Sangam: A Confluence of Knowledge Streams

Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells

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dc.creator Lyu, Pengcheng
dc.creator Settlage, Robert E.
dc.creator Jiang, Honglin
dc.date 2021-12-20T12:43:36Z
dc.date 2021-12-20T12:43:36Z
dc.date 2021-12-16
dc.date 2021-12-19T04:10:18Z
dc.date.accessioned 2023-03-01T18:54:36Z
dc.date.available 2023-03-01T18:54:36Z
dc.identifier BMC Genomics. 2021 Dec 16;22(1):901
dc.identifier http://hdl.handle.net/10919/107129
dc.identifier https://doi.org/10.1186/s12864-021-08224-7
dc.identifier.uri http://localhost:8080/xmlui/handle/CUHPOERS/281846
dc.description Background Satellite cells are the myogenic precursor cells in adult skeletal muscle. The objective of this study was to identify enhancers and transcription factors that regulate gene expression during the differentiation of bovine satellite cells into myotubes. Results Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) was performed to identify genomic regions where lysine 27 of H3 histone is acetylated (H3K27ac), i.e., active enhancers, from bovine satellite cells before and during differentiation into myotubes. A total of 19,027 and 47,669 H3K27ac-marked enhancers were consistently identified from two biological replicates of before- and during-differentiation bovine satellite cells, respectively. Of these enhancers, 5882 were specific to before-differentiation, 35,723 to during-differentiation, and 13,199 common to before- and during-differentiation bovine satellite cells. Whereas most of the before- or during-differentiation-specific H3K27ac-marked enhancers were located distally to the transcription start site, the enhancers common to before- and during-differentiation were located both distally and proximally to the transcription start site. The three sets of H3K27ac-marked enhancers were associated with functionally different genes and enriched with different transcription factor binding sites. Specifically, many of the H3K27ac-marked enhancers specific to during-differentiation bovine satellite cells were associated with genes involved in muscle structure and development, and were enriched with binding sites for the MyoD, AP-1, KLF, TEAD, and MEF2 families of transcription factors. A positive role was validated for Fos and FosB, two AP-1 family transcription factors, in the differentiation of bovine satellite cells into myotubes by siRNA-mediated knockdown. Conclusions Tens of thousands of H3K27ac-marked active enhancers have been identified from bovine satellite cells before or during differentiation. These enhancers contain binding sites not only for transcription factors whose role in satellite cell differentiation is well known but also for transcription factors whose role in satellite cell differentiation is unknown. These enhancers and transcription factors are valuable resources for understanding the complex mechanism that mediates gene expression during satellite cell differentiation. Because satellite cell differentiation is a key step in skeletal muscle growth, the enhancers, the transcription factors, and their target genes identified in this study are also valuable resources for identifying and interpreting skeletal muscle trait-associated DNA variants in cattle.
dc.description Published version
dc.format application/pdf
dc.format application/pdf
dc.language en
dc.rights Creative Commons Attribution 4.0 International
dc.rights http://creativecommons.org/licenses/by/4.0/
dc.rights The Author(s)
dc.title Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells
dc.title BMC Genomics
dc.type Article - Refereed
dc.type Text


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