1
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Bao N, Wang Z, Fu J, Dong H, Jin Y. RNA structure in alternative splicing regulation: from mechanism to therapy. Acta Biochim Biophys Sin (Shanghai) 2024; 57:3-21. [PMID: 39034824 PMCID: PMC11802352 DOI: 10.3724/abbs.2024119] [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: 04/28/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Alternative splicing is a highly intricate process that plays a crucial role in post-transcriptional regulation and significantly expands the functional proteome of a limited number of coding genes in eukaryotes. Its regulation is multifactorial, with RNA structure exerting a significant impact. Aberrant RNA conformations lead to dysregulation of splicing patterns, which directly affects the manifestation of disease symptoms. In this review, the molecular mechanisms of RNA secondary structure-mediated splicing regulation are summarized, with a focus on the complex interplay between aberrant RNA conformations and disease phenotypes resulted from splicing defects. This study also explores additional factors that reshape structural conformations, enriching our understanding of the mechanistic network underlying structure-mediated splicing regulation. In addition, an emphasis has been placed on the clinical role of targeting aberrant splicing corrections in human diseases. The principal mechanisms of action behind this phenomenon are described, followed by a discussion of prospective development strategies and pertinent challenges.
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Affiliation(s)
- Nengcheng Bao
- />MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkCollege of Life SciencesZhejiang UniversityHangzhou310058China
| | - Zhechao Wang
- />MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkCollege of Life SciencesZhejiang UniversityHangzhou310058China
| | - Jiayan Fu
- />MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkCollege of Life SciencesZhejiang UniversityHangzhou310058China
| | - Haiyang Dong
- />MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkCollege of Life SciencesZhejiang UniversityHangzhou310058China
| | - Yongfeng Jin
- />MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling NetworkCollege of Life SciencesZhejiang UniversityHangzhou310058China
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2
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Li H, Ding Z, Fang ZY, Long N, Ang HY, Zhang Y, Fan YJ, Xu YZ. Conserved intronic secondary structures with concealed branch sites regulate alternative splicing of poison exons. Nucleic Acids Res 2024; 52:6002-6016. [PMID: 38499485 PMCID: PMC11162794 DOI: 10.1093/nar/gkae185] [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: 09/15/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Alternative splicing (AS) generates multiple RNA isoforms and increases the complexities of transcriptomes and proteomes. However, it remains unclear how RNA structures contribute to AS regulation. Here, we systematically search transcriptomes for secondary structures with concealed branch sites (BSs) in the alternatively spliced introns and predict thousands of them from six organisms, of which many are evolutionarily conserved. Intriguingly, a highly conserved stem-loop structure with concealed BSs is found in animal SF3B3 genes and colocalizes with a downstream poison exon (PE). Destabilization of this structure allows increased usage of the BSs and results in enhanced PE inclusion in human and Drosophila cells, leading to decreased expression of SF3B3. This structure is experimentally validated using an in-cell SHAPE-MaP assay. Through RNA interference screens of 28 RNA-binding proteins, we find that this stem-loop structure is sensitive to U2 factors. Furthermore, we find that SF3B3 also facilitates DNA repair and protects genome stability by enhancing interaction between ERCC6/CSB and arrested RNA polymerase II. Importantly, both Drosophila and human cells with the secondary structure mutated by genome editing exhibit altered DNA repair in vivo. This study provides a novel and common mechanism for AS regulation of PEs and reveals a physiological function of SF3B3 in DNA repair.
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Affiliation(s)
- Hao Li
- 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 430072, China
| | - Zhan Ding
- 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 430072, China
| | - Zhuo-Ya Fang
- 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 430072, China
| | - Ni Long
- 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 430072, China
| | - Hao-Yang Ang
- 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 430072, China
| | - Yu Zhang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - 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 430072, 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 430072, China
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3
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Lu S, Tang Y, Yin S, Sun L. RNA structure: implications in viral infections and neurodegenerative diseases. ADVANCED BIOTECHNOLOGY 2024; 2:3. [PMID: 39883271 PMCID: PMC11740852 DOI: 10.1007/s44307-024-00010-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/31/2025]
Abstract
RNA is an intermediary between DNA and protein, a catalyzer of biochemical reactions, and a regulator of genes and transcripts. RNA structures are essential for complicated functions. Recent years have witnessed rapid advancements in RNA secondary structure probing techniques. These technological strides provided comprehensive insights into RNA structures, which significantly contributed to our understanding of diverse cellular regulatory processes, including gene regulation, epigenetic regulation, and post-transactional regulation. Meanwhile, they have facilitated the creation of therapeutic tools for tackling human diseases. Despite their therapeutic applications, RNA structure probing methods also offer a promising avenue for exploring the mechanisms of human diseases, potentially providing the key to overcoming existing research constraints and obtaining the in-depth information necessary for a deeper understanding of disease mechanisms.
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Affiliation(s)
- Suiru Lu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China
- Taishan College, Shandong University, Qingdao, 266237, China
| | - Yongkang Tang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Shaozhen Yin
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Lei Sun
- Pingyuan Laboratory, Xinxiang, Henan, 453007, China.
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, 266237, China.
- Taishan College, Shandong University, Qingdao, 266237, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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4
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Dong H, Li J, Wu Q, Jin Y. Confluence and convergence of Dscam and Pcdh cell-recognition codes. Trends Biochem Sci 2023; 48:1044-1057. [PMID: 37839971 DOI: 10.1016/j.tibs.2023.09.001] [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: 07/19/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 10/17/2023]
Abstract
The ability of neurites of the same neuron to avoid each other (self-avoidance) is a conserved feature in both invertebrates and vertebrates. The key to self-avoidance is the generation of a unique subset of cell-surface proteins in individual neurons engaging in isoform-specific homophilic interactions that drive neurite repulsion rather than adhesion. Among these cell-surface proteins are fly Dscam1 and vertebrate clustered protocadherins (cPcdhs), as well as the recently characterized shortened Dscam (sDscam) in the Chelicerata. Herein, we review recent advances in our understanding of how cPcdh, Dscam, and sDscam cell-surface recognition codes are expressed and translated into cellular functions essential for neural wiring.
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Affiliation(s)
- Haiyang Dong
- The First Affiliated Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, China; MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Jinhuan Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Systems Medicine for Cancer, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yongfeng Jin
- The First Affiliated Hospital, School of Medicine, Zhejiang University, 310006, Hangzhou, China; MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China.
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5
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Zhang S, Yang X, Dong H, Xu B, Wu L, Zhang J, Li G, Guo P, Li L, Fu Y, Du Y, Zhu Y, Shi J, Shi F, Huang J, He H, Jin Y. Cis mutagenesis in vivo reveals extensive noncanonical functions of Dscam1 isoforms in neuronal wiring. PNAS NEXUS 2023; 2:pgad135. [PMID: 37152679 PMCID: PMC10156172 DOI: 10.1093/pnasnexus/pgad135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/09/2023]
Abstract
Drosophila Down syndrome cell adhesion molecule 1 (Dscam1) encodes tens of thousands of cell recognition molecules via alternative splicing, which are required for neural function. A canonical self-avoidance model seems to provide a central mechanistic basis for Dscam1 functions in neuronal wiring. Here, we reveal extensive noncanonical functions of Dscam1 isoforms in neuronal wiring. We generated a series of allelic cis mutations in Dscam1, encoding a normal number of isoforms, but with an altered isoform composition. Despite normal dendritic self-avoidance and self-/nonself-discrimination in dendritic arborization (da) neurons, which is consistent with the canonical self-avoidance model, these mutants exhibited strikingly distinct spectra of phenotypic defects in the three types of neurons: up to ∼60% defects in mushroom bodies, a significant increase in branching and growth in da neurons, and mild axonal branching defects in mechanosensory neurons. Remarkably, the altered isoform composition resulted in increased dendrite growth yet inhibited axon growth. Moreover, reducing Dscam1 dosage exacerbated axonal defects in mushroom bodies and mechanosensory neurons but reverted dendritic branching and growth defects in da neurons. This splicing-tuned regulation strategy suggests that axon and dendrite growth in diverse neurons cell-autonomously require Dscam1 isoform composition. These findings provide important insights into the functions of Dscam1 isoforms in neuronal wiring.
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Affiliation(s)
| | | | - Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Lili Wu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Jian Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Guo Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Pengjuan Guo
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Lei Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Yiwen Du
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Jilong Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou ZJ310058, People's Republic of China
| | - Jianhua Huang
- Institute of Insect Sciences, Zhejiang University, Hangzhou ZJ310058, People’s Republic of China
| | - Haihuai He
- To whom correspondence should be addressed: (H.H.); (Y.J.)
| | - Yongfeng Jin
- To whom correspondence should be addressed: (H.H.); (Y.J.)
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6
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Reis RS. Thermomorphogenesis: Opportunities and challenges in posttranscriptional regulation. JOURNAL OF EXPERIMENTAL BOTANY 2023:7134107. [PMID: 37082809 DOI: 10.1093/jxb/erad134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 05/03/2023]
Abstract
Plants exposed to mildly elevated temperatures display morphological and developmental changes collectively termed thermomorphogenesis. This adaptative process has several undesirable consequences to food production, including yield reduction and increased vulnerability to pathogens. Understanding thermomorphogenesis is, thus, critical for understanding how plants will respond to increasingly warmer temperature conditions, such as those caused by climate change. Recently, we have made major advances in that direction, and it has become apparent that plants resource to a broad range of molecules and molecular mechanisms to perceive and respond to increases in environmental temperature. However, most of our efforts have been focused on regulation of transcription and protein abundance and activity, with an important gap encompassing nearly all processes involving RNA (i.e., posttranscriptional regulation). Here, I summarized our current knowledge of thermomorphogenesis involving transcriptional, posttranscriptional, and posttranslational regulation, focused on opportunities and challenges in understanding posttranscriptional regulation-a fertile field for exciting new discoveries.
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Affiliation(s)
- Rodrigo S Reis
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, Bern, Switzerland
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7
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Hou S, Li G, Xu B, Dong H, Zhang S, Fu Y, Shi J, Li L, Fu J, Shi F, Meng Y, Jin Y. Trans-splicing facilitated by RNA pairing greatly expands sDscam isoform diversity but not homophilic binding specificity. SCIENCE ADVANCES 2022; 8:eabn9458. [PMID: 35857463 PMCID: PMC9258826 DOI: 10.1126/sciadv.abn9458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
The Down syndrome cell adhesion molecule 1 (Dscam1) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for nervous and immune functions. Chelicerates generate approximately 50 to 100 shortened Dscam (sDscam) isoforms by alternative promoters, similar to mammalian protocadherins. Here, we reveal that trans-splicing markedly increases the repository of sDscamβ isoforms in Tetranychus urticae. Unexpectedly, every variable exon cassette engages in trans-splicing with constant exons from another cluster. Moreover, we provide evidence that competing RNA pairing not only governs alternative cis-splicing but also facilitates trans-splicing. Trans-spliced sDscam isoforms mediate cell adhesion ability but exhibit the same homophilic binding specificity as their cis-spliced counterparts. Thus, we reveal a single sDscam locus that generates diverse adhesion molecules through cis- and trans-splicing coupled with alternative promoters. These findings expand understanding of the mechanism underlying molecular diversity and have implications for the molecular control of neuronal and/or immune specificity.
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Affiliation(s)
- Shouqing Hou
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Guo Li
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Jilong Shi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Lei Li
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Jiayan Fu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang ZJ310018, P. R. China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, P. R. China
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8
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Xu B, Zhu Y, Cao C, Chen H, Jin Q, Li G, Ma J, Yang SL, Zhao J, Zhu J, Ding Y, Fang X, Jin Y, Kwok CK, Ren A, Wan Y, Wang Z, Xue Y, Zhang H, Zhang QC, Zhou Y. Recent advances in RNA structurome. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1285-1324. [PMID: 35717434 PMCID: PMC9206424 DOI: 10.1007/s11427-021-2116-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 12/27/2022]
Abstract
RNA structures are essential to support RNA functions and regulation in various biological processes. Recently, a range of novel technologies have been developed to decode genome-wide RNA structures and novel modes of functionality across a wide range of species. In this review, we summarize key strategies for probing the RNA structurome and discuss the pros and cons of representative technologies. In particular, these new technologies have been applied to dissect the structural landscape of the SARS-CoV-2 RNA genome. We also summarize the functionalities of RNA structures discovered in different regulatory layers-including RNA processing, transport, localization, and mRNA translation-across viruses, bacteria, animals, and plants. We review many versatile RNA structural elements in the context of different physiological and pathological processes (e.g., cell differentiation, stress response, and viral replication). Finally, we discuss future prospects for RNA structural studies to map the RNA structurome at higher resolution and at the single-molecule and single-cell level, and to decipher novel modes of RNA structures and functions for innovative applications.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Changchang Cao
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Qiongli Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Guangnan Li
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Junfeng Ma
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Siwy Ling Yang
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Jieyu Zhao
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Jianghui Zhu
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection, Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Chun Kit Kwok
- Department of Chemistry, and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, 518057, China.
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
| | - Yue Wan
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yuanchao Xue
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100101, China.
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Yu Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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9
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Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
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Affiliation(s)
- Ilias Georgakopoulos-Soares
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Guillermo E. Parada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5A 1A8, Canada
| | - Martin Hemberg
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
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10
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Dong H, Xu B, Guo P, Zhang J, Yang X, Li L, Fu Y, Shi J, Zhang S, Zhu Y, Shi Y, Zhou F, Bian L, You W, Shi F, Yang X, Huang J, He H, Jin Y. Hidden RNA pairings counteract the "first-come, first-served" splicing principle to drive stochastic choice in Dscam1 splice variants. SCIENCE ADVANCES 2022; 8:eabm1763. [PMID: 35080968 PMCID: PMC8791459 DOI: 10.1126/sciadv.abm1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drosophila melanogaster Dscam1 encodes 38,016 isoforms via mutually exclusive splicing; however, the regulatory mechanism behind this is not fully understood. Here, we found a set of hidden RNA secondary structures that balance the stochastic choice of Dscam1 splice variants (designated balancer RNA secondary structures). In vivo mutational analyses revealed the dual function of these balancer interactions in driving the stochastic choice of splice variants, through enhancement of the inclusion of distal exon 6s by cooperating with docking site–selector pairing to form a stronger multidomain pre-mRNA structure and through simultaneous repression of the inclusion of proximal exon 6s by antagonizing their docking site–selector pairings. Thus, we provide an elegant molecular model based on competition and cooperation between two sets of docking site–selector and balancer pairings, which counteracts the “first-come, first-served” principle. Our findings provide conceptual and mechanistic insight into the dynamics and functions of long-range RNA secondary structures.
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Affiliation(s)
- Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Pengjuan Guo
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xi Yang
- Department of Neurosurgery and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu China
| | - Lei Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jilong Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanda Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fengyan Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lina Bian
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wendong You
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofeng Yang
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianhua Huang
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Haihuai He
- Department of Neurosurgery and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
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11
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Williams DL, Sikora VM, Hammer MA, Amin S, Brinjikji T, Brumley EK, Burrows CJ, Carrillo PM, Cromer K, Edwards SJ, Emri O, Fergle D, Jenkins MJ, Kaushik K, Maydan DD, Woodard W, Clowney EJ. May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression. Front Cell Dev Biol 2022; 9:720798. [PMID: 35087825 PMCID: PMC8787164 DOI: 10.3389/fcell.2021.720798] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 11/24/2021] [Indexed: 12/30/2022] Open
Abstract
How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.
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Affiliation(s)
- Donnell L. Williams
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Veronica Maria Sikora
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Max A. Hammer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Sayali Amin
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Taema Brinjikji
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Emily K. Brumley
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Connor J. Burrows
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Paola Michelle Carrillo
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Kirin Cromer
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Summer J. Edwards
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Olivia Emri
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniel Fergle
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - M. Jamal Jenkins
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
| | - Krishangi Kaushik
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Daniella D. Maydan
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - Wrenn Woodard
- MCDB 464 – Cellular Diversity in the Immune and Nervous Systems, University of Michigan, Ann Arbor, MI, United States
| | - E. Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI, United States
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12
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Li W. Dscam in arthropod immune priming: What is known and what remains unknown. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 125:104231. [PMID: 34390752 DOI: 10.1016/j.dci.2021.104231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
A popular view in the current academic circle is that invertebrates have no adaptive immunity. However, the immune memory and specificity of invertebrates pose a serious challenge to this view and constitute immune priming based on innate immunity. The Down syndrome cell adhesion molecule (Dscam) gene of invertebrates, with approximately 10,000 alternatively spliced isoforms, has a unique characteristic: it specifically binds to different types of bacteria and promotes cell phagocytosis; owing to its antibody-like function, Dscam is a key candidate protein for immune priming. However, the high molecular diversity of Dscam and the gaps and inconsistencies in the existing research make the study of regulation of immune priming by Dscam challenging. In recent years, significant research has been conducted on the Dscam-regulated immune functions in insects and crustaceans, providing preliminary results for Dscam-regulated innate immunity and immune priming, but some important questions remain unresolved. In this review, we summarize the existing knowledge about Dscam-regulated immunity and discuss three yet unanswered questions, the study of which may improve the understanding of the role of Dscam-regulated immune priming in invertebrates.
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Affiliation(s)
- Weiwei Li
- Laboratory of Invertebrate Immunological Defense, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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13
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Meher PK, Satpathy S. Improved recognition of splice sites in A. thaliana by incorporating secondary structure information into sequence-derived features: a computational study. 3 Biotech 2021; 11:484. [PMID: 34790508 DOI: 10.1007/s13205-021-03036-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/18/2021] [Indexed: 10/19/2022] Open
Abstract
Identification of splice sites is an important aspect with regard to the prediction of gene structure. In most of the existing splice site prediction studies, machine learning algorithms coupled with sequence-derived features have been successfully employed for splice site recognition. However, the splice site identification by incorporating the secondary structure information is lacking, particularly in plant species. Thus, we made an attempt in this study to evaluate the performance of structural features on the splice site prediction accuracy in Arabidopsis thaliana. Prediction accuracies were evaluated with the sequence-derived features alone as well as by incorporating the structural features into the sequence-derived features, where support vector machine (SVM) was employed as prediction algorithm. Both short (40 base pairs) and long (105 base pairs) sequence datasets were considered for evaluation. After incorporating the secondary structure features, improvements in accuracies were observed only for the longer sequence dataset and the improvement was found to be higher with the sequence-derived features that accounted nucleotide dependencies. On the other hand, either a little or no improvement in accuracies was found for the short sequence dataset. The performance of SVM was further compared with that of LogitBoost, Random Forest (RF), AdaBoost and XGBoost machine learning methods. The prediction accuracies of SVM, AdaBoost and XGBoost were observed to be at par and higher than that of RF and LogitBoost algorithms. While prediction was performed by taking all the sequence-derived features along with the structural features, a little improvement in accuracies was found as compared to the combination of individual sequence-based features and structural features. To the best of our knowledge, this is the first attempt concerning the computational prediction of splice sites using machine learning methods by incorporating the secondary structure information into the sequence-derived features. All the source codes are available at https://github.com/meher861982/SSFeature. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03036-8.
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14
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Cao D. Reverse complementary matches simultaneously promote both back-splicing and exon-skipping. BMC Genomics 2021; 22:586. [PMID: 34344317 PMCID: PMC8330042 DOI: 10.1186/s12864-021-07910-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Circular RNAs (circRNAs) play diverse roles in different biological and physiological environments and are always expressed in a tissue-specific manner. Especially, circRNAs are enriched in the brain tissues of almost all investigated species, including humans, mice, Drosophila, etc. Although circRNAs were found in C. elegans, the neuron-specific circRNA data is not available yet. Exon-skipping is found to be correlated to circRNA formation, but the mechanisms that link them together are not clear. Results Here, through large-scale neuron isolation from the first larval (L1) stage of C. elegans followed by RNA sequencing with ribosomal RNA depletion, the neuronal circRNA data in C. elegans were obtained. Hundreds of novel circRNAs were annotated with high accuracy. circRNAs were highly expressed in the neurons of C. elegans and were positively correlated to the levels of their cognate linear mRNAs. Disruption of reverse complementary match (RCM) sequences in circRNA flanking introns effectively abolished circRNA formation. In the zip-2 gene, deletion of either upstream or downstream RCMs almost eliminated the production of both the circular and the skipped transcript. Interestingly, the 13-nt RCM in zip-2 is highly conserved across five nematode ortholog genes, which show conserved exon-skipping patterns. Finally, through in vivo one-by-one mutagenesis of all the splicing sites and branch points required for exon-skipping and back-splicing in the zip-2 gene, I showed that back-splicing still happened without exon-skipping, and vice versa. Conclusions Through protocol optimization, total RNA obtained from sorted neurons is increased to hundreds of nanograms. circRNAs highly expressed in the neurons of C. elegans are more likely to be derived from genes also highly expressed in the neurons. RCMs are abundant in circRNA flanking introns, and RCM-deletion is an efficient way to knockout circRNAs. More importantly, these RCMs are not only required for back-splicing but also promote the skipping of exon(s) to be circularized. Finally, RCMs in circRNA flanking introns can directly promote both exon-skipping and back-splicing, providing a new explanation for the correlation between them. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07910-w.
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Affiliation(s)
- Dong Cao
- Information Processing Biology Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, 904-0495, Okinawa, Japan.
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15
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Hong W, Zhang J, Dong H, Shi Y, Ma H, Zhou F, Xu B, Fu Y, Zhang S, Hou S, Li G, Wu Y, Chen S, Zhu X, You W, Shi F, Yang X, Gong Z, Huang J, Jin Y. Intron-targeted mutagenesis reveals roles for Dscam1 RNA pairing architecture-driven splicing bias in neuronal wiring. Cell Rep 2021; 36:109373. [PMID: 34260933 DOI: 10.1016/j.celrep.2021.109373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/05/2021] [Accepted: 06/18/2021] [Indexed: 12/28/2022] Open
Abstract
Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam1) can generate 38,016 different isoforms through largely stochastic, yet highly biased, alternative splicing. These isoforms are required for nervous functions. However, the functional significance of splicing bias remains unknown. Here, we provide evidence that Dscam1 splicing bias is required for mushroom body (MB) axonal wiring. We generate mutant flies with normal overall protein levels and an identical number but global changes in exon 4 and 9 isoform bias (DscamΔ4D-/- and DscamΔ9D-/-), respectively. In contrast to DscamΔ4D-/-, DscamΔ9D-/- exhibits remarkable MB defects, suggesting a variable domain-specific requirement for isoform bias. Importantly, changes in isoform bias cause axonal defects but do not influence the self-avoidance of axonal branches. We conclude that, in contrast to the isoform number that provides the molecular basis for neurite self-avoidance, isoform bias may play a role in MB axonal wiring by influencing non-repulsive signaling.
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Affiliation(s)
- Weiling Hong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Jian Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Hongru Ma
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Fengyan Zhou
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shouqing Hou
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Guo Li
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yandan Wu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shuo Chen
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Xiaohua Zhu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Wendong You
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Xiaofeng Yang
- Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Zhefeng Gong
- Department of Neuroscience, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Jianhua Huang
- Institute of Insect Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China; Department of Neurosurgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China.
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16
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Conboy JG. Unannotated splicing regulatory elements in deep intron space. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1656. [PMID: 33887804 DOI: 10.1002/wrna.1656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/14/2021] [Accepted: 03/23/2021] [Indexed: 12/21/2022]
Abstract
Deep intron space harbors a diverse array of splicing regulatory elements that cooperate with better-known exon-proximal elements to enforce proper tissue-specific and development-specific pre-mRNA processing. Many deep intron elements have been highly conserved through vertebrate evolution, yet remain poorly annotated in the human genome. Recursive splicing exons (RS-exons) and intraexons promote noncanonical, multistep resplicing pathways in long introns, involving transient intermediate structures that are greatly underrepresented in RNA-seq datasets. Decoy splice sites and decoy exons act at a distance to inhibit splicing catalysis at annotated splice sites, with functional consequences such as exon skipping and intron retention. RNA:RNA bridges can juxtapose distant sequences within or across introns to activate deep intron splicing enhancers and silencers, to loop out exons to be skipped, or to select one member of a mutually exclusive set of exons. Similarly, protein bridges mediated by interactions among transcript-bound RNA binding proteins (RBPs) can modulate splicing outcomes. Experimental disruption of deep intron elements serving any of these functions can abrogate normal splicing, strongly suggesting that natural mutations of deep intron elements can do likewise to cause human disease. Understanding noncanonical splicing pathways and discovering deep intron regulatory signals, many of which map hundreds to many thousands of nucleotides from annotated splice junctions, is of great academic interest for basic scientists studying alternative splicing mechanisms. Hopefully, this knowledge coupled with increased analysis of deep intron sequences will also have important medical applications, as better interpretation of deep intron mutations may reveal new disease mechanisms and suggest new therapies. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- John G Conboy
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, California, USA
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17
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Dong H, Li L, Zhu X, Shi J, Fu Y, Zhang S, Shi Y, Xu B, Zhang J, Shi F, Jin Y. Complex RNA Secondary Structures Mediate Mutually Exclusive Splicing of Coleoptera Dscam1. Front Genet 2021; 12:644238. [PMID: 33859670 PMCID: PMC8042237 DOI: 10.3389/fgene.2021.644238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Mutually exclusive splicing is an important mechanism for expanding protein diversity. An extreme example is the Down syndrome cell adhesion molecular (Dscam1) gene of insects, containing four clusters of variable exons (exons 4, 6, 9, and 17), which potentially generates tens of thousands of protein isoforms through mutually exclusive splicing, of which regulatory mechanisms are still elusive. Here, we systematically analyzed the variable exon 4, 6, and 9 clusters of Dscam1 in Coleoptera species. Through comparative genomics and RNA secondary structure prediction, we found apparent evidence that the evolutionarily conserved RNA base pairing mediates mutually exclusive splicing in the Dscam1 exon 4 cluster. In contrast to the fly exon 6, most exon 6 selector sequences in Coleoptera species are partially located in the variable exon region. Besides, bidirectional RNA–RNA interactions are predicted to regulate the mutually exclusive splicing of variable exon 9 of Dscam1. Although the docking sites in exon 4 and 9 clusters are clade specific, the docking sites-selector base pairing is conserved in secondary structure level. In short, our result provided a mechanistic framework for the application of long-range RNA base pairings in regulating the mutually exclusive splicing of Coleoptera Dscam1.
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Affiliation(s)
- Haiyang Dong
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lei Li
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaohua Zhu
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jilong Shi
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ying Fu
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shixin Zhang
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Zhang
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Feng Shi
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis, Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, China
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18
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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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19
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Hong W, Shi Y, Xu B, Jin Y. RNA secondary structures in Dscam1 mutually exclusive splicing: unique evolutionary signature from the midge. RNA (NEW YORK, N.Y.) 2020; 26:1086-1093. [PMID: 32471818 PMCID: PMC7430681 DOI: 10.1261/rna.075259.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/27/2020] [Indexed: 05/12/2023]
Abstract
The Drosophila melanogaster gene Dscam1 potentially generates 38,016 distinct isoforms via mutually exclusive splicing, which are required for both nervous and immune functions. However, the mechanism underlying splicing regulation remains obscure. Here we show apparent evolutionary signatures characteristic of competing RNA secondary structures in exon clusters 6 and 9 of Dscam1 in the two midge species (Belgica antarctica and Clunio marinus). Surprisingly, midge Dscam1 encodes only ∼6000 different isoforms through mutually exclusive splicing. Strikingly, the docking site of the exon 6 cluster is conserved in almost all insects and crustaceans but is specific in the midge; however, the docking site-selector base-pairings are conserved. Moreover, the docking site is complementary to all predicted selector sequences downstream from every variable exon 9 of the midge Dscam1, which is in accordance with the broad spectrum of their isoform expression. This suggests that these cis-elements mainly function through the formation of long-range base-pairings. This study provides a vital insight into the evolution and mechanism of Dscam1 alternative splicing.
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Affiliation(s)
- Weiling Hong
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Yang Shi
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis and Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, China
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20
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Ng TH, Kurtz J. Dscam in immunity: A question of diversity in insects and crustaceans. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 105:103539. [PMID: 31734281 DOI: 10.1016/j.dci.2019.103539] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/07/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
In insects and crustaceans, thousands of Down syndrome cell adhesion molecules (Dscam) can be generated by alternative splicing of variable exons from a single-locus gene, Dscam-hv. This extraordinarily versatile gene (38,016 protein isoforms produced in Drosophila) was first proposed to be involved in exon guidance and subsequently implicated in immunity as a hypervariable immune molecule. Almost 20 y after discovery of Dscam-hv, there have been many studies in insects and crustaceans regarding roles of Dscam in immunity, with many similarities and concurrently, many differences. Here, we review the current status of Dscam-hv, presented as a comparison of similarities and differences in insects and crustaceans and discuss hypotheses of Dscam functions in immunity.
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Affiliation(s)
- Tze Hann Ng
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany
| | - Joachim Kurtz
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, 48149, Münster, Germany.
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21
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Abstract
RNA molecules fold into complex three-dimensional structures that sample alternate conformations ranging from minor differences in tertiary structure dynamics to major differences in secondary structure. This allows them to form entirely different substructures with each population potentially giving rise to a distinct biological outcome. The substructures can be partitioned along an existing energy landscape given a particular static cellular cue or can be shifted in response to dynamic cues such as ligand binding. We review a few key examples of RNA molecules that sample alternate conformations and how these are capitalized on for control of critical regulatory functions.
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Affiliation(s)
- Marie Teng-Pei Wu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Victoria D'Souza
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
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22
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Decio P, Ustaoglu P, Roat TC, Malaspina O, Devaud JM, Stöger R, Soller M. Acute thiamethoxam toxicity in honeybees is not enhanced by common fungicide and herbicide and lacks stress-induced changes in mRNA splicing. Sci Rep 2019; 9:19196. [PMID: 31844097 PMCID: PMC6915785 DOI: 10.1038/s41598-019-55534-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/20/2019] [Indexed: 12/19/2022] Open
Abstract
Securing food supply for a growing population is a major challenge and heavily relies on the use of agrochemicals to maximize crop yield. It is increasingly recognized, that some neonicotinoid insecticides have a negative impact on non-target organisms, including important pollinators such as the European honeybee Apis mellifera. Toxicity of neonicotinoids may be enhanced through simultaneous exposure with additional pesticides, which could help explain, in part, the global decline of honeybee colonies. Here we examined whether exposure effects of the neonicotinoid thiamethoxam on bee viability are enhanced by the commonly used fungicide carbendazim and the herbicide glyphosate. We also analysed alternative splicing changes upon pesticide exposure in the honeybee. In particular, we examined transcripts of three genes: (i) the stress sensor gene X box binding protein-1 (Xbp1), (ii) the Down Syndrome Cell Adhesion Molecule (Dscam) gene and iii) the embryonic lethal/abnormal visual system (elav) gene, which are important for neuronal function. Our results showed that acute thiamethoxam exposure is not enhanced by carbendazim, nor glyphosate. Toxicity of the compounds did not trigger stress-induced, alternative splicing in the analysed mRNAs, thereby leaving dormant a cellular response pathway to these man-made environmental perturbations.
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Affiliation(s)
- Pâmela Decio
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
- MRC Centre for Molecular Bacteriology and Infection, and Department of Life Sciences, Imperial College London, Ground Floor, Flowers Building, South Kensington Campus, London, SW7 2AZ, UK
| | - Thaisa C Roat
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Osmar Malaspina
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Centro de Estudos de Insetos Sociais, Rio Claro, São Paulo, Brazil
| | - Jean-Marc Devaud
- Research Center on Animal Cognition, Center for Integrative Biology, Toulouse University, CNRS, UPS, Toulouse, France
| | - Reinhard Stöger
- School of Biosciences, University of Nottingham, LE12 5RD, Nottingham/Sutton Bonington Campus, United Kingdom.
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom.
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23
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Xu B, Shi Y, Wu Y, Meng Y, Jin Y. Role of RNA secondary structures in regulating Dscam alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194381. [DOI: 10.1016/j.bbagrm.2019.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
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24
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Ustaoglu P, Haussmann IU, Liao H, Torres-Mendez A, Arnold R, Irimia M, Soller M. Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons. RNA (NEW YORK, N.Y.) 2019; 25:1353-1365. [PMID: 31292260 PMCID: PMC6800468 DOI: 10.1261/rna.071316.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/04/2019] [Indexed: 05/24/2023]
Abstract
Alternative splicing of pre-mRNA is a major mechanism to diversify protein functionality in metazoans from a limited number of genes. The Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam) gene, which is important for neuronal wiring and phagocytosis of bacteria, can generate up to 38,016 isoforms by mutually exclusive alternative splicing in four clusters of variable exons. However, it is not understood how a specific exon is chosen from the many variables and how variable exons are prevented from being spliced together. A main role in the regulation of Dscam alternative splicing has been attributed to RNA binding proteins (RBPs), but how they impact on exon selection is not well understood. Serine-arginine rich (SR) proteins and hnRNP proteins are the two main types of RBPs with major roles in exon definition and splice site selection. Here, we analyzed the role of SR and hnRNP proteins in Dscam exon 9 alternative splicing in mutant Drosophila melanogaster embryos because of their essential function for development. Strikingly, loss or overexpression of canonical SR and hnRNP proteins even when multiple proteins are depleted together, does not affect Dscam alternative exon selection very dramatically. Conversely, noncanonical SR protein Serine-arginine repetitive matrix 2/3/4 (Srrm234) is a main determinant of exon inclusion in the Dscam exon 9 cluster. Since long-range base-pairings are absent in the exon 9 cluster, our data argue for a small complement of regulatory factors as main determinants of exon inclusion in the Dscam exon 9 cluster.
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Affiliation(s)
- Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
- Department of Life Science, School of Health Sciences, Birmingham City University, Birmingham B5 3TN, United Kingdom
| | - Hongzhi Liao
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Antonio Torres-Mendez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Roland Arnold
- Institute of Cancer and Genomics Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
- ICREA, Barcelona 08010, Spain
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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25
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Haussmann IU, Ustaoglu P, Brauer U, Hemani Y, Dix TC, Soller M. Plasmid-based gap-repair recombineered transgenes reveal a central role for introns in mutually exclusive alternative splicing in Down Syndrome Cell Adhesion Molecule exon 4. Nucleic Acids Res 2019; 47:1389-1403. [PMID: 30541104 PMCID: PMC6379703 DOI: 10.1093/nar/gky1254] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/22/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing is a key feature of human genes, yet studying its regulation is often complicated by large introns. The Down Syndrome Cell Adhesion Molecule (Dscam) gene from Drosophila is one of the most complex genes generating vast molecular diversity by mutually exclusive alternative splicing. To resolve how alternative splicing in Dscam is regulated, we first developed plasmid-based UAS reporter genes for the Dscam variable exon 4 cluster and show that its alternative splicing is recapitulated by GAL4-mediated expression in neurons. We then developed gap-repair recombineering to very efficiently manipulate these large reporter plasmids in Escherichia coli using restriction enzymes or sgRNA/Cas9 DNA scission to capitalize on the many benefits of plasmids in phiC31 integrase-mediated transgenesis. Using these novel tools, we show that inclusion of Dscam exon 4 variables differs little in development and individual flies, and is robustly determined by sequences harbored in variable exons. We further show that introns drive selection of both proximal and distal variable exons. Since exon 4 cluster introns lack conserved sequences that could mediate robust long-range base-pairing to bring exons into proximity for splicing, our data argue for a central role of introns in mutually exclusive alternative splicing of Dscam exon 4 cluster.
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Affiliation(s)
- Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,School of Life Science, CSELS, Coventry University, Coventry CV1 5FB, UK
| | - Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ulrike Brauer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yash Hemani
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Thomas C Dix
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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26
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Bartys N, Kierzek R, Lisowiec-Wachnicka J. The regulation properties of RNA secondary structure in alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194401. [PMID: 31323437 DOI: 10.1016/j.bbagrm.2019.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/09/2019] [Indexed: 11/30/2022]
Abstract
The RNA secondary structure is important for many functional processes in the cell. The secondary and tertiary structures of cellular RNAs are essential for the activity of these molecules in processes such as transcription, splicing, translation, and localization. New high-throughput analytical methods, including next generation sequencing, have allowed for the in-depth characterization of the 'RNA structurome': a new term describing how the RNA structure controls the activity of RNA by itself and how it regulates the expression of genes. In this review, we present many examples of the influence of structural motifs of RNA, long range interactions and global RNA structure on the alternative splicing processes. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Natalia Bartys
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Jolanta Lisowiec-Wachnicka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704 Poznań, Poland.
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27
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Han R, Hu S, Qin W, Shi J, Hou Q, Wang X, Xu X, Zhang M, Zeng C, Liu Z, Bao H. C3a and suPAR drive versican V1 expression in tubular cells of focal segmental glomerulosclerosis. JCI Insight 2019; 4:122912. [PMID: 30944246 DOI: 10.1172/jci.insight.122912] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 02/14/2019] [Indexed: 12/13/2022] Open
Abstract
Chronic tubulointerstitial injury impacts the prognosis of focal segmental glomerulosclerosis (FSGS). We found that the level of versican V1 was increased in tubular cells of FSGS patients. Tubular cell-derived versican V1 induced proliferation and collagen synthesis by activating the CD44/Smad3 pathway in fibroblasts. Both urine C3a and suPAR were increased and bound to the tubular cells in FSGS patients. C3a promoted the transcription of versican by activating the AKT/β-catenin pathway. C3aR knockout decreased the expression of versican in Adriamycin-treated (ADR-treated) mice. On the other hand, suPAR bound to integrin β6 and activated Rac1, which bound to SRp40 at the 5' end of exon 7 in versican pre-mRNA. This binding inhibited the 3'-end splicing of intron 6 and the base-pair interactions between intron 6 and intron 8, leading to the formation of versican V1. Cotreatment with ADR and suPAR specifically increased the level of versican V1 in tubulointerstitial tissues and caused more obvious interstitial fibrosis in mice than treatment with only ADR. Altogether, our results show that C3a and suPAR drive versican V1 expression in tubular cells by promoting transcription and splicing, respectively, and the increases in tubular cell-derived versican V1 induce interstitial fibrosis by activating fibroblasts in FSGS.
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Affiliation(s)
- Runhong Han
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Southeast University School of Medicine, Nanjing, China
| | - Shuai Hu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Weisong Qin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jinsong Shi
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qin Hou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xia Wang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiaodong Xu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Minchao Zhang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Caihong Zeng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhihong Liu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Southeast University School of Medicine, Nanjing, China
| | - Hao Bao
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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28
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Wan ZC, Li D, Li XJ, Zhu YT, Gao TH, Li WW, Wang Q. B52 promotes alternative splicing of Dscam in Chinese mitten crab, Eriocheir sinensis. FISH & SHELLFISH IMMUNOLOGY 2019; 87:460-469. [PMID: 30685464 DOI: 10.1016/j.fsi.2019.01.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 01/15/2019] [Accepted: 01/21/2019] [Indexed: 06/09/2023]
Abstract
B52 is a member of the classical serine/arginine (SR)-rich proteins, which are phylogenetically conserved and play significant roles in mRNA maturation, including alternative splicing. In the present study, the docking site, selector sequences and locus control region of the Chinese mitten crab (Eriocheir sinensis) Down syndrome cell adhesion molecule (EsDscam) were identified. Alternative splicing of Dscam is essential to generate different isoforms. We also isolated and characterised the B52 gene from E. sinensis (EsB52). The 876 bp open reading frame of EsB52 encodes a 291 amino acid residue polypeptide, and EsB52 has two RNA recognition motifs (RRMs) at the N-terminus and an arginine/serine-rich domain at the C-terminus. Each RRM contains two degenerate short submotifs, RNP-1 and RNP2. Analysis of tissue distribution revealed that EsB52 mRNA expression was widespread in all tested tissues, and especially high in brain and hemocytes. In hemocytes, EsB52 was upregulated significantly after stimulation with pathogen-associated molecular patterns and bacteria. Furthermore, EsB52 RNAi decreased the number of Ig7 inclusion in mRNA rather than Ig2 or Ig3. Taken together, these findings suggest that EsB52 acts as an alternative splicing activator of EsDscam.
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Affiliation(s)
- Zhi-Cheng Wan
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Dan Li
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xue-Jie Li
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - You-Ting Zhu
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Tian-Heng Gao
- Institute of Marine Biology, College of Oceanography, Hohai University, Nanjing, Jiangsu, China
| | - Wei-Wei Li
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China.
| | - Qun Wang
- State Key Laboratory of Estuarine and Coastal Research, Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China.
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29
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Jin Y, Li H. Revisiting Dscam diversity: lessons from clustered protocadherins. Cell Mol Life Sci 2019; 76:667-680. [PMID: 30343321 PMCID: PMC11105660 DOI: 10.1007/s00018-018-2951-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/13/2018] [Accepted: 10/15/2018] [Indexed: 12/14/2022]
Abstract
The complexity of neuronal wiring relies on the extraordinary recognition diversity of cell surface molecules. Drosophila Dscam1 and vertebrate clustered protocadherins (Pcdhs) are two classic examples of the striking diversity from a complex genomic locus, wherein the former encodes more than 10,000 distinct isoforms via alternative splicing, while the latter employs alternative promoters to attain isoform diversity. These structurally unrelated families show remarkably striking molecular parallels and even similar functions. Recent studies revealed a novel Dscam gene family with tandemly arrayed 5' cassettes in Chelicerata (e.g., the scorpion Mesobuthus martensii and the tick Ixodes scapularis), similar to vertebrate clustered Pcdhs. Likewise, octopus shows a more remarkable expansion of the Pcdh isoform repertoire than human. These discoveries of Dscam and Pcdh diversification reshape the evolutionary landscape of recognition molecule diversity and provide a greater understanding of convergent molecular strategies for isoform diversity. This article reviews new insights into the evolution, regulatory mechanisms, and functions of Dscam and Pcdh isoform diversity. In particular, the convergence of clustered Dscams and Pcdhs is highlighted.
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Affiliation(s)
- Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang (ZJ), People's Republic of China.
| | - Hao Li
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang (ZJ), People's Republic of China
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30
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Pan H, Shi Y, Chen S, Yang Y, Yue Y, Zhan L, Dai L, Dong H, Hong W, Shi F, Jin Y. Competing RNA pairings in complex alternative splicing of a 3' variable region. RNA (NEW YORK, N.Y.) 2018; 24:1466-1480. [PMID: 30065023 PMCID: PMC6191721 DOI: 10.1261/rna.066225.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/24/2018] [Indexed: 05/15/2023]
Abstract
Alternative pre-mRNA splicing remarkably expands protein diversity in eukaryotes. Drosophila PGRP-LC can generate three major 3' splice isoforms that exhibit distinct innate immune recognition and defenses against various microbial infections. However, the regulatory mechanisms underlying the uniquely biased splicing pattern at the 3' variable region remain unclear. Here we show that competing RNA pairings control the unique splicing of the 3' variable region of Drosophila PGRP-LC pre-mRNA. We reveal three roles by which these RNA pairings jointly regulate the 3' variant selection through activating the proximal 3' splice site and concurrently masking the intron-proximal 5' splice site, in combination with physical competition of RNA pairing. We also reveal that competing RNA pairings regulate alternative splicing of the highly complex 3' variable regions of Drosophila CG42235 and Pip Our findings will facilitate a better understanding of the regulatory mechanisms of highly complex alternative splicing as well as highly variable 3' processing.
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Affiliation(s)
- Huawei Pan
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Yang Shi
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Shuo Chen
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Yun Yang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Yuan Yue
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Leilei Zhan
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Lanzhi Dai
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Haiyang Dong
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Weiling Hong
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Feng Shi
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
| | - Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, ZJ310058, P.R. China
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31
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An Evolutionary Mechanism for the Generation of Competing RNA Structures Associated with Mutually Exclusive Exons. Genes (Basel) 2018; 9:genes9070356. [PMID: 30018239 PMCID: PMC6071210 DOI: 10.3390/genes9070356] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/06/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing is a commonly-used mechanism of diversifying gene products. Mutually exclusive exons (MXE) represent a particular type of alternative splicing, in which one and only one exon from an array is included in the mature RNA. A number of genes with MXE do so by using a mechanism that depends on RNA structure. Transcripts of these genes contain multiple sites called selector sequences that are all complementary to a regulatory element called the docking site; only one of the competing base pairings can form at a time, which exposes one exon from the cluster to the spliceosome. MXE tend to have similar lengths and sequence content and are believed to originate through tandem genomic duplications. Here, we report that pre-mRNAs of this class of exons have an increased capacity to fold into competing secondary structures. We propose an evolutionary mechanism for the generation of such structures via duplications that affect not only exons, but also their adjacent introns with stem-loop structures. If one of the two arms of a stem-loop is duplicated, it will generate two selector sequences that compete for the same docking site, a pattern that is associated with MXE splicing. A similar partial duplication of two independent stem-loops produces a pattern that is consistent with the so-called bidirectional pairing model. These models explain why tandem exon duplications frequently result in mutually exclusive splicing.
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32
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Pervouchine DD. Towards Long-Range RNA Structure Prediction in Eukaryotic Genes. Genes (Basel) 2018; 9:genes9060302. [PMID: 29914113 PMCID: PMC6027157 DOI: 10.3390/genes9060302] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/13/2018] [Accepted: 06/13/2018] [Indexed: 01/03/2023] Open
Abstract
The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA⁻RNA interactions across the transcriptome.
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Affiliation(s)
- Dmitri D Pervouchine
- Skolkovo Institute for Science and Technology, Ulitsa Nobelya 3, Moscow 121205, Russia.
- The Faculty of Bioengineering and Bioinformatics, Moscow State University 1-73, Moscow 119899, Russia.
- Faculty of Computer Science, Higher School of Economics, Kochnovskiy Proyezd 3, Moscow 125319, Russia.
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33
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Li XJ, Yang L, Li D, Zhu YT, Wang Q, Li WW. Pathogen-Specific Binding Soluble Down Syndrome Cell Adhesion Molecule (Dscam) Regulates Phagocytosis via Membrane-Bound Dscam in Crab. Front Immunol 2018; 9:801. [PMID: 29720978 PMCID: PMC5915466 DOI: 10.3389/fimmu.2018.00801] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/03/2018] [Indexed: 11/13/2022] Open
Abstract
The Down syndrome cell adhesion molecule (Dscam) gene is an extraordinary example of diversity that can produce thousands of isoforms and has so far been found only in insects and crustaceans. Cumulative evidence indicates that Dscam may contribute to the mechanistic foundations of specific immune responses in insects. However, the mechanism and functions of Dscam in relation to pathogens and immunity remain largely unknown. In this study, we identified the genome organization and alternative Dscam exons from Chinese mitten crab, Eriocheir sinensis. These variants, designated EsDscam, potentially produce 30,600 isoforms due to three alternatively spliced immunoglobulin (Ig) domains and a transmembrane domain. EsDscam was significantly upregulated after bacterial challenge at both mRNA and protein levels. Moreover, bacterial specific EsDscam isoforms were found to bind specifically with the original bacteria to facilitate efficient clearance. Furthermore, bacteria-specific binding of soluble EsDscam via the complete Ig1–Ig4 domain significantly enhanced elimination of the original bacteria via phagocytosis by hemocytes; this function was abolished by partial Ig1–Ig4 domain truncation. Further studies showed that knockdown of membrane-bound EsDscam inhibited the ability of EsDscam with the same extracellular region to promote bacterial phagocytosis. Immunocytochemistry indicated colocalization of the soluble and membrane-bound forms of EsDscam at the hemocyte surface. Far-Western and coimmunoprecipitation assays demonstrated homotypic interactions between EsDscam isoforms. This study provides insights into a mechanism by which soluble Dscam regulates hemocyte phagocytosis via bacteria-specific binding and specific interactions with membrane-bound Dscam as a phagocytic receptor.
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Affiliation(s)
- Xue-Jie Li
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Lei Yang
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Dan Li
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - You-Ting Zhu
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Wei-Wei Li
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
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Kaushik K, Sivadas A, Vellarikkal SK, Verma A, Jayarajan R, Pandey S, Sethi T, Maiti S, Scaria V, Sivasubbu S. RNA secondary structure profiling in zebrafish reveals unique regulatory features. BMC Genomics 2018; 19:147. [PMID: 29448945 PMCID: PMC5815192 DOI: 10.1186/s12864-018-4497-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 01/28/2018] [Indexed: 01/08/2023] Open
Abstract
Background RNA is known to play diverse roles in gene regulation. The clues for this regulatory function of RNA are embedded in its ability to fold into intricate secondary and tertiary structure. Results We report the transcriptome-wide RNA secondary structure in zebrafish at single nucleotide resolution using Parallel Analysis of RNA Structure (PARS). This study provides the secondary structure map of zebrafish coding and non-coding RNAs. The single nucleotide pairing probabilities of 54,083 distinct transcripts in the zebrafish genome were documented. We identified RNA secondary structural features embedded in functional units of zebrafish mRNAs. Translation start and stop sites were demarcated by weak structural signals. The coding regions were characterized by the three-nucleotide periodicity of secondary structure and display a codon base specific structural constrain. The splice sites of transcripts were also delineated by distinct signature signals. Relatively higher structural signals were observed at 3’ Untranslated Regions (UTRs) compared to Coding DNA Sequence (CDS) and 5’ UTRs. The 3′ ends of transcripts were also marked by unique structure signals. Secondary structural signals in long non-coding RNAs were also explored to better understand their molecular function. Conclusions Our study presents the first PARS-enabled transcriptome-wide secondary structure map of zebrafish, which documents pairing probability of RNA at single nucleotide precision. Our findings open avenues for exploring structural features in zebrafish RNAs and their influence on gene expression. Electronic supplementary material The online version of this article (10.1186/s12864-018-4497-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kriti Kaushik
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Ambily Sivadas
- G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Shamsudheen Karuthedath Vellarikkal
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Ankit Verma
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India
| | - Rijith Jayarajan
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India
| | - Satyaprakash Pandey
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Tavprithesh Sethi
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - Souvik Maiti
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India.,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India
| | - Vinod Scaria
- G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India.
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Sukhdev Vihar, Mathura Road, New Delhi, 110025, India. .,Academy of Scientific and Innovative Research (AcSIR), New Delhi, 110025, India.
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35
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Jin Y, Dong H, Shi Y, Bian L. Mutually exclusive alternative splicing of pre-mRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1468. [PMID: 29423937 DOI: 10.1002/wrna.1468] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 12/14/2022]
Abstract
Pre-mRNA alternative splicing is an important mechanism used to expand protein diversity in higher eukaryotes, and mutually exclusive splicing is a specific type of alternative splicing in which only one of the exons in a cluster is included in functional transcripts. The most extraordinary example of this is the Drosophila melanogaster Down's syndrome cell adhesion molecule gene (Dscam), which potentially encodes 38,016 different isoforms through mutually exclusive splicing. Mutually exclusive splicing is a unique and challenging model that can be used to elucidate the evolution, regulatory mechanism, and function of alternative splicing. The use of new approaches has not only greatly expanded the mutually exclusive exome, but has also enabled the systematic analyses of single-cell alternative splicing during development. Furthermore, the identification of long-range RNA secondary structures provides a mechanistic framework for the regulation of mutually exclusive splicing (i.e., Dscam splicing). This article reviews recent insights into the identification, underlying mechanism, and roles of mutually exclusive splicing. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Haiyang Dong
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yang Shi
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lina Bian
- Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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36
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Mishra SK, Thakran P. Intron specificity in pre-mRNA splicing. Curr Genet 2018; 64:777-784. [PMID: 29299619 DOI: 10.1007/s00294-017-0802-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 12/26/2017] [Accepted: 12/27/2017] [Indexed: 02/06/2023]
Abstract
The occurrence of spliceosomal introns in eukaryotic genomes is highly diverse and ranges from few introns in an organism to multiple introns per gene. Introns vary with respect to their lengths, strengths of splicing signals, and position in resident genes. Higher intronic density and diversity in genetically complex organisms relies on increased efficiency and accuracy of spliceosomes for pre-mRNA splicing. Since intron diversity is critical for functions in RNA stability, regulation of gene expression and alternative splicing, RNA-binding proteins, spliceosomal regulatory factors and post-translational modifications of splicing factors ought to make the splicing process intron-specific. We recently reported function and regulation of a ubiquitin fold harboring splicing regulator, Sde2, which following activation by ubiquitin-specific proteases facilitates excision of selected introns from a subset of multi-intronic genes in Schizosaccharomyces pombe (Thakran et al. EMBO J, https://doi.org/10.15252/embj.201796751 , 2017). By reviewing our findings with understandings of intron functions and regulated splicing processes, we propose possible functions and mechanism of intron-specific pre-mRNA splicing and suggest that this process is crucial to highlight importance of introns in eukaryotic genomes.
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Affiliation(s)
- Shravan Kumar Mishra
- Max Planck, DST Partner Group, Centre for Protein Science Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Punjab, 140306, India.
| | - Poonam Thakran
- Max Planck, DST Partner Group, Centre for Protein Science Design and Engineering, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Punjab, 140306, India
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37
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Li W, Tang X, Chen Y, Sun W, Liu Y, Gong Y, Wen X, Li S. Characterize a typically Dscam with alternative splicing in mud crab Scylla paramamosain. FISH & SHELLFISH IMMUNOLOGY 2017; 71:305-318. [PMID: 29042325 DOI: 10.1016/j.fsi.2017.10.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/08/2017] [Accepted: 10/13/2017] [Indexed: 06/07/2023]
Abstract
As a member of the immunoglobulin superfamily, Down syndrome cell adhesion molecule (Dscam) could function in the innate immunity of invertebrates. Recently, it is shown that arthropod Dscams play similar functions as antibodies in the adaptive immune system. Dscam could produce thousands of isoforms by alternative splicing and specifically bind to various pathogens. In the present study, we cloned the first Dscam from mud crab Scylla paramamosain (SpDscam), with full-length cDNA 7363 bp containing an open reading frame (ORF) of 6069bp and encoding 2022 amino acids, which had typical domain architecture as other arthropods, i.e., 10 immunoglobulin domains (Ig), 6 fibronectin type 3 domains (FN III), transmembrane and cytoplasmic tail. Quantitative real-time PCR revealed that SpDscam was highly expressed in brain, skin, muscle, intestine and hepatopancreas, but weakly expressed in hemolymph, heart and gill. SpDscam had three alternative splicing regions, located at the N-terminal of Ig2 and Ig3 as well as on the whole Ig7. In these regions, 32, 41 and 14 exons were detected, together with the two exon types of transmembrane domain, indicating SpDscam could potentially encode at least 36,736 unique isoforms. SpDscam induced by Vibrio parahaemolyticus challenge had strong binding ability to V. parahaemolyticus. Further, SpDscam induced by V. parahaemolyticus possessed a clearance of V. parahaemolyticus in S. paramamosain. Collectively, the results indicated SpDscam was a hypervariable pattern-recognition receptor (PRR) by alternative splicing in innate immunity system of mud crab S. paramamosain.
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Affiliation(s)
- Wenshi Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China; Marine Biology Institute, Shantou University, Shantou 515063, China
| | - Xixiang Tang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, China
| | - Yan Chen
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China; Marine Biology Institute, Shantou University, Shantou 515063, China
| | - Wanwei Sun
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China; Marine Biology Institute, Shantou University, Shantou 515063, China
| | - Yan Liu
- Department of Biology, Shantou University, Shantou 515063, China
| | - Yi Gong
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China; Marine Biology Institute, Shantou University, Shantou 515063, China
| | - Xiaobo Wen
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China; Marine Biology Institute, Shantou University, Shantou 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biology, Shantou University, Shantou 515063, China; Marine Biology Institute, Shantou University, Shantou 515063, China.
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38
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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39
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Yue Y, Hou S, Wang X, Zhan L, Cao G, Li G, Shi Y, Zhang P, Hong W, Lin H, Liu B, Shi F, Yang Y, Jin Y. Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing. RNA Biol 2017; 14:1399-1410. [PMID: 28277933 DOI: 10.1080/15476286.2017.1294308] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.
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Affiliation(s)
- Yuan Yue
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Shouqing Hou
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Xiu Wang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China.,b Institute of Ecology, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Leilei Zhan
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Guozheng Cao
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Guoli Li
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yang Shi
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Peng Zhang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Weiling Hong
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Hao Lin
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Baoping Liu
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Feng Shi
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yun Yang
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
| | - Yongfeng Jin
- a Institute of Biochemistry, College of Life Sciences, Zhejiang University , Hangzhou , Zhejiang , P.R. China
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40
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41
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Kralovicova J, Vorechovsky I. Alternative splicing of U2AF1 reveals a shared repression mechanism for duplicated exons. Nucleic Acids Res 2016; 45:417-434. [PMID: 27566151 PMCID: PMC5224494 DOI: 10.1093/nar/gkw733] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 12/30/2022] Open
Abstract
The auxiliary factor of U2 small nuclear ribonucleoprotein (U2AF) facilitates branch point (BP) recognition and formation of lariat introns. The gene for the 35-kD subunit of U2AF gives rise to two protein isoforms (termed U2AF35a and U2AF35b) that are encoded by alternatively spliced exons 3 and Ab, respectively. The splicing recognition sequences of exon 3 are less favorable than exon Ab, yet U2AF35a expression is higher than U2AF35b across tissues. We show that U2AF35b repression is facilitated by weak, closely spaced BPs next to a long polypyrimidine tract of exon Ab. Each BP lacked canonical uridines at position -2 relative to the BP adenines, with efficient U2 base-pairing interactions predicted only for shifted registers reminiscent of programmed ribosomal frameshifting. The BP cluster was compensated by interactions involving unpaired cytosines in an upstream, EvoFold-predicted stem loop (termed ESL) that binds FUBP1/2. Exon Ab inclusion correlated with predicted free energies of mutant ESLs, suggesting that the ESL operates as a conserved rheostat between long inverted repeats upstream of each exon. The isoform-specific U2AF35 expression was U2AF65-dependent, required interactions between the U2AF-homology motif (UHM) and the α6 helix of U2AF35, and was fine-tuned by exon Ab/3 variants. Finally, we identify tandem homologous exons regulated by U2AF and show that their preferential responses to U2AF65-related proteins and SRSF3 are associated with unpaired pre-mRNA segments upstream of U2AF-repressed 3′ss. These results provide new insights into tissue-specific subfunctionalization of duplicated exons in vertebrate evolution and expand the repertoire of exon repression mechanisms that control alternative splicing.
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Affiliation(s)
- Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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42
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Abstract
Pre-mRNA splicing is a key post-transcriptional regulation process in which introns are excised and exons are ligated together. A novel class of structured intron was recently discovered in fish. Simple expansions of complementary AC and GT dimers at opposite boundaries of an intron were found to form a bridging structure, thereby enforcing correct splice site pairing across the intron. In some fish introns, the RNA structures are strong enough to bypass the need of regulatory protein factors for splicing. Here, we discuss the prevalence and potential functions of highly structured introns. In humans, structured introns usually arise through the co-occurrence of C and G-rich repeats at intron boundaries. We explore the potentially instructive example of the HLA receptor genes. In HLA pre-mRNA, structured introns flank the exons that encode the highly polymorphic β sheet cleft, making the processing of the transcript robust to variants that disrupt splicing factor binding. While selective forces that have shaped HLA receptor are fairly atypical, numerous other highly polymorphic genes that encode receptors contain structured introns. Finally, we discuss how the elevated mutation rate associated with the simple repeats that often compose structured intron can make structured introns themselves rapidly evolving elements.
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Affiliation(s)
- Chien-Ling Lin
- a Molecular Biology, Cell Biology and Biochemistry, Brown University , Providence , RI , USA
| | - Allison J Taggart
- a Molecular Biology, Cell Biology and Biochemistry, Brown University , Providence , RI , USA
| | - William G Fairbrother
- a Molecular Biology, Cell Biology and Biochemistry, Brown University , Providence , RI , USA.,b Center for Computational Molecular Biology, Brown University , Providence , RI , USA.,c Hassenfeld Child Health Innovation Institute of Brown University , Providence , RI , USA
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Kawaguchi R, Kiryu H. Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome. BMC Bioinformatics 2016; 17:203. [PMID: 27153986 PMCID: PMC4858847 DOI: 10.1186/s12859-016-1067-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 04/29/2016] [Indexed: 02/08/2023] Open
Abstract
Background RNA secondary structure around splice sites is known to assist normal splicing by promoting spliceosome recognition. However, analyzing the structural properties of entire intronic regions or pre-mRNA sequences has been difficult hitherto, owing to serious experimental and computational limitations, such as low read coverage and numerical problems. Results Our novel software, “ParasoR”, is designed to run on a computer cluster and enables the exact computation of various structural features of long RNA sequences under the constraint of maximal base-pairing distance. ParasoR divides dynamic programming (DP) matrices into smaller pieces, such that each piece can be computed by a separate computer node without losing the connectivity information between the pieces. ParasoR directly computes the ratios of DP variables to avoid the reduction of numerical precision caused by the cancellation of a large number of Boltzmann factors. The structural preferences of mRNAs computed by ParasoR shows a high concordance with those determined by high-throughput sequencing analyses. Using ParasoR, we investigated the global structural preferences of transcribed regions in the human genome. A genome-wide folding simulation indicated that transcribed regions are significantly more structural than intergenic regions after removing repeat sequences and k-mer frequency bias. In particular, we observed a highly significant preference for base pairing over entire intronic regions as compared to their antisense sequences, as well as to intergenic regions. A comparison between pre-mRNAs and mRNAs showed that coding regions become more accessible after splicing, indicating constraints for translational efficiency. Such changes are correlated with gene expression levels, as well as GC content, and are enriched among genes associated with cytoskeleton and kinase functions. Conclusions We have shown that ParasoR is very useful for analyzing the structural properties of long RNA sequences such as mRNAs, pre-mRNAs, and long non-coding RNAs whose lengths can be more than a million bases in the human genome. In our analyses, transcribed regions including introns are indicated to be subject to various types of structural constraints that cannot be explained from simple sequence composition biases. ParasoR is freely available at https://github.com/carushi/ParasoR. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1067-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Risa Kawaguchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Hisanori Kiryu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
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Liu SR, Hu CG, Zhang JZ. Regulatory effects of cotranscriptional RNA structure formation and transitions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:562-74. [PMID: 27028291 DOI: 10.1002/wrna.1350] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 02/25/2016] [Accepted: 03/03/2016] [Indexed: 12/17/2022]
Abstract
RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sheng-Rui Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
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45
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Yan K, Arfat Y, Li D, Zhao F, Chen Z, Yin C, Sun Y, Hu L, Yang T, Qian A. Structure Prediction: New Insights into Decrypting Long Noncoding RNAs. Int J Mol Sci 2016; 17:ijms17010132. [PMID: 26805815 PMCID: PMC4730372 DOI: 10.3390/ijms17010132] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/18/2015] [Accepted: 01/12/2016] [Indexed: 12/31/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), which form a diverse class of RNAs, remain the least understood type of noncoding RNAs in terms of their nature and identification. Emerging evidence has revealed that a small number of newly discovered lncRNAs perform important and complex biological functions such as dosage compensation, chromatin regulation, genomic imprinting, and nuclear organization. However, understanding the wide range of functions of lncRNAs related to various processes of cellular networks remains a great experimental challenge. Structural versatility is critical for RNAs to perform various functions and provides new insights into probing the functions of lncRNAs. In recent years, the computational method of RNA structure prediction has been developed to analyze the structure of lncRNAs. This novel methodology has provided basic but indispensable information for the rapid, large-scale and in-depth research of lncRNAs. This review focuses on mainstream RNA structure prediction methods at the secondary and tertiary levels to offer an additional approach to investigating the functions of lncRNAs.
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Affiliation(s)
- Kun Yan
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yasir Arfat
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Dijie Li
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Fan Zhao
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Zhihao Chen
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Chong Yin
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Yulong Sun
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Lifang Hu
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
| | - Tuanmin Yang
- Department of Bone Disease Oncology, Hong-Hui Hospital, Xi'an Jiaotong University College of Medicine, South Door slightly Friendship Road 555, Xi'an 710054, China.
| | - Airong Qian
- Key Laboratory for Space Bioscience & Biotechnology, Institute of Special Environmental Biophysics, School of Life Sciences, Northwestern Polytechnical University, 127 Youyi Xilu, Xi'an 710072, China.
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46
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Lin CL, Taggart AJ, Lim KH, Cygan KJ, Ferraris L, Creton R, Huang YT, Fairbrother WG. RNA structure replaces the need for U2AF2 in splicing. Genome Res 2016; 26:12-23. [PMID: 26566657 PMCID: PMC4691745 DOI: 10.1101/gr.181008.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 11/10/2015] [Indexed: 01/21/2023]
Abstract
RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.
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Affiliation(s)
- Chien-Ling Lin
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Allison J Taggart
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kian Huat Lim
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kamil J Cygan
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
| | - Luciana Ferraris
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Robbert Creton
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Yen-Tsung Huang
- Departments of Epidemiology and Biostatistics, Brown University, Providence, Rhode Island 02912, USA
| | - William G Fairbrother
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
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47
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Yue Y, Yang Y, Dai L, Cao G, Chen R, Hong W, Liu B, Shi Y, Meng Y, Shi F, Xiao M, Jin Y. Long-range RNA pairings contribute to mutually exclusive splicing. RNA (NEW YORK, N.Y.) 2016; 22:96-110. [PMID: 26554032 PMCID: PMC4691838 DOI: 10.1261/rna.053314.115] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/06/2015] [Indexed: 05/16/2023]
Abstract
Mutually exclusive splicing is an important means of increasing the protein repertoire, by which the Down's syndrome cell adhesion molecule (Dscam) gene potentially generates 38,016 different isoforms in Drosophila melanogaster. However, the regulatory mechanisms remain obscure due to the complexity of the Dscam exon cluster. Here, we reveal a molecular model for the regulation of the mutually exclusive splicing of the serpent pre-mRNA based on competition between upstream and downstream RNA pairings. Such dual RNA pairings confer fine tuning of the inclusion of alternative exons. Moreover, we demonstrate that the splicing outcome of alternative exons is mediated in relative pairing strength-correlated mode. Combined comparative genomics analysis and experimental evidence revealed similar bidirectional structural architectures in exon clusters 4 and 9 of the Dscam gene. Our findings provide a novel mechanistic framework for the regulation of mutually exclusive splicing and may offer potentially applicable insights into long-range RNA-RNA interactions in gene regulatory networks.
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Affiliation(s)
- Yuan Yue
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Yun Yang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Lanzhi Dai
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Guozheng Cao
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Ran Chen
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Weiling Hong
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Baoping Liu
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Yang Shi
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Yijun Meng
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Feng Shi
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Mu Xiao
- Institute of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
| | - Yongfeng Jin
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang, ZJ310058, China
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48
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Endoh T, Hnedzko D, Rozners E, Sugimoto N. Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505938] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; Japan
| | - Dziyana Hnedzko
- Department of Chemistry; Binghamton University; The State University of New York; Binghamton NY 13902 USA
| | - Eriks Rozners
- Department of Chemistry; Binghamton University; The State University of New York; Binghamton NY 13902 USA
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20 Minatojima-minamimachi Kobe 650-0047 Japan
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49
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Endoh T, Hnedzko D, Rozners E, Sugimoto N. Nucleobase-Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells. Angew Chem Int Ed Engl 2015; 55:899-903. [PMID: 26473504 DOI: 10.1002/anie.201505938] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/08/2015] [Indexed: 11/11/2022]
Abstract
Compounds that bind specifically to double-stranded regions of RNA have potential as regulators of structure-based RNA function; however, sequence-selective recognition of double-stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA-RNA triplexes. Herein, we demonstrate that a 9-mer PNA forms a sequence-specific PNA-RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5' untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex-forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double-stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein-RNA interactions.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan
| | - Dziyana Hnedzko
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Japan. .,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
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50
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Abstract
Precursor messenger RNA (pre-mRNA) splicing is a critical step in the posttranscriptional regulation of gene expression, providing significant expansion of the functional proteome of eukaryotic organisms with limited gene numbers. Split eukaryotic genes contain intervening sequences or introns disrupting protein-coding exons, and intron removal occurs by repeated assembly of a large and highly dynamic ribonucleoprotein complex termed the spliceosome, which is composed of five small nuclear ribonucleoprotein particles, U1, U2, U4/U6, and U5. Biochemical studies over the past 10 years have allowed the isolation as well as compositional, functional, and structural analysis of splicing complexes at distinct stages along the spliceosome cycle. The average human gene contains eight exons and seven introns, producing an average of three or more alternatively spliced mRNA isoforms. Recent high-throughput sequencing studies indicate that 100% of human genes produce at least two alternative mRNA isoforms. Mechanisms of alternative splicing include RNA-protein interactions of splicing factors with regulatory sites termed silencers or enhancers, RNA-RNA base-pairing interactions, or chromatin-based effects that can change or determine splicing patterns. Disease-causing mutations can often occur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer elements, as well as in genes that encode splicing factors. Together, these studies provide mechanistic insights into how spliceosome assembly, dynamics, and catalysis occur; how alternative splicing is regulated and evolves; and how splicing can be disrupted by cis- and trans-acting mutations leading to disease states. These findings make the spliceosome an attractive new target for small-molecule, antisense, and genome-editing therapeutic interventions.
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Affiliation(s)
- Yeon Lee
- Center for RNA Systems Biology; Division of Biochemistry, Biophysics, and Structural Biology; Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204;
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