Allele-specific regulatory mechanisms analysis from RNA-seq, ATAC-seq and ChIP-seq data in bovine muscle

Abstract

International initiatives have been conducted to understand the genome-to-phenome relationship. The Functional Annotation of Animal Genomes (FAANG) is a consortium working to discover basic knowledge of genome function. This initiative generated epigenetics and expression data from various tissues and species that enable the identification of regulatory elements. The allele-specific expression (ASE) results from cis-regulation and epigenetic modulation on only one haplotype of a diploid genomic segment, triggering differences in gene expression and phenotype. Previously, we identified thousands of ASE SNPs and putative cis-regulatory variants in Nelore cattle, co-located with epigenetic marks from FAANG, pointing out that an allelic-dependent approach may help understand the epigenetic regulation in each allele. In a second study, we showed that for 1,4 K ASE SNPs, the allelic imbalance was biased towards muscle-related phenotypes (DASE SNPs). Thus, in this Internship Project, we aim to identify ASE SNPs from the FAANG's RNA-seq data to compare them with ASE and DASE SNPs obtained in Nelore cattle. We will search for allele-specific chromatin accessibility regions, allele-specific histone modifications, and allele-specific transcription factor binding from that data, to identify potential regulatory mechanisms affecting the transcription of genes with overlapped ASE SNPs from these two experiments. We hypothesize that we can increase the knowledge about the regulatory machinery affecting relevant genes for important economic traits. (AU)