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Shine M, Gordon J, Schärfen L, Zigackova D, Herzel L, Neugebauer KM. Co-transcriptional gene regulation in eukaryotes and prokaryotes. Nat Rev Mol Cell Biol 2024; 25:534-554. [PMID: 38509203 PMCID: PMC11199108 DOI: 10.1038/s41580-024-00706-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 03/22/2024]
Abstract
Many steps of RNA processing occur during transcription by RNA polymerases. Co-transcriptional activities are deemed commonplace in prokaryotes, in which the lack of membrane barriers allows mixing of all gene expression steps, from transcription to translation. In the past decade, an extraordinary level of coordination between transcription and RNA processing has emerged in eukaryotes. In this Review, we discuss recent developments in our understanding of co-transcriptional gene regulation in both eukaryotes and prokaryotes, comparing methodologies and mechanisms, and highlight striking parallels in how RNA polymerases interact with the machineries that act on nascent RNA. The development of RNA sequencing and imaging techniques that detect transient transcription and RNA processing intermediates has facilitated discoveries of transcription coordination with splicing, 3'-end cleavage and dynamic RNA folding and revealed physical contacts between processing machineries and RNA polymerases. Such studies indicate that intron retention in a given nascent transcript can prevent 3'-end cleavage and cause transcriptional readthrough, which is a hallmark of eukaryotic cellular stress responses. We also discuss how coordination between nascent RNA biogenesis and transcription drives fundamental aspects of gene expression in both prokaryotes and eukaryotes.
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Affiliation(s)
- Morgan Shine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jackson Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Leonard Schärfen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dagmar Zigackova
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Lydia Herzel
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany.
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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2
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Wang Y, Zhang J, Li M, Jia M, Yang L, Wang T, Wang Y, Kang L, Li M, Kong L. Transcriptome and proteomic analysis of mpox virus F3L-expressing cells. Front Cell Infect Microbiol 2024; 14:1354410. [PMID: 38415010 PMCID: PMC10896956 DOI: 10.3389/fcimb.2024.1354410] [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: 12/12/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024] Open
Abstract
Background Monkeypox or mpox virus (mpox) is a double-stranded DNA virus that poses a significant threat to global public health security. The F3 protein, encoded by mpox, is an apoenzyme believed to possess a double-stranded RNA-binding domain (dsRBD). However, limited research has been conducted on its function. In this study, we present data on the transcriptomics and proteomics of F3L-transfected HEK293T cells, aiming to enhance our comprehension of F3L. Methods The gene expression profiles of pCAGGS-HA-F3L transfected HEK293T cells were analyzed using RNA-seq. Proteomics was used to identify and study proteins that interact with F3L. Real-time PCR was used to detect mRNA levels of several differentially expressed genes (DEGs) in HEK293T cells (or Vero cells) after the expression of F3 protein. Results A total of 14,822 genes were obtained in cells by RNA-Seq and 1,672 DEGs were identified, including 1,156 up-regulated genes and 516 down-regulated genes. A total of 27 cellular proteins interacting with F3 proteins were identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and 19 cellular proteins with large differences in abundance ratios were considered to be candidate cellular proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the DEGs were significantly enriched in immune-related pathways, including type I interferon signaling pathway, response to virus, RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, etc. Moreover, some selected DEGs were further confirmed by real-time PCR and the results were consistent with the transcriptome data. Proteomics data show that cellular proteins interacting with F3 proteins are mainly related to RNA splicing and protein translation. Conclusions Our analysis of transcriptomic and proteomic data showed that (1) F3L up-regulates the transcript levels of key genes in the innate immune signaling pathway, such as RIGI, MDA5, IRF5, IRF7, IRF9, ISG15, IFNA14, and elicits a broad spectrum of antiviral immune responses in the host. F3L also increases the expression of the FOS and JNK genes while decreasing the expression of TNFR2, these factors may ultimately induce apoptosis. (2) F3 protein interacts with host proteins involved in RNA splicing and protein translation, such as SNRNP70, POLR2H, HNRNPA1, DDX17, etc. The findings of this study shed light on the function of the F3 protein.
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Affiliation(s)
- Yihao Wang
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Junzhe Zhang
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Mingzhi Li
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Mengle Jia
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lingdi Yang
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Ting Wang
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Yu Wang
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lumei Kang
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Meifeng Li
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
| | - Lingbao Kong
- Institute of Pathogenic Microorganism, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- Nanchang City Key Laboratory of Animal Virus and Genetic Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, Jiangxi, China
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3
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Feng Q, Lin Z, Deng Y, Ran Y, Yu R, Xiang AP, Ye C, Yao C. The U1 antisense morpholino oligonucleotide (AMO) disrupts U1 snRNP structure to promote intronic PCPA modification of pre-mRNAs. J Biol Chem 2023; 299:104854. [PMID: 37224962 PMCID: PMC10404622 DOI: 10.1016/j.jbc.2023.104854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/26/2023] Open
Abstract
Functional depletion of the U1 small nuclear ribonucleoprotein (snRNP) with a 25 nt U1 AMO (antisense morpholino oligonucleotide) may lead to intronic premature cleavage and polyadenylation of thousands of genes, a phenomenon known as U1 snRNP telescripting; however, the underlying mechanism remains elusive. In this study, we demonstrated that U1 AMO could disrupt U1 snRNP structure both in vitro and in vivo, thereby affecting the U1 snRNP-RNAP polymerase II interaction. By performing chromatin immunoprecipitation sequencing for phosphorylation of Ser2 and Ser5 of the C-terminal domain of RPB1, the largest subunit of RNAP polymerase II, we showed that transcription elongation was disturbed upon U1 AMO treatment, with a particular high phosphorylation of Ser2 signal at intronic cryptic polyadenylation sites (PASs). In addition, we showed that core 3'processing factors CPSF/CstF are involved in the processing of intronic cryptic PAS. Their recruitment accumulated toward cryptic PASs upon U1 AMO treatment, as indicated by chromatin immunoprecipitation sequencing and individual-nucleotide resolution CrossLinking and ImmunoPrecipitation sequencing analysis. Conclusively, our data suggest that disruption of U1 snRNP structure mediated by U1 AMO provides a key for understanding the U1 telescripting mechanism.
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Affiliation(s)
- Qiumin Feng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zejin Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yi Ran
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Rui Yu
- Department of Biochemistry, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Andy Peng Xiang
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, Guangdong, China; Advanced Medical Technology Center, The first Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China; Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, China.
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4
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Li Y, Huang J, Zhu J, Bao L, Wang H, Jiang Y, Tian K, Wang R, Zheng H, Duan W, Lai W, Yi X, Zhu Y, Guo T, Ji X. Targeted protein degradation reveals RNA Pol II heterogeneity and functional diversity. Mol Cell 2022; 82:3943-3959.e11. [PMID: 36113479 DOI: 10.1016/j.molcel.2022.08.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 10/14/2022]
Abstract
RNA polymerase II (RNA Pol II) subunits are thought to be involved in various transcription-associated processes, but it is unclear whether they play different regulatory roles in modulating gene expression. Here, we performed nascent and mature transcript sequencing after the acute degradation of 12 mammalian RNA Pol II subunits and profiled their genomic binding sites and protein interactomes to dissect their molecular functions. We found that RNA Pol II subunits contribute differently to RNA Pol II cellular localization and transcription processes and preferentially regulate RNA processing (such as RNA splicing and 3' end maturation). Genes sensitive to the depletion of different RNA Pol II subunits tend to be involved in diverse biological functions and show different RNA half-lives. Sequences, associated protein factors, and RNA structures are correlated with RNA Pol II subunit-mediated differential gene expression. These findings collectively suggest that the heterogeneity of RNA Pol II and different genes appear to depend on some of the subunits.
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Affiliation(s)
- Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Tian
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - WenJia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weifeng Lai
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiao Yi
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Yi Zhu
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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5
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Hu Z, Li M, Huo Z, Chen L, Liu S, Deng K, Lu X, Chen S, Fu Y, Xu A. U1 snRNP proteins promote proximal alternative polyadenylation sites by directly interacting with 3' end processing core factors. J Mol Cell Biol 2022; 14:6694001. [PMID: 36073763 PMCID: PMC9926334 DOI: 10.1093/jmcb/mjac054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/14/2022] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, both alternative splicing and alternative polyadenylation (APA) play essential roles in the gene regulation network. U1 small ribonucleoprotein particle (U1 snRNP) is a major component of spliceosome, and U1 snRNP complex can suppress proximal APA sites through crosstalking with 3' end processing factors. However, here we show that both knockdown and overexpression of SNRPA, SNRPC, SNRNP70, and SNRPD2, the U1 snRNP proteins, promote the usage of proximal APA sites at the transcriptome level. SNRNP70 can drive the phase transition of PABPN1 from droplet to aggregate, which may reduce the repressive effects of PABPN1 on the proximal APA sites. Additionally, SNRNP70 can also promote the proximal APA sites by recruiting CPSF6, suggesting that the function of CPSF6 on APA is related with other RNA-binding proteins and cell context-dependent. Consequently, these results reveal that, on the contrary to U1 snRNP complex, the free proteins of U1 snRNP complex can promote proximal APA sites through the interaction with 3' end processing machinery.
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Affiliation(s)
| | | | | | - Liutao Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Susu Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Ke Deng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Xin Lu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Higher Education Mega Center, Guangzhou 510006, China
| | | | - Anlong Xu
- Correspondence to: Anlong Xu, E-mail:
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6
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Rovira E, Moreno B, Razquin N, Hjerpe R, Gonzalez-Lopez M, Barrio R, Ruiz de los Mozos I, Ule J, Pastor F, Blazquez L, Fortes P. U1A is a positive regulator of the expression of heterologous and cellular genes involved in cell proliferation and migration. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:831-846. [PMID: 35664701 PMCID: PMC9136276 DOI: 10.1016/j.omtn.2022.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 05/07/2022] [Indexed: 11/16/2022]
Abstract
Here, we show that direct recruitment of U1A to target transcripts can increase gene expression. This is a new regulatory role, in addition to previous knowledge showing that U1A decreases the levels of U1A mRNA and other specific targets. In fact, genome-wide, U1A more often increases rather than represses gene expression and many U1A-upregulated transcripts are directly bound by U1A according to individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) studies. Interestingly, U1A-mediated positive regulation can be transferred to a heterologous system for biotechnological purposes. Finally, U1A-bound genes are enriched for those involved in cell cycle and adhesion. In agreement with this, higher U1A mRNA expression associates with lower disease-free survival and overall survival in many cancer types, and U1A mRNA levels positively correlate with those of some oncogenes involved in cell proliferation. Accordingly, U1A depletion leads to decreased expression of these genes and the migration-related gene CCN2/CTGF, which shows the strongest regulation by U1A. A decrease in U1A causes a strong drop in CCN2 expression and CTGF secretion and defects in the expression of CTGF EMT targets, cell migration, and proliferation. These results support U1A as a putative therapeutic target for cancer treatment. In addition, U1A-binding sequences should be considered in biotechnological applications.
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Affiliation(s)
- Eric Rovira
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
| | - Beatriz Moreno
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
| | - Nerea Razquin
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
| | - Roland Hjerpe
- Department of Functional Genomics, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Monika Gonzalez-Lopez
- Department of Functional Genomics, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Rosa Barrio
- Department of Functional Genomics, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Igor Ruiz de los Mozos
- Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK
- RNA Networks Lab, The Francis Crick Institute, NW11BF London, UK
| | - Jernej Ule
- Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK
- RNA Networks Lab, The Francis Crick Institute, NW11BF London, UK
| | - Fernando Pastor
- Department of Molecular Therapy, Aptamer Unit, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
| | - Lorea Blazquez
- Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK
- RNA Networks Lab, The Francis Crick Institute, NW11BF London, UK
- Neurosciences Area, Biodonostia Health Research Institute, 20014 San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
- Corresponding author. Lorea Blazquez, Department of Neuromuscular Diseases, Institute of Neurology, UCL, WC1B5EH London, UK.
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), 31008 Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
- Corresponding author. Puri Fortes, Neurosciences Area, Biodonostia Health Research Institute, 20014 San Sebastian, Spain.
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7
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Abstract
U1 snRNP is one of the most abundant ribonucleoprotein (RNP) complexes in eukaryotic cells and is estimated to be approximately 1 million copies per cell. Apart from its canonical role in mRNA splicing, this complex has emerged as a key regulator of eukaryotic mRNA length via inhibition of mRNA 3'-end processing at numerous intronic polyadenylation sites, in a process that is also termed 'U1 snRNP telescripting'. Several reviews have extensively described the concept of U1 telescripting and subsequently highlighted its potential impacts in mRNA metabolism. Here, we review what is currently known regarding the underlying mechanisms of this important phenomenon and discuss open questions and future challenges.
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Affiliation(s)
- Yi Ran
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Yanhui Deng
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Chengguo Yao
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.,Department of Genetics and Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
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8
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Reimer KA, Mimoso CA, Adelman K, Neugebauer KM. Co-transcriptional splicing regulates 3' end cleavage during mammalian erythropoiesis. Mol Cell 2021; 81:998-1012.e7. [PMID: 33440169 DOI: 10.1016/j.molcel.2020.12.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
Pre-mRNA processing steps are tightly coordinated with transcription in many organisms. To determine how co-transcriptional splicing is integrated with transcription elongation and 3' end formation in mammalian cells, we performed long-read sequencing of individual nascent RNAs and precision run-on sequencing (PRO-seq) during mouse erythropoiesis. Splicing was not accompanied by transcriptional pausing and was detected when RNA polymerase II (Pol II) was within 75-300 nucleotides of 3' splice sites (3'SSs), often during transcription of the downstream exon. Interestingly, several hundred introns displayed abundant splicing intermediates, suggesting that splicing delays can take place between the two catalytic steps. Overall, splicing efficiencies were correlated among introns within the same transcript, and intron retention was associated with inefficient 3' end cleavage. Remarkably, a thalassemia patient-derived mutation introducing a cryptic 3'SS improved both splicing and 3' end cleavage of individual β-globin transcripts, demonstrating functional coupling between the two co-transcriptional processes as a determinant of productive gene output.
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Affiliation(s)
- Kirsten A Reimer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Claudia A Mimoso
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
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