scholarly journals Annotation and differential analysis of alternative splicing using de novo assembly of RNAseq data

2016 ◽  
Author(s):  
Clara Benoit-Pilven ◽  
Camille Marchet ◽  
Emilie Chautard ◽  
Leandro Lima ◽  
Marie-Pierre Lambert ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
De Novo ◽  
Exon Skipping ◽  
Differential Analysis ◽  
Genome Wide ◽  
Human Genes ◽  
Rnaseq Data ◽  
Splicing Variants ◽  
Novel Variants ◽  
Event Based

AbstractGenome-wide analyses reveal that more than 90% of multi exonic human genes produce at least two transcripts through alternative splicing (AS). Various bioinformatics methods are available to analyze AS from RNAseq data. Most methods start by mapping the reads to an annotated reference genome, but some start by a de novo assembly of the reads. In this paper, we present a systematic comparison of a mapping-first approach (FaRLine) and an assembly-first approach (KisSplice). These two approaches are event-based, as they focus on the regions of the transcripts that vary in their exon content. We applied these methods to an RNAseq dataset from a neuroblastoma SK-N-SH cell line (ENCODE) differentiated or not using retinoic acid. We found that the predictions of the two pipelines overlapped (70% of exon skipping events were common), but with noticeable differences. The assembly-first approach allowed to find more novel variants, including novel unannotated exons and splice sites. It also predicted AS in families of paralog genes. The mapping-first approach allowed to find more lowly expressed splicing variants, and was better in predicting exons overlapping repeated elements. This work demonstrates that annotating AS with a single approach leads to missing a large number of candidates. We further show that these candidates cannot be neglected, since many of them are differentially regulated across conditions, and can be validated experimentally. We therefore advocate for the combine use of both mapping-first and assembly-first approaches for the annotation and differential analysis of AS from RNAseq data.

scholarly journals Genome-wide Analysis of Alternative Pre-mRNA Splicing

2007 ◽  
Vol 283 (3) ◽  
pp. 1229-1233 ◽  
Author(s):  
Claudia Ben-Dov ◽  
Britta Hartmann ◽  
Josefin Lundgren ◽  
Juan Valcárcel
Keyword(s):  
Alternative Splicing ◽  
Large Scale ◽  
Mrna Splicing ◽  
Diagnostic Tools ◽  
Primary Transcript ◽  
Genome Wide ◽  
Human Genes ◽  
Multicellular Organisms ◽  
Eukaryotic Genomes ◽  
Key Questions

Alternative splicing of mRNA precursors allows the synthesis of multiple mRNAs from a single primary transcript, significantly expanding the information content and regulatory possibilities of higher eukaryotic genomes. High-throughput enabling technologies, particularly large-scale sequencing and splicing-sensitive microarrays, are providing unprecedented opportunities to address key questions in this field. The picture emerging from these pioneering studies is that alternative splicing affects most human genes and a significant fraction of the genes in other multicellular organisms, with the potential to greatly influence the evolution of complex genomes. A combinatorial code of regulatory signals and factors can deploy physiologically coherent programs of alternative splicing that are distinct from those regulated at other steps of gene expression. Pre-mRNA splicing and its regulation play important roles in human pathologies, and genome-wide analyses in this area are paving the way for improved diagnostic tools and for the identification of novel and more specific pharmaceutical targets.

scholarly journals Alternative Splicing During the Chlamydomonasreinhardtii Cell Cycle

2020 ◽  
Vol 10 (10) ◽  
pp. 3797-3810
Author(s):  
Manishi Pandey ◽  
Gary D. Stormo ◽  
Susan K. Dutcher
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Alternative Splicing ◽  
Chlamydomonas Reinhardtii ◽  
Intron Retention ◽  
Exon Skipping ◽  
Dark Phase ◽  
Periodic Patterns ◽  
Genome Wide ◽  
Splicing Pattern

Genome-wide analysis of transcriptome data in Chlamydomonas reinhardtii shows periodic patterns in gene expression levels when cultures are grown under alternating light and dark cycles so that G1 of the cell cycle occurs in the light phase and S/M/G0 occurs during the dark phase. However, alternative splicing, a process that enables a greater protein diversity from a limited set of genes, remains largely unexplored by previous transcriptome based studies in C. reinhardtii. In this study, we used existing longitudinal RNA-seq data obtained during the light-dark cycle to investigate the changes in the alternative splicing pattern and found that 3277 genes (19.75% of 17,746 genes) undergo alternative splicing. These splicing events include Alternative 5′ (Alt 5′), Alternative 3′ (Alt 3′) and Exon skipping (ES) events that are referred as alternative site selection (ASS) events and Intron retention (IR) events. By clustering analysis, we identified a subset of events (26 ASS events and 10 IR events) that show periodic changes in the splicing pattern during the cell cycle. About two-thirds of these 36 genes either introduce a pre-termination codon (PTC) or introduce insertions or deletions into functional domains of the proteins, which implicate splicing in altering gene function. These findings suggest that alternative splicing is also regulated during the Chlamydomonas cell cycle, although not as extensively as changes in gene expression. The longitudinal changes in the alternative splicing pattern during the cell cycle captured by this study provides an important resource to investigate alternative splicing in genes of interest during the cell cycle in Chlamydomonas reinhardtii and other eukaryotes.

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

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.

scholarly journals Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and Therapeutics

2020 ◽  
Vol 21 (23) ◽  
pp. 9032
Author(s):  
Cláudia Bessa ◽  
Paulo Matos ◽  
Peter Jordan ◽  
Vânia Gonçalves
Keyword(s):  
Alternative Splicing ◽  
Messenger Rna ◽  
Human Cancer ◽  
Genetic Alterations ◽  
Altered Expression ◽  
Genome Wide ◽  
Human Genes ◽  
Transcriptional Regulatory Mechanism ◽  
A Genome ◽  
Wide Scale

Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism used by more than 95% of transcribed human genes and responsible for structural transcript variation and proteome diversity. In the past decade, genome-wide transcriptome sequencing has revealed that AS is tightly regulated in a tissue- and developmental stage-specific manner, and also frequently dysregulated in multiple human cancer types. It is currently recognized that splicing defects, including genetic alterations in the spliced gene, altered expression of both core components or regulators of the precursor messenger RNA (pre-mRNA) splicing machinery, or both, are major drivers of tumorigenesis. Hence, in this review we provide an overview of our current understanding of splicing alterations in cancer, and emphasize the need to further explore the cancer-specific splicing programs in order to obtain new insights in oncology. Furthermore, we also discuss the recent advances in the identification of dysregulated splicing signatures on a genome-wide scale and their potential use as biomarkers. Finally, we highlight the therapeutic opportunities arising from dysregulated splicing and summarize the current approaches to therapeutically target AS in cancer.

scholarly journals Splicing Programs and Cancer

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Sophie Germann ◽  
Lise Gratadou ◽  
Martin Dutertre ◽  
Didier Auboeuf
Keyword(s):  
Alternative Splicing ◽  
Gene Networks ◽  
Large Scale ◽  
Splicing Factors ◽  
Novel Technologies ◽  
Normal Tissues ◽  
Genome Wide ◽  
Splicing Variants ◽  
Cancer Initiation ◽  
Genetic Mechanisms

Numerous studies report splicing alterations in a multitude of cancers by using gene-by-gene analysis. However, understanding of the role of alternative splicing in cancer is now reaching a new level, thanks to the use of novel technologies allowing the analysis of splicing at a large-scale level. Genome-wide analyses of alternative splicing indicate that splicing alterations can affect the products of gene networks involved in key cellular programs. In addition, many splicing variants identified as being misregulated in cancer are expressed in normal tissues. These observations suggest that splicing programs contribute to specific cellular programs that are altered during cancer initiation and progression. Supporting this model, recent studies have identified splicing factors controlling cancer-associated splicing programs. The characterization of splicing programs and their regulation by splicing factors will allow a better understanding of the genetic mechanisms involved in cancer initiation and progression and the development of new therapeutic targets.

scholarly journals Alternative RNA Splicing—The Trojan Horse of Cancer Cells in Chemotherapy

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1085
Author(s):  
Nikolay Mehterov ◽  
Maria Kazakova ◽  
Yordan Sbirkov ◽  
Boyan Vladimirov ◽  
Nikolay Belev ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cancer Cells ◽  
Tumor Cells ◽  
Rna Splicing ◽  
Molecular Mechanisms ◽  
Chemotherapeutic Agents ◽  
Human Genes ◽  
Splicing Variants ◽  
Almost All ◽  
Aberrant Rna

Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays a crucial role in malignant transformation, development, and progression, a fact supported by the distinct splicing profiles identified in both healthy and tumor cells. Drug resistance, resulting in treatment failure, still remains a major challenge for current cancer therapy. Furthermore, tumor cells often take advantage of aberrant RNA splicing to overcome the toxicity of the administered chemotherapeutic agents. Thus, deciphering the alternative RNA splicing variants in tumor cells would provide opportunities for designing novel therapeutics combating cancer more efficiently. In the present review, we provide a comprehensive outline of the recent findings in alternative splicing in the most common neoplasms, including lung, breast, prostate, head and neck, glioma, colon, and blood malignancies. Molecular mechanisms developed by cancer cells to promote oncogenesis as well as to evade anticancer drug treatment and the subsequent chemotherapy failure are also discussed. Taken together, these findings offer novel opportunities for future studies and the development of targeted therapy for cancer-specific splicing variants.

scholarly journals Complementarity of assembly-first and mapping-first approaches for alternative splicing annotation and differential analysis from RNAseq data

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Clara Benoit-Pilven ◽  
Camille Marchet ◽  
Emilie Chautard ◽  
Leandro Lima ◽  
Marie-Pierre Lambert ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Differential Analysis ◽  
Rnaseq Data

scholarly journals LESSeq: Local event-based analysis of alternative splicing using RNA-Seq data

2019 ◽  
Author(s):  
Jing Leng ◽  
Christopher JF Cameron ◽  
Sunghee Oh ◽  
James P Noonan ◽  
Mark B Gerstein
Keyword(s):  
Alternative Splicing ◽  
Likelihood Estimation ◽  
Human Populations ◽  
Species Variation ◽  
Rna Seq ◽  
Data Set ◽  
Genome Wide ◽  
Alternative Splicing Events ◽  
Event Based ◽  
Splicing Patterns

Alternative splicing, which can be observed genome-wide by RNA-Seq, is important in cellular development and evolution. Comparative RNA-Seq experiments between different cellular conditions allow alternative splicing signatures to be detected. However, inferring alternative splicing signatures from short-read technology is unreliable and still presents many challenges before biologically significant signatures may be identified. To enable the robust discovery of differential alternative splicing, we developed the Local Event-based analysis of alternative Splicing using RNA-Seq (LESSeq) pipeline. LESSeq utilizes information of local splicing events (i.e., the partial structures in genes where transcript-splicing patterns diverge) to identify unambiguous alternative splicing. In addition, LESSeq quantifies the abundance of these alternative events using Maximum Likelihood Estimation (MLE) and provides their significance between different cellular conditions. The utility of LESSeq is demonstrated through two case studies relevant to human variation and evolution. Using an RNA-Seq data set of lymphoblastoid cell lines in two human populations, we examined within-species variation and discovered population-differential alternative splicing events. With an RNA-Seq data set of several tissues in human and rhesus macaque, we studied cross-species variation and identified lineage-differential alternative splicing events. LESSeq is implemented in C++ and R, and made publicly available on GitHub at: https://github.com/gersteinlab/LESSeq

scholarly journals Identification of rare de novo epigenetic variations in congenital disorders

2018 ◽  
Author(s):  
Mafalda Barbosa ◽  
Ricky S. Joshi ◽  
Paras Garg ◽  
Alejandro Martin-Trujillo ◽  
Nihir Patel ◽  
...  
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Point Mutations ◽  
Ctcf Binding ◽  
Loss Of Function ◽  
Structural Variations ◽  
Genomic Technologies ◽  
Genome Wide ◽  
Rnaseq Data ◽  
Population Controls

AbstractCertain human traits such as neurodevelopmental disorders (NDs) and congenital anomalies (CAs) are believed to be primarily genetic in origin. With recent dramatic advances in genomic technologies, genome-wide surveys of cohorts of patients with ND/CAs for point mutations and structural variations have greatly advanced our understanding of their genetic etiologies1,2. However, even after whole genome sequencing (WGS), a substantial fraction of such disorders remain unexplained3. In contrast, the possibility that constitutive epigenetic variations (epivariations) might underlie such traits has not been well explored. We hypothesized that some cases of ND/CA are caused by aberrations of DNA methylation that lead to a dysregulation of normal genome function. By comparing DNA methylation profiles from 489 individuals with ND/CAs against 1,534 population controls, we identified epivariations as a frequent occurrence in the human genome. De novo epivariations were significantly enriched in cases when compared to controls. RNAseq data from population studies showed that epivariations often have an impact on gene expression comparable to loss-of-function mutations. Additionally, we detected and replicated an enrichment of rare sequence mutations overlapping CTCF binding sites close to epivariations. Thus, some epivariations occur secondary to cis-linked mutations in regulatory regions, providing a rationale for interpreting non-coding genetic variation. We propose that epivariations likely represent the causative genomic defect in 5-10% of patients with unexplained ND/CAs. This constitutes a yield comparable to CNV microarrays, and as such has significant diagnostic relevance.

scholarly journals Genome-Wide Profiling Reveals Alternative Polyadenylation of Innate Immune-Related mRNA in Patients With COVID-19

2021 ◽  
Vol 12 ◽  
Author(s):  
Sanqi An ◽  
Yueqi Li ◽  
Yao Lin ◽  
Jiemei Chu ◽  
Jinming Su ◽  
...  
Keyword(s):  
Immune Escape ◽  
De Novo ◽  
Human Peripheral Blood ◽  
Alternative Polyadenylation ◽  
Innate Immune ◽  
Peripheral Blood Mononuclear ◽  
Genome Wide ◽  
Human Genes ◽  
Processing Mechanisms

The coronavirus disease 2019 (COVID-19) pandemic has caused many deaths worldwide. To date, the mechanism of viral immune escape remains unclear, which is a great obstacle to developing effective clinical treatment. RNA processing mechanisms, including alternative polyadenylation (APA) and alternative splicing (AS), are crucial in the regulation of most human genes in many types of infectious diseases. Because the role of APA and AS in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains unknown, we performed de novo identification of dynamic APA sites using a public dataset of human peripheral blood mononuclear cell (PBMC) RNA-Seq data in COVID-19 patients. We found that genes with APA were enriched in innate immunity -related gene ontology categories such as neutrophil activation, regulation of the MAPK cascade and cytokine production, response to interferon-gamma and the innate immune response. We also reported genome-wide AS events and enriched viral transcription-related categories upon SARS-CoV-2 infection. Interestingly, we found that APA events may give better predictions than AS in COVID-19 patients, suggesting that APA could act as a potential therapeutic target and novel biomarker in those patients. Our study is the first to annotate genes with APA and AS in COVID-19 patients and highlights the roles of APA variation in SARS-CoV-2 infection.

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