Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues

Alternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. However, despite many efforts, the repertoire of gene splicing variation is still incompletely characterized, even in humans. Here we describe a new computational system, ASprofile, and its application to RNA-seq data from Illumina’s Human Body Map project (>2.5 billion reads). Using the system, we identified putative alternative splicing events in 16 different human tissues, which provide a dynamic picture of splicing variation across the tissues. We detected 26,989 potential exon skipping events representing differences in splicing patterns among the tissues. A large proportion of the events (>60%) were novel, involving new exons (~3000), new introns (~16000), or both. When tracing these events across the sixteen tissues, only a small number (4-7%) appeared to be differentially expressed (‘switched’) between two tissues, while 30-45% showed little variation, and the remaining 50-65% were not present in one or both tissues compared. Novel exon skipping events appeared to be slightly less variable than known events, but were more tissue-specific. Our study represents the first effort to build a comprehensive catalog of alternative splicing in normal human tissues from RNA-seq data, while providing insights into the role of alternative splicing in shaping tissue transcriptome differences. The catalog of events and the ASprofile software are freely available from the Zenodo repository(http://zenodo.org/record/7068; doi:10.5281/zenodo.7068) and from our web site http://ccb.jhu.edu/software/ASprofile.

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Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis

10.1101/259291 ◽

2018 ◽

Author(s):

Jin Li ◽

Peng Yu

Keyword(s):

Alternative Splicing ◽

Computational Analysis ◽

Potential Role ◽

Exon Skipping ◽

Chronic Inflammatory Disease ◽

Splicing Factors ◽

The Novel ◽

Rna Seq ◽

Genome Wide

AbstractPsoriasis is a chronic inflammatory disease that affects the skin, nails, and joints. For understanding the mechanism of psoriasis, though, alternative splicing analysis has received relatively little attention in the field. Here, we developed and applied several computational analysis methods to study psoriasis. Using psoriasis mouse and human datasets, our differential alternative splicing analyses detected hundreds of differential alternative splicing changes. Our analysis of conservation revealed many exon-skipping events conserved between mice and humans. In addition, our splicing signature comparison analysis using the psoriasis datasets and our curated splicing factor perturbation RNA-Seq database, SFMetaDB, identified nine candidate splicing factors that may be important in regulating splicing in the psoriasis mouse model dataset. Three of the nine splicing factors were confirmed upon analyzing the human data. Our computational methods have generated predictions for the potential role of splicing in psoriasis. Future experiments on the novel candidates predicted by our computational analysis are expected to provide a better understanding of the molecular mechanism of psoriasis and to pave the way for new therapeutic treatments.

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PPM1G promotes the progression of hepatocellular carcinoma via phosphorylation regulation of alternative splicing protein SRSF3

Cell Death and Disease ◽

10.1038/s41419-021-04013-y ◽

2021 ◽

Vol 12 (8) ◽

Author(s):

Dawei Chen ◽

Zhenguo Zhao ◽

Lu Chen ◽

Qinghua Li ◽

Jixue Zou ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Alternative Splicing ◽

Protein Function ◽

Vital Role ◽

Normal Tissues ◽

Mechanistic Analysis ◽

Highly Correlated ◽

Splicing Patterns

AbstractEmerging evidence has demonstrated that alternative splicing has a vital role in regulating protein function, but how alternative splicing factors can be regulated remains unclear. We showed that the PPM1G, a protein phosphatase, regulated the phosphorylation of SRSF3 in hepatocellular carcinoma (HCC) and contributed to the proliferation, invasion, and metastasis of HCC. PPM1G was highly expressed in HCC tissues compared to adjacent normal tissues, and higher levels of PPM1G were observed in adverse staged HCCs. The higher levels of PPM1G were highly correlated with poor prognosis, which was further validated in the TCGA cohort. The knockdown of PPM1G inhibited the cell growth and invasion of HCC cell lines. Further studies showed that the knockdown of PPM1G inhibited tumor growth in vivo. The mechanistic analysis showed that the PPM1G interacted with proteins related to alternative splicing, including SRSF3. Overexpression of PPM1G promoted the dephosphorylation of SRSF3 and changed the alternative splicing patterns of genes related to the cell cycle, the transcriptional regulation in HCC cells. In addition, we also demonstrated that the promoter of PPM1G was activated by multiple transcription factors and co-activators, including MYC/MAX and EP300, MED1, and ELF1. Our study highlighted the essential role of PPM1G in HCC and shed new light on unveiling the regulation of alternative splicing in malignant transformation.

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A survey of computational methods in transcriptome-wide alternative splicing analysis

BioMolecular Concepts ◽

10.1515/bmc-2014-0040 ◽

2015 ◽

Vol 6 (1) ◽

pp. 59-66 ◽

Cited By ~ 10

Author(s):

Jianbo Wang ◽

Zhenqing Ye ◽

Tim H.-M. Huang ◽

Huidong Shi ◽

Victor Jin

Keyword(s):

Alternative Splicing ◽

Experimental Validation ◽

Gene Diversity ◽

Exon Skipping ◽

Differential Splicing ◽

Sequencing Data ◽

Future Directions ◽

Specific Analysis ◽

Software Implementations ◽

Expected Outcomes

AbstractAlternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.

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Snaptron: querying and visualizing splicing across tens of thousands of RNA-seq samples

10.1101/097881 ◽

2017 ◽

Cited By ~ 2

Author(s):

Christopher Wilks ◽

Phani Gaddipati ◽

Abhinav Nellore ◽

Ben Langmead

Keyword(s):

Tissue Specificity ◽

Rna Seq ◽

Sequencing Data ◽

Transcription Start ◽

Link Type ◽

Alternative Transcription ◽

Web App ◽

Inverted Indexing ◽

Splice Junctions ◽

Splicing Patterns

AbstractAs more and larger genomics studies appear, there is a growing need for comprehensive and queryable cross-study summaries. Snaptron is a search engine for summarized RNA sequencing data with a query planner that leverages R-tree, B-tree and inverted indexing strategies to rapidly execute queries over 146 million exon-exon splice junctions from over 70,000 human RNA-seq samples. Queries can be tailored by constraining which junctions and samples to consider. Snaptron can also rank and score junctions according to tissue specificity or other criteria. Further, Snaptron can rank and score samples according to the relative frequency of different splicing patterns. We outline biological questions that can be explored with Snaptron queries, including a study of novel exons in annotated genes, of exonization of repetitive element loci, and of a recently discovered alternative transcription start site for the ALK gene. Web app and documentation are at http://snaptron.cs.jhu.edu. Source code is at https://github.com/ChristopherWilks/snaptron under the MIT license.

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Alternative Splicing Regulation of an Alzheimer’s Risk Variant in CLU

International Journal of Molecular Sciences ◽

10.3390/ijms21197079 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7079

Author(s):

Seonggyun Han ◽

Kwangsik Nho ◽

Younghee Lee

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Alternative Splicing ◽

Genetic Variants ◽

Temporal Cortex ◽

Integrative Approach ◽

Splicing Regulation ◽

Rna Seq ◽

Risk Variant

Clusterin (CLU) is one of the risk genes most associated with late onset Alzheimer’s disease (AD), and several genetic variants in CLU are associated with AD risk. However, the functional role of known AD risk genetic variants in CLU has been little explored. We investigated the effect of an AD risk variant (rs7982) in the 5th exon of CLU on alternative splicing by using an integrative approach of brain-tissue-based RNA-Seq and whole genome sequencing data from Accelerating Medicines Partnership—Alzheimer’s Disease (AMP-AD). RNA-Seq data were generated from three regions in the temporal lobe of the brain—the temporal cortex, superior temporal gyrus, and parahippocampal gyrus. The rs7982 was significantly associated with intron retention (IR) of the 5th exon of CLU; as the number of alternative alleles (G) increased, the IR rates decreased more significantly in females than in males. Our results suggest a sex-dependent role of rs7982 in AD pathogenesis via splicing regulation.

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IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

Bioinformatics ◽

10.1093/bioinformatics/btz247 ◽

2019 ◽

Vol 35 (21) ◽

pp. 4469-4471 ◽

Cited By ~ 21

Author(s):

Kristoffer Vitting-Seerup ◽

Albin Sandelin

Keyword(s):

Alternative Splicing ◽

The Cancer Genome Atlas ◽

Supplementary Information ◽

Rna Seq ◽

Genome Wide ◽

Functional Consequences ◽

Cancer Genome Atlas ◽

Health And Disease ◽

Splicing Patterns

Abstract Summary Alternative splicing is an important mechanism involved in health and disease. Recent work highlights the importance of investigating genome-wide changes in splicing patterns and the subsequent functional consequences. Current computational methods only support such analysis on a gene-by-gene basis. Therefore, we extended IsoformSwitchAnalyzeR R library to enable analysis of genome-wide changes in specific types of alternative splicing and predicted functional consequences of the resulting isoform switches. As a case study, we analyzed RNA-seq data from The Cancer Genome Atlas and found systematic changes in alternative splicing and the consequences of the associated isoform switches. Availability and implementation Windows, Linux and Mac OS: http://bioconductor.org/packages/IsoformSwitchAnalyzeR. Supplementary information Supplementary data are available at Bioinformatics online.

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Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle

Scientific Reports ◽

10.1038/srep39094 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 13

Author(s):

Anne-Laure Bougé ◽

Eva Murauer ◽

Emmanuelle Beyne ◽

Julie Miro ◽

Jessica Varilh ◽

...

Keyword(s):

Skeletal Muscle ◽

Alternative Splicing ◽

Cdna Sequence ◽

454 Sequencing ◽

Exon Skipping ◽

Rna Seq ◽

Splicing Pattern ◽

Alternative Splicing Events ◽

Diagnostic Research ◽

Dmd Gene

Abstract We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3′ splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.

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The role of alternative splicing patterns of BCR/ABL transcripts in the generation of the blast crisis of chronic myeloid leukaemia

British Journal of Haematology ◽

10.1111/j.1365-2141.1990.tb07833.x ◽

1990 ◽

Vol 76 (1) ◽

pp. 33-38 ◽

Cited By ~ 27

Author(s):

G. J. Morgan ◽

A. Hernandez ◽

L. C. Chan ◽

T. Hughes ◽

P. Martiat ◽

...

Keyword(s):

Alternative Splicing ◽

Chronic Myeloid Leukaemia ◽

Myeloid Leukaemia ◽

Blast Crisis ◽

Splicing Patterns

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Disruption of Alternative Splicing in the Amygdala of Pigs Exposed to Maternal Immune Activation

Immuno ◽

10.3390/immuno1040035 ◽

2021 ◽

Vol 1 (4) ◽

pp. 499-517

Author(s):

Bruce R. Southey ◽

Marissa R. Keever-Keigher ◽

Haley E. Rymut ◽

Laurie A. Rund ◽

Rodney W. Johnson ◽

...

Keyword(s):

Alternative Splicing ◽

Immune Activation ◽

Fatty Liver Disease ◽

P Value ◽

Rna Seq ◽

Alcoholic Fatty Liver ◽

Maternal Immune Activation ◽

Precise Understanding ◽

Splicing Patterns ◽

Alcoholic Fatty Liver Disease

The inflammatory response of gestating females to infection or stress can disrupt gene expression in the offspring’s amygdala, resulting in lasting neurodevelopmental, physiological, and behavioral disorders. The effects of maternal immune activation (MIA) can be impacted by the offspring’s sex and exposure to additional stressors later in life. The objectives of this study were to investigate the disruption of alternative splicing patterns associated with MIA in the offspring’s amygdala and characterize this disruption in the context of the second stress of weaning and sex. Differential alternative splicing was tested on the RNA-seq profiles of a pig model of viral-induced MIA. Compared to controls, MIA was associated with the differential alternative splicing (FDR-adjusted p-value < 0.1) of 292 and 240 genes in weaned females and males, respectively, whereas 132 and 176 genes were differentially spliced in control nursed female and male, respectively. The majority of the differentially spliced (FDR-adjusted p-value < 0.001) genes (e.g., SHANK1, ZNF672, KCNA6) and many associated enriched pathways (e.g., Fc gamma R-mediated phagocytosis, non-alcoholic fatty liver disease, and cGMP-PKG signaling) have been reported in MIA-related disorders including autism and schizophrenia in humans. Differential alternative splicing associated with MIA was detected in the gene MAG across all sex-stress groups except for unstressed males and SLC2A11 across all groups except unstressed females. Precise understanding of the effect of MIA across second stressors and sexes necessitates the consideration of splicing isoform profiles.

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