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Park J, Nam DH, Kim D, Chung YJ. RPS24 alternative splicing is a marker of cancer progression and epithelial-mesenchymal transition. Sci Rep 2024; 14:13246. [PMID: 38853173 PMCID: PMC11162997 DOI: 10.1038/s41598-024-63976-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: 11/26/2023] [Accepted: 06/04/2024] [Indexed: 06/11/2024] Open
Abstract
Although alternative splicing (AS) is a major mechanism that adds diversity to gene expression patterns, its precise role in generating variability in ribosomal proteins, known as ribosomal heterogeneity, remains unclear. The ribosomal protein S24 (RPS24) gene, encoding a ribosomal component, undergoes AS; however, in-depth studies have been challenging because of three microexons between exons 4 and 6. We conducted a detailed analysis of RPS24 AS isoforms using a direct approach to investigate the splicing junctions related to these microexons, focusing on four AS isoforms. Each of these isoforms showed tissue specificity and relative differences in expression among cancer types. Significant differences in the proportions of these RPS24 AS isoforms between cancerous and normal tissues across diverse cancer types were also observed. Our study highlighted a significant correlation between the expression levels of a specific RPS24 AS isoform and the epithelial-mesenchymal transition process in lung and breast cancers. Our research contributes to a better understanding of the intricate regulatory mechanisms governing AS of ribosomal protein genes and highlights the biological implications of RPS24 AS isoforms in tissue development and tumorigenesis.
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Affiliation(s)
- Jiyeon Park
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea
| | - Da Hae Nam
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dokyeong Kim
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yeun-Jun Chung
- Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, 222 Banpo-daero Seocho-gu, Seoul, 137-701, Republic of Korea.
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
- Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, Republic of Korea.
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2
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Castañeda-Casasola CC, Nieto-Jacobo MF, Soares A, Padilla-Padilla EA, Anducho-Reyes MA, Brown C, Soth S, Esquivel-Naranjo EU, Hampton J, Mendoza-Mendoza A. Unveiling a Microexon Switch: Novel Regulation of the Activities of Sugar Assimilation and Plant-Cell-Wall-Degrading Xylanases and Cellulases by Xlr2 in Trichoderma virens. Int J Mol Sci 2024; 25:5172. [PMID: 38791210 PMCID: PMC11121469 DOI: 10.3390/ijms25105172] [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: 03/20/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Functional microexons have not previously been described in filamentous fungi. Here, we describe a novel mechanism of transcriptional regulation in Trichoderma requiring the inclusion of a microexon from the Xlr2 gene. In low-glucose environments, a long mRNA including the microexon encodes a protein with a GAL4-like DNA-binding domain (Xlr2-α), whereas in high-glucose environments, a short mRNA that is produced encodes a protein lacking this DNA-binding domain (Xlr2-β). Interestingly, the protein isoforms differ in their impact on cellulase and xylanase activity. Deleting the Xlr2 gene reduced both xylanase and cellulase activity and growth on different carbon sources, such as carboxymethylcellulose, xylan, glucose, and arabinose. The overexpression of either Xlr2-α or Xlr2-β in T. virens showed that the short isoform (Xlr2-β) caused higher xylanase activity than the wild types or the long isoform (Xlr2-α). Conversely, cellulase activity did not increase when overexpressing Xlr2-β but was increased with the overexpression of Xlr2-α. This is the first report of a novel transcriptional regulation mechanism of plant-cell-wall-degrading enzyme activity in T. virens. This involves the differential expression of a microexon from a gene encoding a transcriptional regulator.
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Affiliation(s)
- Cynthia Coccet Castañeda-Casasola
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
- Servicio Nacional de Sanidad, Inocuidad y Calidad Agroalimentaria, Centro Nacional de Referencia Fitosanitaria, Tecamac 55740, Mexico
| | | | - Amanda Soares
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Emir Alejandro Padilla-Padilla
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca 04510, Mexico
| | - Miguel Angel Anducho-Reyes
- Laboratorio de AgroBiotecnología, Universidad Politécnica de Pachuca, Carretera Pachuca-Cd. Sahagún, km 20, ExHacienda de Santa Bárbara, Zempoala 43830, Mexico;
| | - Chris Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand;
| | - Sereyboth Soth
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Edgardo Ulises Esquivel-Naranjo
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, Queretaro 76230, Mexico
| | - John Hampton
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
| | - Artemio Mendoza-Mendoza
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand; (C.C.C.-C.); (A.S.); (E.A.P.-P.); (S.S.); (E.U.E.-N.); (J.H.)
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3
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Sanoguera-Miralles L, Llinares-Burguet I, Bueno-Martínez E, Ramadane-Morchadi L, Stuani C, Valenzuela-Palomo A, García-Álvarez A, Pérez-Segura P, Buratti E, de la Hoya M, Velasco-Sampedro EA. Comprehensive splicing analysis of the alternatively spliced CHEK2 exons 8 and 10 reveals three enhancer/silencer-rich regions and 38 spliceogenic variants. J Pathol 2024; 262:395-409. [PMID: 38332730 DOI: 10.1002/path.6243] [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: 08/30/2023] [Revised: 10/26/2023] [Accepted: 11/28/2023] [Indexed: 02/10/2024]
Abstract
Splicing is controlled by a large set of regulatory elements (SREs) including splicing enhancers and silencers, which are involved in exon recognition. Variants at these motifs may dysregulate splicing and trigger loss-of-function transcripts associated with disease. Our goal here was to study the alternatively spliced exons 8 and 10 of the breast cancer susceptibility gene CHEK2. For this purpose, we used a previously published minigene with exons 6-10 that produced the expected minigene full-length transcript and replicated the naturally occurring events of exon 8 [Δ(E8)] and exon 10 [Δ(E10)] skipping. We then introduced 12 internal microdeletions of exons 8 and 10 by mutagenesis in order to map SRE-rich intervals by splicing assays in MCF-7 cells. We identified three minimal (10-, 11-, 15-nt) regions essential for exon recognition: c.863_877del [ex8, Δ(E8): 75%] and c.1073_1083del and c.1083_1092del [ex10, Δ(E10): 97% and 62%, respectively]. Then 87 variants found within these intervals were introduced into the wild-type minigene and tested functionally. Thirty-eight of them (44%) impaired splicing, four of which (c.883G>A, c.883G>T, c.884A>T, and c.1080G>T) induced negligible amounts (<5%) of the minigene full-length transcript. Another six variants (c.886G>A, c.886G>T, c.1075G>A, c.1075G>T, c.1076A>T, and c.1078G>T) showed significantly strong impacts (20-50% of the minigene full-length transcript). Thirty-three of the 38 spliceogenic variants were annotated as missense, three as nonsense, and two as synonymous, underlying the fact that any exonic change is capable of disrupting splicing. Moreover, c.883G>A, c.883G>T, and c.884A>T were classified as pathogenic/likely pathogenic variants according to ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based criteria. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Lara Sanoguera-Miralles
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Inés Llinares-Burguet
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Elena Bueno-Martínez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Lobna Ramadane-Morchadi
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Cristiana Stuani
- Molecular Pathology Lab. International Centre of Genetic Engineering and Biotechnology, Trieste, Italy
| | - Alberto Valenzuela-Palomo
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Alicia García-Álvarez
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
| | - Pedro Pérez-Segura
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Emanuele Buratti
- Molecular Pathology Lab. International Centre of Genetic Engineering and Biotechnology, Trieste, Italy
| | - Miguel de la Hoya
- Molecular Oncology Laboratory CIBERONC, Hospital Clínico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Eladio A Velasco-Sampedro
- Splicing and Genetic Susceptibility to Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular de Valladolid (IBGM), Consejo Superior de Investigaciones Científicas - Universidad de Valladolid (CSIC-UVa), Valladolid, Spain
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4
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Han KA, Yoon TH, Kim J, Lee J, Lee JY, Jang G, Um JW, Kim JK, Ko J. Specification of neural circuit architecture shaped by context-dependent patterned LAR-RPTP microexons. Nat Commun 2024; 15:1624. [PMID: 38388459 PMCID: PMC10883964 DOI: 10.1038/s41467-024-45695-0] [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: 07/13/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
LAR-RPTPs are evolutionarily conserved presynaptic cell-adhesion molecules that orchestrate multifarious synaptic adhesion pathways. Extensive alternative splicing of LAR-RPTP mRNAs may produce innumerable LAR-RPTP isoforms that act as regulatory "codes" for determining the identity and strength of specific synapse signaling. However, no direct evidence for this hypothesis exists. Here, using targeted RNA sequencing, we detected LAR-RPTP mRNAs in diverse cell types across adult male mouse brain areas. We found pronounced cell-type-specific patterns of two microexons, meA and meB, in Ptprd mRNAs. Moreover, diverse neural circuits targeting the same neuronal populations were dictated by the expression of different Ptprd variants with distinct inclusion patterns of microexons. Furthermore, conditional ablation of Ptprd meA+ variants at presynaptic loci of distinct hippocampal circuits impaired distinct modes of synaptic transmission and objection-location memory. Activity-triggered alterations of the presynaptic Ptprd meA code in subicular neurons mediates NMDA receptor-mediated postsynaptic responses in CA1 neurons and objection-location memory. Our data provide the evidence of cell-type- and/or circuit-specific expression patterns in vivo and physiological functions of LAR-RPTP microexons that are dynamically regulated.
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Affiliation(s)
- Kyung Ah Han
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea
| | - Taek-Han Yoon
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Jinhu Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Jusung Lee
- Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Ju Yeon Lee
- Korea Basic Science Institute, Research Center for Bioconvergence Analysis, Cheongju, 28119, Korea
| | - Gyubin Jang
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea
| | - Ji Won Um
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, Daegu, 42988, Korea
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Jaewon Ko
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea.
- Center for Synapse Diversity and Specificity, DGIST, Daegu, 42988, Korea.
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5
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GRP20 regulates micro-exon retention via interaction with the spliceosome during flower development. NATURE PLANTS 2024; 10:11-12. [PMID: 38225353 DOI: 10.1038/s41477-023-01606-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
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6
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Wang J, Ma X, Hu Y, Feng G, Guo C, Zhang X, Ma H. Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development. NATURE PLANTS 2024; 10:66-85. [PMID: 38195906 PMCID: PMC10808074 DOI: 10.1038/s41477-023-01605-8] [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: 11/11/2022] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Pre-mRNA splicing is crucial for gene expression and depends on the spliceosome and splicing factors. Plant exons have an average size of ~180 nucleotides and typically contain motifs for interactions with spliceosome and splicing factors. Micro exons (<51 nucleotides) are found widely in eukaryotes and in genes for plant development and environmental responses. However, little is known about transcript-specific regulation of splicing in plants and about the regulators for micro exon splicing. Here we report that glycine-rich protein 20 (GRP20) is an RNA-binding protein and required for splicing of ~2,100 genes including those functioning in flower development and/or environmental responses. Specifically, GRP20 is required for micro-exon retention in transcripts of floral homeotic genes; these micro exons are conserved across angiosperms. GRP20 is also important for small-exon (51-100 nucleotides) splicing. In addition, GRP20 is required for flower development. Furthermore, GRP20 binds to poly-purine motifs in micro and small exons and a spliceosome component; both RNA binding and spliceosome interaction are important for flower development and micro-exon retention. Our results provide new insights into the mechanisms of micro-exon retention in flower development.
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Affiliation(s)
- Jun Wang
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Xinwei Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yi Hu
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Guanhua Feng
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Xin Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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7
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [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: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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8
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Liu Z, Zhu C, Steinmetz LM, Wei W. Identification and quantification of small exon-containing isoforms in long-read RNA sequencing data. Nucleic Acids Res 2023; 51:e104. [PMID: 37843096 PMCID: PMC10639058 DOI: 10.1093/nar/gkad810] [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: 01/09/2023] [Revised: 08/03/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Small exons are pervasive in transcriptomes across organisms, and their quantification in RNA isoforms is crucial for understanding gene functions. Although long-read RNA-seq based on Oxford Nanopore Technologies (ONT) offers the advantage of covering transcripts in full length, its lower base accuracy poses challenges for identifying individual exons, particularly microexons (≤ 30 nucleotides). Here, we systematically assess small exons quantification in synthetic and human ONT RNA-seq datasets. We demonstrate that reads containing small exons are often not properly aligned, affecting the quantification of relevant transcripts. Thus, we develop a local-realignment method for misaligned exons (MisER), which remaps reads with misaligned exons to the transcript references. Using synthetic and simulated datasets, we demonstrate the high sensitivity and specificity of MisER for the quantification of transcripts containing small exons. Moreover, MisER enabled us to identify small exons with a higher percent spliced-in index (PSI) in neural, particularly neural-regulated microexons, when comparing 14 neural to 16 non-neural tissues in humans. Our work introduces an improved quantification method for long-read RNA-seq and especially facilitates studies using ONT long-reads to elucidate the regulation of genes involving small exons.
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Affiliation(s)
- Zhen Liu
- Lingang Laboratory, Shanghai, Shanghai 200031, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, Shanghai 200031, China
| | - Chenchen Zhu
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lars M Steinmetz
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Wu Wei
- Lingang Laboratory, Shanghai, Shanghai 200031, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, Shanghai 200031, China
- Center for Biomedical Informatics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, Shanghai 200040, China
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9
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Shirokikh NE, Jensen KB, Thakor N. Editorial: RNA machines. Front Genet 2023; 14:1290420. [PMID: 37829284 PMCID: PMC10565666 DOI: 10.3389/fgene.2023.1290420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Affiliation(s)
- Nikolay E. Shirokikh
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Kirk Blomquist Jensen
- School of Biological Sciences, Faculty of Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nehal Thakor
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, Canada
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10
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Dudka D, Akins RB, Lampson MA. FREEDA: An automated computational pipeline guides experimental testing of protein innovation. J Cell Biol 2023; 222:e202212084. [PMID: 37358475 PMCID: PMC10292211 DOI: 10.1083/jcb.202212084] [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: 12/17/2022] [Revised: 04/22/2023] [Accepted: 06/07/2023] [Indexed: 06/27/2023] Open
Abstract
Cell biologists typically focus on conserved regions of a protein, overlooking innovations that can shape its function over evolutionary time. Computational analyses can reveal potential innovations by detecting statistical signatures of positive selection that lead to rapid accumulation of beneficial mutations. However, these approaches are not easily accessible to non-specialists, limiting their use in cell biology. Here, we present an automated computational pipeline FREEDA that provides a simple graphical user interface requiring only a gene name; integrates widely used molecular evolution tools to detect positive selection in rodents, primates, carnivores, birds, and flies; and maps results onto protein structures predicted by AlphaFold. Applying FREEDA to >100 centromere proteins, we find statistical evidence of positive selection within loops and turns of ancient domains, suggesting innovation of essential functions. As a proof-of-principle experiment, we show innovation in centromere binding of mouse CENP-O. Overall, we provide an accessible computational tool to guide cell biology research and apply it to experimentally demonstrate functional innovation.
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Affiliation(s)
- Damian Dudka
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - R. Brian Akins
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael A. Lampson
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
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11
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Sznajder L, Khan M, Tadross M, Ciesiołka A, Nutter C, Taylor K, Pearson C, Sobczak K, Lewis M, Swanson M, Yuen R. Autistic traits in myotonic dystrophy type 1 due to MBNL inhibition and RNA mis-splicing. RESEARCH SQUARE 2023:rs.3.rs-3221704. [PMID: 37645891 PMCID: PMC10462192 DOI: 10.21203/rs.3.rs-3221704/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tandem repeat expansions are enriched in autism spectrum disorder, including CTG expansion in the DMPK gene that underlines myotonic muscular dystrophy type 1. Although the clinical connection of autism to myotonic dystrophy is corroborated, the molecular links remained unknown. Here, we show a mechanistic path of autism via repeat expansion in myotonic dystrophy. We found that inhibition of muscleblind-like (MBNL) splicing factors by expanded CUG RNAs alerts the splicing of autism-risk genes during brain development especially a class of autism-relevant microexons. To provide in vivo evidence that the CTG expansion and MBNL inhibition axis leads to the presentation of autistic traits, we demonstrate that CTG expansion and MBNL-null mouse models recapitulate autism-relevant mis-splicing profiles and demonstrate social deficits. Our findings indicate that DMPK CTG expansion-associated autism arises from developmental mis-splicing. Understanding this pathomechanistic connection provides an opportunity for greater in-depth investigations of mechanistic threads in autism.
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Lederer I, Shahid B, Dao U, Brogdon A, Byrtus H, Delva M, Deva O, Hatfield P, Hertz M, Justice J, Mavor S, Pilbeam E, Rice Z, Simpson A, Temar H, Wynn R, Xhangolli J, Graves C, Seidel H. A frameshift variant in the melanophilin gene is associated with loss of pigment from shed skin in ball pythons ( Python regius ). MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000896. [PMID: 37637270 PMCID: PMC10448248 DOI: 10.17912/micropub.biology.000896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/19/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023]
Abstract
Melanophilin is a myosin adaptor required for transporting the pigment melanin within cells. Loss of melanophilin in fish, birds, and mammals causes pigmentation defects, but little is known about the role of melanophilin in non-avian reptiles. Here we show that a frameshift in the melanophilin gene in ball python ( P. regius ) is associated with loss of pigment from shed skin. This variant is predicted to remove the myosin-binding domain of melanophilin and thereby impair transport of melanin-containing organelles. Our study represents the first description of a melanophilin variant in a non-avian reptile and confirms the role of melanophilin across vertebrates.
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13
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Rezvykh A, Ustyugov A, Chaprov K, Teterina E, Nebogatikov V, Spasskaya D, Evgen’ev M, Morozov A, Funikov S. Cytoplasmic aggregation of mutant FUS causes multistep RNA splicing perturbations in the course of motor neuron pathology. Nucleic Acids Res 2023; 51:5810-5830. [PMID: 37115004 PMCID: PMC10287951 DOI: 10.1093/nar/gkad319] [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: 08/29/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Dysfunction of the RNA-binding protein (RBP) FUS implicated in RNA metabolism can cause amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases. Mutations affecting FUS nuclear localization can drive RNA splicing defects and stimulate the formation of non-amyloid inclusions in affected neurons. However, the mechanism by which FUS mutations contribute to the development of ALS remains uncertain. Here we describe a pattern of RNA splicing changes in the dynamics of the continuous proteinopathy induced by mislocalized FUS. We show that the decrease in intron retention of FUS-associated transcripts represents the hallmark of the pathogenesis of ALS and is the earliest molecular event in the course of progression of the disease. As FUS aggregation increases, the pattern of RNA splicing changes, becoming more complex, including a decrease in the inclusion of neuron-specific microexons and induction of cryptic exon splicing due to the sequestration of additional RBPs into FUS aggregates. Crucially, the identified features of the pathological splicing pattern are also observed in ALS patients in both sporadic and familial cases. Our data provide evidence that both a loss of nuclear FUS function due to mislocalization and the subsequent cytoplasmic aggregation of mutant protein lead to the disruption of RNA splicing in a multistep fashion during FUS aggregation.
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Affiliation(s)
- Alexander P Rezvykh
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Aleksey A Ustyugov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Kirill D Chaprov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Ekaterina V Teterina
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Vladimir O Nebogatikov
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences, Chernogolovka, 142432, Russian Federation
| | - Daria S Spasskaya
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Michael B Evgen’ev
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Alexey V Morozov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
| | - Sergei Yu Funikov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow, 119991, Russian Federation
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14
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Dudka D, Akins RB, Lampson MA. FREEDA: an automated computational pipeline guides experimental testing of protein innovation by detecting positive selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530329. [PMID: 36909479 PMCID: PMC10002610 DOI: 10.1101/2023.02.27.530329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Cell biologists typically focus on conserved regions of a protein, overlooking innovations that can shape its function over evolutionary time. Computational analyses can reveal potential innovations by detecting statistical signatures of positive selection that leads to rapid accumulation of beneficial mutations. However, these approaches are not easily accessible to non-specialists, limiting their use in cell biology. Here, we present an automated computational pipeline FREEDA (Finder of Rapidly Evolving Exons in De novo Assemblies) that provides a simple graphical user interface requiring only a gene name, integrates widely used molecular evolution tools to detect positive selection, and maps results onto protein structures predicted by AlphaFold. Applying FREEDA to >100 mouse centromere proteins, we find evidence of positive selection in intrinsically disordered regions of ancient domains, suggesting innovation of essential functions. As a proof-of-principle experiment, we show innovation in centromere binding of CENP-O. Overall, we provide an accessible computational tool to guide cell biology research and apply it to experimentally demonstrate functional innovation.
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15
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Choi S, Lee HS, Cho N, Kim I, Cheon S, Park C, Kim EM, Kim W, Kim KK. RBFOX2-regulated TEAD1 alternative splicing plays a pivotal role in Hippo-YAP signaling. Nucleic Acids Res 2022; 50:8658-8673. [PMID: 35699208 PMCID: PMC9410899 DOI: 10.1093/nar/gkac509] [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: 10/15/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
Alternative pre-mRNA splicing is key to proteome diversity; however, the biological roles of alternative splicing (AS) in signaling pathways remain elusive. Here, we focus on TEA domain transcription factor 1 (TEAD1), a YAP binding factor in the Hippo signaling pathway. Public database analyses showed that expression of YAP-TEAD target genes negatively correlated with the expression of a TEAD1 isoform lacking exon 6 (TEAD1ΔE6) but did not correlate with overall TEAD1 expression. We confirmed that the transcriptional activity and oncogenic properties of the full-length TEAD1 isoform were greater than those of TEAD1ΔE6, with the difference in transcription related to YAP interaction. Furthermore, we showed that RNA-binding Fox-1 homolog 2 (RBFOX2) promoted the inclusion of TEAD1 exon 6 via binding to the conserved GCAUG element in the downstream intron. These results suggest a regulatory mechanism of RBFOX2-mediated TEAD1 AS and provide insight into AS-specific modulation of signaling pathways.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hyo Seong Lee
- 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
| | - Inyoung Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seongmin Cheon
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea.,Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Eun-Mi Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea
| | - Wantae Kim
- 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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16
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Hinkle ER, Wiedner HJ, Torres EV, Jackson M, Black AJ, Blue RE, Harris SE, Guzman BB, Gentile GM, Lee EY, Tsai YH, Parker J, Dominguez D, Giudice J. Alternative splicing regulation of membrane trafficking genes during myogenesis. RNA (NEW YORK, N.Y.) 2022; 28:523-540. [PMID: 35082143 PMCID: PMC8925968 DOI: 10.1261/rna.078993.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Alternative splicing transitions occur during organ development, and, in numerous diseases, splicing programs revert to fetal isoform expression. We previously found that extensive splicing changes occur during postnatal mouse heart development in genes encoding proteins involved in vesicle-mediated trafficking. However, the regulatory mechanisms of this splicing-trafficking network are unknown. Here, we found that membrane trafficking genes are alternatively spliced in a tissue-specific manner, with striated muscles exhibiting the highest levels of alternative exon inclusion. Treatment of differentiated muscle cells with chromatin-modifying drugs altered exon inclusion in muscle cells. Examination of several RNA-binding proteins revealed that the poly-pyrimidine tract binding protein 1 (PTBP1) and quaking regulate splicing of trafficking genes during myogenesis, and that removal of PTBP1 motifs prevented PTBP1 from binding its RNA target. These findings enhance our understanding of developmental splicing regulation of membrane trafficking proteins which might have implications for muscle disease pathogenesis.
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Affiliation(s)
- Emma R Hinkle
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Hannah J Wiedner
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Eduardo V Torres
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Micaela Jackson
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Adam J Black
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - R Eric Blue
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Sarah E Harris
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Bryan B Guzman
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Gabrielle M Gentile
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Eunice Y Lee
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Yi-Hsuan Tsai
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Joel Parker
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel Dominguez
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Jimena Giudice
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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17
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Pitolli C, Marini A, Sette C, Pagliarini V. Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer. Int J Mol Sci 2022; 23:ijms23052811. [PMID: 35269953 PMCID: PMC8911335 DOI: 10.3390/ijms23052811] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Alberto Marini
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
- Correspondence:
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18
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Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants. Nat Commun 2022; 13:820. [PMID: 35145097 PMCID: PMC8831610 DOI: 10.1038/s41467-022-28449-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/26/2022] [Indexed: 12/31/2022] Open
Abstract
It is challenging to identify the smallest microexons (≤15-nt) due to their small size. Consequently, these microexons are often misannotated or missed entirely during genome annotation. Here, we develop a pipeline to accurately identify 2,398 small microexons in 10 diverse plant species using 990 RNA-seq datasets, and most of them have not been annotated in the reference genomes. Analysis reveals that microexons tend to have increased detained flanking introns that require post-transcriptional splicing after polyadenylation. Examination of 45 conserved microexon clusters demonstrates that microexons and associated gene structures can be traced back to the origin of land plants. Based on these clusters, we develop an algorithm to genome-wide model coding microexons in 132 plants and find that microexons provide a strong phylogenetic signal for plant organismal relationships. Microexon modeling reveals diverse evolutionary trajectories, involving microexon gain and loss and alternative splicing. Our work provides a comprehensive view of microexons in plants. The small size (≤15-nt) of micorexons poses difficulties for genome annotation and identification using standard RNA sequence mapping approaches. Here, the authors develop computational pipelines to discover and predict microexons in plants and reveal diverse evolutionary trajectories via genomewide microexon modeling.
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19
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Parada GE, Hemberg M. Identification and Quantification of Microexons Using Bulk and Single-Cell RNA-Seq Data. Methods Mol Biol 2022; 2537:129-147. [PMID: 35895262 DOI: 10.1007/978-1-0716-2521-7_8] [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] [Indexed: 06/15/2023]
Abstract
The analysis of RNA-seq has greatly improved the characterization and understanding of the transcriptome. In particular, RNA-seq experiments have extended catalogs of alternative splicing events. However, the analysis of RNAs-seq data for detection and quantification of microexons, extremely short exons of length up to 30 nt, require specialized computational workflows. Here, we describe MicroExonator, a reproducible computational workflow for microexon splicing analysis using bulk or single-cell RNA-seq data.
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Affiliation(s)
- Guillermo E Parada
- Wellcome Sanger Institute, Cambridge, UK
- Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Martin Hemberg
- Wellcome Sanger Institute, Cambridge, UK.
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
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20
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Cheng Q, He B, Zhao C, Bi H, Chen D, Han S, Gao H, Feng W. Prediction of functional microexons by transfer learning. BMC Genomics 2021; 22:855. [PMID: 34836511 PMCID: PMC8627023 DOI: 10.1186/s12864-021-08187-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
Background Microexons are a particular kind of exon of less than 30 nucleotides in length. More than 60% of annotated human microexons were found to have high levels of sequence conservation, suggesting their potential functions. There is thus a need to develop a method for predicting functional microexons. Results Given the lack of a publicly available functional label for microexons, we employed a transfer learning skill called Transfer Component Analysis (TCA) to transfer the knowledge obtained from feature mapping for the prediction of functional microexons. To provide reference knowledge, microindels were chosen because of their similarities to microexons. Then, Support Vector Machine (SVM) was used to train a classification model in the newly built feature space for the functional microindels. With the trained model, functional microexons were predicted. We also built a tool based on this model to predict other functional microexons. We then used this tool to predict a total of 19 functional microexons reported in the literature. This approach successfully predicted 16 out of 19 samples, giving accuracy greater than 80%. Conclusions In this study, we proposed a method for predicting functional microexons and applied it, with the predictive results being largely consistent with records in the literature.
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Affiliation(s)
- Qi Cheng
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Bo He
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China.
| | - Chengkui Zhao
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Hongyuan Bi
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Duojiao Chen
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Shuangze Han
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Haikuan Gao
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China
| | - Weixing Feng
- College of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China.
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21
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Rahimi K, Venø MT, Dupont DM, Kjems J. Nanopore sequencing of brain-derived full-length circRNAs reveals circRNA-specific exon usage, intron retention and microexons. Nat Commun 2021; 12:4825. [PMID: 34376658 PMCID: PMC8355340 DOI: 10.1038/s41467-021-24975-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022] Open
Abstract
Circular RNA (circRNA) is a class of covalently joined non-coding RNAs with functional roles in a wide variety of cellular processes. Their composition shows extensive overlap with exons found in linear mRNAs making it difficult to delineate their composition using short-read RNA sequencing, particularly for long and multi-exonic circRNAs. Here, we use long-read nanopore sequencing of nicked circRNAs (circNick-LRS) and characterize a total of 18,266 and 39,623 circRNAs in human and mouse brain, respectively. We further develop an approach for targeted long-read sequencing of a panel of circRNAs (circPanel-LRS), eliminating the need for prior circRNA enrichment and find >30 circRNA isoforms on average per targeted locus. Our data show that circRNAs exhibit a large number of splicing events such as novel exons, intron retention and microexons that preferentially occur in circRNAs. We propose that altered exon usage in circRNAs may reflect resistance to nonsense-mediated decay in the absence of translation.
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Affiliation(s)
- Karim Rahimi
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
| | - Morten T Venø
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
- Omiics ApS, Aarhus, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus, Denmark.
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22
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Enriched Alternative Splicing in Islets of Diabetes-Susceptible Mice. Int J Mol Sci 2021; 22:ijms22168597. [PMID: 34445304 PMCID: PMC8395343 DOI: 10.3390/ijms22168597] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/28/2021] [Accepted: 08/05/2021] [Indexed: 12/30/2022] Open
Abstract
Dysfunctional islets of Langerhans are a hallmark of type 2 diabetes (T2D). We hypothesize that differences in islet gene expression alternative splicing which can contribute to altered protein function also participate in islet dysfunction. RNA sequencing (RNAseq) data from islets of obese diabetes-resistant and diabetes-susceptible mice were analyzed for alternative splicing and its putative genetic and epigenetic modulators. We focused on the expression levels of chromatin modifiers and SNPs in regulatory sequences. We identified alternative splicing events in islets of diabetes-susceptible mice amongst others in genes linked to insulin secretion, endocytosis or ubiquitin-mediated proteolysis pathways. The expression pattern of 54 histones and chromatin modifiers, which may modulate splicing, were markedly downregulated in islets of diabetic animals. Furthermore, diabetes-susceptible mice carry SNPs in RNA-binding protein motifs and in splice sites potentially responsible for alternative splicing events. They also exhibit a larger exon skipping rate, e.g., in the diabetes gene Abcc8, which might affect protein function. Expression of the neuronal splicing factor Srrm4 which mediates inclusion of microexons in mRNA transcripts was markedly lower in islets of diabetes-prone compared to diabetes-resistant mice, correlating with a preferential skipping of SRRM4 target exons. The repression of Srrm4 expression is presumably mediated via a higher expression of miR-326-3p and miR-3547-3p in islets of diabetic mice. Thus, our study suggests that an altered splicing pattern in islets of diabetes-susceptible mice may contribute to an elevated T2D risk.
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23
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Mochizuki Y, Funayama R, Shirota M, Kikukawa Y, Ohira M, Karasawa H, Kobayashi M, Ohnuma S, Unno M, Nakayama K. Alternative microexon splicing by RBFOX2 and PTBP1 is associated with metastasis in colorectal cancer. Int J Cancer 2021; 149:1787-1800. [PMID: 34346508 DOI: 10.1002/ijc.33758] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/09/2022]
Abstract
The splicing of microexons (very small exons) is frequently dysregulated in the brain of individuals with autism spectrum disorder. However, little is known of the patterns, regulatory mechanisms and roles of microexon splicing in cancer. We here examined the transcriptome-wide profile of microexon splicing in matched colorectal cancer (CRC) and normal tissue specimens. Out of 1492 microexons comprising 3 to 15 nucleotides, 21 (1%) manifested differential splicing between CRC and normal tissue. The 21 genes harboring the differentially spliced microexons were enriched in gene ontology terms related to cell adhesion and migration. RNA interference-mediated knockdown experiments identified two splicing factors, RBFOX2 and PTBP1, as regulators of microexon splicing in CRC cells. RBFOX2 and PTBP1 were found to directly bind to microexon-containing pre-mRNAs and to control their splicing in such cells. Differential microexon splicing was shown to be due, at least in part, to altered expression of RBFOX2 and PTBP1 in CRC tissue compared to matched normal tissue. Finally, we found that changes in the pattern of microexon splicing were associated with CRC metastasis. Our data thus suggest that altered expression of RBFOX2 and PTBP1 might influence CRC metastasis through the regulation of microexon splicing.
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Affiliation(s)
- Yasushi Mochizuki
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ryo Funayama
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Science, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yuna Kikukawa
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masahiro Ohira
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hideaki Karasawa
- Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Minoru Kobayashi
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinobu Ohnuma
- Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
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24
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Choudhary B, Marx O, Norris AD. Spliceosomal component PRP-40 is a central regulator of microexon splicing. Cell Rep 2021; 36:109464. [PMID: 34348142 PMCID: PMC8378409 DOI: 10.1016/j.celrep.2021.109464] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 05/31/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
Microexons (≤27 nt) play critical roles in nervous system development and function but create unique challenges for the splicing machinery. The mechanisms of microexon regulation are therefore of great interest. We performed a genetic screen for alternative splicing regulators in the C. elegans nervous system and identify PRP-40, a core component of the U1 snRNP. RNA-seq reveals that PRP-40 is required for inclusion of alternatively spliced, but not constitutively spliced, exons. PRP-40 is particularly required for inclusion of neuronal microexons, and our data indicate that PRP-40 is a central regulator of microexon splicing. Microexons can be relieved from PRP-40 dependence by artificially increasing exon size or reducing flanking intron size, indicating that PRP-40 is specifically required for microexons surrounded by conventionally sized introns. Knockdown of the orthologous PRPF40A in mouse neuroblastoma cells causes widespread dysregulation of microexons but not conventionally sized exons. PRP-40 regulation of neuronal microexons is therefore a widely conserved phenomenon.
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Affiliation(s)
- Bikash Choudhary
- Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Olivia Marx
- Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Adam D Norris
- Biological Sciences, Southern Methodist University, Dallas, TX 75275, USA.
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25
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Akinyi MV, Frilander MJ. At the Intersection of Major and Minor Spliceosomes: Crosstalk Mechanisms and Their Impact on Gene Expression. Front Genet 2021; 12:700744. [PMID: 34354740 PMCID: PMC8329584 DOI: 10.3389/fgene.2021.700744] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
Many eukaryotic species contain two separate molecular machineries for removing non-coding intron sequences from pre-mRNA molecules. The majority of introns (more than 99.5% in humans) are recognized and excised by the major spliceosome, which utilizes relatively poorly conserved sequence elements at the 5′ and 3′ ends of the intron that are used for intron recognition and in subsequent catalysis. In contrast, the minor spliceosome targets a rare group of introns (approximately 0.5% in humans) with highly conserved sequences at the 5′ and 3′ ends of the intron. Minor introns coexist in the same genes with major introns and while the two intron types are spliced by separate spliceosomes, the two splicing machineries can interact with one another to shape mRNA processing events in genes containing minor introns. Here, we review known cooperative and competitive interactions between the two spliceosomes and discuss the mechanistic basis of the spliceosome crosstalk, its regulatory significance, and impact on spliceosome diseases.
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Affiliation(s)
- Maureen V Akinyi
- Institute of Biotechnology/Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology/Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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26
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Herbrechter R, Hube N, Buchholz R, Reiner A. Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data. Cell Mol Life Sci 2021; 78:5605-5630. [PMID: 34100982 PMCID: PMC8257547 DOI: 10.1007/s00018-021-03865-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/12/2021] [Accepted: 05/22/2021] [Indexed: 12/11/2022]
Abstract
Ionotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantification of alternative splice and editing events. We detected all canonical iGluR splice junctions, assessed the abundance of alternative events described in the literature, and identified new splice events in AMPA, kainate, delta, and NMDA receptor subunits. Notable events include an abundant transcript encoding the GluA4 amino-terminal domain, GluA4-ATD, a novel C-terminal GluD1 (delta receptor 1) isoform, GluD1-b, and potentially new GluK4 and GluN2C isoforms. C-terminal GluN1 splicing may be controlled by inclusion of a cassette exon, which shows preference for one of the two acceptor sites in the last exon. Moreover, we identified alternative untranslated regions (UTRs) and species-specific differences in splicing. In contrast, editing in exonic iGluR regions appears to be mostly limited to ten previously described sites, two of which result in silent amino acid changes. Coupling of proximal editing/editing and editing/splice events occurs to variable degree. Overall, this analysis provides the first inventory of alternative splicing and editing in human brain iGluRs and provides the impetus for further transcriptome-based and functional investigations.
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Affiliation(s)
- Robin Herbrechter
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Nadine Hube
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Raoul Buchholz
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany
| | - Andreas Reiner
- Department of Biology and Biotechnology, Ruhr University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.
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27
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Mazin PV, Khaitovich P, Cardoso-Moreira M, Kaessmann H. Alternative splicing during mammalian organ development. Nat Genet 2021; 53:925-934. [PMID: 33941934 PMCID: PMC8187152 DOI: 10.1038/s41588-021-00851-w] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/19/2021] [Indexed: 12/30/2022]
Abstract
Alternative splicing (AS) is pervasive in mammalian genomes, yet cross-species comparisons have been largely restricted to adult tissues and the functionality of most AS events remains unclear. We assessed AS patterns across pre- and postnatal development of seven organs in six mammals and a bird. Our analyses revealed that developmentally dynamic AS events, which are especially prevalent in the brain, are substantially more conserved than nondynamic ones. Cassette exons with increasing inclusion frequencies during development show the strongest signals of conserved and regulated AS. Newly emerged cassette exons are typically incorporated late in testis development, but those retained during evolution are predominantly brain specific. Our work suggests that an intricate interplay of programs controlling gene expression levels and AS is fundamental to organ development, especially for the brain and heart. In these regulatory networks, AS affords substantial functional diversification of genes through the generation of tissue- and time-specific isoforms from broadly expressed genes.
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Affiliation(s)
- Pavel V Mazin
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Philipp Khaitovich
- V. Zelman Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Margarida Cardoso-Moreira
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
- Evolutionary Developmental Biology Laboratory, The Francis Crick Institute, London, UK.
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.
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28
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Banerjee S, Bhandary P, Woodhouse M, Sen TZ, Wise RP, Andorf CM. FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. BMC Bioinformatics 2021; 22:205. [PMID: 33879057 PMCID: PMC8056616 DOI: 10.1186/s12859-021-04120-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally active regions of the genome that contain overlapping genes, genes that produce numerous transcripts, transposable elements and numerous diverse sequence repeats. Currently available gene annotation software applications depend on pre-constructed full-length gene sequence assemblies which are not guaranteed to be error-free. The origins of these sequences are often uncertain, making it difficult to identify and rectify errors in them. This hinders the creation of an accurate and holistic representation of the transcriptomic landscape across multiple tissue types and experimental conditions. Therefore, to gauge the extent of diversity in gene structures, a comprehensive analysis of genome-wide expression data is imperative. RESULTS We present FINDER, a fully automated computational tool that optimizes the entire process of annotating genes and transcript structures. Unlike current state-of-the-art pipelines, FINDER automates the RNA-Seq pre-processing step by working directly with raw sequence reads and optimizes gene prediction from BRAKER2 by supplementing these reads with associated proteins. The FINDER pipeline (1) reports transcripts and recognizes genes that are expressed under specific conditions, (2) generates all possible alternatively spliced transcripts from expressed RNA-Seq data, (3) analyzes read coverage patterns to modify existing transcript models and create new ones, and (4) scores genes as high- or low-confidence based on the available evidence across multiple datasets. We demonstrate the ability of FINDER to automatically annotate a diverse pool of genomes from eight species. CONCLUSIONS FINDER takes a completely automated approach to annotate genes directly from raw expression data. It is capable of processing eukaryotic genomes of all sizes and requires no manual supervision-ideal for bench researchers with limited experience in handling computational tools.
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Affiliation(s)
- Sagnik Banerjee
- Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Statistics, Iowa State University, Ames, IA, 50011, USA
| | - Priyanka Bhandary
- Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Margaret Woodhouse
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, 50011, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, USDA-Agricultural Research Service, Albany, CA, 94710, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, 50011, USA
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Carson M Andorf
- Corn Insects and Crop Genetics Research Unit, USDA-Agricultural Research Service, Ames, IA, 50011, USA.
- Department of Computer Science, Iowa State University, Ames, IA, 50011, USA.
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29
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Gehring NH, Roignant JY. Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation. Trends Genet 2021; 37:355-372. [DOI: 10.1016/j.tig.2020.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
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30
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Pang TL, Ding Z, Liang SB, Li L, Zhang B, Zhang Y, Fan YJ, Xu YZ. Comprehensive Identification and Alternative Splicing of Microexons in Drosophila. Front Genet 2021; 12:642602. [PMID: 33859668 PMCID: PMC8042270 DOI: 10.3389/fgene.2021.642602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/05/2021] [Indexed: 11/29/2022] Open
Abstract
Interrupted exons in the pre-mRNA transcripts are ligated together through RNA splicing, which plays a critical role in the regulation of gene expression. Exons with a length ≤ 30 nt are defined as microexons that are unique in identification. However, microexons, especially those shorter than 8 nt, have not been well studied in many organisms due to difficulties in mapping short segments from sequencing reads. Here, we analyzed mRNA-seq data from a variety of Drosophila samples with a newly developed bioinformatic tool, ce-TopHat. In addition to the Flybase annotated, 465 new microexons were identified. Differentially alternatively spliced (AS) microexons were investigated between the Drosophila tissues (head, body, and gonad) and genders. Most of the AS microexons were found in the head and two AS microexons were identified in the sex-determination pathway gene fruitless.
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Affiliation(s)
- Ting-Lin Pang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Zhan Ding
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Shao-Bo Liang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Liang Li
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Bei Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
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31
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Head SA, Hernandez-Alias X, Yang JS, Ciampi L, Beltran-Sastre V, Torres-Méndez A, Irimia M, Schaefer MH, Serrano L. Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers. PLoS Biol 2021; 19:e3001138. [PMID: 33621242 PMCID: PMC7935315 DOI: 10.1371/journal.pbio.3001138] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 03/05/2021] [Accepted: 02/04/2021] [Indexed: 01/14/2023] Open
Abstract
RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors (SFs). Microexons are extremely small exons (3–27 nucleotides long) that are highly evolutionarily conserved and play critical roles in promoting neuronal differentiation and development. Inclusion of microexons in mRNA transcripts is mediated by the SF Serine/Arginine Repetitive Matrix 4 (SRRM4), whose expression is largely restricted to neural tissues. However, microexons have been largely overlooked in prior analyses of splicing in cancer, as their small size necessitates specialized computational approaches for their detection. Here, we demonstrate that despite having low expression in normal nonneural tissues, SRRM4 is further silenced in tumors, resulting in the suppression of normal microexon inclusion. Remarkably, SRRM4 is the most consistently silenced SF across all tumor types analyzed, implying a general advantage of microexon down-regulation in cancer independent of its tissue of origin. We show that this silencing is favorable for tumor growth, as decreased SRRM4 expression in tumors is correlated with an increase in mitotic gene expression, and up-regulation of SRRM4 in cancer cell lines dose-dependently inhibits proliferation in vitro and in a mouse xenograft model. Further, this proliferation inhibition is accompanied by induction of neural-like expression and splicing patterns in cancer cells, suggesting that SRRM4 expression shifts the cell state away from proliferation and toward differentiation. We therefore conclude that SRRM4 acts as a proliferation brake, and tumors gain a selective advantage by cutting off this brake. Using data from The Cancer Genome Atlas, this study shows that the splicing factor SRRM4 and its program of differentiation-promoting microexons are downregulated across tumor types with remarkable consistency, providing tumors with a proliferative advantage.
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Affiliation(s)
- Sarah A. Head
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- * E-mail: (SAH); (MHS); (LS)
| | - Xavier Hernandez-Alias
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jae-Seong Yang
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centre de Recerca en Agrigenòmica, Consortium CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, Spain
| | - Ludovica Ciampi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Violeta Beltran-Sastre
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Torres-Méndez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Martin H. Schaefer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- IEO European Institute of Oncology IRCCS, Department of Experimental Oncology, Milan, Italy
- * E-mail: (SAH); (MHS); (LS)
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
- * E-mail: (SAH); (MHS); (LS)
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32
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Parada GE, Munita R, Georgakopoulos-Soares I, Fernandes HJR, Kedlian VR, Metzakopian E, Andres ME, Miska EA, Hemberg M. MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development. Genome Biol 2021; 22:43. [PMID: 33482885 PMCID: PMC7821500 DOI: 10.1186/s13059-020-02246-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Microexons, exons that are ≤ 30 nucleotides, are a highly conserved and dynamically regulated set of cassette exons. They have key roles in nervous system development and function, as evidenced by recent results demonstrating the impact of microexons on behaviour and cognition. However, microexons are often overlooked due to the difficulty of detecting them using standard RNA-seq aligners. RESULTS Here, we present MicroExonator, a novel pipeline for reproducible de novo discovery and quantification of microexons. We process 289 RNA-seq datasets from eighteen mouse tissues corresponding to nine embryonic and postnatal stages, providing the most comprehensive survey of microexons available for mice. We detect 2984 microexons, 332 of which are differentially spliced throughout mouse embryonic brain development, including 29 that are not present in mouse transcript annotation databases. Unsupervised clustering of microexons based on their inclusion patterns segregates brain tissues by developmental time, and further analysis suggests a key function for microexons in axon growth and synapse formation. Finally, we analyse single-cell RNA-seq data from the mouse visual cortex, and for the first time, we report differential inclusion between neuronal subpopulations, suggesting that some microexons could be cell type-specific. CONCLUSIONS MicroExonator facilitates the investigation of microexons in transcriptome studies, particularly when analysing large volumes of data. As a proof of principle, we use MicroExonator to analyse a large collection of both mouse bulk and single-cell RNA-seq datasets. The analyses enabled the discovery of previously uncharacterized microexons, and our study provides a comprehensive microexon inclusion catalogue during mouse development.
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Affiliation(s)
- Guillermo E Parada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Roberto Munita
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ilias Georgakopoulos-Soares
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Hugo J R Fernandes
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK
| | - Emmanouil Metzakopian
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Maria Estela Andres
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eric A Miska
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, UK.
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
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33
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SRRM4 Expands the Repertoire of Circular RNAs by Regulating Microexon Inclusion. Cells 2020; 9:cells9112488. [PMID: 33207694 PMCID: PMC7697094 DOI: 10.3390/cells9112488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/27/2020] [Accepted: 11/13/2020] [Indexed: 12/25/2022] Open
Abstract
High-throughput RNA sequencing (RNA-seq) and dedicated bioinformatics pipelines have synergized to identify an expansive repertoire of unique circular RNAs (circRNAs), exceeding 100,000 variants. While the vast majority of these circRNAs comprise canonical exonic and intronic sequences, microexons (MEs)-which occur in 30% of functional mRNA transcripts-have been entirely overlooked. CircRNAs which contain these known MEs (ME-circRNAs) could be identified with commonly utilized circRNA prediction pipelines, CIRCexplorer2 and CIRI2, but were not previously recognized as ME-circRNAs. In addition, when employing a bespoke bioinformatics pipeline for identifying RNA chimeras, called Hyb, we could also identify over 2000 ME-circRNAs which contain novel MEs at their backsplice junctions, that are uncalled by either CIRCexplorer2 or CIRI2. Analysis of circRNA-seq datasets from gliomas of varying clinical grades compared with matched control tissue has shown circRNAs have potential as prognostic markers for stratifying tumor from healthy tissue. Furthermore, the abundance of microexon-containing circRNAs (ME-circRNAs) between tumor and normal tissues is correlated with the expression of a splicing associated factor, Serine/arginine repetitive matrix 4 (SRRM4). Overexpressing SRRM4, known for regulating ME inclusion in mRNAs critical for neural differentiation, in human HEK293 cells resulted in the biogenesis of over 2000 novel ME-circRNAs, including ME-circEIF4G3, and changes in the abundance of many canonical circRNAs, including circSETDB2 and circLBRA. This shows SRRM4, in which its expression is correlated with poor prognosis in gliomas, acts as a bona fide circRNA biogenesis factor. Given the known roles of MEs and circRNAs in oncogenesis, the identification of these previously unrecognized ME-circRNAs further increases the complexity and functional purview of this non-coding RNA family.
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34
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First Identification of RNA-Binding Proteins That Regulate Alternative Exons in the Dystrophin Gene. Int J Mol Sci 2020; 21:ijms21207803. [PMID: 33096920 PMCID: PMC7589424 DOI: 10.3390/ijms21207803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/29/2022] Open
Abstract
The Duchenne muscular dystrophy (DMD) gene has a complex expression pattern regulated by multiple tissue-specific promoters and by alternative splicing (AS) of the resulting transcripts. Here, we used an RNAi-based approach coupled with DMD-targeted RNA-seq to identify RNA-binding proteins (RBPs) that regulate splicing of its skeletal muscle isoform (Dp427m) in a human muscular cell line. A total of 16 RBPs comprising the major regulators of muscle-specific splicing events were tested. We show that distinct combinations of RBPs maintain the correct inclusion in the Dp427m of exons that undergo spatio-temporal AS in other dystrophin isoforms. In particular, our findings revealed the complex networks of RBPs contributing to the splicing of the two short DMD exons 71 and 78, the inclusion of exon 78 in the adult Dp427m isoform being crucial for muscle function. Among the RBPs tested, QKI and DDX5/DDX17 proteins are important determinants of DMD exon inclusion. This is the first large-scale study to determine which RBP proteins act on the physiological splicing of the DMD gene. Our data shed light on molecular mechanisms contributing to the expression of the different dystrophin isoforms, which could be influenced by a change in the function or expression level of the identified RBPs.
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35
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Chang LW, Tseng IC, Wang LH, Sun YH. Isoform-specific functions of an evolutionarily conserved 3 bp micro-exon alternatively spliced from another exon in Drosophila homothorax gene. Sci Rep 2020; 10:12783. [PMID: 32732884 PMCID: PMC7392893 DOI: 10.1038/s41598-020-69644-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/14/2020] [Indexed: 12/03/2022] Open
Abstract
Micro-exons are exons of very small size (usually 3–30 nts). Some micro-exons are alternatively spliced. Their functions, regulation and evolution are largely unknown. Here, we present an example of an alternatively spliced 3 bp micro-exon (micro-Ex8) in the homothorax (hth) gene in Drosophila. Hth is involved in many developmental processes. It contains a MH domain and a TALE-class homeodomain (HD). It binds to another homeodomain Exd via its MH domain to promote the nuclear import of the Hth-Exd complex and serve as a cofactor for Hox proteins. The MH and HD domains in Hth as well as the HTh-Exd interaction are highly conserved in evolution. The alternatively spliced micro-exon lies between the exons encoding the MH and HD domains. We provide clear proof that the micro-Ex8 is produced by alternative splicing from a 48 bp full-length exon 8 (FL-Ex8) and the micro-Ex8 is the first three nt is FL-Ex8. We found that the micro-Ex8 is the ancient form and the 3 + 48 organization of alternatively spliced overlapping exons only emerged in the Schizophora group of Diptera and is absolutely conserved in this group. We then used several strategies to test the in vivo function of the two types of isoforms and found that the micro-Ex8 and FL-Ex8 isoforms have largely overlapping functions but also have non-redundant functions that are tissue-specific, which supports their strong evolutionary conservation. Since the different combinations of protein interaction of Hth with Exd and/or Hox can have different DNA target specificity, our finding of alternatively spliced isoforms adds to the spectrum of structural and functional diversity under developmental regulation.
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Affiliation(s)
- Ling-Wen Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - I-Chieh Tseng
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Institute of Genomic Sciences, National Yang-Ming University, Taipei, Taiwan, ROC.,Department of Life Science, Chinese Culture University, Taipei, Taiwan, ROC
| | - Lan-Hsin Wang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.
| | - Y Henry Sun
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC. .,Institute of Genomic Sciences, National Yang-Ming University, Taipei, Taiwan, ROC.
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36
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Brain Translation: A Feather Tips the Scale. Mol Cell 2020; 77:1155-1156. [PMID: 32200794 DOI: 10.1016/j.molcel.2020.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this issue of Molecular Cell, Gonatopoulos-Pournatzis et al. (2020) report a neuron-specific microexon in eIF4G translation initiation factors that dampens synaptic protein translation. Autism-associated disruption of this exon results in increased protein production, likely through reduced coalescence with cytoplasmic ribonucleoprotein granule components, including FMRP.
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37
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Microexons: at the nexus of nervous system development, behaviour and autism spectrum disorder. Curr Opin Genet Dev 2020; 65:22-33. [PMID: 32535349 DOI: 10.1016/j.gde.2020.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
The discovery and characterization of a network of highly conserved neuronal microexons has provided fundamental new insight into mechanisms underlying nervous system development and function, as well as an important basis for pathway convergence in autism spectrum disorder. In the past few years, considerable progress has been made in comprehensively determining the repertoires of factors that control neuronal microexons. These results have illuminated molecular mechanisms that activate the splicing of microexons, including those that control gene expression programs critical for neurogenesis, as well as synaptic protein translation and neuronal activity. Remarkably, individual disruption of specific microexons in these pathways results in autism-like phenotypes and cognitive impairment in mice. This review discusses these findings and their implications for delivering new therapeutic strategies for neurological disorders.
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38
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Kaur B, Záhonová K, Valach M, Faktorová D, Prokopchuk G, Burger G, Lukeš J. Gene fragmentation and RNA editing without borders: eccentric mitochondrial genomes of diplonemids. Nucleic Acids Res 2020; 48:2694-2708. [PMID: 31919519 PMCID: PMC7049700 DOI: 10.1093/nar/gkz1215] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/14/2019] [Accepted: 01/08/2020] [Indexed: 11/20/2022] Open
Abstract
Diplonemids are highly abundant heterotrophic marine protists. Previous studies showed that their strikingly bloated mitochondrial genome is unique because of systematic gene fragmentation and manifold RNA editing. Here we report a comparative study of mitochondrial genome architecture, gene structure and RNA editing of six recently isolated, phylogenetically diverse diplonemid species. Mitochondrial gene fragmentation and modes of RNA editing, which include cytidine-to-uridine (C-to-U) and adenosine-to-inosine (A-to-I) substitutions and 3′ uridine additions (U-appendage), are conserved across diplonemids. Yet as we show here, all these features have been pushed to their extremes in the Hemistasiidae lineage. For example, Namystynia karyoxenos has its genes fragmented into more than twice as many modules than other diplonemids, with modules as short as four nucleotides. Furthermore, we detected in this group multiple A-appendage and guanosine-to-adenosine (G-to-A) substitution editing events not observed before in diplonemids and found very rarely elsewhere. With >1,000 sites, C-to-U and A-to-I editing in Namystynia is nearly 10 times more frequent than in other diplonemids. The editing density of 12% in coding regions makes Namystynia’s the most extensively edited transcriptome described so far. Diplonemid mitochondrial genome architecture, gene structure and post-transcriptional processes display such high complexity that they challenge all other currently known systems.
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Affiliation(s)
- Binnypreet Kaur
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic.,Faculty of Science, Charles University, BIOCEV, 25250 Vestec, Czech Republic
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, H3T 1J4 Montreal, Canada
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, H3T 1J4 Montreal, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic.,Faculty of Sciences, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
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39
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Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
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40
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Gonatopoulos-Pournatzis T, Niibori R, Salter EW, Weatheritt RJ, Tsang B, Farhangmehr S, Liang X, Braunschweig U, Roth J, Zhang S, Henderson T, Sharma E, Quesnel-Vallières M, Permanyer J, Maier S, Georgiou J, Irimia M, Sonenberg N, Forman-Kay JD, Gingras AC, Collingridge GL, Woodin MA, Cordes SP, Blencowe BJ. Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions. Mol Cell 2020; 77:1176-1192.e16. [PMID: 31999954 DOI: 10.1016/j.molcel.2020.01.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/15/2019] [Accepted: 01/02/2020] [Indexed: 12/21/2022]
Abstract
Microexons represent the most highly conserved class of alternative splicing, yet their functions are poorly understood. Here, we focus on closely related neuronal microexons overlapping prion-like domains in the translation initiation factors, eIF4G1 and eIF4G3, the splicing of which is activity dependent and frequently disrupted in autism. CRISPR-Cas9 deletion of these microexons selectively upregulates synaptic proteins that control neuronal activity and plasticity and further triggers a gene expression program mirroring that of activated neurons. Mice lacking the Eif4g1 microexon display social behavior, learning, and memory deficits, accompanied by altered hippocampal synaptic plasticity. We provide evidence that the eIF4G microexons function as a translational brake by causing ribosome stalling, through their propensity to promote the coalescence of cytoplasmic granule components associated with translation repression, including the fragile X mental retardation protein FMRP. The results thus reveal an autism-disrupted mechanism by which alternative splicing specializes neuronal translation to control higher order cognitive functioning.
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Affiliation(s)
| | - Rieko Niibori
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Eric W Salter
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Brian Tsang
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shaghayegh Farhangmehr
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Xinyi Liang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | | | - Jonathan Roth
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Tyler Henderson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eesha Sharma
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mathieu Quesnel-Vallières
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Jon Permanyer
- Centre for Genomic Regulation, Barcelona 08003, Spain
| | - Stefan Maier
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - John Georgiou
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain; ICREA, Barcelona 08010, Spain
| | - Nahum Sonenberg
- Goodman Cancer Research Center, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Julie D Forman-Kay
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Graham L Collingridge
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Melanie A Woodin
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Sabine P Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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41
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Nimeth BA, Riegler S, Kalyna M. Alternative Splicing and DNA Damage Response in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:91. [PMID: 32140165 PMCID: PMC7042379 DOI: 10.3389/fpls.2020.00091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/21/2020] [Indexed: 05/06/2023]
Abstract
Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.
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42
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Saposin-like proteins in Opisthorchis felineus and related opisthorchids. INFECTION GENETICS AND EVOLUTION 2019; 78:104132. [PMID: 31805380 DOI: 10.1016/j.meegid.2019.104132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/25/2019] [Accepted: 11/30/2019] [Indexed: 12/12/2022]
Abstract
Saposin B domain-containing or saposin-like proteins (SAPs, SAPLIPs) have been described as lipid/membrane-binding and often show antibacterial and cytolytic activity. Members of this protein family are present in phylogenetically distant organisms, pointing to their functional importance. Several SAPs are found in trematodes and some of them apparently are related to host-parasite interaction as they show cytolytic activity or immunogenicity. In the present study, we search for SAP genes of Opisthorchis felineus, Clonorchis sinensis and O. viverrini, compare and analyze their structure and expression patterns. We define three orthologous groups of SAPs in opisthorchids and suggest a unique protein motif with unknown function in one group of orthologs.
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43
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Lopez Soto EJ, Gandal MJ, Gonatopoulos-Pournatzis T, Heller EA, Luo D, Zheng S. Mechanisms of Neuronal Alternative Splicing and Strategies for Therapeutic Interventions. J Neurosci 2019; 39:8193-8199. [PMID: 31619487 PMCID: PMC6794923 DOI: 10.1523/jneurosci.1149-19.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 01/15/2023] Open
Abstract
Many cellular and physiological processes are coordinated by regulatory networks that produce a remarkable complexity of transcript isoforms. In the mammalian nervous system, alternative pre-mRNA splicing generates functionally distinct isoforms that play key roles in normal physiology, supporting development, plasticity, complex behaviors, and cognition. Neuronal splicing programs controlled by RNA-binding proteins, are influenced by chromatin modifications and can exhibit neuronal subtype specificity. As highlighted in recent publications, aberrant alternative splicing is a major contributor to disease phenotypes. Therefore, understanding the underlying mechanisms of alternative splicing regulation and identifying functional splicing isoforms with critical phenotypic roles are expected to provide a comprehensive resource for therapeutic development, as illuminated by recent successful interventions of spinal muscular atrophy. Here, we discuss the latest progress in the study of the emerging complexity of alternative splicing mechanisms in neurons, and how these findings inform new therapies to correct and control splicing defects.
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Affiliation(s)
| | - Michael J Gandal
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095
| | | | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5158
| | - Diou Luo
- Department of Biomedical Sciences, Iowa State University, Ames, Iowa 50011, and
| | - Sika Zheng
- Division of Biomedical Sciences, University of California at Riverside, Riverside, California 92521
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44
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Ultra-deep sequencing reveals pre-mRNA splicing as a sequence driven high-fidelity process. PLoS One 2019; 14:e0223132. [PMID: 31581208 PMCID: PMC6776343 DOI: 10.1371/journal.pone.0223132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/13/2019] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing diversifies mRNA transcripts in human cells. While the spliceosome pairs exons with a high degree of accuracy, the rates of rare aberrant and non-canonical pre-mRNA splicing have not been evaluated at the nucleotide level to determine the quantity and identity of these events across splice junctions. Using ultra-deep sequencing the frequency of aberrant and non-canonical splicing events for three splice junctions flanking exon 7 of SMN1 were determined at single nucleotide resolution. After correction for background noise introduced by PCR amplification and sequencing steps, pre-mRNA splicing was shown to maintain a low overall rate of aberrant and non-canonically spliced events. Several previously unannotated splicing events across 3 exon|intron junctions in SMN1 were identified. Mutations within SMN exon 7 were shown to affect splicing fidelity by modulating RNA secondary structures, by altering the binding site of regulatory proteins and by changing the 5’ splice site strength. Mutations also create a truncated SMN1 exon 7 through the introduction of a de novo non-canonical 5’ splice site. The results from the ultra-deep sequencing approach highlight the impressive fidelity of pre-mRNA splicing and demonstrate that the immediate sequence context around splice sites is the main driving force behind non-canonical splice site pairing.
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45
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Hatje K, Mühlhausen S, Simm D, Kollmar M. The Protein-Coding Human Genome: Annotating High-Hanging Fruits. Bioessays 2019; 41:e1900066. [PMID: 31544971 DOI: 10.1002/bies.201900066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/07/2019] [Indexed: 12/19/2022]
Abstract
The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.
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Affiliation(s)
- Klas Hatje
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstr. 124, 4070, Basel, Switzerland
| | - Stefanie Mühlhausen
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Dominic Simm
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Goldschmidtstr. 7, 37077, Göttingen, Germany
| | - Martin Kollmar
- Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
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46
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Identification and Analysis of Micro-Exon Genes in the Rice Genome. Int J Mol Sci 2019; 20:ijms20112685. [PMID: 31159166 PMCID: PMC6600660 DOI: 10.3390/ijms20112685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/25/2019] [Accepted: 05/29/2019] [Indexed: 11/24/2022] Open
Abstract
Micro-exons are a kind of exons with lengths no more than 51 nucleotides. They are generally ignored in genome annotation due to the short length, whereas recent studies indicate that they have special splicing properties and important functions. Considering that there has been no genome-wide study of micro-exons in plants up to now, we screened and analyzed genes containing micro-exons in two indica rice varieties in this study. According to the annotation of Zhenshan 97 (ZS97) and Minghui 63 (MH63), ~23% of genes possess micro-exons. We then identified micro-exons from RNA-seq data and found that >65% micro-exons had been annotated and most of novel micro-exons were located in gene regions. About 60% micro-exons were constitutively spliced, and the others were alternatively spliced in different tissues. Besides, we observed that approximately 54% of genes harboring micro-exons tended to be ancient genes, and 13% were Oryza genus-specific. Micro-exon genes were highly conserved in Oryza genus with consistent domains. In particular, the predicted protein structures showed that alternative splicing of in-frame micro-exons led to a local structural recombination, which might affect some core structure of domains, and alternative splicing of frame-shifting micro-exons usually resulted in premature termination of translation by introducing a stop codon or missing functional domains. Overall, our study provided the genome-wide distribution, evolutionary conservation, and potential functions of micro-exons in rice.
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47
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Ratcliffe CDH, Siddiqui N, Coelho PP, Laterreur N, Cookey TN, Sonenberg N, Park M. HGF-induced migration depends on the PI(3,4,5)P 3-binding microexon-spliced variant of the Arf6 exchange factor cytohesin-1. J Cell Biol 2018; 218:285-298. [PMID: 30404949 PMCID: PMC6314551 DOI: 10.1083/jcb.201804106] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/19/2018] [Accepted: 10/17/2018] [Indexed: 12/19/2022] Open
Abstract
Splice variants of the Arf6 guanine exchange factor cytohesin-1 display differential affinity for PI(4,5)P2 and PI(3,4,5)P3. Ratcliffe et al. show that the specific lipid binding of the diglycine variant of cytohesin-1 is needed for HGF-dependent cell migration and establishment of the leading edge, thereby regulating cancer cell migration following activation of the proto-oncogenic receptor tyrosine kinase Met. Differential inclusion or skipping of microexons is an increasingly recognized class of alternative splicing events. However, the functional significance of microexons and their contribution to signaling diversity is poorly understood. The Met receptor tyrosine kinase (RTK) modulates invasive growth and migration in development and cancer. Here, we show that microexon switching in the Arf6 guanine nucleotide exchange factor cytohesin-1 controls Met-dependent cell migration. Cytohesin-1 isoforms, differing by the inclusion of an evolutionarily conserved three-nucleotide microexon in the pleckstrin homology domain, display differential affinity for PI(4,5)P2 (triglycine) and PI(3,4,5)P3 (diglycine). We show that selective phosphoinositide recognition by cytohesin-1 isoforms promotes distinct subcellular localizations, whereby the triglycine isoform localizes to the plasma membrane and the diglycine to the leading edge. These data highlight microexon skipping as a mechanism to spatially restrict signaling and provide a mechanistic link between RTK-initiated phosphoinositide microdomains and Arf6 during signal transduction and cancer cell migration.
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Affiliation(s)
- Colin D H Ratcliffe
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Nadeem Siddiqui
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Paula P Coelho
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Nancy Laterreur
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Tumini N Cookey
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Nahum Sonenberg
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada .,Department of Biochemistry, McGill University, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada.,Department of Oncology, McGill University, Montreal, Quebec, Canada
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48
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Quesnel-Vallières M, Weatheritt RJ, Cordes SP, Blencowe BJ. Autism spectrum disorder: insights into convergent mechanisms from transcriptomics. Nat Rev Genet 2018; 20:51-63. [DOI: 10.1038/s41576-018-0066-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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49
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Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons. Mol Cell 2018; 72:510-524.e12. [DOI: 10.1016/j.molcel.2018.10.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/27/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022]
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50
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Event Analysis: Using Transcript Events To Improve Estimates of Abundance in RNA-seq Data. G3-GENES GENOMES GENETICS 2018; 8:2923-2940. [PMID: 30021829 PMCID: PMC6118309 DOI: 10.1534/g3.118.200373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Alternative splicing leverages genomic content by allowing the synthesis of multiple transcripts and, by implication, protein isoforms, from a single gene. However, estimating the abundance of transcripts produced in a given tissue from short sequencing reads is difficult and can result in both the construction of transcripts that do not exist, and the failure to identify true transcripts. An alternative approach is to catalog the events that make up isoforms (splice junctions and exons). We present here the Event Analysis (EA) approach, where we project transcripts onto the genome and identify overlapping/unique regions and junctions. In addition, all possible logical junctions are assembled into a catalog. Transcripts are filtered before quantitation based on simple measures: the proportion of the events detected, and the coverage. We find that mapping to a junction catalog is more efficient at detecting novel junctions than mapping in a splice aware manner. We identify 99.8% of true transcripts while iReckon identifies 82% of the true transcripts and creates more transcripts not included in the simulation than were initially used in the simulation. Using PacBio Iso-seq data from a mouse neural progenitor cell model, EA detects 60% of the novel junctions that are combinations of existing exons while only 43% are detected by STAR. EA further detects ∼5,000 annotated junctions missed by STAR. Filtering transcripts based on the proportion of the transcript detected and the number of reads on average supporting that transcript captures 95% of the PacBio transcriptome. Filtering the reference transcriptome before quantitation, results in is a more stable estimate of isoform abundance, with improved correlation between replicates. This was particularly evident when EA is applied to an RNA-seq study of type 1 diabetes (T1D), where the coefficient of variation among subjects (n = 81) in the transcript abundance estimates was substantially reduced compared to the estimation using the full reference. EA focuses on individual transcriptional events. These events can be quantitate and analyzed directly or used to identify the probable set of expressed transcripts. Simple rules based on detected events and coverage used in filtering result in a dramatic improvement in isoform estimation without the use of ancillary data (e.g., ChIP, long reads) that may not be available for many studies.
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