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Title: Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.)

Abstract

Background: Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. Results: This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. Conclusions: The genome-wide histone modifications reported here can be utilized in understanding the regulation of genesmore » important in the phenylpropanoid–monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [5];  [1]
  1. Delaware State Univ., Dover, DE (United States). College of Agriculture and Related Sciences. Molecular Genetics and Epigenomics Lab.
  2. Alabama A&M Univ., Normal, AL (United States). Life and Natural Sciences. Molecular Biology and Bioinformatics Lab.
  3. (. Kal) [Delaware State Univ., Dover, DE (United States). College of Agriculture and Related Sciences. Molecular Genetics and Epigenomics Lab.; Delaware State Univ., Dover, DE (United States). Center for Integrated Biological and Environmental Research
  4. Noble Research Ins., Ardmore, OK (United States)
  5. Purdue Univ., West Lafayette, IN (United States). Bioinformatics Core
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1626825
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 20; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity; Switchgrass; Epigenome; ChIP-Seq; Histone modifications; Differential binding; Phenylpropanoid pathway; And monolignols

Citation Formats

Ayyappan, Vasudevan, Sripathi, Venkateswara R., Kalavacharla, Venu, Saha, Malay C., Thimmapuram, Jyothi, Bhide, Ketaki P., and Fiedler, Elizabeth. Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). United States: N. p., 2019. Web. https://doi.org/10.1186/s12864-019-6038-x.
Ayyappan, Vasudevan, Sripathi, Venkateswara R., Kalavacharla, Venu, Saha, Malay C., Thimmapuram, Jyothi, Bhide, Ketaki P., & Fiedler, Elizabeth. Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.). United States. https://doi.org/10.1186/s12864-019-6038-x
Ayyappan, Vasudevan, Sripathi, Venkateswara R., Kalavacharla, Venu, Saha, Malay C., Thimmapuram, Jyothi, Bhide, Ketaki P., and Fiedler, Elizabeth. Thu . "Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.)". United States. https://doi.org/10.1186/s12864-019-6038-x. https://www.osti.gov/servlets/purl/1626825.
@article{osti_1626825,
title = {Genome-wide identification of histone methylation (H3K9me2) and acetylation (H4K12ac) marks in two ecotypes of switchgrass (Panicum virgatum L.)},
author = {Ayyappan, Vasudevan and Sripathi, Venkateswara R. and Kalavacharla, Venu and Saha, Malay C. and Thimmapuram, Jyothi and Bhide, Ketaki P. and Fiedler, Elizabeth},
abstractNote = {Background: Histone modifications play a significant role in the regulation of transcription and various biological processes, such as development and regeneration. Though a few genomic (including DNA methylation patterns) and transcriptomic studies are currently available in switchgrass, the genome-wide distribution of histone modifications has not yet been studied to help elucidate gene regulation and its application to switchgrass improvement. Results: This study provides a comprehensive epigenomic analyses of two contrasting switchgrass ecotypes, lowland (AP13) and upland (VS16), by employing chromatin immunoprecipitation sequencing (ChIP-Seq) with two histone marks (suppressive- H3K9me2 and active- H4K12ac). In this study, most of the histone binding was in non-genic regions, and the highest enrichment was seen between 0 and 2 kb regions from the transcriptional start site (TSS). Considering the economic importance and potential of switchgrass as a bioenergy crop, we focused on genes, transcription factors (TFs), and pathways that were associated with C4-photosynthesis, biomass, biofuel production, biotic stresses, and abiotic stresses. Using quantitative real-time PCR (qPCR) the relative expression of five genes selected from the phenylpropanoid-monolignol pathway showed preferential binding of acetylation marks in AP13 rather than in VS16. Conclusions: The genome-wide histone modifications reported here can be utilized in understanding the regulation of genes important in the phenylpropanoid–monolignol biosynthesis pathway, which in turn, may help understand the recalcitrance associated with conversion of biomass to biofuel, a major roadblock in utilizing lignocellulosic feedstocks.},
doi = {10.1186/s12864-019-6038-x},
journal = {BMC Genomics},
number = 1,
volume = 20,
place = {United States},
year = {2019},
month = {8}
}

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