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

Access to Document

10.1016/j.febslet.2013.01.032

Fingerprint Dive into the research topics of 'Computational analysis of associations between alternative splicing and histone modifications'. Together they form a unique fingerprint.

Cite this

@article{4f52abb1e2334015a1fca25d156ea869,

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.",

keywords = "Computational analysis, Histone modification, Splicing",

author = "Yuki Shindo and Tadasu Nozaki and Rintaro Saito and Masaru Tomita",

year = "2013",

month = mar,

day = "1",

doi = "10.1016/j.febslet.2013.01.032",

language = "English",

volume = "587",

pages = "516--521",

journal = "FEBS Letters",

issn = "0014-5793",

publisher = "Elsevier",

number = "5",

}

TY - JOUR

T1 - Computational analysis of associations between alternative splicing and histone modifications

AU - Shindo, Yuki

AU - Nozaki, Tadasu

AU - Saito, Rintaro

AU - Tomita, Masaru

PY - 2013/3/1

Y1 - 2013/3/1

N2 - 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.

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.

KW - Computational analysis

KW - Histone modification

KW - Splicing

UR - http://www.scopus.com/inward/record.url?scp=84874189918&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84874189918&partnerID=8YFLogxK

U2 - 10.1016/j.febslet.2013.01.032

DO - 10.1016/j.febslet.2013.01.032

M3 - Article

C2 - 23353998

AN - SCOPUS:84874189918

VL - 587

SP - 516

EP - 521

JO - FEBS Letters

JF - FEBS Letters

SN - 0014-5793

IS - 5

ER -

Computational analysis of associations between alternative splicing and histone modifications

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Cite this