1
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Zhang KY, Joshi H, Marchant RG, Bryen SJ, Dawes R, Yuen M, Cooper ST, Evesson FJ. Refining clinically relevant parameters for mis-splicing risk in shortened introns with donor-to-branchpoint space constraint. Eur J Hum Genet 2024; 32:972-979. [PMID: 38802528 PMCID: PMC11291888 DOI: 10.1038/s41431-024-01632-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/16/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
Intronic deletions that critically shorten donor-to-branchpoint (D-BP) distance of a precursor mRNA impose biophysical space constraint on assembly of the U1/U2 spliceosomal complex, leading to canonical splicing failure. Here we use a series of β-globin (HBB) gene constructs with intron 1 deletions to define D-BP lengths that present low/no risk of mis-splicing and lengths which are critically short and likely elicit clinically relevant mis-splicing. We extend our previous observation in EMD intron 5 of 46 nt as the minimal productive D-BP length, demonstrating spliceosome assembly constraint persists at D-BP lengths of 47-56 nt. We exploit the common HBB exon 1 β-thalassemia variant that strengthens a cryptic donor (NM_000518.5(HBB):c.79G > A) to provide a simple barometer for the earliest signs of space constraint, via cryptic donor activation. For clinical evaluation of intronic deletions, we assert D-BP lengths > 60 nt present low mis-splicing risk while space constraint increases exponentially with D-BP lengths < 55 nt, with critical risk and profound splicing abnormalities with D-BP lengths < 50 nt.
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Affiliation(s)
- Katharine Y Zhang
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
| | - Rhett G Marchant
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Samantha J Bryen
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research, UNSW & Murdoch Children's Research Institute, Sydney & Melbourne, Australia
| | - Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Big Data Institute and Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michaela Yuen
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Frances J Evesson
- Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, NSW, Australia.
- Functional Neuromics, Children's Medical Research Institute, Westmead, NSW, Australia.
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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2
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Zeuli R, Karali M, de Bruijn SE, Rodenburg K, Scarpato M, Capasso D, Astuti GDN, Gilissen C, Rodríguez-Hidalgo M, Ruiz-Ederra J, Testa F, Simonelli F, Cremers FPM, Banfi S, Roosing S. Whole genome sequencing identifies elusive variants in genetically unsolved Italian inherited retinal disease patients. HGG ADVANCES 2024; 5:100314. [PMID: 38816995 PMCID: PMC11225895 DOI: 10.1016/j.xhgg.2024.100314] [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: 03/15/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/01/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of rare monogenic diseases with high genetic heterogeneity (pathogenic variants identified in over 280 causative genes). The genetic diagnostic rate for IRDs is around 60%, mainly thanks to the routine application of next-generation sequencing (NGS) approaches such as extensive gene panels or whole exome analyses. Whole-genome sequencing (WGS) has been reported to improve this diagnostic rate by revealing elusive variants, such as structural variants (SVs) and deep intronic variants (DIVs). We performed WGS on 33 unsolved cases with suspected autosomal recessive IRD, aiming to identify causative genetic variants in non-coding regions or to detect SVs that were unexplored in the initial screening. Most of the selected cases (30 of 33, 90.9%) carried monoallelic pathogenic variants in genes associated with their clinical presentation, hence we first analyzed the non-coding regions of these candidate genes. Whenever additional pathogenic variants were not identified with this approach, we extended the search for SVs and DIVs to all IRD-associated genes. Overall, we identified the missing causative variants in 11 patients (11 of 33, 33.3%). These included three DIVs in ABCA4, CEP290 and RPGRIP1; one non-canonical splice site (NCSS) variant in PROM1 and three SVs (large deletions) in EYS, PCDH15 and USH2A. For the previously unreported DIV in CEP290 and for the NCCS variant in PROM1, we confirmed the effect on splicing by reverse transcription (RT)-PCR on patient-derived RNA. This study demonstrates the power and clinical utility of WGS as an all-in-one test to identify disease-causing variants missed by standard NGS diagnostic methodologies.
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Affiliation(s)
- Roberta Zeuli
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Marianthi Karali
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Margherita Scarpato
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Dalila Capasso
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomic and Experimental Medicine Program, Naples, Italy
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sandro Banfi
- Medical Genetics, Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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3
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Masuda A, Okamoto T, Kawachi T, Takeda JI, Hamaguchi T, Ohno K. Blending and separating dynamics of RNA-binding proteins develop architectural splicing networks spreading throughout the nucleus. Mol Cell 2024:S1097-2765(24)00544-6. [PMID: 39053456 DOI: 10.1016/j.molcel.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 01/28/2024] [Accepted: 07/02/2024] [Indexed: 07/27/2024]
Abstract
The eukaryotic nucleus has a highly organized structure. Although the spatiotemporal arrangement of spliceosomes on nascent RNA drives splicing, the nuclear architecture that directly supports this process remains unclear. Here, we show that RNA-binding proteins (RBPs) assembled on RNA form meshworks in human and mouse cells. Core and accessory RBPs in RNA splicing make two distinct meshworks adjacently but distinctly distributed throughout the nucleus. This is achieved by mutual exclusion dynamics between the charged and uncharged intrinsically disordered regions (IDRs) of RBPs. These two types of meshworks compete for spatial occupancy on pre-mRNA to regulate splicing. Furthermore, the optogenetic enhancement of the RBP meshwork causes aberrant splicing, particularly of genes involved in neurodegeneration. Genetic mutations associated with neurodegenerative diseases are often found in the IDRs of RBPs, and cells harboring these mutations exhibit impaired meshwork formation. Our results uncovered the spatial organization of RBP networks to drive RNA splicing.
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Affiliation(s)
- Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Takaaki Okamoto
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshihiko Kawachi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Jun-Ichi Takeda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tomonari Hamaguchi
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan; Graduate School of Nutritional Sciences, Nagoya University of Arts and Sciences, Nisshin, Japan
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4
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Huang AC, Su JY, Hung YJ, Chiang HL, Chen YT, Huang YT, Yu CHA, Lin HN, Lin CL. SpliceAPP: an interactive web server to predict splicing errors arising from human mutations. BMC Genomics 2024; 25:600. [PMID: 38877417 PMCID: PMC11179192 DOI: 10.1186/s12864-024-10512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/07/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Splicing variants are a major class of pathogenic mutations, with their severity equivalent to nonsense mutations. However, redundant and degenerate splicing signals hinder functional assessments of sequence variations within introns, particularly at branch sites. We have established a massively parallel splicing assay to assess the impact on splicing of 11,191 disease-relevant variants. Based on the experimental results, we then applied regression-based methods to identify factors determining splicing decisions and their respective weights. RESULTS Our statistical modeling is highly sensitive, accurately annotating the splicing defects of near-exon intronic variants, outperforming state-of-the-art predictive tools. We have incorporated the algorithm and branchpoint information into a web-based tool, SpliceAPP, to provide an interactive application. This user-friendly website allows users to upload any genetic variants with genome coordinates (e.g., chr15 74,687,208 A G), and the tool will output predictions for splicing error scores and evaluate the impact on nearby splice sites. Additionally, users can query branch site information within the region of interest. CONCLUSIONS In summary, SpliceAPP represents a pioneering approach to screening pathogenic intronic variants, contributing to the development of precision medicine. It also facilitates the annotation of splicing motifs. SpliceAPP is freely accessible using the link https://bc.imb.sinica.edu.tw/SpliceAPP . Source code can be downloaded at https://github.com/hsinnan75/SpliceAPP .
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Affiliation(s)
- Ang-Chu Huang
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Jia-Ying Su
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yu-Jen Hung
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Hung-Lun Chiang
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Yi-Ting Chen
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Yen-Tsung Huang
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Chen-Hsin Albert Yu
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan
| | - Hsin-Nan Lin
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan.
| | - Chien-Ling Lin
- Institute of Molecular Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nangang District, Taipei City, 115014, Taiwan.
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan.
- Bioinformatics Program, International Graduate Program, Academia Sinica, Taipei, Taiwan.
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5
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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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6
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Zhang Y, Zhang X, Tang Q, Li L, Jiang T, Fang Y, Zhang H, Zhai J, Ren G, Zheng B. A repertoire of intronic lariat RNAs reveals tissue-specific regulation and target mimicry potential in plants. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1280-1291. [PMID: 38489006 DOI: 10.1007/s11427-023-2466-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 03/17/2024]
Abstract
Lariat RNA is concomitantly produced by excised intron during RNA splicing, which is usually debranched by DBR1, an RNA debranching enzyme. However, increasing evidence showed that some lariat RNA could escape debranching. Little is known about how and why these lariat RNAs could be retained. By comparing the atlas of lariat RNAs between the non-dividing cell (mature pollen) and three actively dividing tissues (young shoot apex, young seeds, and young roots), we identified hundreds to thousands of lariat RNA naturally retained in each tissue, and the incidence of lariat RNA retention is much less in shoot apex while much more in pollen. Many lariat RNAs derived from the same intron or different lariat RNAs from the same pre-mRNA could be retained in one tissue while degraded in the other tissues. By deciphering lariat RNA sequences, we identified an AG-rich (RAAAAVAAAR) motif and a UC-rich (UCUCUYUCUC) motif for pollen-specific and the other three tissues-retained lariat RNAs, respectively. Reconstitution of the pollen-specific AG-rich motif indeed enhanced lariat RNA retention in plants. Biologically, hundreds of lariat RNAs harbored miRNA binding sites, and dual-luciferase reporter assay showed that these natural lariat RNAs had the potential to protect expression of miRNA target genes. Collectively, our results uncover that selective retention of lariat RNA is an actively regulatory process, and provide new insights into understanding how lariat RNA metabolism may impact miRNA activity.
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Affiliation(s)
- Yong Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaotuo Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qi Tang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ting Jiang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yixiao Fang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hong Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jixian Zhai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Binglian Zheng
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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7
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Buerer L, Clark NE, Welch A, Duan C, Taggart AJ, Townley BA, Wang J, Soemedi R, Rong S, Lin CL, Zeng Y, Katolik A, Staley JP, Damha MJ, Mosammaparast N, Fairbrother WG. The debranching enzyme Dbr1 regulates lariat turnover and intron splicing. Nat Commun 2024; 15:4617. [PMID: 38816363 PMCID: PMC11139901 DOI: 10.1038/s41467-024-48696-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/05/2024] [Indexed: 06/01/2024] Open
Abstract
The majority of genic transcription is intronic. Introns are removed by splicing as branched lariat RNAs which require rapid recycling. The branch site is recognized during splicing catalysis and later debranched by Dbr1 in the rate-limiting step of lariat turnover. Through generation of a viable DBR1 knockout cell line, we find the predominantly nuclear Dbr1 enzyme to encode the sole debranching activity in human cells. Dbr1 preferentially debranches substrates that contain canonical U2 binding motifs, suggesting that branchsites discovered through sequencing do not necessarily represent those favored by the spliceosome. We find that Dbr1 also exhibits specificity for particular 5' splice site sequences. We identify Dbr1 interactors through co-immunoprecipitation mass spectrometry. We present a mechanistic model for Dbr1 recruitment to the branchpoint through the intron-binding protein AQR. In addition to a 20-fold increase in lariats, Dbr1 depletion increases exon skipping. Using ADAR fusions to timestamp lariats, we demonstrate a defect in spliceosome recycling. In the absence of Dbr1, spliceosomal components remain associated with the lariat for a longer period of time. As splicing is co-transcriptional, slower recycling increases the likelihood that downstream exons will be available for exon skipping.
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Affiliation(s)
- Luke Buerer
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Nathaniel E Clark
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Allison J Taggart
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Brittany A Townley
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jing Wang
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Rachel Soemedi
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
| | - Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
- Department of Genetics, Yale University, New Haven, CT, 06520, USA
| | - Chien-Ling Lin
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA
- Institute of Molecular Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Yi Zeng
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Adam Katolik
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, QC, H3A 0B8, Canada
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Center for Genome Integrity, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02903, USA.
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
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8
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Ares M, Igel H, Katzman S, Donohue JP. Intron lariat spliceosomes convert lariats to true circles: implications for intron transposition. Genes Dev 2024; 38:322-335. [PMID: 38724209 PMCID: PMC11146597 DOI: 10.1101/gad.351764.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Rare, full-length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envisioned and tested a hypothesis for their formation using Saccharomyces cerevisiae, documenting full-length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle. Human U2 and U12 spliceosomes produce analogous full-length and processed circles. Postsplicing catalytic activity of the spliceosome may promote intron transposition during eukaryotic genome evolution.
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Affiliation(s)
- Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA;
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - John P Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz, Santa Cruz, California 95064, USA
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9
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Damianov A, Lin CH, Huang J, Zhou L, Jami-Alahmadi Y, Peyda P, Wohlschlegel J, Black DL. The splicing regulators RBM5 and RBM10 are subunits of the U2 snRNP engaged with intron branch sites on chromatin. Mol Cell 2024; 84:1496-1511.e7. [PMID: 38537639 PMCID: PMC11057915 DOI: 10.1016/j.molcel.2024.02.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 04/09/2024]
Abstract
Understanding the mechanisms of pre-mRNA splicing is limited by the technical challenges to examining spliceosomes in vivo. Here, we report the isolation of RNP complexes derived from precatalytic A or B-like spliceosomes solubilized from the chromatin pellet of mammalian cell nuclei. We found that these complexes contain U2 snRNP proteins and a portion of the U2 snRNA bound with protected RNA fragments that precisely map to intronic branch sites across the transcriptome. These U2 complexes also contained the splicing regulators RBM5 and RBM10. We found RBM5 and RBM10 bound to nearly all branch site complexes and not simply those at regulated exons. The deletion of a conserved RBM5/RBM10 peptide sequence, including a zinc finger motif, disrupted U2 interaction and rendered the proteins inactive for the repression of many alternative exons. We propose a model where RBM5 and RBM10 regulate splicing as components of the U2 snRNP complex following branch site base pairing.
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Affiliation(s)
- Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jeffrey Huang
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lin Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Parham Peyda
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
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10
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Shi W, Tang J, Xiang J. Therapeutic strategies for aberrant splicing in cancer and genetic disorders. Clin Genet 2024; 105:345-354. [PMID: 38165092 DOI: 10.1111/cge.14478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
Accurate pre-mRNA splicing is essential for proper protein translation; however, aberrant splicing is commonly observed in the context of cancer and genetic disorders. Notably, in genetic diseases, these splicing abnormalities often play a pivotal role. Substantial challenges persist in accurately identifying and classifying disease-induced aberrant splicing, as well as in development of targeted therapeutic strategies. In this review, we examine prevalent forms of aberrant splicing and explore potential therapeutic approaches aimed at addressing these splicing-related diseases. This summary contributes to a deeper understanding of the complexities about aberrant splicing and provide a foundation for the development of effective therapeutic interventions in the field of genetic disorders and cancer.
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Affiliation(s)
- Wenhua Shi
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingqun Tang
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Juanjuan Xiang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- NHC Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, Hunan, China
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11
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Ares M, Igel H, Katzman S, Donohue JP. Intron-lariat spliceosomes convert lariats to true circles: implications for intron transposition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586863. [PMID: 38585890 PMCID: PMC10996645 DOI: 10.1101/2024.03.26.586863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Rare, full length circular intron RNAs distinct from lariats have been reported in several species, but their biogenesis is not understood. We envision and test a hypothesis for their formation using Saccharomyces cerevisiae, documenting full length and novel processed circular RNAs from multiple introns. Evidence implicates a previously undescribed catalytic activity of the intron-lariat spliceosome (ILS) in which the 3'-OH of the lariat tail (with optional trimming and adenylation by the nuclear 3' processing machinery) attacks the branch, joining the intron 3' end to the 5' splice site in a 3'-5' linked circle. Human U2 and U12 spliceosomes produce analogous full length and processed circles. Post-splicing catalytic activity of the spliceosome may promote intron transposition during eukaryotic genome evolution.
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Affiliation(s)
- Manuel Ares
- Center for Molecular Biology of RNA, University of California, Santa Cruz
- Genomics Institute, Santa Cruz, CA 95064 USA
| | - Haller Igel
- Center for Molecular Biology of RNA, University of California, Santa Cruz
| | - Sol Katzman
- Center for Molecular Biology of RNA, University of California, Santa Cruz
- Genomics Institute, Santa Cruz, CA 95064 USA
| | - John P. Donohue
- Center for Molecular Biology of RNA, University of California, Santa Cruz
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12
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Chen K, Zhou Y, Ding M, Wang Y, Ren Z, Yang Y. Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. Brief Bioinform 2024; 25:bbae163. [PMID: 38605640 PMCID: PMC11009468 DOI: 10.1093/bib/bbae163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/22/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Language models pretrained by self-supervised learning (SSL) have been widely utilized to study protein sequences, while few models were developed for genomic sequences and were limited to single species. Due to the lack of genomes from different species, these models cannot effectively leverage evolutionary information. In this study, we have developed SpliceBERT, a language model pretrained on primary ribonucleic acids (RNA) sequences from 72 vertebrates by masked language modeling, and applied it to sequence-based modeling of RNA splicing. Pretraining SpliceBERT on diverse species enables effective identification of evolutionarily conserved elements. Meanwhile, the learned hidden states and attention weights can characterize the biological properties of splice sites. As a result, SpliceBERT was shown effective on several downstream tasks: zero-shot prediction of variant effects on splicing, prediction of branchpoints in humans, and cross-species prediction of splice sites. Our study highlighted the importance of pretraining genomic language models on a diverse range of species and suggested that SSL is a promising approach to enhance our understanding of the regulatory logic underlying genomic sequences.
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Affiliation(s)
- Ken Chen
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yue Zhou
- Peng Cheng Laboratory, Shenzhen, China
| | - Maolin Ding
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Yu Wang
- Peng Cheng Laboratory, Shenzhen, China
| | | | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Machine Intelligence and Advanced Computing (Sun Yat-sen University), Ministry of Education, China
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13
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Liu S, Huang J, Zhou J, Chen S, Zheng W, Liu C, Lin Q, Zhang P, Wu D, He S, Ye J, Liu S, Zhou K, Li B, Qu L, Yang J. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun 2024; 15:2425. [PMID: 38499544 PMCID: PMC10948791 DOI: 10.1038/s41467-024-46596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Junhong Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Siyan Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Wujian Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Qiao Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Ping Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Di Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Simeng He
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jiayi Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China.
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14
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Bakhtiar D, Vondraskova K, Pengelly RJ, Chivers M, Kralovicova J, Vorechovsky I. Exonic splicing code and coordination of divalent metals in proteins. Nucleic Acids Res 2024; 52:1090-1106. [PMID: 38055834 PMCID: PMC10853796 DOI: 10.1093/nar/gkad1161] [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: 06/16/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Exonic sequences contain both protein-coding and RNA splicing information but the interplay of the protein and splicing code is complex and poorly understood. Here, we have studied traditional and auxiliary splicing codes of human exons that encode residues coordinating two essential divalent metals at the opposite ends of the Irving-Williams series, a universal order of relative stabilities of metal-organic complexes. We show that exons encoding Zn2+-coordinating amino acids are supported much less by the auxiliary splicing motifs than exons coordinating Ca2+. The handicap of the former is compensated by stronger splice sites and uridine-richer polypyrimidine tracts, except for position -3 relative to 3' splice junctions. However, both Ca2+ and Zn2+ exons exhibit close-to-constitutive splicing in multiple tissues, consistent with their critical importance for metalloprotein function and a relatively small fraction of expendable, alternatively spliced exons. These results indicate that constraints imposed by metal coordination spheres on RNA splicing have been efficiently overcome by the plasticity of exon-intron architecture to ensure adequate metalloprotein expression.
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Affiliation(s)
- Dara Bakhtiar
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Katarina Vondraskova
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben J Pengelly
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Martin Chivers
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
| | - Jana Kralovicova
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre of Biosciences, 840 05 Bratislava, Slovak Republic
| | - Igor Vorechovsky
- University of Southampton, Faculty of Medicine, Southampton SO16 6YD, UK
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15
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Haack DB, Rudolfs B, Zhang C, Lyumkis D, Toor N. Structural basis of branching during RNA splicing. Nat Struct Mol Biol 2024; 31:179-189. [PMID: 38057551 PMCID: PMC10968580 DOI: 10.1038/s41594-023-01150-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/04/2023] [Indexed: 12/08/2023]
Abstract
Branching is a critical step in RNA splicing that is essential for 5' splice site selection. Recent spliceosome structures have led to competing models for the recognition of the invariant adenosine at the branch point. However, there are no structures of any splicing complex with the adenosine nucleophile docked in the active site and positioned to attack the 5' splice site. Thus we lack a mechanistic understanding of adenosine selection and splice site recognition during RNA splicing. Here we present a cryo-electron microscopy structure of a group II intron that reveals that active site dynamics are coupled to the formation of a base triple within the branch-site helix that positions the 2'-OH of the adenosine for nucleophilic attack on the 5' scissile phosphate. This structure, complemented with biochemistry and comparative analyses to splicing complexes, supports a base triple model of adenosine recognition for branching within group II introns and the evolutionarily related spliceosome.
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Affiliation(s)
- Daniel B Haack
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
| | - Boris Rudolfs
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Cheng Zhang
- Salk Institute, La Jolla, CA, USA
- Amgen, Thousand Oaks, CA, USA
| | | | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
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16
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Zheng ZM. RNA therapy is shining for genetic diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102042. [PMID: 37876533 PMCID: PMC10590990 DOI: 10.1016/j.omtn.2023.102042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Affiliation(s)
- Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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17
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Nosková A, Li C, Wang X, Leonard AS, Pausch H, Kadri N. Exploiting public databases of genomic variation to quantify evolutionary constraint on the branch point sequence in 30 plant and animal species. Nucleic Acids Res 2023; 51:12069-12075. [PMID: 37953306 PMCID: PMC10711541 DOI: 10.1093/nar/gkad970] [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: 05/08/2023] [Revised: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
The branch point sequence is a degenerate intronic heptamer required for the assembly of the spliceosome during pre-mRNA splicing. Disruption of this motif may promote alternative splicing and eventually cause phenotype variation. Despite its functional relevance, the branch point sequence is not included in most genome annotations. Here, we predict branch point sequences in 30 plant and animal species and attempt to quantify their evolutionary constraints using public variant databases. We find an implausible variant distribution in the databases from 16 of 30 examined species. Comparative analysis of variants from whole-genome sequencing shows that variants submitted from exome sequencing or false positive variants are widespread in public databases and cause these irregularities. We then investigate evolutionary constraint with largely unbiased public variant databases in 14 species and find that the fourth and sixth position of the branch point sequence are more constrained than coding nucleotides. Our findings show that public variant databases should be scrutinized for possible biases before they qualify to analyze evolutionary constraint.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Chao Li
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaolong Wang
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs/Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Naveen Kumar Kadri
- Animal Genomics, ETH Zürich, Universitätstrasse 2, 8092 Zürich, Switzerland
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18
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Ma XK, Zhai SN, Yang L. Approaches and challenges in genome-wide circular RNA identification and quantification. Trends Genet 2023; 39:897-907. [PMID: 37839990 DOI: 10.1016/j.tig.2023.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023]
Abstract
Numerous circular RNAs (circRNAs) produced from back-splicing of exon(s) have been recently revealed on a genome-wide scale across species. Although generally expressed at a low level, some relatively abundant circRNAs can play regulatory roles in various biological processes, prompting continuous profiling of circRNA in broader conditions. Over the past decade, distinct strategies have been applied in both transcriptome enrichment and bioinformatic tools for detecting and quantifying circRNAs. Understanding the scope and limitations of these strategies is crucial for the subsequent annotation and characterization of circRNAs, especially those with functional potential. Here, we provide an overview of different transcriptome enrichment, deep sequencing and computational approaches for genome-wide circRNA identification, and discuss strategies for accurate quantification and characterization of circRNA.
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Affiliation(s)
- Xu-Kai Ma
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Si-Nan Zhai
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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19
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Xie J, Wang L, Lin RJ. Variations of intronic branchpoint motif: identification and functional implications in splicing and disease. Commun Biol 2023; 6:1142. [PMID: 37949953 PMCID: PMC10638238 DOI: 10.1038/s42003-023-05513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The branchpoint (BP) motif is an essential intronic element for spliceosomal pre-mRNA splicing. In mammals, its sequence composition, distance to the downstream exon, and number of BPs per 3´ splice site are highly variable, unlike the GT/AG dinucleotides at the intron ends. These variations appear to provide evolutionary advantages for fostering alternative splicing, satisfying more diverse cellular contexts, and promoting resilience to genetic changes, thus contributing to an extra layer of complexity for gene regulation. Importantly, variants in the BP motif itself or in genes encoding BP-interacting factors cause human genetic diseases or cancers, highlighting the critical function of BP motif and the need to precisely identify functional BPs for faithful interpretation of their roles in splicing. In this perspective, we will succinctly summarize the major findings related to BP motif variations, discuss the relevant issues/challenges, and provide our insights.
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Affiliation(s)
- Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Ren-Jang Lin
- Center for RNA Biology & Therapeutics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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20
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Theil AF, Pines A, Kalayci T, Heredia‐Genestar JM, Raams A, Rietveld MH, Sridharan S, Tanis SEJ, Mulder KW, Büyükbabani N, Karaman B, Uyguner ZO, Kayserili H, Hoeijmakers JHJ, Lans H, Demmers JAA, Pothof J, Altunoglu U, El Ghalbzouri A, Vermeulen W. Trichothiodystrophy-associated MPLKIP maintains DBR1 levels for proper lariat debranching and ectodermal differentiation. EMBO Mol Med 2023; 15:e17973. [PMID: 37800682 PMCID: PMC10630875 DOI: 10.15252/emmm.202317973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
The brittle hair syndrome Trichothiodystrophy (TTD) is characterized by variable clinical features, including photosensitivity, ichthyosis, growth retardation, microcephaly, intellectual disability, hypogonadism, and anaemia. TTD-associated mutations typically cause unstable mutant proteins involved in various steps of gene expression, severely reducing steady-state mutant protein levels. However, to date, no such link to instability of gene-expression factors for TTD-associated mutations in MPLKIP/TTDN1 has been established. Here, we present seven additional TTD individuals with MPLKIP mutations from five consanguineous families, with a newly identified MPLKIP variant in one family. By mass spectrometry-based interaction proteomics, we demonstrate that MPLKIP interacts with core splicing factors and the lariat debranching protein DBR1. MPLKIP-deficient primary fibroblasts have reduced steady-state DBR1 protein levels. Using Human Skin Equivalents (HSEs), we observed impaired keratinocyte differentiation associated with compromised splicing and eventually, an imbalanced proteome affecting skin development and, interestingly, also the immune system. Our data show that MPLKIP, through its DBR1 stabilizing role, is implicated in mRNA splicing, which is of particular importance in highly differentiated tissue.
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Affiliation(s)
- Arjan F Theil
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Alex Pines
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Tuğba Kalayci
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
| | | | - Anja Raams
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Marion H Rietveld
- Department of DermatologyLeiden University Medical Center (LUMC)LeidenThe Netherlands
| | - Sriram Sridharan
- Cancer Science Institute of SingaporeNational University of SingaporeSingaporeSingapore
| | - Sabine EJ Tanis
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life SciencesRadboud UniversityNijmegenThe Netherlands
| | - Klaas W Mulder
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life SciencesRadboud UniversityNijmegenThe Netherlands
| | - Nesimi Büyükbabani
- Department of Pathology, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Medical GeneticsKoc University HospitalIstanbulTurkey
| | - Birsen Karaman
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Pediatric Basic Sciences, Child Health InstituteIstanbul UniversityIstanbulTurkey
| | - Zehra O Uyguner
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
| | - Hülya Kayserili
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Medical GeneticsKoc University School of Medicine (KUSOM)IstanbulTurkey
| | - Jan HJ Hoeijmakers
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
- Institute for Genome Stability in Aging and Disease, CECAD ForschungszentrumUniversity Hospital of CologneKölnGermany
- Princess Máxima Center for Pediatric OncologyONCODE InstituteUtrechtThe Netherlands
| | - Hannes Lans
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | | | - Joris Pothof
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Umut Altunoglu
- Department of Medical Genetics, Istanbul Faculty of MedicineIstanbul UniversityIstanbulTurkey
- Department of Medical GeneticsKoc University School of Medicine (KUSOM)IstanbulTurkey
| | | | - Wim Vermeulen
- Department of Molecular GeneticsErasmus MC Cancer InstituteRotterdamThe Netherlands
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21
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Hunter OV, Ruiz JC, Flaherty JN, Conrad NK. Functional analysis of 3'-UTR hairpins supports a two-tiered model for posttranscriptional regulation of MAT2A by METTL16. RNA (NEW YORK, N.Y.) 2023; 29:1725-1737. [PMID: 37567786 PMCID: PMC10578476 DOI: 10.1261/rna.079695.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023]
Abstract
S-adenosylmethionine (SAM) is the methyl donor for nearly all cellular methylation events, so cells need to carefully control SAM levels. MAT2A encodes the only SAM synthetase expressed in the majority of human cells, and its 3'-UTR has six conserved regulatory hairpins (hp1-6) that can be methylated by the N6-methyladenosine methyltransferase METTL16. Hp1 begins 8 nt from the stop codon, whereas hp2-6 are clustered further downstream (∼800 nt). These hairpins have been proposed to regulate MAT2A mRNA levels in response to intracellular SAM levels by regulating intron detention of the last intron of MAT2A and by modulating the stability of the fully spliced mRNA. However, a dissection of these two posttranscriptional mechanisms has not been previously reported. Using a modular reporter system, we show that hp1 functions primarily when the detained intron is included in the reporter and when that intron has a suboptimal polypyrimidine tract. In contrast, the hp2-6 cluster modulates mRNA stability independent of the detained intron, although hp1 may make a minor contribution to the regulation of decay as well. Taken with previously published reports, these data support a two-tiered model for MAT2A posttranscriptional regulation by METTL16 through its interactions with hp1 and hp2-6. In the upstream tier, hp1 and METTL16 control MAT2A intron detention, whereas the second tier involves METTL16-dependent methylation of hp2-6 to control MAT2A mRNA stability. Thus, cells use a similar set of molecular factors to achieve considerable complexity in the posttranscriptional regulation of SAM homeostasis.
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Affiliation(s)
- Olga V Hunter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Julio C Ruiz
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Juliana N Flaherty
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Nicholas K Conrad
- Department of Microbiology, UT Southwestern Medical Center, Dallas, Texas 75390, USA
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22
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Damianov A, Lin CH, Huang J, Zhou L, Jami-Alahmadi Y, Wohlschlegel J, Black DL. The apoptotic splicing regulators RBM5 and RBM10 are subunits of the U2 snRNP engaged with intron branch sites on chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558883. [PMID: 37790489 PMCID: PMC10542197 DOI: 10.1101/2023.09.21.558883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Understanding the mechanisms of pre-mRNA splicing and spliceosome assembly is limited by technical challenges to examining spliceosomes in vivo. Here we report the isolation of RNP complexes derived from precatalytic A or B-like spliceosomes solubilized from the chromatin pellet of lysed nuclei. We found that these complexes contain U2 snRNP proteins and a portion of the U2 snRNA, bound with intronic branch sites prior to the first catalytic step of splicing. Sequencing these pre-mRNA fragments allowed the transcriptome-wide mapping of branch sites with high sensitivity. In addition to known U2 snRNP proteins, these complexes contained the proteins RBM5 and RBM10. RBM5 and RBM10 are alternative splicing regulators that control exons affecting apoptosis and cell proliferation in cancer, but were not previously shown to associate with the U2 snRNP or to play roles in branch site selection. We delineate a common segment of RBM5 and RBM10, separate from their known functional domains, that is required for their interaction with the U2 snRNP. We identify a large set of splicing events regulated by RBM5 and RBM10 and find that they predominantly act as splicing silencers. Disruption of their U2 interaction renders the proteins inactive for repression of many alternative exons. We further find that these proteins assemble on branch sites of nearly all exons across the transcriptome, including those whose splicing is not altered by them. We propose a model where RBM5 and RBM10 act as components of the U2 snRNP complex. From within this complex, they sense structural features of branchpoint recognition to either allow progression to functional spliceosome or rejection of the complex to inhibit splicing.
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23
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Ohara H, Hosokawa M, Awaya T, Hagiwara A, Kurosawa R, Sako Y, Ogawa M, Ogasawara M, Noguchi S, Goto Y, Takahashi R, Nishino I, Hagiwara M. Branchpoints as potential targets of exon-skipping therapies for genetic disorders. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:404-412. [PMID: 37547287 PMCID: PMC10403725 DOI: 10.1016/j.omtn.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Fukutin (FKTN) c.647+2084G>T creates a pseudo-exon with a premature stop codon, which causes Fukuyama congenital muscular dystrophy (FCMD). We aimed to ameliorate aberrant splicing of FKTN caused by this variant. We screened compounds focusing on splicing regulation using the c.647+2084G>T splicing reporter and discovered that the branchpoint, which is essential for splicing reactions, could be a potential therapeutic target. To confirm the effectiveness of branchpoints as targets for exon skipping, we designed branchpoint-targeted antisense oligonucleotides (BP-AONs). This restored normal FKTN mRNA and protein production in FCMD patient myotubes. We identified a functional BP by detecting splicing intermediates and creating BP mutations in the FKTN reporter gene; this BP was non-redundant and sufficiently blocked by BP-AONs. Next, a BP-AON was designed for a different FCMD-causing variant, which induces pathogenic exon trapping by a common SINE-VNTR-Alu-type retrotransposon. Notably, this BP-AON also restored normal FKTN mRNA and protein production in FCMD patient myotubes. Our findings suggest that BPs could be potential targets in exon-skipping therapeutic strategies for genetic disorders.
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Affiliation(s)
- Hiroaki Ohara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
- Department of Drug Discovery for Intractable Diseases, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Motoyasu Hosokawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Tomonari Awaya
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Tumor Microenvironment and Immunity, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Atsuko Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Ryo Kurosawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yukiya Sako
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Megumu Ogawa
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Masashi Ogasawara
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Satoru Noguchi
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Yuichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neurology, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Ryosuke Takahashi
- Department of Neurology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8502, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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24
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Rasmussen A, Okholm T, Knudsen M, Vang S, Dyrskjøt L, Hansen T, Pedersen J. Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer. NAR Cancer 2023; 5:zcad041. [PMID: 37554968 PMCID: PMC10405568 DOI: 10.1093/narcan/zcad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Until recently, intronic lariats were regarded as short-lasting splicing byproducts with no apparent function; however, increasing evidence of stable derivatives suggests regulatory roles. Yet little is known about their characteristics, functions, distribution, and expression in healthy and tumor tissue. Here, we profiled and characterized circular stable intronic sequence RNAs (sisRNAs) using total RNA-Seq data from bladder cancer (BC; n = 457, UROMOL cohort), healthy tissue (n = 46), and fractionated cell lines (n = 5). We found that the recently-discovered full-length intronic circles and the stable lariats formed distinct subclasses, with a surprisingly high intronic circle fraction in BC (∼45%) compared to healthy tissues (0-20%). The stable lariats and their host introns were characterized by small transcript sizes, highly conserved BP regions, enriched BP motifs, and localization in multiple cell fractions. Additionally, circular sisRNAs showed tissue-specific expression patterns. We found nine circular sisRNAs as differentially expressed across early-stage BC patients with different prognoses, and sisHNRNPK expression correlated with progression-free survival. In conclusion, we identify distinguishing biological features of circular sisRNAs and point to specific candidates (incl. sisHNRNPK, sisWDR13 and sisMBNL1) that were highly expressed, had evolutionary conserved sequences, or had clinical correlations, which may facilitate future studies and further insights into their functional roles.
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Affiliation(s)
- Asta M Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
| | - Trine Line H Okholm
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Michael Knudsen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Søren Vang
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus 8000, Denmark
| | - Jakob S Pedersen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
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25
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Walker LC, Hoya MDL, Wiggins GAR, Lindy A, Vincent LM, Parsons MT, Canson DM, Bis-Brewer D, Cass A, Tchourbanov A, Zimmermann H, Byrne AB, Pesaran T, Karam R, Harrison SM, Spurdle AB. Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing Subgroup. Am J Hum Genet 2023; 110:1046-1067. [PMID: 37352859 PMCID: PMC10357475 DOI: 10.1016/j.ajhg.2023.06.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) framework for classifying variants uses six evidence categories related to the splicing potential of variants: PVS1, PS3, PP3, BS3, BP4, and BP7. However, the lack of guidance on how to apply such codes has contributed to variation in the specifications developed by different Clinical Genome Resource (ClinGen) Variant Curation Expert Panels. The ClinGen Sequence Variant Interpretation Splicing Subgroup was established to refine recommendations for applying ACMG/AMP codes relating to splicing data and computational predictions. We utilized empirically derived splicing evidence to (1) determine the evidence weighting of splicing-related data and appropriate criteria code selection for general use, (2) outline a process for integrating splicing-related considerations when developing a gene-specific PVS1 decision tree, and (3) exemplify methodology to calibrate splice prediction tools. We propose repurposing the PVS1_Strength code to capture splicing assay data that provide experimental evidence for variants resulting in RNA transcript(s) with loss of function. Conversely, BP7 may be used to capture RNA results demonstrating no splicing impact for intronic and synonymous variants. We propose that the PS3/BS3 codes are applied only for well-established assays that measure functional impact not directly captured by RNA-splicing assays. We recommend the application of PS1 based on similarity of predicted RNA-splicing effects for a variant under assessment in comparison with a known pathogenic variant. The recommendations and approaches for consideration and evaluation of RNA-assay evidence described aim to help standardize variant pathogenicity classification processes when interpreting splicing-based evidence.
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Affiliation(s)
- Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | | | - Michael T Parsons
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Daffodil M Canson
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | | | | | - Alicia B Byrne
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Steven M Harrison
- Ambry Genetics, Aliso Viejo, CA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Amanda B Spurdle
- Population Health Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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26
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Hoppe ER, Udy DB, Bradley RK. Recursive splicing discovery using lariats in total RNA sequencing. Life Sci Alliance 2023; 6:e202201889. [PMID: 37137707 PMCID: PMC10156609 DOI: 10.26508/lsa.202201889] [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: 12/23/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Recursive splicing is a non-canonical splicing mechanism in which an intron is removed in segments via multiple splicing reactions. Relatively few recursive splice sites have been identified with high confidence in human introns, and more comprehensive analyses are needed to better characterize where recursive splicing happens and whether or not it has a regulatory function. In this study, we use an unbiased approach using intron lariats to search for recursive splice sites in constitutive introns and alternative exons in the human transcriptome. We find evidence for recursive splicing in a broader range of intron sizes than previously reported and detail a new location for recursive splicing at the distal ends of cassette exons. In addition, we identify evidence for the conservation of these recursive splice sites among higher vertebrates and the use of these sites to influence alternative exon exclusion. Together, our data demonstrate the prevalence of recursive splicing and its potential influence on gene expression through alternatively spliced isoforms.
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Affiliation(s)
- Emma R Hoppe
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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27
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McBeath E, Fujiwara K, Hofmann MC. Evidence-Based Guide to Using Artificial Introns for Tissue-Specific Knockout in Mice. Int J Mol Sci 2023; 24:10258. [PMID: 37373404 PMCID: PMC10299402 DOI: 10.3390/ijms241210258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/09/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Up until recently, methods for generating floxed mice either conventionally or by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 (CRISPR-associated protein 9) editing have been technically challenging, expensive and error-prone, or time-consuming. To circumvent these issues, several labs have started successfully using a small artificial intron to conditionally knockout (KO) a gene of interest in mice. However, many other labs are having difficulty getting the technique to work. The key problem appears to be either a failure in achieving correct splicing after the introduction of the artificial intron into the gene or, just as crucial, insufficient functional KO of the gene's protein after Cre-induced removal of the intron's branchpoint. Presented here is a guide on how to choose an appropriate exon and where to place the recombinase-regulated artificial intron (rAI) in that exon to prevent disrupting normal gene splicing while maximizing mRNA degradation after recombinase treatment. The reasoning behind each step in the guide is also discussed. Following these recommendations should increase the success rate of this easy, new, and alternative technique for producing tissue-specific KO mice.
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Affiliation(s)
- Elena McBeath
- Department of Endocrine Neoplasia & Hormonal Disorders, MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Keigi Fujiwara
- National Coalition of Independent Scholars, Brattleboro, VT 05301, USA;
| | - Marie-Claude Hofmann
- Department of Endocrine Neoplasia & Hormonal Disorders, MD Anderson Cancer Center, Houston, TX 77030, USA;
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28
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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29
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Hamanaka K, Yamauchi D, Koshimizu E, Watase K, Mogushi K, Ishikawa K, Mizusawa H, Tsuchida N, Uchiyama Y, Fujita A, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N. Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans. Genome Res 2023; 33:435-447. [PMID: 37307504 PMCID: PMC10078293 DOI: 10.1101/gr.277335.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a genome-wide catalog of 9537 spl-TRs with a total of 58,290 significant TR-splicing associations across 49 tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci for repeat expansion diseases, spinocerebellar ataxia 6 (SCA6) and 12 (SCA12). Splicing alterations by these spl-TRs were compatible with those observed in SCA6 and SCA12. Thus, our comprehensive spl-TR catalog may help elucidate the pathomechanism of genetic diseases.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kei Watase
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kaoru Mogushi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kinya Ishikawa
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hidehiro Mizusawa
- Department of Neurology, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
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30
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Chuang TJ, Chiang TW, Chen CY. Assessing the impacts of various factors on circular RNA reliability. Life Sci Alliance 2023; 6:6/5/e202201793. [PMID: 36849251 PMCID: PMC9971162 DOI: 10.26508/lsa.202201793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 03/01/2023] Open
Abstract
Circular RNAs (circRNAs) are non-polyadenylated RNAs with a continuous loop structure characterized by a non-colinear back-splice junction (BSJ). Although millions of circRNA candidates have been identified, it remains a major challenge for determining circRNA reliability because of various types of false positives. Here, we systematically assess the impacts of numerous factors related to circRNA identification, conservation, biogenesis, and function on circRNA reliability by comparisons of circRNA expression from mock and the corresponding colinear/polyadenylated RNA-depleted datasets based on three different RNA treatment approaches. Eight important indicators of circRNA reliability are determined. The relative contribution to variability explained analyses reveal that the relative importance of these factors in affecting circRNA reliability in descending order is the conservation level of circRNA, full-length circular sequences, supporting BSJ read count, both BSJ donor and acceptor splice sites at the same colinear transcript isoforms, both BSJ donor and acceptor splice sites at the annotated exon boundaries, BSJs detected by multiple tools, supporting functional features, and both BSJ donor and acceptor splice sites undergoing alternative splicing. This study thus provides a useful guideline and an important resource for selecting high-confidence circRNAs for further investigations.
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Affiliation(s)
| | - Tai-Wei Chiang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
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31
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Tran KM, Kawauchi S, Kramár EA, Rezaie N, Liang HY, Sakr JS, Gomez-Arboledas A, Arreola MA, Cunha CD, Phan J, Wang S, Collins S, Walker A, Shi KX, Neumann J, Filimban G, Shi Z, Milinkeviciute G, Javonillo DI, Tran K, Gantuz M, Forner S, Swarup V, Tenner AJ, LaFerla FM, Wood MA, Mortazavi A, MacGregor GR, Green KN. A Trem2 R47H mouse model without cryptic splicing drives age- and disease-dependent tissue damage and synaptic loss in response to plaques. Mol Neurodegener 2023; 18:12. [PMID: 36803190 PMCID: PMC9938579 DOI: 10.1186/s13024-023-00598-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/19/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND The TREM2 R47H variant is one of the strongest genetic risk factors for late-onset Alzheimer's Disease (AD). Unfortunately, many current Trem2 R47H mouse models are associated with cryptic mRNA splicing of the mutant allele that produces a confounding reduction in protein product. To overcome this issue, we developed the Trem2R47H NSS (Normal Splice Site) mouse model in which the Trem2 allele is expressed at a similar level to the wild-type Trem2 allele without evidence of cryptic splicing products. METHODS Trem2R47H NSS mice were treated with the demyelinating agent cuprizone, or crossed with the 5xFAD mouse model of amyloidosis, to explore the impact of the TREM2 R47H variant on inflammatory responses to demyelination, plaque development, and the brain's response to plaques. RESULTS Trem2R47H NSS mice display an appropriate inflammatory response to cuprizone challenge, and do not recapitulate the null allele in terms of impeded inflammatory responses to demyelination. Utilizing the 5xFAD mouse model, we report age- and disease-dependent changes in Trem2R47H NSS mice in response to development of AD-like pathology. At an early (4-month-old) disease stage, hemizygous 5xFAD/homozygous Trem2R47H NSS (5xFAD/Trem2R47H NSS) mice have reduced size and number of microglia that display impaired interaction with plaques compared to microglia in age-matched 5xFAD hemizygous controls. This is associated with a suppressed inflammatory response but increased dystrophic neurites and axonal damage as measured by plasma neurofilament light chain (NfL) level. Homozygosity for Trem2R47H NSS suppressed LTP deficits and loss of presynaptic puncta caused by the 5xFAD transgene array in 4-month-old mice. At a more advanced (12-month-old) disease stage 5xFAD/Trem2R47H NSS mice no longer display impaired plaque-microglia interaction or suppressed inflammatory gene expression, although NfL levels remain elevated, and a unique interferon-related gene expression signature is seen. Twelve-month old Trem2R47H NSS mice also display LTP deficits and postsynaptic loss. CONCLUSIONS The Trem2R47H NSS mouse is a valuable model that can be used to investigate age-dependent effects of the AD-risk R47H mutation on TREM2 and microglial function including its effects on plaque development, microglial-plaque interaction, production of a unique interferon signature and associated tissue damage.
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Affiliation(s)
- Kristine M. Tran
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Shimako Kawauchi
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
- Transgenic Mouse Facility, Office of Research, ULAR, Irvine, USA
| | - Enikö A. Kramár
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Narges Rezaie
- Department of Developmental and Cell Biology, University of California, Irvine, USA
- Center for Complex Biological Systems, Irvine, USA
| | - Heidi Yahan Liang
- Department of Developmental and Cell Biology, University of California, Irvine, USA
- Center for Complex Biological Systems, Irvine, USA
| | - Jasmine S. Sakr
- Department of Pharmaceutical Sciences, University of California, Irvine, USA
| | | | - Miguel A. Arreola
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Celia da Cunha
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Jimmy Phan
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Shuling Wang
- Transgenic Mouse Facility, Office of Research, ULAR, Irvine, USA
| | - Sherilyn Collins
- Transgenic Mouse Facility, Office of Research, ULAR, Irvine, USA
| | - Amber Walker
- Transgenic Mouse Facility, Office of Research, ULAR, Irvine, USA
| | - Kai-Xuan Shi
- Transgenic Mouse Facility, Office of Research, ULAR, Irvine, USA
| | - Jonathan Neumann
- Transgenic Mouse Facility, Office of Research, ULAR, Irvine, USA
| | - Ghassan Filimban
- Department of Developmental and Cell Biology, University of California, Irvine, USA
| | - Zechuan Shi
- Department of Neurobiology and Behavior, University of California, Irvine, USA
| | - Giedre Milinkeviciute
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Dominic I. Javonillo
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Katelynn Tran
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Magdalena Gantuz
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Stefania Forner
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Vivek Swarup
- Department of Neurobiology and Behavior, University of California, Irvine, USA
- Center for Complex Biological Systems, Irvine, USA
| | - Andrea J. Tenner
- Department of Neurobiology and Behavior, University of California, Irvine, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, USA
- Department of Pathology and Laboratory Medicine, University of California, Irvine, USA
| | - Frank M. LaFerla
- Department of Neurobiology and Behavior, University of California, Irvine, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Marcelo A. Wood
- Department of Neurobiology and Behavior, University of California, Irvine, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, USA
- Center for Complex Biological Systems, Irvine, USA
| | - Grant R. MacGregor
- Transgenic Mouse Facility, Office of Research, ULAR, Irvine, USA
- Department of Developmental and Cell Biology, University of California, Irvine, USA
| | - Kim N. Green
- Department of Neurobiology and Behavior, University of California, Irvine, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, USA
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Viering DH, Hureaux M, Neveling K, Latta F, Kwint M, Blanchard A, Konrad M, Bindels RJ, Schlingmann KP, Vargas-Poussou R, de Baaij JH. Long-Read Sequencing Identifies Novel Pathogenic Intronic Variants in Gitelman Syndrome. J Am Soc Nephrol 2023; 34:333-345. [PMID: 36302598 PMCID: PMC10103101 DOI: 10.1681/asn.2022050627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/17/2022] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gitelman syndrome is a salt-losing tubulopathy characterized by hypokalemic alkalosis and hypomagnesemia. It is caused by homozygous recessive or compound heterozygous pathogenic variants in SLC12A3 , which encodes the Na + -Cl - cotransporter (NCC). In up to 10% of patients with Gitelman syndrome, current genetic techniques detect only one specific pathogenic variant. This study aimed to identify a second pathogenic variant in introns, splice sites, or promoters to increase the diagnostic yield. METHODS Long-read sequencing of SLC12A3 was performed in 67 DNA samples from individuals with suspected Gitelman syndrome in whom a single likely pathogenic or pathogenic variant was previously detected. In addition, we sequenced DNA samples from 28 individuals with one variant of uncertain significance or no candidate variant. Midigene splice assays assessed the pathogenicity of novel intronic variants. RESULTS A second likely pathogenic/pathogenic variant was identified in 45 (67%) patients. Those with two likely pathogenic/pathogenic variants had a more severe electrolyte phenotype than other patients. Of the 45 patients, 16 had intronic variants outside of canonic splice sites (nine variants, mostly deep intronic, six novel), whereas 29 patients had an exonic variant or canonic splice site variant. Midigene splice assays of the previously known c.1670-191C>T variant and intronic candidate variants demonstrated aberrant splicing patterns. CONCLUSION Intronic pathogenic variants explain an important part of the missing heritability in Gitelman syndrome. Long-read sequencing should be considered in diagnostic workflows for Gitelman syndrome.
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Affiliation(s)
- Daan H.H.M. Viering
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marguerite Hureaux
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Department of Genetics, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Paris CardioVascular Research Center, Institut National de la Santé et de Recherche Médicale (INSERM) U970, Paris City University, Paris, France
| | - Kornelia Neveling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Femke Latta
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anne Blanchard
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Clinical Investigations Center, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Centre de Recherche des Cordeliers, Sorbonne Université, INSERM, University of Paris, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Martin Konrad
- Department of General Pediatrics, University Children’s Hospital, Münster, Germany
| | - René J.M. Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Rosa Vargas-Poussou
- Reference Center for Hereditary Kidney and Childhood Diseases (Maladies Rénales Héréditaires de l’Enfant et de l’Adulte, MARHEA), Paris, France
- Department of Genetics, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
- Clinical Investigations Center, Hôpital Européen Georges-Pompidou, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Jeroen H.F. de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
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33
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Barbagallo C, Stella M, Broggi G, Russo A, Caltabiano R, Ragusa M. Genetics and RNA Regulation of Uveal Melanoma. Cancers (Basel) 2023; 15:775. [PMID: 36765733 PMCID: PMC9913768 DOI: 10.3390/cancers15030775] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Uveal melanoma (UM) is the most common intraocular malignant tumor and the most frequent melanoma not affecting the skin. While the rate of UM occurrence is relatively low, about 50% of patients develop metastasis, primarily to the liver, with lethal outcome despite medical treatment. Notwithstanding that UM etiopathogenesis is still under investigation, a set of known mutations and chromosomal aberrations are associated with its pathogenesis and have a relevant prognostic value. The most frequently mutated genes are BAP1, EIF1AX, GNA11, GNAQ, and SF3B1, with mutually exclusive mutations occurring in GNAQ and GNA11, and almost mutually exclusive ones in BAP1 and SF3B1, and BAP1 and EIF1AX. Among chromosomal aberrations, monosomy of chromosome 3 is the most frequent, followed by gain of chromosome 8q, and full or partial loss of chromosomes 1 and 6. In addition, epigenetic mechanisms regulated by non-coding RNAs (ncRNA), namely microRNAs and long non-coding RNAs, have also been investigated. Several papers investigating the role of ncRNAs in UM have reported that their dysregulated expression affects cancer-related processes in both in vitro and in vivo models. This review will summarize current findings about genetic mutations, chromosomal aberrations, and ncRNA dysregulation establishing UM biology.
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Affiliation(s)
- Cristina Barbagallo
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Michele Stella
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
| | - Giuseppe Broggi
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Andrea Russo
- Department of Ophthalmology, University of Catania, 95123 Catania, Italy
| | - Rosario Caltabiano
- Department of Medical, Surgical Sciences and Advanced Technologies G.F. Ingrassia—Section of Anatomic Pathology, University of Catania, 95123 Catania, Italy
| | - Marco Ragusa
- Department of Biomedical and Biotechnological Sciences—Section of Biology and Genetics, University of Catania, 95123 Catania, Italy
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34
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Zeng Y, Fair BJ, Zeng H, Krishnamohan A, Hou Y, Hall JM, Ruthenburg AJ, Li YI, Staley JP. Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing. Mol Cell 2022; 82:4681-4699.e8. [PMID: 36435176 PMCID: PMC10448999 DOI: 10.1016/j.molcel.2022.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 09/10/2022] [Accepted: 11/02/2022] [Indexed: 11/27/2022]
Abstract
Long introns with short exons in vertebrate genes are thought to require spliceosome assembly across exons (exon definition), rather than introns, thereby requiring transcription of an exon to splice an upstream intron. Here, we developed CoLa-seq (co-transcriptional lariat sequencing) to investigate the timing and determinants of co-transcriptional splicing genome wide. Unexpectedly, 90% of all introns, including long introns, can splice before transcription of a downstream exon, indicating that exon definition is not obligatory for most human introns. Still, splicing timing varies dramatically across introns, and various genetic elements determine this variation. Strong U2AF2 binding to the polypyrimidine tract predicts early splicing, explaining exon definition-independent splicing. Together, our findings question the essentiality of exon definition and reveal features beyond intron and exon length that are determinative for splicing timing.
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Affiliation(s)
- Yi Zeng
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Benjamin J Fair
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Huilin Zeng
- 855 Jefferson Ave. Redwood City, CA 94063, USA
| | - Aiswarya Krishnamohan
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yichen Hou
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Johnathon M Hall
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry & Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yang I Li
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA.
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Her HL, Boyle E, Yeo GW. Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites. BIOINFORMATICS ADVANCES 2022; 2:vbac083. [PMID: 36388152 PMCID: PMC9653213 DOI: 10.1093/bioadv/vbac083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/15/2022] [Accepted: 11/07/2022] [Indexed: 09/19/2023]
Abstract
Motivation Cross-linking and immunoprecipitation (CLIP) is a technology to map the binding sites of RNA-binding proteins (RBPs). The region where an RBP binds within RNA is often indicative of its molecular function in RNA processing. As an example, the binding sites of splicing factors are found within or proximal to alternatively spliced exons. To better reveal the function of RBPs, we developed a tool to visualize the distribution of CLIP signals around various transcript features. Results Here, we present Metadensity (https://github.com/YeoLab/Metadensity), a software that allows users to generate metagene plots. Metadensity allows users to input features such as branchpoints and preserves the near-nucleotide resolution of CLIP technologies by not scaling the features by length. Metadensity normalizes immunoprecipitated libraries with background controls, such as size-matched inputs, then windowing in various user-defined features. Finally, the signals are averaged across a provided set of transcripts. Availability and implementation Metadensity is available at https://github.com/YeoLab/Metadensity, with example notebooks at https://metadensity.readthedocs.io/en/latest/tutorial.html. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Hsuan-Lin Her
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Evan Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA
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36
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Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing. Nat Struct Mol Biol 2022; 29:1043-1055. [PMID: 36303034 DOI: 10.1038/s41594-022-00844-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 08/23/2022] [Indexed: 12/24/2022]
Abstract
It is estimated that 10%-30% of disease-associated genetic variants affect splicing. Splicing variants may generate deleteriously altered gene product and are potential therapeutic targets. However, systematic diagnosis or prediction of splicing variants is yet to be established, especially for the near-exon intronic splice region. The major challenge lies in the redundant and ill-defined branch sites and other splicing motifs therein. Here, we carried out unbiased massively parallel splicing assays on 5,307 disease-associated variants that overlapped with branch sites and collected 5,884 variants across the 5' splice region. We found that strong splice sites and exonic features preserve splicing from intronic sequence variation. Whereas the splice-altering mechanism of the 3' intronic variants is complex, that of the 5' is mainly splice-site destruction. Statistical learning combined with these molecular features allows precise prediction of altered splicing from an intronic variant. This statistical model provides the identity and ranking of biological features that determine splicing, which serves as transferable knowledge and out-performs the benchmarking predictive tool. Moreover, we demonstrated that intronic splicing variants may associate with disease risks in the human population. Our study elucidates the mechanism of splicing response of intronic variants, which classify disease-associated splicing variants for the promise of precision medicine.
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Genome-wide detection of human variants that disrupt intronic branchpoints. Proc Natl Acad Sci U S A 2022; 119:e2211194119. [PMID: 36306325 PMCID: PMC9636908 DOI: 10.1073/pnas.2211194119] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 human genes have been reported to alter splicing and cause disease by disrupting BP. However, until now, no computational approach was available to efficiently detect such variants in massively parallel sequencing data. We established a comprehensive human genome-wide BP database by integrating existing BP data and generating new BP data from RNA sequencing of lariat debranching enzyme DBR1-mutated patients and from machine-learning predictions. We characterized multiple features of BP in major and minor introns and found that BP and BP-2 (two nucleotides upstream of BP) positions exhibit a lower rate of variation in human populations and higher evolutionary conservation than the intronic background, while being comparable to the exonic background. We developed BPHunter as a genome-wide computational approach to systematically and efficiently detect intronic variants that may disrupt BP recognition. BPHunter retrospectively identified 40 of the 48 known pathogenic BP variants, in which we summarized a strategy for prioritizing BP variant candidates. The remaining eight variants all create AG-dinucleotides between the BP and acceptor site, which is the likely reason for missplicing. We demonstrated the practical utility of BPHunter prospectively by using it to identify a novel germline heterozygous BP variant of
STAT2
in a patient with critical COVID-19 pneumonia and a novel somatic intronic 59-nucleotide deletion of
ITPKB
in a lymphoma patient, both of which were validated experimentally. BPHunter is publicly available from
https://hgidsoft.rockefeller.edu/BPHunter
and
https://github.com/casanova-lab/BPHunter
.
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Bryen SJ, Yuen M, Joshi H, Dawes R, Zhang K, Lu JK, Jones KJ, Liang C, Wong WK, Peduto AJ, Waddell LB, Evesson FJ, Cooper ST. Prevalence, parameters, and pathogenic mechanisms for splice-altering acceptor variants that disrupt the AG exclusion zone. HGG ADVANCES 2022; 3:100125. [PMID: 35847480 PMCID: PMC9284458 DOI: 10.1016/j.xhgg.2022.100125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/19/2022] [Indexed: 10/26/2022] Open
Abstract
Predicting the pathogenicity of acceptor splice-site variants outside the essential AG is challenging, due to high sequence diversity of the extended splice-site region. Critical analysis of 24,445 intronic extended acceptor splice-site variants reported in ClinVar and the Leiden Open Variation Database (LOVD) demonstrates 41.9% of pathogenic variants create an AG dinucleotide between the predicted branchpoint and acceptor (AG-creating variants in the AG exclusion zone), 28.4% result in loss of a pyrimidine at the -3 position, and 15.1% result in loss of one or more pyrimidines in the polypyrimidine tract. Pathogenicity of AG-creating variants was highly influenced by their position. We define a high-risk zone for pathogenicity: > 6 nucleotides downstream of the predicted branchpoint and >5 nucleotides upstream from the acceptor, where 93.1% of pathogenic AG-creating variants arise and where naturally occurring AG dinucleotides are concordantly depleted (5.8% of natural AGs). SpliceAI effectively predicts pathogenicity of AG-creating variants, achieving 95% sensitivity and 69% specificity. We highlight clinical examples showing contrasting mechanisms for mis-splicing arising from AG variants: (1) cryptic acceptor created; (2) splicing silencer created: an introduced AG silences the acceptor, resulting in exon skipping, intron retention, and/or use of an alternative existing cryptic acceptor; and (3) splicing silencer disrupted: loss of a deep intronic AG activates inclusion of a pseudo-exon. In conclusion, we establish AG-creating variants as a common class of pathogenic extended acceptor variant and outline factors conferring critical risk for mis-splicing for AG-creating variants in the AG exclusion zone, between the branchpoint and acceptor.
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Affiliation(s)
- Samantha J. Bryen
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Michaela Yuen
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Himanshu Joshi
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Ruebena Dawes
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Katharine Zhang
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Jessica K. Lu
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Kristi J. Jones
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Department of Clinical Genetics, Children’s Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Christina Liang
- Department of Neurology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
- Department of Neurogenetics, Northern Clinical School, Kolling Institute, University of Sydney, NSW 2065, Australia
| | - Wui-Kwan Wong
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Anthony J. Peduto
- Department of Radiology, Westmead Hospital, Western Clinical School, University of Sydney, Westmead, NSW 2145, Australia
| | - Leigh B. Waddell
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Frances J. Evesson
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
| | - Sandra T. Cooper
- Kids Neuroscience Centre, Kids Research, The Children’s Hospital at Westmead, Locked Bag 4001, Westmead, NSW 2145, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
- Functional Neuromics, Children’s Medical Research Institute, The University of Sydney, Locked Bag 4001, Westmead, NSW 2145, Australia
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Anil AT, Choudhary K, Pandian R, Gupta P, Thakran P, Singh A, Sharma M, Mishra SK. Splicing of branchpoint-distant exons is promoted by Cactin, Tls1 and the ubiquitin-fold-activated Sde2. Nucleic Acids Res 2022; 50:10000-10014. [PMID: 36095128 PMCID: PMC9508853 DOI: 10.1093/nar/gkac769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/27/2022] [Indexed: 11/13/2022] Open
Abstract
Intron diversity facilitates regulated gene expression and alternative splicing. Spliceosomes excise introns after recognizing their splicing signals: the 5'-splice site (5'ss), branchpoint (BP) and 3'-splice site (3'ss). The latter two signals are recognized by U2 small nuclear ribonucleoprotein (snRNP) and its accessory factors (U2AFs), but longer spacings between them result in weaker splicing. Here, we show that excision of introns with a BP-distant 3'ss (e.g. rap1 intron 2) requires the ubiquitin-fold-activated splicing regulator Sde2 in Schizosaccharomyces pombe. By monitoring splicing-specific ura4 reporters in a collection of S. pombe mutants, Cay1 and Tls1 were identified as additional regulators of this process. The role of Sde2, Cay1 and Tls1 was further confirmed by increasing BP-3'ss spacings in a canonical tho5 intron. We also examined BP-distant exons spliced independently of these factors and observed that RNA secondary structures possibly bridged the gap between the two signals. These proteins may guide the 3'ss towards the spliceosome's catalytic centre by folding the RNA between the BP and 3'ss. Orthologues of Sde2, Cay1 and Tls1, although missing in the intron-poor Saccharomyces cerevisiae, are present in intron-rich eukaryotes, including humans. This type of intron-specific pre-mRNA splicing appears to have evolved for regulated gene expression and alternative splicing of key heterochromatin factors.
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Affiliation(s)
- Anupa T Anil
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Karan Choudhary
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Rakesh Pandian
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Praver Gupta
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Poonam Thakran
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Arashdeep Singh
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
| | - Shravan Kumar Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, 140306 Punjab, India
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Biscontin A, Zarantonello L, Russo A, Costa R, Montagnese S. Toward a Molecular Approach to Chronotype Assessment. J Biol Rhythms 2022; 37:272-282. [PMID: 35583112 DOI: 10.1177/07487304221099365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The aim of the present study was to develop a Polygenic Score-based model for molecular chronotype assessment. Questionnaire-based phenotypical chronotype assessment was used as a reference. In total, 54 extremely morning/morning (MM/M; 35 females, 39.7 ± 3.8 years) and 44 extremely evening/evening (EE/E; 20 females, 27.3 ± 7.7 years) individuals donated a buccal DNA sample for genotyping by sequencing of the entire genetic variability of 19 target genes known to be involved in circadian rhythmicity and/or sleep duration. Targeted genotyping was performed using the single primer enrichment technology and a specifically designed panel of 5526 primers. Among 2868 high-quality polymorphisms, a cross-validation approach lead to the identification of 83 chronotype predictive variants, including previously known and also novel chronotype-associated polymorphisms. A large (35 single-nucleotide polymorphisms [SNPs]) and also a small (13 SNPs) panel were obtained, both with an estimated predictive validity of approximately 80%. Potential mechanistic hypotheses for the role of some of the newly identified variants in modulating chronotype are formulated. Once validated in independent populations encompassing the whole range of chronotypes, the identified panels might become useful within the setting of both circadian public health initiatives and precision medicine.
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Affiliation(s)
| | | | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padova, Italy.,Institute of Neuroscience, National Research Council, Padova, Italy.,Chronobiology Section, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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41
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Torrado M, Maneiro E, Lamounier Junior A, Fernández-Burriel M, Sánchez Giralt S, Martínez-Carapeto A, Cazón L, Santiago E, Ochoa JP, McKenna WJ, Santomé L, Monserrat L. Identification of an elusive spliceogenic MYBPC3 variant in an otherwise genotype-negative hypertrophic cardiomyopathy pedigree. Sci Rep 2022; 12:7284. [PMID: 35508642 PMCID: PMC9068804 DOI: 10.1038/s41598-022-11159-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/13/2022] [Indexed: 11/10/2022] Open
Abstract
The finding of a genotype-negative hypertrophic cardiomyopathy (HCM) pedigree with several affected members indicating a familial origin of the disease has driven this study to discover causative gene variants. Genetic testing of the proband and subsequent family screening revealed the presence of a rare variant in the MYBPC3 gene, c.3331−26T>G in intron 30, with evidence supporting cosegregation with the disease in the family. An analysis of potential splice-altering activity using several splicing algorithms consistently yielded low scores. Minigene expression analysis at the mRNA and protein levels revealed that c.3331−26T>G is a spliceogenic variant with major splice-altering activity leading to undetectable levels of properly spliced transcripts or the corresponding protein. Minigene and patient mRNA analyses indicated that this variant induces complete and partial retention of intron 30, which was expected to lead to haploinsufficiency in carrier patients. As most spliceogenic MYBPC3 variants, c.3331−26T>G appears to be non-recurrent, since it was identified in only two additional unrelated probands in our large HCM cohort. In fact, the frequency analysis of 46 known splice-altering MYBPC3 intronic nucleotide substitutions in our HCM cohort revealed 9 recurrent and 16 non-recurrent variants present in a few probands (≤ 4), while 21 were not detected. The identification of non-recurrent elusive MYBPC3 spliceogenic variants that escape detection by in silico algorithms represents a challenge for genetic diagnosis of HCM and contributes to solving a fraction of genotype-negative HCM cases.
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Affiliation(s)
- Mario Torrado
- Cardiovascular Research Group, University of A Coruña, Campus de Oza, Building Fortín, 15006, A Coruña, Spain. .,Biomedical Research Institute of A Coruña, A Coruña, Spain.
| | - Emilia Maneiro
- Biomedical Research Institute of A Coruña, A Coruña, Spain. .,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain.
| | - Arsonval Lamounier Junior
- Cardiovascular Research Group, University of A Coruña, Campus de Oza, Building Fortín, 15006, A Coruña, Spain.,Biomedical Research Institute of A Coruña, A Coruña, Spain.,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain.,Medical School, Universidade Vale do Rio Doce, Governador Valadares, MG, Brazil
| | | | | | | | - Laura Cazón
- Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - Elisa Santiago
- Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - Juan Pablo Ochoa
- Biomedical Research Institute of A Coruña, A Coruña, Spain.,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - William J McKenna
- Cardiovascular Research Group, University of A Coruña, Campus de Oza, Building Fortín, 15006, A Coruña, Spain.,Biomedical Research Institute of A Coruña, A Coruña, Spain.,Institute of Cardiovascular Science, University College London, London, UK
| | - Luis Santomé
- Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
| | - Lorenzo Monserrat
- Biomedical Research Institute of A Coruña, A Coruña, Spain.,Cardiovascular Genetics, Health in Code, Business Center Marineda, Avenida de Arteixo 43, Local 1A, 15008, A Coruña, Spain
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42
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Robic A, Cerutti C, Demars J, Kühn C. From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194815. [PMID: 35513260 DOI: 10.1016/j.bbagrm.2022.194815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Circular intronic RNAs (ciRNAs) are still unexplored regarding mechanisms for their emergence. We considered the ATXN2L intron lariat-derived circular RNA (ciRNA-ATXN2L) as an opportunity to conduct a cross-species examination of ciRNA genesis. To this end, we investigated 207 datasets from 4 tissues and from 13 mammalian species. While in eight species, ciRNA-ATXN2L was never detected, in pigs and rabbits, ciRNA-ATXN2L was expressed in all tissues and sometimes at very high levels. Bovine tissues were an intermediate case and in macaques and cats, only ciRNA-ATXN2L traces were detected. The pattern of ciRNA-ATXN2L restricted to only five species is not related to a particular evolution of intronic sequences. To empower our analysis, we considered 221 additional introns including 80 introns where a lariat-derived ciRNA was previously described. The primary driver of micro-ciRNA genesis (< 155 nt as ciRNA-ATXN2L) appears to be the absence of a canonical "A" (i.e. a "tnA" located in the usual branching region) to build the lariat around this adenosine. The balance between available "non canonical-A" (no ciRNA genesis) and "non-A" (ciRNA genesis) for use as a branch point to build the lariat could modify the expression level of ciRNA-ATXN2L. In addition, the rare localization of the 2'-5' bond in an open RNA secondary structure could also negatively affect the lifetime of ciRNAs (macaque ciRNA-ATXN2L). Our analyses suggest that ciRNA-ATXN2L is likely a functionless splice remnant. This study provides a better understanding of the ciRNAs origin, especially drivers for micro ciRNA genesis.
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Affiliation(s)
- Annie Robic
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Chloé Cerutti
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany.
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43
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Liu H, Akhatayeva Z, Pan C, Liao M, Lan X. Comprehensive comparison of two types of algorithm for circRNA detection from short-read RNA-Seq. Bioinformatics 2022; 38:3037-3043. [PMID: 35482518 DOI: 10.1093/bioinformatics/btac302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Circular RNA is generally formed by the "back-splicing" process between the upstream splice acceptor and the downstream donor in/not in the regulation of the corresponding RNA-binding proteins or cis-elements. Therefore, more and more software packages have been developed and they are mostly based on the identification of the back-spliced junction reads. However, recent studies developed two software tools that can detect circRNA candidates by constructing k-mer table or/and de bruijn graph rather than reads mapping. RESULTS Here, we compared the precision, sensitivity and detection efficiency between software tools based on different algorithms. Eleven representative detection tools with two types of algorithm were selected for the overall pipeline analysis of RNA-seq datasets with/without RNase R treatment in two cell lines. Precision, sensitivity, AUC, F1 score and detection efficiency metrics were assessed to compare the prediction tools. Meanwhile, the sensitivity and distribution of highly expressed circRNAs before and after RNase R treatment were also revealed by their enrichment, unaffected and depleted candidate frequencies. Eventually, we found that compared to the k-mer based tools, CIRI2 and KNIFE based on reads mapping had relatively superior and more balanced detection performance regardless of the cell line or RNase R (-/+) datasets. AVAILABILITY AND IMPLEMENTATION All predicted results and source codes can be retrieved from https://github.com/luffy563/circRNA_tools_comparison. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hongfei Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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44
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Jacquier V, Prévot M, Gostan T, Bordonné R, Benkhelifa-Ziyyat S, Barkats M, Soret J. Splicing efficiency of minor introns in a mouse model of SMA predominantly depends on their branchpoint sequence and can involve the contribution of major spliceosome components. RNA (NEW YORK, N.Y.) 2022; 28:303-319. [PMID: 34893560 PMCID: PMC8848931 DOI: 10.1261/rna.078329.120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Spinal muscular atrophy (SMA) is a devastating neurodegenerative disease caused by reduced amounts of the ubiquitously expressed Survival of Motor Neuron (SMN) protein. In agreement with its crucial role in the biogenesis of spliceosomal snRNPs, SMN-deficiency is correlated to numerous splicing alterations in patient cells and various tissues of SMA mouse models. Among the snRNPs whose assembly is impacted by SMN-deficiency, those involved in the minor spliceosome are particularly affected. Importantly, splicing of several, but not all U12-dependent introns has been shown to be affected in different SMA models. Here, we have investigated the molecular determinants of this differential splicing in spinal cords from SMA mice. We show that the branchpoint sequence (BPS) is a key element controlling splicing efficiency of minor introns. Unexpectedly, splicing of several minor introns with suboptimal BPS is not affected in SMA mice. Using in vitro splicing experiments and oligonucleotides targeting minor or major snRNAs, we show for the first time that splicing of these introns involves both the minor and major machineries. Our results strongly suggest that splicing of a subset of minor introns is not affected in SMA mice because components of the major spliceosome compensate for the loss of minor splicing activity.
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Affiliation(s)
- Valentin Jacquier
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Manon Prévot
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Thierry Gostan
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
| | - Sofia Benkhelifa-Ziyyat
- Centre de Recherche en Myologie (CRM), Institut de Myologie, Sorbonne Universités, UPMC Univ Paris 06, Inserm UMRS974, GH Pitié Salpêtrière, Paris 75013, France
| | - Martine Barkats
- Centre de Recherche en Myologie (CRM), Institut de Myologie, Sorbonne Universités, UPMC Univ Paris 06, Inserm UMRS974, GH Pitié Salpêtrière, Paris 75013, France
| | - Johann Soret
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier 34293, France
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45
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Choi S, Cho N, Kim KK. Non-canonical splice junction processing increases the diversity of RBFOX2 splicing isoforms. Int J Biochem Cell Biol 2022; 144:106172. [PMID: 35124219 DOI: 10.1016/j.biocel.2022.106172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/23/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022]
Abstract
The underlying mechanisms of splicing regulation through non-canonical splice junction processing remain largely unknown. Here, we identified two RBFOX2 splicing isoforms by alternative 3' splice site selection of exon 9; the non-canonical splice junction processed RBFOX2 transcript (RBFOX2-N.C.) was expressed by the selection of the 3' splice GG acceptor sequence. The cytoplasmic localization of RBFOX2-C., a canonical splice junction-processed RBFOX2 transcript, was different from that of RBFOX2-N.C., which showed nuclear localization. In addition, we confirmed that RBFOX2-C. showed a significantly stronger localization into stress granules than RBFOX2-N.C. upon sodium arsenite treatment. Next, we investigated the importance of non-canonical 3' splice GG sequence selection of specific cis-regulatory elements using minigene constructs of the RBFOX2 gene. We found that the non-canonical 3' splice GG sequence and suboptimal branch point site adjacent region were critical for RBFOX2-N.C. expression through a non-canonical 3' splice selection. Our results suggest a regulatory mechanism for the non-canonical 3' splice selection in the RBFOX2 gene, providing a basis for studies related to the regulation of alternative pre-mRNA splicing through non-canonical splice junction processing.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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46
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Martinez NM, Su A, Burns MC, Nussbacher JK, Schaening C, Sathe S, Yeo GW, Gilbert WV. Pseudouridine synthases modify human pre-mRNA co-transcriptionally and affect pre-mRNA processing. Mol Cell 2022; 82:645-659.e9. [PMID: 35051350 PMCID: PMC8859966 DOI: 10.1016/j.molcel.2021.12.023] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/04/2021] [Accepted: 12/17/2021] [Indexed: 02/05/2023]
Abstract
Pseudouridine is a modified nucleotide that is prevalent in human mRNAs and is dynamically regulated. Here, we investigate when in their life cycle mRNAs become pseudouridylated to illuminate the potential regulatory functions of endogenous mRNA pseudouridylation. Using single-nucleotide resolution pseudouridine profiling on chromatin-associated RNA from human cells, we identified pseudouridines in nascent pre-mRNA at locations associated with alternatively spliced regions, enriched near splice sites, and overlapping hundreds of binding sites for RNA-binding proteins. In vitro splicing assays establish a direct effect of individual endogenous pre-mRNA pseudouridines on splicing efficiency. We validate hundreds of pre-mRNA sites as direct targets of distinct pseudouridine synthases and show that PUS1, PUS7, and RPUSD4-three pre-mRNA-modifying pseudouridine synthases with tissue-specific expression-control widespread changes in alternative pre-mRNA splicing and 3' end processing. Our results establish a vast potential for cotranscriptional pre-mRNA pseudouridylation to regulate human gene expression via alternative pre-mRNA processing.
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Affiliation(s)
- Nicole M Martinez
- Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA
| | - Amanda Su
- Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA
| | - Margaret C Burns
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Julia K Nussbacher
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Cassandra Schaening
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
| | - Wendy V Gilbert
- Yale School of Medicine, Department of Molecular Biophysics & Biochemistry, New Haven, CT 06520, USA.
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47
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Canson DM, Dumenil T, Parsons MT, O'Mara TA, Davidson AL, Okano S, Signal B, Mercer TR, Glubb DM, Spurdle AB. The splicing effect of variants at branchpoint elements in cancer genes. Genet Med 2022; 24:398-409. [PMID: 34906448 DOI: 10.1016/j.gim.2021.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/24/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Branchpoint elements are required for intron removal, and variants at these elements can result in aberrant splicing. We aimed to assess the value of branchpoint annotations generated from recent large-scale studies to select branchpoint-abrogating variants, using hereditary cancer genes as model. METHODS We identified branchpoint elements in 119 genes associated with hereditary cancer from 3 genome-wide experimentally-inferred and 2 predicted branchpoint data sets. We then identified variants that occur within branchpoint elements from public databases. We compared conservation, unique variant observations, and population frequencies at different nucleotides within branchpoint motifs. Finally, selected minigene assays were performed to assess the splicing effect of variants at branchpoint elements within mismatch repair genes. RESULTS There was poor overlap between predicted and experimentally-inferred branchpoints. Our analysis of cancer genes suggested that variants at -2 nucleotide, -1 nucleotide, and branchpoint positions in experimentally-inferred canonical motifs are more likely to be clinically relevant. Minigene assay data showed the -2 nucleotide to be more important to branchpoint motif integrity but also showed fluidity in branchpoint usage. CONCLUSION Data from cancer gene analysis suggest that there are few high-risk alleles that severely impact function via branchpoint abrogation. Results of this study inform a general scheme to prioritize branchpoint motif variants for further study.
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Affiliation(s)
- Daffodil M Canson
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Troy Dumenil
- Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Michael T Parsons
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Tracy A O'Mara
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Aimee L Davidson
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Satomi Okano
- Statistics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Bethany Signal
- Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Tim R Mercer
- Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia; Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Dylan M Glubb
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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48
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Zaimoku Y, Patel BA, Adams SD, Shalhoub R, Groarke EM, Lee AAC, Kajigaya S, Feng X, Rios OJ, Eager H, Alemu L, Quinones Raffo D, Wu CO, Flegel WA, Young NS. HLA associations, somatic loss of HLA expression, and clinical outcomes in immune aplastic anemia. Blood 2021; 138:2799-2809. [PMID: 34724566 PMCID: PMC8718630 DOI: 10.1182/blood.2021012895] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Immune aplastic anemia (AA) features somatic loss of HLA class I allele expression on bone marrow cells, consistent with a mechanism of escape from T-cell-mediated destruction of hematopoietic stem and progenitor cells. The clinical significance of HLA abnormalities has not been well characterized. We examined the somatic loss of HLA class I alleles and correlated HLA loss and mutation-associated HLA genotypes with clinical presentation and outcomes after immunosuppressive therapy in 544 AA patients. HLA class I allele loss was detected in 92 (22%) of the 412 patients tested, in whom there were 393 somatic HLA gene mutations and 40 instances of loss of heterozygosity. Most frequently affected was HLA-B*14:02, followed by HLA-A*02:01, HLA-B*40:02, HLA-B*08:01, and HLA-B*07:02. HLA-B*14:02, HLA-B*40:02, and HLA-B*07:02 were also overrepresented in AA. High-risk clonal evolution was correlated with HLA loss, HLA-B*14:02 genotype, and older age, which yielded a valid prediction model. In 2 patients, we traced monosomy 7 clonal evolution from preexisting clones harboring somatic mutations in HLA-A*02:01 and HLA-B*40:02. Loss of HLA-B*40:02 correlated with higher blood counts. HLA-B*07:02 and HLA-B*40:01 genotypes and their loss correlated with late-onset of AA. Our results suggest the presence of specific immune mechanisms of molecular pathogenesis with clinical implications. HLA genotyping and screening for HLA loss may be of value in the management of immune AA. This study was registered at clinicaltrials.gov as NCT00001964, NCT00061360, NCT00195624, NCT00260689, NCT00944749, NCT01193283, and NCT01623167.
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Affiliation(s)
- Yoshitaka Zaimoku
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Sharon D Adams
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Ruba Shalhoub
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Audrey Ai Chin Lee
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Olga Julia Rios
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Holly Eager
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Lemlem Alemu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Colin O Wu
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD; and
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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49
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Kumari A, Sedehizadeh S, Brook JD, Kozlowski P, Wojciechowska M. Differential fates of introns in gene expression due to global alternative splicing. Hum Genet 2021; 141:31-47. [PMID: 34907472 PMCID: PMC8758631 DOI: 10.1007/s00439-021-02409-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023]
Abstract
The discovery of introns over four decades ago revealed a new vision of genes and their interrupted arrangement. Throughout the years, it has appeared that introns play essential roles in the regulation of gene expression. Unique processing of excised introns through the formation of lariats suggests a widespread role for these molecules in the structure and function of cells. In addition to rapid destruction, these lariats may linger on in the nucleus or may even be exported to the cytoplasm, where they remain stable circular RNAs (circRNAs). Alternative splicing (AS) is a source of diversity in mature transcripts harboring retained introns (RI-mRNAs). Such RNAs may contain one or more entire retained intron(s) (RIs), but they may also have intron fragments resulting from sequential excision of smaller subfragments via recursive splicing (RS), which is characteristic of long introns. There are many potential fates of RI-mRNAs, including their downregulation via nuclear and cytoplasmic surveillance systems and the generation of new protein isoforms with potentially different functions. Various reports have linked the presence of such unprocessed transcripts in mammals to important roles in normal development and in disease-related conditions. In certain human neurological-neuromuscular disorders, including myotonic dystrophy type 2 (DM2), frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS) and Duchenne muscular dystrophy (DMD), peculiar processing of long introns has been identified and is associated with their pathogenic effects. In this review, we discuss different mechanisms involved in the processing of introns during AS and the functions of these large sections of the genome in our biology.
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Affiliation(s)
- Anjani Kumari
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Saam Sedehizadeh
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - John David Brook
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. .,Department of Rare Human Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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50
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Yu KHO, Shi CH, Wang B, Chow SHC, Chung GTY, Lung RWM, Tan KE, Lim YY, Tsang ACM, Lo KW, Yip KY. Quantifying full-length circular RNAs in cancer. Genome Res 2021; 31:2340-2353. [PMID: 34663689 PMCID: PMC8647826 DOI: 10.1101/gr.275348.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 10/12/2021] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discover and validate circRNA isoforms differentially expressed between the two groups. Compared with the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain substantially fewer microRNA response elements, showing the importance of quantifying full-length circRNA isoforms.
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Affiliation(s)
- Ken Hung-On Yu
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Christina Huan Shi
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Bo Wang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Savio Ho-Chit Chow
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Grace Tin-Yun Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Raymond Wai-Ming Lung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ke-En Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yat-Yuen Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Anna Chi-Man Tsang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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