scholarly journals Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Wu-yi Liu ◽  
Chun-jiang Zhao
Keyword(s):  
Transcription Factor ◽  
Phylogenetic Analyses ◽  
Bhlh Transcription Factor ◽  
Transcription Factor Family ◽  
Early Date ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

scholarly journals Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis

2021 ◽  
Vol 22 (13) ◽  
pp. 7152
Author(s):  
Yaqi Hao ◽  
Xiumei Zong ◽  
Pan Ren ◽  
Yuqi Qian ◽  
Aigen Fu
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Target Genes ◽  
Gene Families ◽  
Bhlh Transcription Factor ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Wide Range ◽  
Range Of Functions ◽  
Eukaryotic Organisms

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor gene families in Arabidopsis thaliana, and contains a bHLH motif that is highly conserved throughout eukaryotic organisms. Members of this family have two conserved motifs, a basic DNA binding region and a helix-loop-helix (HLH) region. These proteins containing bHLH domain usually act as homo- or heterodimers to regulate the expression of their target genes, which are involved in many physiological processes and have a broad range of functions in biosynthesis, metabolism and transduction of plant hormones. Although there are a number of articles on different aspects to provide detailed information on this family in plants, an overall summary is not available. In this review, we summarize various aspects of related studies that provide an overview of insights into the pleiotropic regulatory roles of these transcription factors in plant growth and development, stress response, biochemical functions and the web of signaling networks. We then provide an overview of the functional profile of the bHLH family and the regulatory mechanisms of other proteins.

scholarly journals Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

2020 ◽  
Author(s):  
Songfeng Diao ◽  
Hong Liu ◽  
Zhongrui Lv ◽  
Caiyun He ◽  
Aiguo Duan ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Gene Families ◽  
Sea Buckthorn ◽  
Bhlh Transcription Factor ◽  
Systematic Analysis ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
A Genome

Abstract Background The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, organ development, and stress responses. However, limited studies are available on the gene family in sea buckthorn. Results In this study, we focused on 144 HrbHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 15 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 108 HrbHLH genes that expressed in five sea buckthorn tissue, including root nodule, root, leaf, stem and fruit. Furthermore, we found 11 increased expressed HrbHLH genes during sea buckthorn fruit development. We validated the expression pattern of HrbHLH genes using reverse transcription quantitative real-time PCR. Conclusions This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms. We performed a genome-wide, systematic analysis of bHLH proteins in sea buckthorn. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs.

scholarly journals Genome-wide Identification, Evolution and Expression Analysis of Basic Helix-loop-helix (bHLH) Gene Family in Barley (Hordeum vulgare L.)

2020 ◽  
Vol 21 (8) ◽  
pp. 624-644
Author(s):  
Qinglin Ke ◽  
Wenjing Tao ◽  
Tingting Li ◽  
Wenqiu Pan ◽  
Xiaoyun Chen ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Expression Analysis ◽  
Expression Profiles ◽  
Regulatory Function ◽  
Bhlh Transcription Factor ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
A Genome ◽  
Bhlh Genes

Background: The basic helix-loop-helix (bHLH) transcription factor is one of the most important gene families in plants, playing a key role in diverse metabolic, physiological, and developmental processes. Although it has been well characterized in many plants, the significance of the bHLH family in barley is not well understood at present. Methods: Through a genome-wide search against the updated barley reference genome, the genomic organization, evolution and expression of the bHLH family in barley were systematically analyzed. Results: We identified 141 bHLHs in the barley genome (HvbHLHs) and further classified them into 24 subfamilies based on phylogenetic analysis. It was found that HvbHLHs in the same subfamily shared a similar conserved motif composition and exon-intron structures. Chromosome distribution and gene duplication analysis revealed that segmental duplication mainly contributed to the expansion of HvbHLHs and the duplicated genes were subjected to strong purifying selection. Furthermore, expression analysis revealed that HvbHLHs were widely expressed in different tissues and also involved in response to diverse abiotic stresses. The co-expression network was further analyzed to underpin the regulatory function of HvbHLHs. Finally, 25 genes were selected for qRT-PCR validation, the expression profiles of HvbHLHs showed diverse patterns, demonstrating their potential roles in relation to stress tolerance regulation. Conclusion: This study reported the genome organization, evolutionary characteristics and expression profile of the bHLH family in barley, which not only provide the targets for further functional analysis, but also facilitate better understanding of the regulatory network bHLH genes involved in stress tolerance in barley.

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