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Title: Exploring the relationship between intron retention and chromatin accessibility in plants

Abstract

Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality. Splicing is known to occur co-transcriptionally and is influenced by the speed of transcription which in turn, is affected by chromatin structure. It follows that chromatin structure may have an important role in the regulation of splicing, and there is preliminary evidence in metazoans to suggest that this is indeed the case; however, nothing is known about the role of chromatin structure in regulating IR in plants. DNase I-seq is a useful experimental tool for genome-wide interrogation of chromatin accessibility, providing information on regions of chromatin with very high likelihood of cleavage by the enzyme DNase I, known as DNase I Hypersensitive Sites (DHSs). While it is well-established that promoter regions are highly accessible and are over-represented with DHSs, not much is known about DHSs in the bodies of genes, and their relationship to splicing in general, and IR in particular.

Authors:
 [1];  [1];  [1]; ORCiD logo [1]
  1. Colorado State Univ., Fort Collins, CO (United States)
Publication Date:
Research Org.:
Colorado State Univ., Fort Collins, (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1504903
Grant/Contract Number:  
SC0010733
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 19; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Intron retention; Chromatin accessibility; DNase I hypersensitive sites

Citation Formats

Ullah, Fahad, Hamilton, Michael, Reddy, Anireddy S. N., and Ben-Hur, Asa. Exploring the relationship between intron retention and chromatin accessibility in plants. United States: N. p., 2018. Web. doi:10.1186/s12864-017-4393-z.
Ullah, Fahad, Hamilton, Michael, Reddy, Anireddy S. N., & Ben-Hur, Asa. Exploring the relationship between intron retention and chromatin accessibility in plants. United States. doi:10.1186/s12864-017-4393-z.
Ullah, Fahad, Hamilton, Michael, Reddy, Anireddy S. N., and Ben-Hur, Asa. Fri . "Exploring the relationship between intron retention and chromatin accessibility in plants". United States. doi:10.1186/s12864-017-4393-z. https://www.osti.gov/servlets/purl/1504903.
@article{osti_1504903,
title = {Exploring the relationship between intron retention and chromatin accessibility in plants},
author = {Ullah, Fahad and Hamilton, Michael and Reddy, Anireddy S. N. and Ben-Hur, Asa},
abstractNote = {Intron retention (IR) is the most prevalent form of alternative splicing in plants. IR, like other forms of alternative splicing, has an important role in increasing gene product diversity and regulating transcript functionality. Splicing is known to occur co-transcriptionally and is influenced by the speed of transcription which in turn, is affected by chromatin structure. It follows that chromatin structure may have an important role in the regulation of splicing, and there is preliminary evidence in metazoans to suggest that this is indeed the case; however, nothing is known about the role of chromatin structure in regulating IR in plants. DNase I-seq is a useful experimental tool for genome-wide interrogation of chromatin accessibility, providing information on regions of chromatin with very high likelihood of cleavage by the enzyme DNase I, known as DNase I Hypersensitive Sites (DHSs). While it is well-established that promoter regions are highly accessible and are over-represented with DHSs, not much is known about DHSs in the bodies of genes, and their relationship to splicing in general, and IR in particular.},
doi = {10.1186/s12864-017-4393-z},
journal = {BMC Genomics},
number = 1,
volume = 19,
place = {United States},
year = {2018},
month = {1}
}

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Works referenced in this record:

Clustal W and Clustal X version 2.0
journal, September 2007


WebLogo: A Sequence Logo Generator
journal, May 2004

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