNAs are extensively processed to generate functional transcripts, which are 5′ capped, spliced and 3′ polyadenylated. Accumulation of unprocessed (aberrant) mRNAs can be deleterious for the cell, hence processing fidelity is closely monitored by QC (quality control) mechanisms that identify erroneous transcripts and initiate their selective removal. Nucleases including Xrn2/Rat1 and the nuclear exosome have been shown to play an important role in the turnover of aberrant mRNAs. Recently, with the growing appreciation that mRNA processing occurs concomitantly with polII (RNA polymerase II) transcription, it has become evident that QC acts at the transcriptional level in addition to degrading aberrant RNAs. In the present review, we discuss mechanisms that allow cells to co-transcriptionally initiate the removal of RNAs as well as down-regulate transcription of transcripts where processing repeatedly fails.
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Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L. Patterns of positive selection in seven ant genomes. Mol Biol Evol 2014; 31:1661-85. [PMID: 24782441 PMCID: PMC4069625 DOI: 10.1093/molbev/msu141] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The evolution of ants is marked by remarkable adaptations that allowed the development of very complex social systems. To identify how ant-specific adaptations are associated with patterns of molecular evolution, we searched for signs of positive selection on amino-acid changes in proteins. We identified 24 functional categories of genes which were enriched for positively selected genes in the ant lineage. We also reanalyzed genome-wide data sets in bees and flies with the same methodology to check whether positive selection was specific to ants or also present in other insects. Notably, genes implicated in immunity were enriched for positively selected genes in the three lineages, ruling out the hypothesis that the evolution of hygienic behaviors in social insects caused a major relaxation of selective pressure on immune genes. Our scan also indicated that genes implicated in neurogenesis and olfaction started to undergo increased positive selection before the evolution of sociality in Hymenoptera. Finally, the comparison between these three lineages allowed us to pinpoint molecular evolution patterns that were specific to the ant lineage. In particular, there was ant-specific recurrent positive selection on genes with mitochondrial functions, suggesting that mitochondrial activity was improved during the evolution of this lineage. This might have been an important step toward the evolution of extreme lifespan that is a hallmark of ants.
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Affiliation(s)
- Julien Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Eyal Privman
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sébastien Moretti
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandVital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Josephine T Daub
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, SwitzerlandCMPG, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, SwitzerlandSIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Laurent Keller
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Taboada X, Robledo D, Del Palacio L, Rodeiro A, Felip A, Martínez P, Viñas A. Comparative expression analysis in mature gonads, liver and brain of turbot (Scophthalmus maximus) by cDNA-AFLPS. Gene 2011; 492:250-61. [PMID: 22037609 DOI: 10.1016/j.gene.2011.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 09/08/2011] [Accepted: 10/10/2011] [Indexed: 11/28/2022]
Abstract
Turbot is one of the most important farmed fish in Europe. This species exhibits a considerable sexual dimorphism in growth and sexual maturity that makes the all-female production recommended for turbot farming. Our knowledge about the genetic basis of sex determination and the molecular regulation of gonad differentiation in this species is still limited. Our goal was to identify and compare gene expression and functions between testes and ovaries in adults in order to ascertain the relationship between the genes that could be involved in the gonad differentiation or related to the sex determination system. The identification of differentially expressed sex related genes is an initial step towards understanding the molecular mechanisms of gonad differentiation. For this, we carried out a transcriptome analysis based on cDNA-AFLP technique which allowed us to obtain an initial frame on sex-specific gene expression that will facilitate further analysis especially along the critical gonad differentiating period. With the aim of widening the study on sex-biased gene expression we reproduced the same experiments in two somatic tissues: liver and brain. We have selected the liver because it is the most analyzed one regarding sexual dimorphic gene expression and due to its importance in steroid hormones metabolism and the brain because the functional relationship between brain and gonad is documented. We found slight but important differences between sexes which deserve further investigation.
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Affiliation(s)
- Xoana Taboada
- Departamento de Genética, Facultad de Biología (CIBUS), Universidad de Santiago de Compostela Avda Lope Gómez de Marzoa, 15782 Santiago de Compostela, Spain
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