1
|
Wang M, Liang AM, Zhou ZZ, Pang TL, Fan YJ, Xu YZ. Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation. PLoS Genet 2023; 19:e1011021. [PMID: 37917726 PMCID: PMC10645366 DOI: 10.1371/journal.pgen.1011021] [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] [Received: 03/12/2023] [Revised: 11/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Small nuclear RNAs (snRNAs) are structural and functional cores of the spliceosome. In metazoan genomes, each snRNA has multiple copies/variants, up to hundreds in mammals. However, the expressions and functions of each copy/variant in one organism have not been systematically studied. Focus on U1 snRNA genes, we investigated all five copies in Drosophila melanogaster using two series of constructed strains. Analyses of transgenic flies that each have a U1 promoter-driven gfp revealed that U1:21D is the major and ubiquitously expressed copy, and the other four copies have specificities in developmental stages and tissues. Mutant strains that each have a precisely deleted copy of U1-gene exhibited various extents of defects in fly morphology or mobility, especially deletion of U1:82Eb. Interestingly, splicing was changed at limited levels in the deletion strains, while large amounts of differentially-expressed genes and alternative polyadenylation events were identified, showing preferences in the down-regulation of genes with 1-2 introns and selection of proximal sites for 3'-end polyadenylation. In vitro assays suggested that Drosophila U1 variants pulled down fewer SmD2 proteins compared to the canonical U1. This study demonstrates that all five U1-genes in Drosophila have physiological functions in development and play regulatory roles in transcription and 3'-end formation.
Collapse
Affiliation(s)
- Mei Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China, University of Chinese Academy of Sciences, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
- Shanghai Institute of Biological Products, Shanghai, China
| | - An-Min Liang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Zhen-Zhen Zhou
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Ting-Lin Pang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China, University of Chinese Academy of Sciences, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| |
Collapse
|
2
|
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: 38] [Impact Index Per Article: 12.7] [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.
Collapse
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
| |
Collapse
|
3
|
Miladi M, Montaseri S, Backofen R, Raden M. Integration of accessibility data from structure probing into RNA-RNA interaction prediction. Bioinformatics 2020; 35:2862-2864. [PMID: 30590479 PMCID: PMC6691327 DOI: 10.1093/bioinformatics/bty1029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/20/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
SUMMARY Experimental structure probing data has been shown to improve thermodynamics-based RNA secondary structure prediction. To this end, chemical reactivity information (as provided e.g. by SHAPE) is incorporated, which encodes whether or not individual nucleotides are involved in intra-molecular structure. Since inter-molecular RNA-RNA interactions are often confined to unpaired RNA regions, SHAPE data is even more promising to improve interaction prediction. Here, we show how such experimental data can be incorporated seamlessly into accessibility-based RNA-RNA interaction prediction approaches, as implemented in IntaRNA. This is possible via the computation and use of unpaired probabilities that incorporate the structure probing information. We show that experimental SHAPE data can significantly improve RNA-RNA interaction prediction. We evaluate our approach by investigating interactions of a spliceosomal U1 snRNA transcript with its target splice sites. When SHAPE data is incorporated, known target sites are predicted with increased precision and specificity. AVAILABILITY AND IMPLEMENTATION https://github.com/BackofenLab/IntaRNA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Milad Miladi
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany
| | - Soheila Montaseri
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany
| | - Rolf Backofen
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany.,Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg D-79104, Germany
| | - Martin Raden
- Department of Computer Science, Bioinformatics Group, University of Freiburg, Freiburg D-79110, Germany
| |
Collapse
|
4
|
Del Corpo O, Goguen RP, Malard CMG, Daher A, Colby-Germinario S, Scarborough RJ, Gatignol A. A U1i RNA that Enhances HIV-1 RNA Splicing with an Elongated Recognition Domain Is an Optimal Candidate for Combination HIV-1 Gene Therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 18:815-830. [PMID: 31734561 PMCID: PMC6861678 DOI: 10.1016/j.omtn.2019.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/27/2019] [Accepted: 10/12/2019] [Indexed: 11/30/2022]
Abstract
U1 interference (U1i) RNAs can be designed to correct splicing defects and target pathogenic RNA, such as HIV-1 RNA. In this study, we show that U1i RNAs that enhance HIV-1 RNA splicing are more effective at inhibiting HIV-1 production compared to top U1i RNAs that inhibit polyadenylation of HIV-1 RNA. A U1i RNA was also identified targeting a site upstream of the first splice acceptor site in the Gag coding region that was effective at inhibiting HIV-1 production. U1-T6, which enhanced HIV-1 RNA splicing, was superior to an antiviral short hairpin RNA (shRNA) currently in clinical trials. To increase specificity, the recognition domain of U1-T6 was elongated by 3–6 nt. The elongated molecules inhibited HIV-1 production from different HIV-1 strains, including one with a mismatch in the target site. These results suggest that lengthening the recognition domain can enhance the specificity of U1i RNAs for their intended target sites while at the same time allowing them to tolerate single mismatch mutations. Overall, our results demonstrate that U1-T6 with an elongated recognition domain inhibits HIV-1 production and has both the efficacy and specificity to be a promising candidate for HIV-1 gene therapy.
Collapse
Affiliation(s)
- Olivier Del Corpo
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada
| | - Ryan P Goguen
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada
| | - Camille M G Malard
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada
| | - Aïcha Daher
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada
| | | | - Robert J Scarborough
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada.
| | - Anne Gatignol
- Lady Davis Institute for Medical Research, Montréal, QC H3T 1E2, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 0G4, Canada.
| |
Collapse
|
5
|
Yeh CS, Wang Z, Miao F, Ma H, Kao CT, Hsu TS, Yu JH, Hung ET, Lin CC, Kuan CY, Tsai NC, Zhou C, Qu GZ, Jiang J, Liu G, Wang JP, Li W, Chiang VL, Chang TH, Lin YCJ. A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time. Genome Res 2019; 29:1343-1351. [PMID: 31186303 PMCID: PMC6673709 DOI: 10.1101/gr.245951.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/06/2019] [Indexed: 12/18/2022]
Abstract
Eukaryotic gene expression is often tightly regulated by interactions between transcription factors (TFs) and their DNA cis targets. Yeast one-hybrid (Y1H) is one of the most extensively used methods to discover these interactions. We developed a high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis. The system has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method. The system also offers the highest accuracy in identifying TF–DNA interactions that can be authenticated in vivo by chromatin immunoprecipitation. With these unique features, this meiosis-directed Y1H system is particularly suited for constructing novel and comprehensive genome-scale gene regulatory networks for various organisms.
Collapse
Affiliation(s)
- Chung-Shu Yeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Zhifeng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Fang Miao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Chung-Ting Kao
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Shu Hsu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biomedical Informatics and Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Jhong-He Yu
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Er-Tsi Hung
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Chang Lin
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Yu Kuan
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ni-Chiao Tsai
- Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guan-Zheng Qu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jing Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Guifeng Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.,Department of Life Sciences and Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695, USA
| |
Collapse
|