Genome-wide identification, classification, and functional analysis of the basic helix–loop–helix transcription factors in the cattle, Bos Taurus

Abstract

The basic helix-loop-helix (bHLH) transcription factors (TFs) form a huge superfamily and play crucial roles in many essential developmental, genetic, and physiological-biochemical processes of eukaryotes. In total, 109 putative bHLH TFs were identified and categorized successfully in the genomic databases of cattle, Bos Taurus, after removing redundant sequences and merging genetic isoforms. Through phylogenetic analyses, 105 proteins among these bHLH TFs were classified into 44 families with 46, 25, 14, 3, 13, and 4 members in the high-order groups A, B, C, D, E, and F, respectively. The remaining 4 bHLH proteins were sorted out as 'orphans.' Next, these 109 putative bHLH proteins identified were further characterized as significantly enriched in 524 significant Gene Ontology (GO) annotations (corrected P value ≤ 0.05) and 21 significantly enriched pathways (corrected P value ≤ 0.05) that had been mapped by the web server KOBAS 2.0. Furthermore, 95 bHLH proteins were further screened and analyzed together with two uncharacterized proteins in the STRING online database to reconstruct the protein-protein interaction network of cattle bHLH TFs. Ultimately, 89 bHLH proteins were fully mapped in a network with 67 biological process, 13 molecular functions, 5 KEGG pathways, 12 PFAM protein domains, and 25 INTERPRO classified protein domains and features. These results provide much useful information and a good reference for further functional investigations and updated researches on cattle bHLH TFs.

Association between the expression of carbonic anhydrase�II and clinicopathological features of hepatocellular carcinoma

“…Gene analysis based on interaction between genes can effectively produce biological information, providing valid scientific reference for the diagnosis, treatment and improvement of prognosis. Following the rapid development of genomic science, a large quantity of genomic data and gene expression data have provided a novel basis for the investigation of gene-gene and gene-environment interactions (23)(24)(25). By analyzing the existing data through systems biology approaches, it is possible to investigate the association between gene function, protein interaction and the occurrence of diseases, and construct a detailed network of the occurrence and progression of diseases.…”

GROWTH AND DEVELOPMENT SYMPOSIUM: STEM AND PROGENITOR CELLS IN ANIMAL GROWTH: The regulation of beef quality by resident progenitor cells1

“…In addition, TCF4 was identified as an indispensable mediator in the inhibitory effect of tumor necrosis factor α (TNFα) on adipogenesis (Cawthorn et al, 2007), suggesting that TCF4 is pro-fibrogenic and is important for the fibrogenic fate determination of FAPs. The expression of TCF4 in cattle has not been extensively studied possibly due to the presence of large number of TCF4 transcription isoforms in cattle (Li and Liu, 2017). However, a study reported a possible single nucleotide polymorphism (SNP) effect of TCF4 on the lean mass of beef cattle (Zhang et al, 2018), which might be related to the reported role of TCF4 + fibroblasts in skeletal muscle development and growth (Mathew et al, 2011;Murphy et al, 2011).…”

Identification and Characterization of the Basic Helix-Loop-Helix Transcription Factor Family in Pinus massoniana

“…bHLH family members contain two highly conserved and different functional domains, namely, the basic region and the helix-loop-helix (HLH) region, with a total of approximately 50-60 amino acids [7]. The basic region consists of approximately 15 amino acids, is located at the N-terminus of the domain, and can recognize and bind the E-box and G-box.…”