Genome-wide identification of histone methylation (H3K9 me2 ) and acetylation (H4K12 ac ) marks in two ecotypes of switchgrass (Panicum virgatum L.).

Autor: Ayyappan V; Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA., Sripathi VR; Molecular Biology and Bioinformatics Laboratory, College of Agricultural, Life and Natural Sciences, Alabama A&M University, Normal, AL, USA., Kalavacharla VK; Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA. vkalavacharla@desu.edu.; Center for Integrated Biological and Environmental Research, Delaware State University, Dover, DE, USA. vkalavacharla@desu.edu., Saha MC; Noble Research Institute, Ardmore, OK, USA., Thimmapuram J; Bioinformatics Core, Purdue University, West Lafayette, IN, USA., Bhide KP; Bioinformatics Core, Purdue University, West Lafayette, IN, USA., Fiedler E; Molecular Genetics and Epigenomics Laboratory, College of Agriculture and Related Sciences, Delaware State University, Dover, DE, USA.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2019 Aug 22; Vol. 20 (1), pp. 667. Date of Electronic Publication: 2019 Aug 22.
DOI: 10.1186/s12864-019-6038-x
Abstrakt: 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- H3K9 me2 and active- H4K12 ac ). 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.
Databáze: MEDLINE
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