Cis-regulatory modules prediction in spliced genes associated with carcass and meat traits of Nelore cattle

The cis-regulatory modules are non-coding DNA regions responsible for controlling gene transcription and being involved in the anatomical and embryonic development of animal species. This study aimed to perform a prediction analysis of cis-regulatory modules in spliced genes associated, commonly, with ribeye area (REA) and intramuscular fat (IF) of Nelore cattle. For this, JuncBASE v.0.9 (Junction-Based Analysis of Splicing Events) software was used to identify and classify exon-centered alternative splicing events in the group of animals selected for REA and IF. The prediction of transcription factors and cis-regulatory modules was performed for the genes found using iRegulon v.1.3. The prediction analysis exhibited 45 cis-regulatory modules, of which module 11 had the highest number (N = 9) of binding sites shared commonly by 11 spliced genes and five transcription factors from the MEF2 family. These modules could potentially regulate spliced exons and, thus, contribute to the production of isoforms, which may be involved in essential pathways and biological processes involved in the evaluated animals muscular development and lipid metabolism.