451 Identification and characterization of euchromatic regions associated with gene expression and intramuscular fat in Nelore cattle.

Abstract

In eukaryotes, DNA is organized along with histones in nucleoprotein complexes known as chromatin, which has nucleosomes as their fundamental unit. Chromatin exists in two forms: euchromatin, corresponding to a lightly condensed structure and an easily transcribed region, and heterochromatin, a highly condensed and transcriptionally silent region. Therefore, the chromatin compaction degree interferes with regulation of gene expression, and nucleosomes act as gene silencers. In this context, using Assay for Transposase-Accessible Chromatin technique (ATAC-seq), the aims of the present study were to identify, map and characterize euchromatin regions in Longissimus dorsi muscle of Nellore cattle to understand if these regions are associated with gene expression and intramuscular fat content. Different transposase-treated nuclei concentrations were tested: 50 thousand, 75 thousand and 100 thousand, and their nucleosomal periodicity was analyzed to check the efficiency of ATAC-seq enzymatic activity. From these, 6,811, 11,121, and 11,473 euchromatin peaks were respectively found by using Model-based Analysis of ChIP-Seq (MACS2). A total of 6,212 open chromatin regions were coincident among the three nuclei concentrations, and this data was used in subsequent analyzes. Enrichment analysis performed using package RegioneR in R, considering significance of p < 0.05, revealed over-representation of peaks in 1) transcription start sites of genes expressed in skeletal muscle; 2) differentially expressed genes (GDE) associated with intramuscular fat content; 3) expression quantitative trait loci (eQTL) identified in skeletal muscle tissue. Our results indicate that skeletal muscle regulatory regions identified by ATAC-seq are involved in the control of gene expression and intramuscular fat content in cattle.