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Title: Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.

Abstract

Abiotic stresses including drought are major limiting factors of crop yields and cause significant crop losses. Acquisition of stress tolerance to abiotic stresses requires coordinated regulation of a multitude of biochemical and physiological changes, and most of these changes depend on alterations in gene expression. The goal of this work is to perform global analysis of differential regulation of gene expression and alternative splicing, and their relationship with chromatin landscape in drought sensitive and tolerant cultivars. our Iso-Seq study revealed transcriptome-wide full-length isoforms at an unprecedented scale with over 11000 novel splice isoforms. Additionally, we uncovered alternative polyadenylation sites of ~11000 expressed genes and many novel genes. Overall, Iso-Seq results greatly enhanced sorghum gene annotations that are not only useful in analyzing all our RNA-seq, ChIP-seq and ATAC-seq data but also serve as a great resource to the plant biology community. Our studies identified differentially expressed genes and splicing events that are correlated with the drought-resistant phenotype. An association between alternative splicing and chromatin accessibility was also revealed. Several computational tools developed here (TAPIS and iDiffIR) have been made freely available to the research community in analyzing alternative splicing and differential alternative splicing.

Authors:
 [1];  [1]
  1. Colorado State Univ., Fort Collins, CO (United States)
Publication Date:
Research Org.:
Colorado State Univ., Fort Collins, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1409851
Report Number(s):
Fianl Report_DOE_CSU_SC0010733
DOE Contract Number:
SC0010733
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS

Citation Formats

Reddy, Anireddy, and Ben-Hur, Asa. Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.. United States: N. p., 2017. Web. doi:10.2172/1409851.
Reddy, Anireddy, & Ben-Hur, Asa. Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.. United States. doi:10.2172/1409851.
Reddy, Anireddy, and Ben-Hur, Asa. 2017. "Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.". United States. doi:10.2172/1409851. https://www.osti.gov/servlets/purl/1409851.
@article{osti_1409851,
title = {Global analysis of epigenetic regulation of gene expression in response to drought stress in Sorghum.},
author = {Reddy, Anireddy and Ben-Hur, Asa},
abstractNote = {Abiotic stresses including drought are major limiting factors of crop yields and cause significant crop losses. Acquisition of stress tolerance to abiotic stresses requires coordinated regulation of a multitude of biochemical and physiological changes, and most of these changes depend on alterations in gene expression. The goal of this work is to perform global analysis of differential regulation of gene expression and alternative splicing, and their relationship with chromatin landscape in drought sensitive and tolerant cultivars. our Iso-Seq study revealed transcriptome-wide full-length isoforms at an unprecedented scale with over 11000 novel splice isoforms. Additionally, we uncovered alternative polyadenylation sites of ~11000 expressed genes and many novel genes. Overall, Iso-Seq results greatly enhanced sorghum gene annotations that are not only useful in analyzing all our RNA-seq, ChIP-seq and ATAC-seq data but also serve as a great resource to the plant biology community. Our studies identified differentially expressed genes and splicing events that are correlated with the drought-resistant phenotype. An association between alternative splicing and chromatin accessibility was also revealed. Several computational tools developed here (TAPIS and iDiffIR) have been made freely available to the research community in analyzing alternative splicing and differential alternative splicing.},
doi = {10.2172/1409851},
journal = {},
number = ,
volume = ,
place = {United States},
year = 2017,
month =
}

Technical Report:

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