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Article

Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families

1
Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
2
Department of Mathematics, Tulane University, New Orleans, LA 70118, USA
3
Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA 70112, USA
*
Author to whom correspondence should be addressed.
Received: 24 December 2019 / Revised: 21 January 2020 / Accepted: 28 January 2020 / Published: 30 January 2020
(This article belongs to the Special Issue Recent Advances in Biological Methylation)
Much remains to be discovered about the intersection of tissue-specific transcription control and the epigenetics of skeletal muscle (SkM), a very complex and dynamic organ. From four gene families, Leucine-Rich Repeat Containing (LRRC), Oxysterol Binding Protein Like (OSBPL), Ankyrin Repeat and Socs Box (ASB), and Transmembrane Protein (TMEM), we chose 21 genes that are preferentially expressed in human SkM relative to 52 other tissue types and analyzed relationships between their tissue-specific epigenetics and expression. We also compared their genetics, proteomics, and descriptions in the literature. For this study, we identified genes with little or no previous descriptions of SkM functionality (ASB4, ASB8, ASB10, ASB12, ASB16, LRRC14B, LRRC20, LRRC30, TMEM52, TMEM233, OSBPL6/ORP6, and OSBPL11/ORP11) and included genes whose SkM functions had been previously addressed (ASB2, ASB5, ASB11, ASB15, LRRC2, LRRC38, LRRC39, TMEM38A/TRIC-A, and TMEM38B/TRIC-B). Some of these genes have associations with SkM or heart disease, cancer, bone disease, or other diseases. Among the transcription-related SkM epigenetic features that we identified were: super-enhancers, promoter DNA hypomethylation, lengthening of constitutive low-methylated promoter regions, and SkM-related enhancers for one gene embedded in a neighboring gene (e.g., ASB8-PFKM, LRRC39-DBT, and LRRC14B-PLEKHG4B gene-pairs). In addition, highly or lowly co-expressed long non-coding RNA (lncRNA) genes probably regulate several of these genes. Our findings give insights into tissue-specific epigenetic patterns and functionality of related genes in a gene family and can elucidate normal and disease-related regulation of gene expression in SkM. View Full-Text
Keywords: skeletal muscle; heart; myoblasts; enhancer; super-enhancers; DNA methylation; Leucine-rich Repeat; Oxysterol-Binding Protein-Like; Ankyrin Repeat and Suppressor of Cytokine Signaling Box; transmembrane protein skeletal muscle; heart; myoblasts; enhancer; super-enhancers; DNA methylation; Leucine-rich Repeat; Oxysterol-Binding Protein-Like; Ankyrin Repeat and Suppressor of Cytokine Signaling Box; transmembrane protein
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MDPI and ACS Style

Ehrlich, K.C.; Lacey, M.; Ehrlich, M. Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families. Epigenomes 2020, 4, 1. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4010001

AMA Style

Ehrlich KC, Lacey M, Ehrlich M. Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families. Epigenomes. 2020; 4(1):1. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4010001

Chicago/Turabian Style

Ehrlich, Kenneth C.; Lacey, Michelle; Ehrlich, Melanie. 2020. "Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families" Epigenomes 4, no. 1: 1. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes4010001

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