Genome-Wide Identification of Histone Acetylation (H4K12ac) and Methylation (H3K9me2) Marks in Switchgrass (Panicum virgatum L.)

In eukaryotes gene expression involves the complex interplay among transcription factors and chromatin proteins that compact chromosomal DNA into confined space of the nucleus that either trigger the activation or repression of genes. At the whole-genome level, the molecular mechanism of regulation of gene expression is an important process where the accessibility of DNA sequences is determined by the structure of chromatin. Transcription is an important process that is regulated by both genetic and epigenetic factors. Epigenetic marks, such as histone modification and DNA methylation play an important role in the regulation of transcription and in various biological processes such as development, regeneration, and oncogenesis. In plants, there is an increasing evidence of regulation of gene expression by chromatin modification. Chromatin modification is an epigenetic process that has evolved among diverse eukaryotes enhancing the capabilities of the DNA code.

Switchgrass (Panicum virgatum), is a perennial, warm-season grass. It is commonly used for livestock feed, erosion control, wildlife, and recently as a biofuel source. It is native to the continental United States, and it is classified as a C4 plant. Its ability to have a high yield potential in various geographical areas and on marginal land, plus its low nutrient requirements and few pest and erosion problems, made it a very marketable crop worth researching. The genomic resources including bacterial artificial chromosomes (BAC) library, expressed sequence tags (EST), and exome sequences have been available for switchgrass. The molecular markers for the identification of the genetic diversity and germplasm classification have been reported in switchgrass. The complete switchgrass genetic maps have been available. There are few transcriptomic reports are also available for switchgrass. Though several genomic resources available, the genome-wide distribution of histone-specific modification haven’t reported yet in switchgrass. In this study, we report the genome-wide profiling of histone methylation H3K9_me2 and histone acetylation H4K12_ac by using ChIP-Seq in switchgrass.