1
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Chan SN, Pek JW. Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA. EMBO Rep 2023; 24:e54350. [PMID: 36533631 PMCID: PMC9900350 DOI: 10.15252/embr.202154350] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/28/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022] Open
Abstract
Stable intronic sequence RNAs (sisRNAs) are stable, long noncoding RNAs containing intronic sequences. While sisRNAs have been found across diverse species, their level of conservation remains poorly understood. Here we report that the biogenesis and functions of a sisRNA transcribed from the highly conserved Arglu1 locus are distinct in human and Drosophila melanogaster. The Arglu1 genes in both species show similar exon-intron structures where the intron 2 is orthologous and positionally conserved. In humans, Arglu1 sisRNA retains the entire intron 2 and promotes host gene splicing. Mechanistically, Arglu1 sisRNA represses the splicing-inhibitory activity of ARGLU1 protein by binding to ARGLU1 protein and promoting its localization to nuclear speckles, away from the Arglu1 gene locus. In contrast, Drosophila dArglu1 sisRNA forms via premature cleavage of intron 2 and represses host gene splicing. This repression occurs through a local accumulation of dARGLU1 protein and inhibition of telescripting by U1 snRNPs at the dArglu1 locus. We propose that distinct biogenesis of positionally conserved Arglu1 sisRNAs in both species may have led to functional divergence.
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Affiliation(s)
- Seow Neng Chan
- Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
| | - Jun Wei Pek
- Temasek Life Sciences LaboratoryNational University of SingaporeSingaporeSingapore
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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2
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Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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3
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Rambout X, Cho H, Maquat LE. Transcriptional Coactivator PGC-1α Binding to Newly Synthesized RNA via CBP80: A Nexus for Co- and Posttranscriptional Gene Regulation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:47-54. [PMID: 32295928 DOI: 10.1101/sqb.2019.84.040212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mammalian cells have many quality-control mechanisms that regulate protein-coding gene expression to ensure proper transcript synthesis, processing, and translation. Should a step in transcript metabolism fail to fulfill requisite spatial, temporal, or structural criteria, including the proper acquisition of RNA-binding proteins, then that step will halt, fail to proceed to the next step, and ultimately result in transcript degradation. Quality-control mechanisms constitute a continuum of processes that initiate in the nucleus and extend to the cytoplasm. Here, we present published and unpublished data for protein-coding genes whose expression is activated by the transcriptional coactivator PGC-1α. We show that PGC-1α movement from chromatin, to which it is recruited by DNA-binding proteins, to CBP80 at the 5' cap of nascent transcripts begins a series of co- and posttranscriptional quality- and quantity-control steps that, in total, ensure proper gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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4
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Cuevas-Bermúdez A, Garrido-Godino AI, Navarro F. A novel yeast chromatin-enriched fractions purification approach, yChEFs, for the chromatin-associated protein analysis used for chromatin-associated and RNA-dependent chromatin-associated proteome studies from Saccharomyces cerevisiae. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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5
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Barbier J, Chen X, Sanchez G, Cai M, Helsmoortel M, Higuchi T, Giraud P, Contreras X, Yuan G, Feng Z, Nait-Saidi R, Deas O, Bluy L, Judde JG, Rouquier S, Ritchie W, Sakamoto S, Xie D, Kiernan R. An NF90/NF110-mediated feedback amplification loop regulates dicer expression and controls ovarian carcinoma progression. Cell Res 2018; 28:556-571. [PMID: 29563539 DOI: 10.1038/s41422-018-0016-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 01/16/2023] Open
Abstract
Reduced expression of DICER, a key enzyme in the miRNA pathway, is frequently associated with aggressive, invasive disease, and poor survival in various malignancies. Regulation of DICER expression is, however, poorly understood. Here, we show that NF90/NF110 facilitates DICER expression by controlling the processing of a miRNA, miR-3173, which is embedded in DICER pre-mRNA. As miR-3173 in turn targets NF90, a feedback amplification loop controlling DICER expression is established. In a nude mouse model, NF90 overexpression reduced proliferation of ovarian cancer cells and significantly reduced tumor size and metastasis, whereas overexpression of miR-3173 dramatically increased metastasis in an NF90- and DICER-dependent manner. Clinically, low NF90 expression and high miR-3173-3p expression were found to be independent prognostic markers of poor survival in a cohort of ovarian carcinoma patients. These findings suggest that, by facilitating DICER expression, NF90 can act as a suppressor of ovarian carcinoma.
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Affiliation(s)
- Jérôme Barbier
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | - Xin Chen
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Gabriel Sanchez
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | - Muyan Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Marion Helsmoortel
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | - Takuma Higuchi
- Laboratory of Molecular Biology, Science Research Center, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Pierre Giraud
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | - Xavier Contreras
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | - Gangjun Yuan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zihao Feng
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510060, China
| | - Rima Nait-Saidi
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | - Olivier Deas
- XenTech SAS, 4 rue Pierre Fontaine, Evry, 91000, France
| | - Lisa Bluy
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | | | - Sylvie Rouquier
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France
| | - William Ritchie
- Institut de Génétique Humaine, CNRS, University of Montpellier, Machine Learning and Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, 34396, France
| | - Shuji Sakamoto
- Laboratory of Molecular Biology, Science Research Center, Kochi Medical School, Kochi University, Kochi, 783-8505, Japan
| | - Dan Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
| | - Rosemary Kiernan
- Institut de Génétique Humaine, CNRS, University of Montpellier, Gene Regulation Laboratory, 141 rue de la cardonille, Montpellier, France.
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6
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De Amicis F, Guido C, Santoro M, Giordano F, Donà A, Rizza P, Pellegrino M, Perrotta I, Bonofiglio D, Sisci D, Panno ML, Tramontano D, Aquila S, Andò S. Ligand activated progesterone receptor B drives autophagy-senescence transition through a Beclin-1/Bcl-2 dependent mechanism in human breast cancer cells. Oncotarget 2018; 7:57955-57969. [PMID: 27462784 PMCID: PMC5295403 DOI: 10.18632/oncotarget.10799] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/09/2016] [Indexed: 12/21/2022] Open
Abstract
Loss of progesterone-receptors (PR) expression is associated with breast cancer progression. Herein we provide evidence that OHPg/PR-B through Beclin-1 evoke autophagy-senescence transition, in breast cancer cells. Specifically, OHPg increases Beclin-1 expression through a transcriptional mechanism due to the occupancy of Beclin-1 promoter by PR-B, together with the transcriptional coactivator SRC-2. This complex binds at a canonical half progesterone responsive element, which is fundamental for OHPg effects, as shown by site-directed mutagenesis. Beside, OHPg via non-genomic action rapidly activates JNK, which phosphorylates Bcl-2, producing the functional release from Beclin-1 interaction. This is not linked to an efficient autophagic flux, since p62 levels, marker of degradation via lysosomes, were not reduced after sustained OHPg stimulus. Instead, the cell cycle inhibitor p27 was induced, together with an irreversible G1 arrest, hallmark of cellular senescence. Specifically the increase of senescence-associated β-galactosidase activity was blocked by Bcl-2 siRNA but also by Beclin-1 siRNA. Collectively these findings support the importance of PR-B expression in breast cancer cells, thus targeting PR-B may be a useful strategy to provide additional approaches to existing therapies for breast cancer patients.
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Affiliation(s)
- Francesca De Amicis
- Centro Sanitario, University of Calabria, Rende, Italy.,Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Carmela Guido
- Centro Sanitario, University of Calabria, Rende, Italy.,Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Marta Santoro
- Centro Sanitario, University of Calabria, Rende, Italy
| | - Francesca Giordano
- Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Ada Donà
- Centro Sanitario, University of Calabria, Rende, Italy.,Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Pietro Rizza
- Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Michele Pellegrino
- Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | | | - Daniela Bonofiglio
- Centro Sanitario, University of Calabria, Rende, Italy.,Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Diego Sisci
- Centro Sanitario, University of Calabria, Rende, Italy.,Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Maria Luisa Panno
- Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Donatella Tramontano
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Naples, Italy
| | - Saveria Aquila
- Centro Sanitario, University of Calabria, Rende, Italy.,Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
| | - Sebastiano Andò
- Centro Sanitario, University of Calabria, Rende, Italy.,Department of Pharmacy, Health Science and Nutrition, University of Calabria, Rende, Italy
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7
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Naftelberg S, Schor IE, Ast G, Kornblihtt AR. Regulation of alternative splicing through coupling with transcription and chromatin structure. Annu Rev Biochem 2015; 84:165-98. [PMID: 26034889 DOI: 10.1146/annurev-biochem-060614-034242] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays a pivotal role in the flow of genetic information from DNA to proteins by expanding the coding capacity of genomes. Regulation of alternative splicing is as important as regulation of transcription to determine cell- and tissue-specific features, normal cell functioning, and responses of eukaryotic cells to external cues. Its importance is confirmed by the evolutionary conservation and diversification of alternative splicing and the fact that its deregulation causes hereditary disease and cancer. This review discusses the multiple layers of cotranscriptional regulation of alternative splicing in which chromatin structure, DNA methylation, histone marks, and nucleosome positioning play a fundamental role in providing a dynamic scaffold for interactions between the splicing and transcription machineries. We focus on evidence for how the kinetics of RNA polymerase II (RNAPII) elongation and the recruitment of splicing factors and adaptor proteins to chromatin components act in coordination to regulate alternative splicing.
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Affiliation(s)
- Shiran Naftelberg
- Sackler Medical School, Tel Aviv University, Tel Aviv 69978, Israel;
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8
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Dardenne E, Polay Espinoza M, Fattet L, Germann S, Lambert MP, Neil H, Zonta E, Mortada H, Gratadou L, Deygas M, Chakrama FZ, Samaan S, Desmet FO, Tranchevent LC, Dutertre M, Rimokh R, Bourgeois CF, Auboeuf D. RNA helicases DDX5 and DDX17 dynamically orchestrate transcription, miRNA, and splicing programs in cell differentiation. Cell Rep 2014; 7:1900-13. [PMID: 24910439 DOI: 10.1016/j.celrep.2014.05.010] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 04/08/2014] [Accepted: 05/05/2014] [Indexed: 02/07/2023] Open
Abstract
The RNA helicases DDX5 and DDX17 are members of a large family of highly conserved proteins that are involved in gene-expression regulation; however, their in vivo targets and activities in biological processes such as cell differentiation, which requires reprogramming of gene-expression programs at multiple levels, are not well characterized. Here, we uncovered a mechanism by which DDX5 and DDX17 cooperate with heterogeneous nuclear ribonucleoprotein (hnRNP) H/F splicing factors to define epithelial- and myoblast-specific splicing subprograms. We then observed that downregulation of DDX5 and DDX17 protein expression during myogenesis and epithelial-to-mesenchymal transdifferentiation contributes to the switching of splicing programs during these processes. Remarkably, this downregulation is mediated by the production of miRNAs induced upon differentiation in a DDX5/DDX17-dependent manner. Since DDX5 and DDX17 also function as coregulators of master transcriptional regulators of differentiation, we propose to name these proteins "master orchestrators" of differentiation that dynamically orchestrate several layers of gene expression.
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Affiliation(s)
- Etienne Dardenne
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Micaela Polay Espinoza
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Laurent Fattet
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Sophie Germann
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Marie-Pierre Lambert
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Helen Neil
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Eleonora Zonta
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Hussein Mortada
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Lise Gratadou
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Mathieu Deygas
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Fatima Zahra Chakrama
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Samaan Samaan
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - François-Olivier Desmet
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Léon-Charles Tranchevent
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Martin Dutertre
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Ruth Rimokh
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France
| | - Cyril F Bourgeois
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France.
| | - Didier Auboeuf
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France; Université Claude Bernard Lyon 1, 69008 Lyon, France; Centre Léon Bérard, 69008 Lyon, France.
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9
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RNA splicing regulates the temporal order of TNF-induced gene expression. Proc Natl Acad Sci U S A 2013; 110:11934-9. [PMID: 23812748 DOI: 10.1073/pnas.1309990110] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
When cells are induced to express inflammatory genes by treatment with TNF, the mRNAs for the induced genes appear in three distinct waves, defining gene groups I, II, and III, or early, intermediate, and late genes. To examine the basis for these different kinetic classes, we have developed a PCR-based procedure to distinguish pre-mRNAs from mRNAs. It shows that the three groups initiate transcription virtually simultaneously but that delays in splicing characterize groups II and III. We also examined the elongation times, concluding that pre-mRNA synthesis is coordinate but splicing differences directly regulate the timing of mRNA production.
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10
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Bhat-Nakshatri P, Song EK, Collins NR, Uversky VN, Dunker AK, O'Malley BW, Geistlinger TR, Carroll JS, Brown M, Nakshatri H. Interplay between estrogen receptor and AKT in estradiol-induced alternative splicing. BMC Med Genomics 2013; 6:21. [PMID: 23758675 PMCID: PMC3687557 DOI: 10.1186/1755-8794-6-21] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 06/03/2013] [Indexed: 02/07/2023] Open
Abstract
Background Alternative splicing is critical for generating complex proteomes in response to extracellular signals. Nuclear receptors including estrogen receptor alpha (ERα) and their ligands promote alternative splicing. The endogenous targets of ERα:estradiol (E2)-mediated alternative splicing and the influence of extracellular kinases that phosphorylate ERα on E2-induced splicing are unknown. Methods MCF-7 and its anti-estrogen derivatives were used for the majority of the assays. CD44 mini gene was used to measure the effect of E2 and AKT on alternative splicing. ExonHit array analysis was performed to identify E2 and AKT-regulated endogenous alternatively spliced apoptosis-related genes. Quantitative reverse transcription polymerase chain reaction was performed to verify alternative splicing. ERα binding to alternatively spliced genes was verified by chromatin immunoprecipitation assay. Bromodeoxyuridine incorporation-ELISA and Annexin V labeling assays were done to measure cell proliferation and apoptosis, respectively. Results We identified the targets of E2-induced alternative splicing and deconstructed some of the mechanisms surrounding E2-induced splicing by combining splice array with ERα cistrome and gene expression array. E2-induced alternatively spliced genes fall into at least two subgroups: coupled to E2-regulated transcription and ERα binding to the gene without an effect on rate of transcription. Further, AKT, which phosphorylates both ERα and splicing factors, influenced ERα:E2 dependent splicing in a gene-specific manner. Genes that are alternatively spliced include FAS/CD95, FGFR2, and AXIN-1. E2 increased the expression of FGFR2 C1 isoform but reduced C3 isoform at mRNA level. E2-induced alternative splicing of FAS and FGFR2 in MCF-7 cells correlated with resistance to FAS activation-induced apoptosis and response to keratinocyte growth factor (KGF), respectively. Resistance of MCF-7 breast cancer cells to the anti-estrogen tamoxifen was associated with ERα-dependent overexpression of FGFR2, whereas resistance to fulvestrant was associated with ERα-dependent isoform switching, which correlated with altered response to KGF. Conclusion E2 may partly alter cellular proteome through alternative splicing uncoupled to its effects on transcription initiation and aberration in E2-induced alternative splicing events may influence response to anti-estrogens.
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Affiliation(s)
- Poornima Bhat-Nakshatri
- Department of Surgery, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN 46202, USA
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11
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G9a functions as a molecular scaffold for assembly of transcriptional coactivators on a subset of glucocorticoid receptor target genes. Proc Natl Acad Sci U S A 2012; 109:19673-8. [PMID: 23151507 DOI: 10.1073/pnas.1211803109] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Histone H3 lysine-9 methyltransferase G9a/EHMT2/KMT1C is a key corepressor of gene expression. However, activation of a limited number of genes by G9a (independent of its catalytic activity) has also been observed, although the precise molecular mechanisms are unknown. By using RNAi in combination with gene expression microarray analysis, we found that G9a functions as a positive and a negative transcriptional coregulator for discrete subsets of genes that are regulated by the hormone-activated Glucocorticoid Receptor (GR). G9a was recruited to GR-binding sites (but not to the gene body) of its target genes and interacted with GR, suggesting recruitment of G9a by GR. In contrast to its corepressor function, positive regulation of gene expression by G9a involved G9a-mediated enhanced recruitment of coactivators CARM1 and p300 to GR target genes. Further supporting a role for G9a as a molecular scaffold for its coactivator function, the G9a-specific methyltransferase inhibitor UNC0646 did not affect G9a coactivator function but selectively decreased G9a corepressor function for endogenous target genes. Overall, G9a functioned as a coactivator for hormone-activated genes and as a corepressor in support of hormone-induced gene repression, suggesting that the positive or negative actions of G9a are determined by the gene-specific regulatory environment and chromatin architecture. These findings indicate distinct mechanisms of G9a coactivator vs. corepressor functions in transcriptional regulation and provide insight into the molecular mechanisms of G9a coactivator function. Our results also suggest a physiological role of G9a in fine tuning the set of genes that respond to glucocorticoids.
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Zonta E, Bittencourt D, Samaan S, Germann S, Dutertre M, Auboeuf D. The RNA helicase DDX5/p68 is a key factor promoting c-fos expression at different levels from transcription to mRNA export. Nucleic Acids Res 2012; 41:554-64. [PMID: 23143267 PMCID: PMC3592390 DOI: 10.1093/nar/gks1046] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
It is widely accepted that pre-mRNA maturation, including splicing, is tightly coupled to both transcription and mRNA export, but factors linking the three processes are less understood. By analysing the estrogen-regulated expression of the c-fos mRNA that is processed during transcription, we show that the ddx5 RNA helicase, is required throughout the major nuclear steps of the expression of the c-fos gene, from transcription to mRNA export. Indeed, ddx5, whose recruitment on the c-fos gene was increased upon estrogen treatment, was required for the full transcriptional activation of the c-fos gene. In addition, ddx5 was required for c-fos co-transcriptional RNA splicing. When splicing occurred post-transcriptionally in the absence of ddx5, the c-fos mRNA was poorly exported into the cytosol because of inefficient recruitment of the TAP mRNA export receptor. Finally, ddx5 was present in the c-fos messenger ribonucleoprotein together with mRNA export factors, which further supports that ddx5 is a key operator in the c-fos ‘mRNA factory’.
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Affiliation(s)
- Eleonora Zonta
- Université de Lyon, Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, 28 Rue Laennec, F-69008 Lyon, France and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Danielle Bittencourt
- Université de Lyon, Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, 28 Rue Laennec, F-69008 Lyon, France and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Samaan Samaan
- Université de Lyon, Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, 28 Rue Laennec, F-69008 Lyon, France and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Sophie Germann
- Université de Lyon, Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, 28 Rue Laennec, F-69008 Lyon, France and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Martin Dutertre
- Université de Lyon, Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, 28 Rue Laennec, F-69008 Lyon, France and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Didier Auboeuf
- Université de Lyon, Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Centre Léon Bérard, 28 Rue Laennec, F-69008 Lyon, France and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
- *To whom correspondence should be addressed. Tel: +33 4 26 55 67 46; Fax: +33 4 78 78 27 20;
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Sanchez G, Dury AY, Murray LM, Biondi O, Tadesse H, El Fatimy R, Kothary R, Charbonnier F, Khandjian EW, Côté J. A novel function for the survival motoneuron protein as a translational regulator. Hum Mol Genet 2012; 22:668-84. [PMID: 23136128 DOI: 10.1093/hmg/dds474] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
SMN1, the causative gene for spinal muscular atrophy (SMA), plays a housekeeping role in the biogenesis of small nuclear RNA ribonucleoproteins. SMN is also present in granular foci along axonal projections of motoneurons, which are the predominant cell type affected in the pathology. These so-called RNA granules mediate the transport of specific mRNAs along neurites and regulate mRNA localization, stability, as well as local translation. Recent work has provided evidence suggesting that SMN may participate in the assembly of RNA granules, but beyond that, the precise nature of its role within these structures remains unclear. Here, we demonstrate that SMN associates with polyribosomes and can repress translation in an in vitro translation system. We further identify the arginine methyltransferase CARM1 as an mRNA that is regulated at the translational level by SMN and find that CARM1 is abnormally up-regulated in spinal cord tissue from SMA mice and in severe type I SMA patient cells. We have previously characterized a novel regulatory pathway in motoneurons involving the SMN-interacting RNA-binding protein HuD and CARM1. Thus, our results suggest the existence of a potential negative feedback loop in this pathway. Importantly, an SMA-causing mutation in the Tudor domain of SMN completely abolished translational repression, a strong indication for the functional significance of this novel SMN activity in the pathology.
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Affiliation(s)
- Gabriel Sanchez
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8M5
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Dardenne E, Pierredon S, Driouch K, Gratadou L, Lacroix-Triki M, Espinoza MP, Zonta E, Germann S, Mortada H, Villemin JP, Dutertre M, Lidereau R, Vagner S, Auboeuf D. Splicing switch of an epigenetic regulator by RNA helicases promotes tumor-cell invasiveness. Nat Struct Mol Biol 2012; 19:1139-46. [PMID: 23022728 DOI: 10.1038/nsmb.2390] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 08/24/2012] [Indexed: 12/11/2022]
Abstract
Both epigenetic and splicing regulation contribute to tumor progression, but the potential links between these two levels of gene-expression regulation in pathogenesis are not well understood. Here, we report that the mouse and human RNA helicases Ddx17 and Ddx5 contribute to tumor-cell invasiveness by regulating alternative splicing of several DNA- and chromatin-binding factors, including the macroH2A1 histone. We show that macroH2A1 splicing isoforms differentially regulate the transcription of a set of genes involved in redox metabolism. In particular, the SOD3 gene that encodes the extracellular superoxide dismutase and plays a part in cell migration is regulated in an opposite manner by macroH2A1 splicing isoforms. These findings reveal a new regulatory pathway in which splicing factors control the expression of histone variant isoforms that in turn drive a transcription program to switch tumor cells to an invasive phenotype.
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Affiliation(s)
- Etienne Dardenne
- Institut National de la Santé et de la Recherche Médicale, U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
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Hnilicová J, Staněk D. Where splicing joins chromatin. Nucleus 2012; 2:182-8. [PMID: 21818411 DOI: 10.4161/nucl.2.3.15876] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 12/14/2022] Open
Abstract
There are numerous data suggesting that two key steps in gene expression-transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and methylation and potential mechanisms of their role in splicing. It seems that whereas histone acetylation acts mainly by alterating the transcription rate, histone methylation can also influence splicing directly by recruiting various splicing components.
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Affiliation(s)
- Jarmila Hnilicová
- Department of RNA Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague
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Germann S, Gratadou L, Zonta E, Dardenne E, Gaudineau B, Fougère M, Samaan S, Dutertre M, Jauliac S, Auboeuf D. Dual role of the ddx5/ddx17 RNA helicases in the control of the pro-migratory NFAT5 transcription factor. Oncogene 2012; 31:4536-49. [PMID: 22266867 DOI: 10.1038/onc.2011.618] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ddx5 and ddx17 are two highly related RNA helicases involved in both transcription and splicing. These proteins coactivate transcription factors involved in cancer such as the estrogen receptor alpha, p53 and beta-catenin. Ddx5 and ddx17 are part of the splicing machinery and can modulate alternative splicing, the main mechanism increasing the proteome diversity. Alternative splicing also has a role in gene expression level regulation when it is coupled to the nonsense-mediated mRNA decay (NMD) pathway. In this work, we report that ddx5 and ddx17 have a dual role in the control of the pro-migratory NFAT5 transcription factor. First, ddx5 and ddx17 act as transcriptional coactivators of NFAT5 and are required for activating NFAT5 target genes involved in tumor cell migration. Second, at the splicing level, ddx5 and ddx17 increase the inclusion of NFAT5 exon 5. As exon 5 contains a pre-mature translation termination codon, its inclusion leads to the regulation of NFAT5 mRNAs by the NMD pathway and to a decrease in NFAT5 protein level. Therefore, we demonstrated for the first time that a transcriptional coregulator can simultaneously regulate the transcriptional activity and alternative splicing of a transcription factor. This dual regulation, where ddx5 and ddx17 enhance the transcriptional activity of NFAT5 although reducing its protein expression level, suggests a critical role for ddx5 and ddx17 in tumor cell migration through the fine regulation of NFAT5 pathway.
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Abstract
It was initially assumed that RNA biogenesis and processing were two independent processes with transcripts undergoing splicing only after being completely synthesized and released from the DNA template. However, transcription and splicing are tightly linked and increasing evidence shows that nascent transcripts can undergo splicing in the vicinity of chromatin while still attached to the RNA polymerase II (RNAPII) transcriptional machinery. These co-transcriptionally spliced RNA molecules are very labile due to dynamic processing and represent a minor subpopulation among total cellular RNA species. Thus, it is difficult to isolate these RNAs in order to study the dynamics and mechanisms of co-transcriptional RNA splicing. To overcome this problem, the RNA-chromatin immunoprecipitation (ChIP) assay, adapted from classical ChIP, allows to co-purify and isolate nascent RNAs after immunoprecipitation of RNAPII. Thanks to this technique, we have shown that co-transcriptional RNA splicing occurs with distinct efficiencies for different genes and different exons of a given transcript and can represent a rate-limiting step in the biological response of messenger RNA synthesis to extracellular stimuli and drug treatments.
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Cotranscriptional exon skipping in the genotoxic stress response. Nat Struct Mol Biol 2010; 17:1358-66. [PMID: 20972445 DOI: 10.1038/nsmb.1912] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 08/19/2010] [Indexed: 12/14/2022]
Abstract
Pre-mRNA splicing is functionally coupled to transcription, and genotoxic stresses can enhance alternative exon inclusion by affecting elongating RNA polymerase II. We report here that various genotoxic stress inducers, including camptothecin (CPT), inhibit the interaction between Ewing's sarcoma proto-oncoprotein (EWS), an RNA polymerase II-associated factor, and YB-1, a spliceosome-associated factor. This results in the cotranscriptional skipping of several exons of the MDM2 gene, which encodes the main p53 ubiquitin ligase. This reversible exon skipping participates in the regulation of MDM2 expression that may contribute to the accumulation of p53 during stress exposure and its rapid shut-off when stress is removed. Finally, a splicing-sensitive microarray identified numerous exons that are skipped in response to CPT and EWS-YB-1 depletion. These data demonstrate genotoxic stress-induced alteration of the communication between the transcriptional and splicing machineries, which results in widespread exon skipping and plays a central role in the genotoxic stress response.
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Dutertre M, Gratadou L, Dardenne E, Germann S, Samaan S, Lidereau R, Driouch K, de la Grange P, Auboeuf D. Estrogen regulation and physiopathologic significance of alternative promoters in breast cancer. Cancer Res 2010; 70:3760-70. [PMID: 20406972 DOI: 10.1158/0008-5472.can-09-3988] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Alternative promoters (AP) occur in >30% protein-coding genes and contribute to proteome diversity. However, large-scale analyses of AP regulation are lacking, and little is known about their potential physiopathologic significance. To better understand the transcriptomic effect of estrogens, which play a major role in breast cancer, we analyzed gene and AP regulation by estradiol in MCF7 cells using pan-genomic exon arrays. We thereby identified novel estrogen-regulated genes (ERG) and determined the regulation of AP-encoded transcripts in 150 regulated genes. In <30% cases, APs were regulated in a similar manner by estradiol, whereas in >70% cases, they were regulated differentially. The patterns of AP regulation correlated with the patterns of estrogen receptor alpha (ERalpha) and CCCTC-binding factor (CTCF) binding sites at regulated gene loci. Interestingly, among genes with differentially regulated (DR) APs, we identified cases where estradiol regulated APs in an opposite manner, sometimes without affecting global gene expression levels. This promoter switch was mediated by the DDX5/DDX17 family of ERalpha coregulators. Finally, genes with DR promoters were preferentially involved in specific processes (e.g., cell structure and motility, and cell cycle). We show, in particular, that isoforms encoded by the NET1 gene APs, which are inversely regulated by estradiol, play distinct roles in cell adhesion and cell cycle regulation and that their expression is differentially associated with prognosis in ER(+) breast cancer. Altogether, this study identifies the patterns of AP regulation in ERGs and shows the contribution of AP-encoded isoforms to the estradiol-regulated transcriptome as well as their physiopathologic significance in breast cancer.
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Affiliation(s)
- Martin Dutertre
- Institut National de la Sante et de la Recherche Medicale, U590, Centre Léon Bérard, Lyon, France
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Pawlicki JM, Steitz JA. Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function. Trends Cell Biol 2009; 20:52-61. [PMID: 20004579 DOI: 10.1016/j.tcb.2009.10.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Revised: 10/15/2009] [Accepted: 10/20/2009] [Indexed: 10/20/2022]
Abstract
The expression of protein-coding genes is enhanced by the exquisite coupling of transcription by RNA polymerase II with pre-messenger RNA processing reactions, such as 5'-end capping, splicing and 3'-end formation. Integration between cotranscriptional processing events extends beyond the nucleus, as proteins that bind cotranscriptionally can affect the localization, translation and degradation of the mature messenger RNA. MicroRNAs are RNA polymerase II transcripts with crucial roles in the regulation of gene expression. Recent data demonstrate that processing of primary microRNA transcripts might be yet another cotranscriptional event that is woven into this elaborate nuclear network. This review discusses the extensive molecular interactions that couple the earliest steps in gene expression and therefore influence the final fate and function of the mature messenger RNA or microRNA produced.
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Affiliation(s)
- Jan M Pawlicki
- Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA
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Pawlicki JM, Steitz JA. Subnuclear compartmentalization of transiently expressed polyadenylated pri-microRNAs: processing at transcription sites or accumulation in SC35 foci. Cell Cycle 2009; 8:345-56. [PMID: 19177009 DOI: 10.4161/cc.8.3.7494] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally regulate expression of their target messenger RNAs. We recently demonstrated that primary miRNA transcripts (pri-miRNAs) retained at transcription sites are processed with enhanced efficiency, suggesting that pri-miRNA processing is coupled to transcription in mammalian cells. We also observed that transiently expressed pri-miRNAs accumulate in nuclear foci with splicing factor SC35 and Microprocessor components, Drosha and DGCR8. Here, we show that pri-miRNAs containing a self-cleaving hepatitis delta ribozyme accumulate in the nucleoplasm after release from their transcription sites, but are not efficiently processed. Pri-miRNAs with ribozyme-generated 3' ends do not localize to SC35-containing foci, whereas cleaved and polyadenylated pri-miRNA transcripts with or without the pre-miRNA hairpin do. Pri-miRNA/SC35 foci contain a number of proteins normally associated with SC35 domains, including ASF/SF2, PABII, and the prolyl isomerase, Pin1. In contrast, RNA polymerase II and PM/Scl-100 do not strongly colocalize with pri-miRNAs in SC35-containing foci. These data argue that pri-miRNA/SC35-containing foci are not major sites of pri-miRNA processing and that pri-miRNA processing is coupled to transcription. We discuss the implications of our findings relative to recent insights into miRNA biogenesis, mRNA metabolism, and the nuclear organization of gene expression.
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Affiliation(s)
- Jan M Pawlicki
- Department of Pharmacology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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