Exploring the relationship between intron retention and chromatin accessibility in plants

Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy S. N.; Ben-Hur, Asa

doi:10.1186/s12864-017-4393-z

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

Journal Article · Fri Jan 05 00:00:00 EST 2018 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-017-4393-z· OSTI ID:1618555

Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy S. N.;

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.

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Research Organization:: Colorado State Univ., Fort Collins, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0010733

OSTI ID:: 1618555

Alternate ID(s):: OSTI ID: 1504903

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Vol. 19 Journal Issue: 1; ISSN 1471-2164

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 35 works

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59 BASIC BIOLOGICAL SCIENCES
Intron retention
Chromatin accessibility
DNase I hypersensitive sites

Additional file 1 of Exploring the relationship between intron retention and chromatin accessibility in plants Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy https://doi.org/10.6084/m9.figshare.5765037.v1 The current record is supplemented by this text	text	January 2018
Additional file 2 of Exploring the relationship between intron retention and chromatin accessibility in plants Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy https://doi.org/10.6084/m9.figshare.5765052.v1 The current record is supplemented by this dataset	dataset	January 2018
Additional file 3 of Exploring the relationship between intron retention and chromatin accessibility in plants Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy https://doi.org/10.6084/m9.figshare.5765073.v1 The current record is supplemented by this dataset	dataset	January 2018
Exploring the relationship between intron retention and chromatin accessibility in plants Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy https://doi.org/10.6084/m9.figshare.c.3970362.v1 The current record is supplemented by this collection	collection	January 2018
Additional file 1 of Exploring the relationship between intron retention and chromatin accessibility in plants Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy https://doi.org/10.6084/m9.figshare.5765037 The current record is supplemented by this text	text	January 2018
Additional file 2 of Exploring the relationship between intron retention and chromatin accessibility in plants Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy https://doi.org/10.6084/M9.FIGSHARE.5765052 The current record is supplemented by this dataset	dataset	January 2018
Additional file 3 of Exploring the relationship between intron retention and chromatin accessibility in plants Ullah, Fahad; Hamilton, Michael; Reddy, Anireddy https://doi.org/10.6084/m9.figshare.5765073 The current record is supplemented by this dataset	dataset	January 2018