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.
- 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:
- Journal Article: 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},
issn = {1471-2164},
number = 1,
volume = 19,
place = {United States},
year = {2018},
month = {1}
}
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Figures / Tables:
Table 1: Enrichment of DHSs in IR and IE events
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Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.