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Vo K, Sharma Y, Paul A, Mohamadi R, Mohamadi A, Fields PE, Rumi MAK. Importance of Transcript Variants in Transcriptome Analyses. Cells 2024; 13:1502. [PMID: 39273072 PMCID: PMC11394320 DOI: 10.3390/cells13171502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 09/01/2024] [Accepted: 09/05/2024] [Indexed: 09/15/2024] Open
Abstract
RNA sequencing (RNA-Seq) has become a widely adopted technique for studying gene expression. However, conventional RNA-Seq analyses rely on gene expression (GE) values that aggregate all the transcripts produced under a single gene identifier, overlooking the complexity of transcript variants arising from different transcription start sites or alternative splicing. Transcript variants may encode proteins with diverse functional domains, or noncoding RNAs. This study explored the implications of neglecting transcript variants in RNA-Seq analyses. Among the 1334 transcription factor (TF) genes expressed in mouse embryonic stem (ES) or trophoblast stem (TS) cells, 652 were differentially expressed in TS cells based on GE values (365 upregulated and 287 downregulated, ≥absolute 2-fold changes, false discovery rate (FDR) p-value ≤ 0.05). The 365 upregulated genes expressed 883 transcript variants. Further transcript expression (TE) based analyses identified only 174 (<20%) of the 883 transcripts to be upregulated. The remaining 709 transcripts were either downregulated or showed no significant changes. Meanwhile, the 287 downregulated genes expressed 856 transcript variants and only 153 (<20%) of the 856 transcripts were downregulated. The other 703 transcripts were either upregulated or showed no significant change. Additionally, the 682 insignificant TF genes (GE values < absolute 2-fold changes and/or FDR p-values > 0.05) between ES and TS cells expressed 2215 transcript variants. These included 477 (>21%) differentially expressed transcripts (276 upregulated and 201 downregulated, ≥absolute 2-fold changes, FDR p-value ≤ 0.05). Hence, GE based RNA-Seq analyses do not represent accurate expression levels due to divergent transcripts expression from the same gene. Our findings show that by including transcript variants in RNA-Seq analyses, we can generate a precise understanding of a gene's functional and regulatory landscape; ignoring the variants may result in an erroneous interpretation.
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Affiliation(s)
- Kevin Vo
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Yashica Sharma
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Anohita Paul
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ryan Mohamadi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Amelia Mohamadi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Patrick E Fields
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - M A Karim Rumi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Fair B, Buen Abad Najar CF, Zhao J, Lozano S, Reilly A, Mossian G, Staley JP, Wang J, Li YI. Global impact of unproductive splicing on human gene expression. Nat Genet 2024; 56:1851-1861. [PMID: 39223315 PMCID: PMC11387194 DOI: 10.1038/s41588-024-01872-x] [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: 12/19/2023] [Accepted: 07/16/2024] [Indexed: 09/04/2024]
Abstract
Alternative splicing (AS) in human genes is widely viewed as a mechanism for enhancing proteomic diversity. AS can also impact gene expression levels without increasing protein diversity by producing 'unproductive' transcripts that are targeted for rapid degradation by nonsense-mediated decay (NMD). However, the relative importance of this regulatory mechanism remains underexplored. To better understand the impact of AS-NMD relative to other regulatory mechanisms, we analyzed population-scale genomic data across eight molecular assays, covering various stages from transcription to cytoplasmic decay. We report threefold more unproductive splicing compared with prior estimates using steady-state RNA. This unproductive splicing compounds across multi-intronic genes, resulting in 15% of transcript molecules from protein-coding genes being unproductive. Leveraging genetic variation across cell lines, we find that GWAS trait-associated loci explained by AS are as often associated with NMD-induced expression level differences as with differences in protein isoform usage. Our findings suggest that much of the impact of AS is mediated by NMD-induced changes in gene expression rather than diversification of the proteome.
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Affiliation(s)
- Benjamin Fair
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Junxing Zhao
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stephanie Lozano
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Center for Neuroscience, University of California Davis, Davis, CA, USA
| | - Austin Reilly
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Gabriela Mossian
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
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Dulski J, Muthusamy K, Lund TC, Wszolek ZK. CSF1R-related disorder: State of the art, challenges, and proposition of a new terminology. Parkinsonism Relat Disord 2024; 121:105894. [PMID: 37839910 DOI: 10.1016/j.parkreldis.2023.105894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Recent developments in adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP) and other disorders due to CSF1R variants led to the emergence of symptomatic and prophylactic treatment options. The growing body of knowledge on genetics, pathomechanisms, clinical, and radiological features in patients harboring CSF1R variants challenges the current concepts and terminology to define the disorders, in addition to bringing up new questions on genotype-phenotype relationships. Therefore, this paper discusses the present complexities and challenges in the research on ALSP due to CSF1R variants. We illustrate our new concepts with two cases that are compound heterozygotes for CSF1R variants. Although their clinical phenotype resembles ALSP, the diagnosis of brain abnormalities, neurodegeneration, and dysosteosclerosis (BANDDOS) seems more appropriate based on their genotype. As the diagnostic classification dilemma cannot be resolved with currently used concepts and terminology on these disorders, we propose a new nomenclature of "CSF1R-related disorder" with subcategories of "early-onset (<18 years old) and late-onset (≥18 years old) forms". We highlight the heterogeneity of CSF1R variant carriers in age at onset, spectrum and severity of clinical presentation, and progression rate, even within the same family. We argue that multiple factors, including genetic architecture and environment, converge to result in an individual's disease phenotype.
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Affiliation(s)
- Jarosław Dulski
- Department of Neurology, Mayo Clinic, Jacksonville, FL, USA; Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, Gdansk, Poland; Neurology Department, St Adalbert Hospital, Copernicus PL Ltd., Gdansk, Poland
| | | | - Troy C Lund
- Department of Pediatrics, Division of Blood and Marrow Transplant, University of Minnesota, Minneapolis, MN, USA
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Carrard J, Lejeune F. Nonsense-mediated mRNA decay, a simplified view of a complex mechanism. BMB Rep 2023; 56:625-632. [PMID: 38052423 PMCID: PMC10761751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 12/07/2023] Open
Abstract
Nonsense-mediated mRNA decay (NMD) is both a quality control mechanism and a gene regulation pathway. It has been studied for more than 30 years, with an accumulation of many mechanistic details that have often led to debate and hence to different models of NMD activation, particularly in higher eukaryotes. Two models seem to be opposed, since the first requires intervention of the exon junction complex (EJC) to recruit NMD factors downstream of the premature termination codon (PTC), whereas the second involves an EJC-independent mechanism in which NMD factors concentrate in the 3'UTR to initiate NMD in the presence of a PTC. In this review we describe both models, giving recent molecular details and providing experimental arguments supporting one or the other model. In the end it is certainly possible to imagine that these two mechanisms co-exist, rather than viewing them as mutually exclusive. [BMB Reports 2023; 56(12): 625-632].
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Affiliation(s)
- Julie Carrard
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
| | - Fabrice Lejeune
- Univ. Lille, CNRS, Inserm, UMR9020-U1277 - CANTHER - Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille F-59000, France
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Fair B, Najar CBA, Zhao J, Lozano S, Reilly A, Mossian G, Staley JP, Wang J, Li YI. Global impact of aberrant splicing on human gene expression levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557588. [PMID: 37745605 PMCID: PMC10515962 DOI: 10.1101/2023.09.13.557588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Alternative splicing (AS) is pervasive in human genes, yet the specific function of most AS events remains unknown. It is widely assumed that the primary function of AS is to diversify the proteome, however AS can also influence gene expression levels by producing transcripts rapidly degraded by nonsense-mediated decay (NMD). Currently, there are no precise estimates for how often the coupling of AS and NMD (AS-NMD) impacts gene expression levels because rapidly degraded NMD transcripts are challenging to capture. To better understand the impact of AS on gene expression levels, we analyzed population-scale genomic data in lymphoblastoid cell lines across eight molecular assays that capture gene regulation before, during, and after transcription and cytoplasmic decay. Sequencing nascent mRNA transcripts revealed frequent aberrant splicing of human introns, which results in remarkably high levels of mRNA transcripts subject to NMD. We estimate that ~15% of all protein-coding transcripts are degraded by NMD, and this estimate increases to nearly half of all transcripts for lowly-expressed genes with many introns. Leveraging genetic variation across cell lines, we find that GWAS trait-associated loci explained by AS are similarly likely to associate with NMD-induced expression level differences as with differences in protein isoform usage. Additionally, we used the splice-switching drug risdiplam to perturb AS at hundreds of genes, finding that ~3/4 of the splicing perturbations induce NMD. Thus, we conclude that AS-NMD substantially impacts the expression levels of most human genes. Our work further suggests that much of the molecular impact of AS is mediated by changes in protein expression levels rather than diversification of the proteome.
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Affiliation(s)
- Benjamin Fair
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Carlos Buen Abad Najar
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Junxing Zhao
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Stephanie Lozano
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Present address: Center for Neuroscience, University of California Davis, Davis, CA 95618, USA
| | - Austin Reilly
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Gabriela Mossian
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Jingxin Wang
- Department of Medicinal Chemistry, University of Kansas, Lawrence, KS 66047, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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Kim YJ, Lee Y, Chae W, Kim JW. Recessive COL17A1 Mutations and a Dominant LAMB3 Mutation Cause Hypoplastic Amelogenesis Imperfecta. J Pers Med 2023; 13:1494. [PMID: 37888105 PMCID: PMC10608278 DOI: 10.3390/jpm13101494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/02/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Hereditary conditions that affect tooth enamel in quantity and/or quality are called amelogenesis imperfecta (AI). AI can occur as an isolated condition or as a symptom of a syndrome. An OMIM search with the term "AI" yielded 79 result entries. Mutations in the same gene cause syndromic or non-syndromic AI, depending on the nature of the mutations. In this study, we recruited two AI families and performed mutational analysis using whole-exome sequencing. The proband of family 1, with hypoplastic pitted AI and mild localized atopic dermatitis, had compound heterozygous COL17A1 mutations (paternal NM_000494.4: c.3598G>T, p.Asp1200Tyr and maternal c.1700G>A, p.Gly567Glu). The proband of family 2, with hypoplastic pitted AI and Jervell and Lange-Nielsen syndrome, had a recurrent LAMB3 mutation (NM_000228.3: c.3463_3475del, p.(Glu1155Thrfs*51)) in addition to compound heterozygous mutations in the KCNQ1 gene.
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Affiliation(s)
- Youn Jung Kim
- Department of Pediatric Dentistry & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea; (Y.J.K.); (Y.L.); (W.C.)
| | - Yejin Lee
- Department of Pediatric Dentistry & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea; (Y.J.K.); (Y.L.); (W.C.)
| | - Wonseon Chae
- Department of Pediatric Dentistry & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea; (Y.J.K.); (Y.L.); (W.C.)
| | - Jung-Wook Kim
- Department of Pediatric Dentistry & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea; (Y.J.K.); (Y.L.); (W.C.)
- Department of Molecular Genetics & DRI, School of Dentistry, Seoul National University, Seoul 03080, Republic of Korea
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