Computational analysis of associations between alternative splicing and histone modifications

Yuki Shindo; Tadasu Nozaki; Rintaro Saito; Masaru Tomita

doi:10.1016/j.febslet.2013.01.032

Computational analysis of associations between alternative splicing and histone modifications

Yuki Shindo, Tadasu Nozaki, Rintaro Saito, Masaru Tomita

Faculty of Environment and Information Studies

Research output: Contribution to journal › Article › peer-review

17 Citations (Scopus)

Abstract

Pre-mRNA splicing is a complex process involving combinatorial effects of cis- and trans-elements. Here, we focused on histone modifications as typical trans-regulatory elements and performed systematic analyses of associations between splicing patterns and histone modifications by using publicly available ChIP-Seq, mRNA-Seq, and exon-array data obtained in two human cell lines. We found that several types of histone modifications including H3K36me3 were associated with the inclusion or exclusion of alternative exons. Furthermore, we observed that the levels of H3K36me3 and H3K79me1 in the cell lines were well correlated with the differences in alternative splicing patterns between the cell lines.

Original language	English
Pages (from-to)	516-521
Number of pages	6
Journal	FEBS Letters
Volume	587
Issue number	5
DOIs	https://doi.org/10.1016/j.febslet.2013.01.032
Publication status	Published - 2013 Mar 1

Keywords

Computational analysis
Histone modification
Splicing

ASJC Scopus subject areas

Biophysics
Structural Biology
Biochemistry
Molecular Biology
Genetics
Cell Biology

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title = "Computational analysis of associations between alternative splicing and histone modifications",

abstract = "Pre-mRNA splicing is a complex process involving combinatorial effects of cis- and trans-elements. Here, we focused on histone modifications as typical trans-regulatory elements and performed systematic analyses of associations between splicing patterns and histone modifications by using publicly available ChIP-Seq, mRNA-Seq, and exon-array data obtained in two human cell lines. We found that several types of histone modifications including H3K36me3 were associated with the inclusion or exclusion of alternative exons. Furthermore, we observed that the levels of H3K36me3 and H3K79me1 in the cell lines were well correlated with the differences in alternative splicing patterns between the cell lines.",

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AU - Shindo, Yuki

AU - Nozaki, Tadasu

AU - Saito, Rintaro

AU - Tomita, Masaru

N1 - Funding Information: This research was supported by research funds from the Yamagata Prefectural Government and Tsuruoka City, Japan.

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AB - Pre-mRNA splicing is a complex process involving combinatorial effects of cis- and trans-elements. Here, we focused on histone modifications as typical trans-regulatory elements and performed systematic analyses of associations between splicing patterns and histone modifications by using publicly available ChIP-Seq, mRNA-Seq, and exon-array data obtained in two human cell lines. We found that several types of histone modifications including H3K36me3 were associated with the inclusion or exclusion of alternative exons. Furthermore, we observed that the levels of H3K36me3 and H3K79me1 in the cell lines were well correlated with the differences in alternative splicing patterns between the cell lines.

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