Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo

Abstract

Bromodomain (BRD) is an evolutionarily conserved protein–protein interaction module that is critical in gene regulation, cellular homeostasis, and epigenetics. This study aimed to conduct an identification, evolution, and expression analysis of the BRD gene family in the swamp buffalo (Bubalus bubalis). A total of 101 BRD protein sequences deduced from 22 BRD genes were found in the buffalo genome. The BRD proteins were classified into six groups based on phylogenetic relationships, conserved motifs, and conserved domains. The BRD genes were irregularly distributed in 13 chromosomes. Collinearity analysis revealed 20 BRD gene pairs that had remarkable homologous relationships between the buffalo and cattle, although no tandem or segmental duplication event was found in the buffalo BRD genes. Comparative transcriptomics using a 10x sequencing platform analysis showed that 22 BRD genes were identified in the Sertoli cells (SCs) at different developmental stages of buffalo. Further, the mRNA expression levels of bromodomain and the extraterminal (BET) family in SCs at the pubertal stage were higher than that at the prepubertal stage of buffalo. However, the SMARCA2, PHIP, BRD9, and TAF1 genes exhibited the opposite trend. The maturation process of SCs may be regulated by the BRD family members expressed differentially in SCs at different developmental stages of buffalo. In summary, our findings provide an understanding of the evolutionary, structural, and functional properties of the buffalo BRD family members, and further characterize the function of the BRD family in the maturation of SCs. It also provides a theoretical basis for further understanding in the future of the mechanism of SCs regulating spermatogenesis.

Genome-Wide Identification and Characterization of the BRD Family in Nile Tilapia (Oreochromis niloticus)

“…Previously, 43 different BRDs were identified and divided into eight subfamilies according to the sequence similarity in humans [ 3 , 5 ]. However, 22 BRDs were identified and classified into six groups on the basis of the conserved sequences in buffalo [ 9 ], which was incomplete and inconclusive. Therefore, the number and evolution of the BRD family require clarification.…”

“…For example, these proteins can act as a scaffold for larger protein complexes to facilitate their assembly, function as transcription factors and transcriptional co-regulators [ 5 ], and engage in various chromatin modifications [ 6 , 7 ]. Bromodomain was first identified in the fruit fly [ 8 ], and later in humans [ 3 , 5 ] and the buffalo [ 9 ]. However, to date, no study was systematically performed to analyze the evolution of the BRD family.…”