ArticleNucleic acids research2007
A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- SpliceTransformer predicts tissue-specific splicing linked to human diseases.Nature communications · 2024Article
- Expression of Smyd1b_tv1 by Alternative Splicing in Cardiac Muscle is Critical for Sarcomere Organization in Cardiomyocytes and Heart Function.Molecular and cellular biology · 2024Article
- The Role of Alternative Splicing Factors hnRNP G and Fox-2 in the Progression and Prognosis of Esophageal Cancer.Disease markers · 2022Article
- Sensitive period-regulating genetic pathways and exposure to adversity shape risk for depression.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2022Article
- Restriction of an intron size en route to endothermy.Nucleic acids research · 2021Article
- The evolution of hemocyanin genes in Tectipleura: a multitude of conserved introns in highly diverse gastropods.BMC ecology and evolution · 2021Article
- The regulatory genome of the malaria vectorNAR genomics and bioinformatics · 2021Article
- Diversification of the muscle proteome through alternative splicing.Skeletal muscle · 2018Review
- Developmental regulation of RNA processing by Rbfox proteins.Wiley interdisciplinary reviews. RNA · 2017Review
- Computational Identification of Tissue-Specific Splicing Regulatory Elements in Human Genes from RNA-Seq Data.PloS one · 2016Article
- Identification of Targets of CUG-BP, Elav-Like Family Member 1 (CELF1) Regulation in Embryonic Heart Muscle.PloS one · 2016Article
- The RNA-binding protein Rbfox1 regulates splicing required for skeletal muscle structure and function.Human molecular genetics · 2015Article
- Article
- RBFOX and SUP-12 sandwich a G base to cooperatively regulate tissue-specific splicing.Nature structural & molecular biology · 2014Article
- ARH-seq: identification of differential splicing in RNA-seq data.Nucleic acids research · 2014Article
- Pressure-overload cardiac hypertrophy is associated with distinct alternative splicing due to altered expression of splicing factors.Molecules and cells · 2014Article
- RNA binding proteins in the regulation of heart development.The international journal of biochemistry & cell biology · 2013Review
- Quaking and PTB control overlapping splicing regulatory networks during muscle cell differentiation.RNA (New York, N.Y.) · 2013Article
- Function of alternative splicing.Gene · 2013Review
- A biophysical model for identifying splicing regulatory elements and their interactions.PloS one · 2013Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify cis-regulatory elements for alternative pre-mRNA splicing. Using data from a human exon microarray, we identified 56 cassette exons that exhibited higher transcript-normalized expression in muscle than in other normal adult tissues. Intron sequences flanking these exons were then analyzed to identify candidate regulatory motifs for muscle-specific alternative splicing. Correlation of motif parameters with gene-normalized exon expression levels was examined using linear regression and linear splines on RNA words and degenerate weight matrices, respectively. Our unbiased analysis uncovered multiple candidate regulatory motifs for muscle-specific splicing, many of which are phylogenetically conserved among vertebrate genomes. The most prominent downstream motifs were binding sites for Fox1- and CELF-related splicing factors, and a branchpoint-like element acuaac; pyrimidine-rich elements resembling PTB-binding sites were most significant in upstream introns. Intriguingly, our systematic study indicates a paucity of novel muscle-specific elements that are dominant in short proximal intronic regions. We propose that Fox and CELF proteins play major roles in enforcing the muscle-specific alternative splicing program, facilitating expression of unique isoforms of cytoskeletal proteins critical to muscle cell function.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.