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Li F, Karimi N, Wang S, Pan T, Dong J, Wang X, Ma S, Shan Q, Liu C, Zhang Y, Li W, Feng G. mRNA isoform switches during mouse zygotic genome activation. Cell Prolif 2024; 57:e13655. [PMID: 38764347 PMCID: PMC11216927 DOI: 10.1111/cpr.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/29/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Affiliation(s)
- Fan Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Najmeh Karimi
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Tianshi Pan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
| | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Medical SchoolUniversity of Chinese Academy of SciencesBeijingChina
| | - Sinan Ma
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Qingtong Shan
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- College of Life SciencesNortheast Agricultural UniversityHarbinChina
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- Key Laboratory of Organ Regeneration and ReconstructionChinese Academy of SciencesBeijingChina
- Beijing Institute for Stem Cell and Regenerative MedicineBeijingChina
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2
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Rosa PMDS, Guedes PHE, Garcia JM, Oliveira CS. Cytoplasmic granules in bovine oocytes do not affect embryonic or fetal development. ZYGOTE 2024; 32:28-37. [PMID: 38047350 DOI: 10.1017/s0967199423000576] [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] [Indexed: 12/05/2023]
Abstract
Oocyte cytoplasmic evaluation is based on homogeneity and granular appearance. Our study investigated if a granular cytoplasm, highly heterogeneous, would affect oocyte competence in bovine. In two experiments, bovine cumulus-oocyte complexes (COCs) with homogeneous cytoplasm (control, CC) and granulated cytoplasm (granular, GC) were selected from a regular pool of COCs. Experiment 1 was performed with slaughterhouse ovaries, and Experiment 2 was carried out in Girolando COCs obtained from ovum pick-up. Granular oocytes had higher caspase 3 levels (66.17 ± 11.61 vs 172.08 ± 16.95, P < 0.01) and similar GAP junction activity (5.64 ± 0.45 vs 6.29 ± 0.29). ZAR1 relative mRNA amount was lower in granular oocytes (178.27 ± 151.63 vs 0.89 ± 0.89, P = 0.01) and no effect was detected for MATER, PPP2R1A, ENY2, IGF2R, and BMP15 genes. Despite molecular differences, no detrimental effect was detected on oocyte competence in GC oocytes. Cleavage (Experiment 1: 59.52 ± 7.21% vs 59.79 ± 6.10% and Experiment 2: 68.88 ± 4.82 vs 74.41 ± 5.89%) and blastocyst (Experiment 1: 29.28 ± 4.14% vs 23.15 ± 2.96% and Experiment 2: 21.11 ± 3.28% vs 21.02 ± 6.08%) rates were similar between CC and GC (Experiments 1 and 2, respectively). Post-transfer embryo development revealed that pregnancy (CC: 24.27 ± 9.70% vs GC: 26.31 ± 7.23%) and calving (23.68% vs 33.33%) rates and fetal growth were not affected by the presence of cytoplasmic granules. Our results demonstrated that oocytes with granular cytoplasm present equivalent efficiency for IVF and calf production compared with homogenous cytoplasm oocytes. This could be observed through similar cleavage, blastocyst rates, and fetal growth development. In addition to differences in oocyte gene expression related to oocyte quality, it seems not to affect oocyte developmental competence.
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Affiliation(s)
- Paola Maria da Silva Rosa
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave, Juiz de Fora, MG, Brazil36038-330
- Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University, Jaboticabal, SP14884-900, Brazil
| | | | - Joaquim Mansano Garcia
- Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University, Jaboticabal, SP14884-900, Brazil
| | - Clara Slade Oliveira
- Embrapa Dairy Cattle, 610 Eugenio do Nascimento Ave, Juiz de Fora, MG, Brazil36038-330
- Department of Preventive Veterinary Medicine and Animal Reproduction, São Paulo State University, Jaboticabal, SP14884-900, Brazil
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3
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An integrative analysis of enhancer of yellow 2 homolog (ENY2) as a molecular biomarker in pan-cancer. Funct Integr Genomics 2023; 23:72. [PMID: 36862319 DOI: 10.1007/s10142-023-01000-8] [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: 12/29/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023]
Abstract
ENY2 (Enhancer of yellow 2 transcription factor) is a transcription nuclear protein and primarily participates in the course of mRNA export and histone deubiquitination to influence gene expression. Current studies have shown that the expression of ENY2 is significantly upregulated in multiple cancers. However, the exact association between ENY2 and pan-cancers has not been fully established. Here, we comprehensively analyzed ENY2 from the online public database and The Cancer Genome Atlas (TCGA) database, including gene expression level in pan-cancer, comparison of ENY2 expression in different molecular and immune subtypes of pan-cancer, targeted protein, biological functions, molecular signatures, diagnostic and prognostic value in pan-cancer. Moreover, we focused on head and neck squamous cell carcinoma (HNSC) and explored ENY2 from the perspective of the correlations with clinical characteristics, prognosis, co-expression genes, differentially expressed genes (DEGs) and immune Infiltration. Our findings showed that the expression of ENY2 differed enormously not only in most cancer types but also in different molecular and immune subtypes of cancers. High accuracy in predicting cancers and notable correlations with prognosis of certain cancers suggested that ENY2 might be a potential diagnostic and prognostic biomarker of cancers. In addition, ENY2 was identified to be significantly correlated with clinical stage, gender, histologic grade and lymphovascular invasion in HNSC. Overexpression of ENY2 could lead to a worse overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI) in HNSC, especially in different clinical subgroups of HNSC. Taken together, ENY2 showed strong correlation with the diagnosis and prognosis of pan-cancer, and was an independent prognostic risk factor of HNSC, which may serve as a potential target for cancer management.
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4
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Oliete-Calvo P, Serrano-Quílez J, Nuño-Cabanes C, Pérez-Martínez ME, Soares LM, Dichtl B, Buratowski S, Pérez-Ortín JE, Rodríguez-Navarro S. A role for Mog1 in H2Bub1 and H3K4me3 regulation affecting RNAPII transcription and mRNA export. EMBO Rep 2018; 19:embr.201845992. [PMID: 30249596 DOI: 10.15252/embr.201845992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 12/11/2022] Open
Abstract
Monoubiquitination of histone H2B (to H2Bub1) is required for downstream events including histone H3 methylation, transcription, and mRNA export. The mechanisms and players regulating these events have not yet been completely delineated. Here, we show that the conserved Ran-binding protein Mog1 is required to sustain normal levels of H2Bub1 and H3K4me3 in Saccharomyces cerevisiae Mog1 is needed for gene body recruitment of Rad6, Bre1, and Rtf1 that are involved in H2B ubiquitination and genetically interacts with these factors. We provide evidence that the absence of MOG1 impacts on cellular processes such as transcription, DNA replication, and mRNA export, which are linked to H2Bub1. Importantly, the mRNA export defect in mog1Δ strains is exacerbated by the absence of factors that decrease H2Bub1 levels. Consistent with a role in sustaining H2Bub and H3K4me3 levels, Mog1 co-precipitates with components that participate in these modifications such as Bre1, Rtf1, and the COMPASS-associated factors Shg1 and Sdc1. These results reveal a novel role for Mog1 in H2B ubiquitination, transcription, and mRNA biogenesis.
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Affiliation(s)
- Paula Oliete-Calvo
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Joan Serrano-Quílez
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Gene expression and mRNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Carme Nuño-Cabanes
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.,Gene expression and mRNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - María E Pérez-Martínez
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Facultad de Biología, Universitat de València, Burjassot, Spain
| | - Luis M Soares
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Centre for Cellular and Molecular Biology, Deakin University, Geelong, Vic., Australia
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - José E Pérez-Ortín
- Departamento de Bioquímica y Biología Molecular and E.R.I. Biotecmed, Facultad de Biología, Universitat de València, Burjassot, Spain
| | - Susana Rodríguez-Navarro
- Gene expression and mRNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain .,Gene expression and mRNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
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5
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AbuQattam A, Serrano-Quílez J, Rodríguez-Navarro S, Gallego J. An exon three-way junction structure modulates splicing and degradation of the SUS1 yeast pre-mRNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:673-686. [PMID: 29966763 DOI: 10.1016/j.bbagrm.2018.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 06/04/2018] [Accepted: 06/22/2018] [Indexed: 12/18/2022]
Abstract
The SUS1 gene of Saccharomyces cerevisiae is unusual as it contains two introns and undergoes alternative splicing, retaining one or both introns depending on growth conditions. The exon located between the two introns can be skipped during splicing and has been detected in circular form. This exon (E2) has also been found to influence the splicing of the flanking introns, an unusual situation in budding yeast where splicing mainly relies on intron recognition. Using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), NMR spectroscopy, gel electrophoresis and UV thermal denaturation experiments combined with computational predictions, we show that E2 of SUS1 comprises a conserved double-helical stem topped by a three-way junction. One of the hairpins emerging from the junction exhibited significant thermal stability and was capped by a purine-rich loop structurally related to the substrate loop of the VS ribozyme. Cellular assays revealed that three mutants containing altered E2 structures had impaired SUS1 expression, and that a compensatory mutation restoring the conserved stem recovered expression to wild-type levels. Semi-quantitative RT-PCR measurements paralleled these results, and revealed that mutations in E2 altered splicing and transcript degradation processes. Thus, exon structure plays an important role in SUS1 RNA metabolism.
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Affiliation(s)
- Ali AbuQattam
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain; Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, C/ E. Primo Yúfera 3, 46012 Valencia, Spain
| | - Joan Serrano-Quílez
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), C/ Jaime Roig 11, 46010 Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, C/ E. Primo Yúfera 3, 46012 Valencia, Spain; Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (CSIC), C/ Jaime Roig 11, 46010 Valencia, Spain.
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, C/Quevedo 2, 46001 Valencia, Spain.
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6
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Pfab A, Bruckmann A, Nazet J, Merkl R, Grasser KD. The Adaptor Protein ENY2 Is a Component of the Deubiquitination Module of the Arabidopsis SAGA Transcriptional Co-activator Complex but not of the TREX-2 Complex. J Mol Biol 2018; 430:1479-1494. [PMID: 29588169 DOI: 10.1016/j.jmb.2018.03.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/20/2018] [Accepted: 03/20/2018] [Indexed: 12/26/2022]
Abstract
The conserved nuclear protein ENY2 (Sus1 in yeast) is involved in coupling transcription and mRNA export in yeast and metazoa, as it is a component both of the transcriptional co-activator complex SAGA and of the mRNA export complex TREX-2. Arabidopsis thaliana ENY2 is widely expressed in the plant and it localizes to the nucleoplasm, but unlike its yeast/metazoan orthologs, it is not enriched in the nuclear envelope. Affinity purification of ENY2 in combination with mass spectrometry revealed that it co-purified with SAGA components, but not with the nuclear pore-associated TREX-2. In addition, further targeted proteomics analyses by reciprocal tagging established the composition of the Arabidopsis SAGA complex consisting of the four modules HATm, SPTm, TAFm and DUBm, and that several SAGA subunits occur in alternative variants. While the HATm, SPTm and TAFm robustly co-purified with each other, the deubiquitination module (DUBm) appears to associate with the other SAGA modules more weakly/dynamically. Consistent with a homology model of the Arabidopsis DUBm, the SGF11 protein interacts directly with ENY2 and UBP22. Plants depleted in the DUBm components, SGF11 or ENY2, are phenotypically only mildly affected, but they contain increased levels of ubiquitinated histone H2B, indicating that the SAGA-DUBm has histone deubiquitination activity in plants. In addition to transcription-related proteins (i.e., transcript elongation factors, Mediator), many splicing factors were found to associate with SAGA, linking the SAGA complex and ongoing transcription with mRNA processing.
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Affiliation(s)
- Alexander Pfab
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Julian Nazet
- Department for Biochemistry II, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Rainer Merkl
- Department for Biochemistry II, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, Universitätsstr. 31, D-93053 Regensburg, Germany.
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7
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The evolutionarily conserved factor Sus1/ENY2 plays a role in telomere length maintenance. Curr Genet 2017; 64:635-644. [DOI: 10.1007/s00294-017-0778-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/02/2017] [Accepted: 11/03/2017] [Indexed: 11/26/2022]
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8
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AbuQattam A, Gallego J, Rodríguez-Navarro S. An intronic RNA structure modulates expression of the mRNA biogenesis factor Sus1. RNA (NEW YORK, N.Y.) 2016; 22:75-86. [PMID: 26546116 PMCID: PMC4691836 DOI: 10.1261/rna.054049.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/03/2015] [Indexed: 06/05/2023]
Abstract
Sus1 is a conserved protein involved in chromatin remodeling and mRNA biogenesis. Unlike most yeast genes, the SUS1 pre-mRNA of Saccharomyces cerevisiae contains two introns and is alternatively spliced, retaining one or both introns in response to changes in environmental conditions. SUS1 splicing may allow the cell to control Sus1 expression, but the mechanisms that regulate this process remain unknown. Using in silico analyses together with NMR spectroscopy, gel electrophoresis, and UV thermal denaturation experiments, we show that the downstream intron (I2) of SUS1 forms a weakly stable, 37-nucleotide stem-loop structure containing the branch site near its apical loop and the 3' splice site after the stem terminus. A cellular assay revealed that two of four mutants containing altered I2 structures had significantly impaired SUS1 expression. Semiquantitative RT-PCR experiments indicated that all mutants accumulated unspliced SUS1 pre-mRNA and/or induced distorted levels of fully spliced mRNA relative to wild type. Concomitantly, Sus1 cellular functions in histone H2B deubiquitination and mRNA export were affected in I2 hairpin mutants that inhibited splicing. This work demonstrates that I2 structure is relevant for SUS1 expression, and that this effect is likely exerted through modulation of splicing.
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Affiliation(s)
- Ali AbuQattam
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain Facultad de Medicina, Universidad Católica de Valencia, Valencia 46001, Spain
| | - José Gallego
- Facultad de Medicina, Universidad Católica de Valencia, Valencia 46001, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
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9
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Maksimenko O, Kyrchanova O, Bonchuk A, Stakhov V, Parshikov A, Georgiev P. Highly conserved ENY2/Sus1 protein binds to Drosophila CTCF and is required for barrier activity. Epigenetics 2014; 9:1261-70. [PMID: 25147918 DOI: 10.4161/epi.32086] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chromatin insulators affect interactions between promoters and enhancers/silencers and function as barriers for the spreading of repressive chromatin. Drosophila insulator protein dCTCF marks active promoters and boundaries of many histone H3K27 trimethylation domains associated with repressed chromatin. In particular, dCTCF binds to such boundaries between the parasegment-specific regulatory domains of the Bithorax complex. Here we demonstrate that the evolutionarily conserved protein ENY2 is recruited to the zinc-finger domain of dCTCF and is required for the barrier activity of dCTCF-dependent insulators in transgenic lines. Inactivation of ENY2 by RNAi in BG3 cells leads to the spreading of H3K27 trimethylation and Pc protein at several dCTCF boundaries. The results suggest that evolutionarily conserved ENY2 is responsible for barrier activity mediated by the dCTCF protein.
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Affiliation(s)
- Oksana Maksimenko
- Laboratory of Gene Expression Regulation in Development; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Olga Kyrchanova
- Group of Transcriptional Regulation; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Artem Bonchuk
- Group of Transcriptional Regulation; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Viacheslav Stakhov
- Laboratory of Gene Expression Regulation in Development; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Alexander Parshikov
- Department of the Control of Genetic Processes; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes; Institute of Gene Biology; Russian Academy of Sciences; Moscow, Russia
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10
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Hamperl S, Cimprich KA. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 2014; 19:84-94. [PMID: 24746923 PMCID: PMC4051866 DOI: 10.1016/j.dnarep.2014.03.023] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell.
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Affiliation(s)
- Stephan Hamperl
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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11
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Durairaj G, Sen R, Uprety B, Shukla A, Bhaumik SR. Sus1p facilitates pre-initiation complex formation at the SAGA-regulated genes independently of histone H2B de-ubiquitylation. J Mol Biol 2014; 426:2928-2941. [PMID: 24911582 DOI: 10.1016/j.jmb.2014.05.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/29/2014] [Accepted: 05/31/2014] [Indexed: 12/23/2022]
Abstract
Sus1p is a common component of transcriptional co-activator, SAGA (Spt-Ada-Gcn5-Acetyltransferase), and mRNA export complex, TREX-2 (Transcription-export 2), and is involved in promoting transcription and mRNA export. However, it is not clearly understood how Sus1p promotes transcription. Here, we show that Sus1p is predominantly recruited to the upstream activating sequence of a SAGA-dependent gene, GAL1, under transcriptionally active conditions as a component of SAGA to promote the formation of pre-initiation complex (PIC) at the core promoter and, consequently, transcriptional initiation. Likewise, Sus1p promotes the PIC formation at other SAGA-dependent genes and hence transcriptional initiation. Such function of Sus1p in promoting PIC formation and transcriptional initiation is not mediated via its role in regulation of SAGA's histone H2B de-ubiquitylation activity. However, Sus1p's function in regulation of histone H2B ubiquitylation is associated with transcriptional elongation, DNA repair and replication. Collectively, our results support that Sus1p promotes PIC formation (and hence transcriptional initiation) at the SAGA-regulated genes independently of histone H2B de-ubiquitylation and further controls transcriptional elongation, DNA repair and replication via orchestration of histone H2B ubiquitylation, thus providing distinct functional insights of Sus1p in regulation of DNA transacting processes.
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Affiliation(s)
- Geetha Durairaj
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Rwik Sen
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Bhawana Uprety
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Abhijit Shukla
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology Southern Illinois University School of Medicine Carbondale, IL-62901 USA
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12
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Pamblanco M, Oliete-Calvo P, García-Oliver E, Luz Valero M, Sanchez del Pino MM, Rodríguez-Navarro S. Unveiling novel interactions of histone chaperone Asf1 linked to TREX-2 factors Sus1 and Thp1. Nucleus 2014; 5:247-59. [PMID: 24824343 DOI: 10.4161/nucl.29155] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Anti-silencing function 1 (Asf1) is a conserved key eukaryotic histone H3/H4 chaperone that participates in a variety of DNA and chromatin-related processes. These include the assembly and disassembly of histones H3 and H4 from chromatin during replication, transcription, and DNA repair. In addition, Asf1 is required for H3K56 acetylation activity dependent on histone acetyltransferase Rtt109. Thus, Asf1 impacts on many aspects of DNA metabolism. To gain insights into the functional links of Asf1 with other cellular machineries, we employed mass spectrometry coupled to tandem affinity purification (TAP) to investigate novel physical interactions of Asf1. Under different TAP-MS analysis conditions, we describe a new repertoire of Asf1 physical interactions and novel Asf1 post-translational modifications as ubiquitination, methylation and acetylation that open up new ways to regulate Asf1 functions. Asf1 co-purifies with several subunits of the TREX-2, SAGA complexes, and with nucleoporins Nup2, Nup60, and Nup57, which are all involved in transcription coupled to mRNA export in eukaryotes. Reciprocally, Thp1 and Sus1 interact with Asf1. Albeit mRNA export and GAL1 transcription are not affected in asf1Δ a strong genetic interaction exists between ASF1 and SUS1. Notably, supporting a functional link between Asf1 and TREX-2, both Sus1 and Thp1 affect the levels of Asf1-dependent histone H3K56 acetylation and histone H3 and H4 incorporation onto chromatin. Additionally, we provide evidence for a role of Asf1 in histone H2B ubiquitination. This work proposes a functional link between Asf1 and TREX-2 components in histone metabolism at the vicinity of the nuclear pore complex.
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Affiliation(s)
- Mercè Pamblanco
- Departament de Bioquímica i Biologia Molecular; Universitat de València; Burjassot, Spain
| | - Paula Oliete-Calvo
- Gene Expression and RNA Metabolism Laboratory; Centro de Investigación Príncipe Felipe (CIPF); València, Spain
| | - Encar García-Oliver
- Gene Expression and RNA Metabolism Laboratory; Centro de Investigación Príncipe Felipe (CIPF); València, Spain
| | - M Luz Valero
- Secció de Proteòmica; Servei Central de Suport a la Investigació Experimental (SCSIE); Universitat de València; Burjassot, Spain
| | | | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory; Centro de Investigación Príncipe Felipe (CIPF); València, Spain
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13
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Gurskiy DY, Kopytova DV, Georgieva SG, Nabirochkina EN. SAGA complex: Role in viability and development. Mol Biol 2013. [DOI: 10.1134/s0026893313060071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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14
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Cunningham CN, Schmidt CA, Schramm NJ, Gaylord MR, Resendes KK. Human TREX2 components PCID2 and centrin 2, but not ENY2, have distinct functions in protein export and co-localize to the centrosome. Exp Cell Res 2013; 320:209-18. [PMID: 24291146 DOI: 10.1016/j.yexcr.2013.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 11/15/2022]
Abstract
TREX-2 is a five protein complex, conserved from yeast to humans, involved in linking mRNA transcription and export. The centrin 2 subunit of TREX-2 is also a component of the centrosome and is additionally involved in a distinctly different process of nuclear protein export. While centrin 2 is a known multifunctional protein, the roles of other human TREX-2 complex proteins other than mRNA export are not known. In this study, we found that human TREX-2 member PCID2 but not ENY2 is involved in some of the same cellular processes as those of centrin 2 apart from the classical TREX-2 function. PCID2 is present at the centrosome in a subset of HeLa cells and this localization is centrin 2 dependent. Furthermore, the presence of PCID2 at the centrosome is prevalent throughout the cell cycle as determined by co-staining with cyclins E, A and B. PCID2 but not ENY2 is also involved in protein export. Surprisingly, siRNA knockdown of PCID2 delayed the rate of nuclear protein export, a mechanism distinct from the effects of centrin 2, which when knocked down inhibits export. Finally we showed that co-depletion of centrin 2 and PCID2 leads to blocking rather than delaying nuclear protein export, indicating the dominance of the centrin 2 phenotype. Together these results represent the first discovery of specific novel functions for PCID2 other than mRNA export and suggest that components of the TREX-2 complex serve alternative shared roles in the regulation of nuclear transport and cell cycle progression.
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Affiliation(s)
- Corey N Cunningham
- Westminster College, Department of Biology, 319 South Market Street, New Wilmington, PA 16172, USA
| | - Casey A Schmidt
- Westminster College, Department of Biology, 319 South Market Street, New Wilmington, PA 16172, USA
| | - Nathaniel J Schramm
- Westminster College, Department of Biology, 319 South Market Street, New Wilmington, PA 16172, USA
| | - Michelle R Gaylord
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California - San Diego, 9500 Gilman Drive, #0347, La Jolla, CA 92093-0347, USA
| | - Karen K Resendes
- Westminster College, Department of Biology, 319 South Market Street, New Wilmington, PA 16172, USA.
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15
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LABRECQUE RÉMI, VIGNEAULT CHRISTIAN, BLONDIN PATRICK, SIRARD MARCANDRÉ. Gene Expression Analysis of Bovine Oocytes With High Developmental Competence Obtained From FSH-Stimulated Animals. Mol Reprod Dev 2013; 80:428-40. [DOI: 10.1002/mrd.22177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 03/21/2013] [Indexed: 11/11/2022]
Affiliation(s)
- RÉMI LABRECQUE
- Centre de recherche en biologie de la reproduction, Faculté des sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon INAF; Université Laval; Québec; Québec; Canada
| | | | | | - MARC-ANDRÉ SIRARD
- Centre de recherche en biologie de la reproduction, Faculté des sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon INAF; Université Laval; Québec; Québec; Canada
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