scholarly journals Quantitative visualization of alternative exon expression from RNA-seq data

2015 ◽  
Vol 31 (14) ◽  
pp. 2400-2402 ◽  
Author(s):  
Yarden Katz ◽  
Eric T. Wang ◽  
Jacob Silterra ◽  
Schraga Schwartz ◽  
Bang Wong ◽  
...  
Keyword(s):  
Alternative Exon ◽  
Rna Seq ◽  
Exon Expression ◽  
Quantitative Visualization

scholarly journals Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data

2014 ◽  
Author(s):  
Yarden Katz ◽  
Eric T Wang ◽  
Jacob Stilterra ◽  
Schraga Schwartz ◽  
Bang Wong ◽  
...  
Keyword(s):  
Region Of Interest ◽  
Splice Junction ◽  
Genomic Region ◽  
Rna Seq ◽  
Mrna Isoforms ◽  
Experimental Conditions ◽  
Human Genes ◽  
Quantitative Visualization ◽  
Isoform Expression ◽  
Multiple Samples

Analysis of RNA sequencing (RNA-Seq) data revealed that the vast majority of human genes express multiple mRNA isoforms, produced by alternative pre-mRNA splicing and other mechanisms, and that most alternative isoforms vary in expression between human tissues. As RNA-Seq datasets grow in size, it remains challenging to visualize isoform expression across multiple samples. We present Sashimi plots, a quantitative multi-sample visualization of RNA-Seq reads aligned to gene annotations, which enables quantitative comparison of isoform usage across samples or experimental conditions. Given an input annotation and spliced alignments of reads from a sample, a region of interest is visualized in a Sashimi plot as follows: (i) alignments in exons are represented as read densities (optionally normalized by length of genomic region and coverage), and (ii) splice junction reads are drawn as arcs connecting a pair of exons, where arc width is drawn proportional to the number of reads aligning to the junction.

scholarly journals Non-coding Class Switch Recombination-related transcription in human normal and pathological immune responses

2018 ◽  
Author(s):  
Helena Kuri-Magaña ◽  
Leonardo Collado-Torres ◽  
Andrew E. Jaffe ◽  
Humberto Valdovinos-Torres ◽  
Marbella Ovilla-Muñoz ◽  
...  
Keyword(s):  
B Cells ◽  
Immune Responses ◽  
Class Switch Recombination ◽  
Rna Seq ◽  
Ileal Mucosa ◽  
Exon Expression ◽  
Class Switch ◽  
Cytokine Milieu ◽  
Antibody Class ◽  
Cancer Tissues

AbstractBackgroundAntibody class switch recombination (CSR) to IgG, IgA or IgE is a hallmark of adaptive immunity, allowing antibody function diversification beyond IgM. CSR involves a deletion of the IgM/IgD constant region genes placing a new acceptor Constant (CH) gene, downstream of the VDJH exon. CSR depends on non-coding (CSRnc) transcription of donor Iμ and acceptor IH exons, located 5’ upstream of each CH coding gene. Although our knowledge of the role of CSRnc transcription has advanced greatly, its extension and importance in healthy and diseased humans is scarce.MethodsWe analyzed CSRnc transcription in 70,603 publicly available RNA-seq samples, including GTEx, TCGA and the Sequence Read Archive (SRA) using recount2, an online resource consisting of normalized RNA-seq gene and exon counts, as well as coverage BigWig files that can be programmatically accessed through R. CSRnc transcription was validated with a qRT-PCR assay for Iμ, Iγ3 and Iγ1 in humans in response to vaccination.ResultsWe mapped IH transcription for the human IgH locus, including the less understood IGHD gene. CSRnc transcription was restricted to B cells and is widely distributed in normal adult tissues, but predominant in blood, spleen, MALT-containing tissues, visceral adipose tissue and some so-called “immune privileged” tissues. However, significant Iγ4 expression was found even in non-lymphoid fetal tissues. CSRnc expression in cancer tissues mimicked the expression of their normal counterparts, with notable pattern changes in some common cancer subsets. CSRnc transcription in tumors appears to result from tumor infiltration by B cells, since CSRnc transcription was not detected in corresponding tumor-derived immortal cell lines. Additionally, significantly increased I5 transcription in ileal mucosa in Crohn’s disease with ulceration was found.ConclusionsCSRnc transcription occurs in multiple anatomical locations beyond classical secondary lymphoid organs, representing a potentially useful marker of effector B cell responses in normal and pathological immune responses. The pattern of IH exon expression may reveal clues of the local immune response (i.e. cytokine milieu) in health and disease. This is a great example of how the public recount2 data can be used to further our understanding of transcription, including regions outside the known transcriptome.

scholarly journals Coordinated analysis of exon and intron data reveals novel differential gene expression changes

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hamid R. Eghbalnia ◽  
William W. Wilfinger ◽  
Karol Mackey ◽  
Piotr Chomczynski
Keyword(s):  
Gene Networks ◽  
Expression Data ◽  
Rna Seq ◽  
Data Set ◽  
Exon Expression ◽  
Regulatory Processes ◽  
Pathway Gene ◽  
Immune Pathway ◽  
Archived Data

Abstract RNA-Seq expression analysis currently relies primarily upon exon expression data. The recognized role of introns during translation, and the presence of substantial RNA-Seq counts attributable to introns, provide the rationale for the simultaneous consideration of both exon and intron data. We describe here a method for the coordinated analysis of exon and intron data by investigating their relationship within individual genes and across samples, while taking into account changes in both variability and expression level. This coordinated analysis of exon and intron data offers strong evidence for significant differences that distinguish the profiles of the exon-only expression data from the combined exon and intron data. One advantage of our proposed method, called matched change characterization for exons and introns (MEI), is its straightforward applicability to existing archived data using small modifications to standard RNA-Seq pipelines. Using MEI, we demonstrate that when data are examined for changes in variability across control and case conditions, novel differential changes can be detected. Notably, when MEI criteria were employed in the analysis of an archived data set involving polyarthritic subjects, the number of differentially expressed genes was expanded by sevenfold. More importantly, the observed changes in exon and intron variability with statistically significant false discovery rates could be traced to specific immune pathway gene networks. The application of MEI analysis provides a strategy for incorporating the significance of exon and intron variability and further developing the role of using both exons and intron sequencing counts in studies of gene regulatory processes.

scholarly journals Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse brain

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Lindsay Liang ◽  
Siavash Fazel Darbandi ◽  
Sirisha Pochareddy ◽  
Forrest O. Gulden ◽  
Michael C. Gilson ◽  
...  
Keyword(s):  
Human Brain ◽  
Developmental Trajectories ◽  
Autism Spectrum ◽  
Rna Seq ◽  
Splice Isoforms ◽  
Protein Coding ◽  
Voltage Gated ◽  
Exon Expression ◽  
Voltage Gated Sodium Channels ◽  
Exon Level

Abstract Background Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes vary across development in the rodent brain, including mutually exclusive copies of the fifth protein-coding exon detected in the neonate (5N) and adult (5A). A second pair of mutually exclusive exons is reported in SCN8A only (18N and 18A). We aimed to quantify the expression of individual exons in the developing human brain. Methods RNA-seq data from 783 human brain samples across development were analyzed to estimate exon-level expression. Developmental changes in exon utilization were validated by assessing intron splicing. Exon expression was also estimated in RNA-seq data from 58 developing mouse neocortical samples. Results In the mature human neocortex, exon 5A is consistently expressed at least 4-fold higher than exon 5N in all four genes. For SCN2A, SCN3A, and SCN8A, a brain-wide synchronized 5N to 5A transition occurs between 24 post-conceptual weeks (2nd trimester) and 6 years of age. In mice, the equivalent 5N to 5A transition begins at or before embryonic day 15.5. In SCN8A, over 90% of transcripts in the mature human cortex include exon 18A. Early in fetal development, most transcripts include 18N or skip both 18N and 18A, with a transition to 18A inclusion occurring from 13 post-conceptual weeks to 6 months of age. No other protein-coding exons showed comparably dynamic developmental trajectories. Conclusions Exon usage in SCN1A, SCN2A, SCN3A, and SCN8A changes dramatically during human brain development. These splice isoforms, which alter the biophysical properties of the encoded channels, may account for some of the observed phenotypic differences across development and between specific variants. Manipulation of the proportion of splicing isoforms at appropriate stages of development may act as a therapeutic strategy for specific mutations or even epilepsy in general.

scholarly journals RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0240895
Author(s):  
Joel D. Leal-Gutiérrez ◽  
Mauricio A. Elzo ◽  
Chad Carr ◽  
Raluca G. Mateescu
Keyword(s):  
Meat Quality ◽  
Quality Index ◽  
Transcriptional Profiling ◽  
Cytoskeletal Proteins ◽  
P Value ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Exon Expression ◽  
Continuous Response ◽  
Slaughter Age

RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through the identification of differentially expressed (DE) genes and pathways. A total of 80 steers with extreme phenotypes were selected from the University of Florida multibreed Angus-Brahman herd. The average slaughter age was 12.91±8.69 months. Tenderness, juiciness and connective tissue assessed by sensory panel, along with marbling, Warner-Bratzler Shear Force (WBSF) and cooking loss, were measured in longissimus dorsi muscle. Total RNA was extracted from muscle and one RNA-seq library per sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq-3000 platform to generate 2×101 bp paired-end reads. The overall read mapping rate using the Btau_4.6.1 reference genome was 63%. A total of 8,799 genes were analyzed using two different methodologies, an expression association and a DE analysis. A gene and exon expression association analysis was carried out using a meat quality index on all 80 samples as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). A gene and isoform DE evaluation was performed analyzing two groups with extreme WBSF, tenderness and marbling. A total of 676 (adjusted p-value≤0.05), 70 (adjusted p-value≤0.1) and 198 (adjusted p-value≤0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR≤0.1) were DE. Cytoskeletal and transmembrane anchoring genes and pathways were identified in the expression association, DE and the gene enrichment analyses; these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal interaction with myocyte and organelle membranes, contributing to cytoskeletal structure and architecture maintenance postmortem.

scholarly journals RNA-seq analysis identifies cytoskeletal structural genes and pathways for meat quality in beef

2019 ◽  
Author(s):  
Joel David Leal Gutierrez ◽  
Mauricio A. Elzo ◽  
Raluca G. Mateescu
Keyword(s):  
Meat Quality ◽  
Quality Index ◽  
Transcriptional Profiling ◽  
Cytoskeletal Proteins ◽  
P Value ◽  
Rna Seq ◽  
Microtubule Network ◽  
Illumina Hiseq ◽  
Exon Expression ◽  
Longissimus Dorsi Muscle

Abstract Background RNA sequencing (RNA-seq) has allowed for transcriptional profiling of biological systems through identification of differentially expressed (DE) genes and pathways. Results A total of 80 steers were selected from the multibreed Angus-Brahman herd of the University of Florida. Sensory panel tenderness, juiciness and connective tissue as well as marbling, WBSF and cooking loss were assessed in longissimus dorsi muscle. Nuclear RNA was extracted from muscle and an RNA-seq library for each sample was constructed, multiplexed, and sequenced based on protocols by Illumina HiSeq 3000 PE100 platform to generate 2 × 101 bp paired-end reads. On average, 34.9 million high-quality paired reads were uniquely mapped to the Btau_4.6.1 reference genome and a total of 8,799 genes were analyzed. Including all 80 animals, gene and exon expression analysis was carried out using a meat quality index as a continuous response variable. The expression of 208 genes and 3,280 exons from 1,565 genes was associated with the meat quality index (p-value ≤ 0.05). Out of the 80 samples sequenced, 40 animals with extreme low and high WBSF, tenderness and marbling values were selected for a differential expression (DE) analysis for gene and isoforms. A total of 676 (adjusted p-value ≤ 0.05), 70 (adjusted p-value ≤ 0.1) and 198 (adjusted p-value ≤ 0.1) genes were DE for WBSF, tenderness and marbling, respectively. A total of 106 isoforms from 98 genes for WBSF, 13 isoforms from 13 genes for tenderness and 43 isoforms from 42 genes for marbling (FDR ≤ 0.1) were DE. Conclusion A number of cytoskeletal and transmembrane anchoring related genes and pathways were identified in the expression, DE and gene enrichment analyses, and these proteins can have a direct effect on meat quality. Cytoskeletal proteins and transmembrane anchoring molecules can influence meat quality by allowing cytoskeletal filament interaction with myocyte and organelle membranes, contributing to cytoskeletal structure, microtubule network stability, and cellular architecture maintenance during the postmortem.

scholarly journals Quantitative RNA-seq meta-analysis of alternative exon usage in C. elegans

2017 ◽  
Vol 27 (12) ◽  
pp. 2120-2128 ◽  
Author(s):  
Nicolas J. Tourasse ◽  
Jonathan R.M. Millet ◽  
Denis Dupuy
Keyword(s):  
Meta Analysis ◽  
Alternative Exon ◽  
Rna Seq ◽  
C Elegans ◽  
Exon Usage

scholarly journals Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

2010 ◽  
Vol 38 (10) ◽  
pp. e112-e112 ◽  
Author(s):  
Hugues Richard ◽  
Marcel H. Schulz ◽  
Marc Sultan ◽  
Asja Nürnberger ◽  
Sabine Schrinner ◽  
...  
Keyword(s):  
Rna Seq ◽  
Expression Levels ◽  
Exon Expression ◽  
Alternative Isoforms

scholarly journals Developmental dynamics of voltage-gated sodium channel isoform expression in the human and mouse neocortex

2020 ◽  
Author(s):  
Lindsay Liang ◽  
Siavash Fazel Darbandi ◽  
Sirisha Pochareddy ◽  
Forrest O. Gulden ◽  
Michael C. Gilson ◽  
...  
Keyword(s):  
Developmental Trajectories ◽  
Autism Spectrum ◽  
Rna Seq ◽  
Splice Isoforms ◽  
Protein Coding ◽  
Voltage Gated ◽  
Human Neocortex ◽  
Exon Expression ◽  
Voltage Gated Sodium Channels ◽  
Dorsolateral Prefrontal

AbstractObjectiveGenetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, and autism spectrum disorder. The mRNA splicing patterns of all four genes vary across development in the rodent brain, including mutually exclusive copies of the fifth protein-coding exon detected in the neonate (5N) and adult (5A). A second pair of mutually exclusive exons is reported in SCN8A only (18N and 18A). We aimed to quantify the expression of individual exons in the developing human neocortex.MethodsRNA-seq data from 176 human dorsolateral prefrontal cortex samples across development were analyzed to estimate exon-level expression. Developmental changes in exon utilization were validated by assessing intron splicing. Exon expression was also estimated in RNA-seq data from 58 developing mouse neocortical samples.ResultsIn the mature human neocortex, exon 5A is consistently expressed at least 4-fold higher than exon 5N in all four genes. For SCN2A, SCN3A, and SCN8A a synchronized 5N/5A transition occurs between 24 post-conceptual weeks (2nd trimester) and six years of age. In mice, the equivalent 5N/5A transition begins at or before embryonic day 15.5. In SCN8A, over 90% of transcripts in the mature human cortex include exon 18A. Early in fetal development, most transcripts include 18N or skip both 18N and 18A, with a transition to 18A inclusion occurring from 13 post-conceptual weeks to 6 months of age. No other protein-coding exons showed comparably dynamic developmental trajectories.SignificanceSplice isoforms, which alter the biophysical properties of the encoded channels, may account for some of the observed phenotypic differences across development and between specific variants. Manipulation of the proportion of splicing isoforms at appropriate stages of development may act as a therapeutic strategy for specific mutations or even epilepsy in general.

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