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Das AS, Sherry EC, Vaughan RM, Henderson ML, Zieba J, Uhl KL, Koehn O, Bupp CP, Rajasekaran S, Li X, Chhetri SB, Nissim S, Williams CL, Prokop JW. The complex, dynamic SpliceOme of the small GTPase transcripts altered by technique, sex, genetics, tissue specificity, and RNA base editing. Front Cell Dev Biol 2022; 10:1033695. [PMID: 36467401 PMCID: PMC9714508 DOI: 10.3389/fcell.2022.1033695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/01/2022] [Indexed: 04/04/2024] Open
Abstract
The small GTPase family is well-studied in cancer and cellular physiology. With 162 annotated human genes, the family has a broad expression throughout cells of the body. Members of the family have multiple exons that require splicing. Yet, the role of splicing within the family has been underexplored. We have studied the splicing dynamics of small GTPases throughout 41,671 samples by integrating Nanopore and Illumina sequencing techniques. Within this work, we have made several discoveries. 1). Using the GTEx long read data of 92 samples, each small GTPase gene averages two transcripts, with 83 genes (51%) expressing two or more isoforms. 2). Cross-tissue analysis of GTEx from 17,382 samples shows 41 genes (25%) expressing two or more protein-coding isoforms. These include protein-changing transcripts in genes such as RHOA, RAB37, RAB40C, RAB4B, RAB5C, RHOC, RAB1A, RAN, RHEB, RAC1, and KRAS. 3). The isolation and library technique of the RNAseq influences the abundance of non-sense-mediated decay and retained intron transcripts of small GTPases, which are observed more often in genes than appreciated. 4). Analysis of 16,243 samples of "Blood PAXgene" identified seven genes (3.7%; RHOA, RAB40C, RAB4B, RAB37, RAB5B, RAB5C, RHOC) with two or more transcripts expressed as the major isoform (75% of the total gene), suggesting a role of genetics in altering splicing. 5). Rare (ARL6, RAB23, ARL13B, HRAS, NRAS) and common variants (GEM, RHOC, MRAS, RAB5B, RERG, ARL16) can influence splicing and have an impact on phenotypes and diseases. 6). Multiple genes (RAB9A, RAP2C, ARL4A, RAB3A, RAB26, RAB3C, RASL10A, RAB40B, and HRAS) have sex differences in transcript expression. 7). Several exons are included or excluded for small GTPase genes (RASEF, KRAS, RAC1, RHEB, ARL4A, RHOA, RAB30, RHOBTB1, ARL16, RAP1A) in one or more forms of cancer. 8). Ten transcripts are altered in hypoxia (SAR1B, IFT27, ARL14, RAB11A, RAB10, RAB38, RAN, RIT1, RAB9A) with RHOA identified to have a transient 3'UTR RNA base editing at a conserved site found in all of its transcripts. Overall, we show a remarkable and dynamic role of splicing within the small GTPase family that requires future explorations.
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Affiliation(s)
- Akansha S. Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Biology, Washington and Jefferson College, Washington, PA, United States
| | - Emily C. Sherry
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, United States
| | - Robert M. Vaughan
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Marian L. Henderson
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- The Department of Biology, Calvin University, Grand Rapids, MI, United States
| | - Jacob Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
| | - Katie L. Uhl
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Olivia Koehn
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Caleb P. Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Medical Genetics, Spectrum Health and Helen DeVos Children’s Hospital, Grand Rapids, MI, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Department of Pediatric Critical Care Medicine, Helen DeVos Children’s Hospital Spectrum Health, Grand Rapids, MI, United States
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Xiaopeng Li
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Surya B. Chhetri
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MA, United States
| | - Sahar Nissim
- Genetics and Gastroenterology Divisions, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, United States
| | - Carol L. Williams
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
- Genetics and Genome Sciences Program, BioMolecular Science, Michigan State University, East Lansing, MI, United States
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
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Wang SE, Amir AS, Nguyen T, Poole AM, Simoes-Barbosa A. Spliceosomal introns in Trichomonas vaginalis revisited. Parasit Vectors 2018; 11:607. [PMID: 30482228 PMCID: PMC6260720 DOI: 10.1186/s13071-018-3196-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/09/2018] [Indexed: 11/16/2022] Open
Abstract
Background The human protozoan parasite Trichomonas vaginalis is an organism of interest for understanding eukaryotic evolution. Despite having an unusually large genome and a rich gene repertoire among protists, spliceosomal introns in T. vaginalis appear rare: only 62 putative introns have been annotated in this genome, and little or no experimental evidence exists to back up these predictions. Results This study revisited the 62 annotated introns of T. vaginalis derived from the genome sequencing plus previous publications. After experimental validation and a new genome-wide search, we confirmed the presence of introns in 32 genes and 18 others were concluded to be intronless. Sequence analyses classified the validated introns into two types, based on distinctive features such as length and conservation of splice site motifs. Conclusions Our study provides an updated list of intron-containing genes in the genome of T. vaginalis. Our findings suggests the existence of two intron ‘families’ spread among T. vaginalis protein-coding genes. Additional studies are needed to understand the functional separation of these two classes of introns and to assess the existence of further introns in the T. vaginalis genome. Electronic supplementary material The online version of this article (10.1186/s13071-018-3196-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuqi E Wang
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Abdul S Amir
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Tai Nguyen
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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