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

被引:28
作者
Ehrlich, Kenneth C. [1 ]
Lacey, Michelle [2 ,3 ]
Ehrlich, Melanie [1 ,3 ]
机构
[1] Tulane Univ, Ctr Bioinformat & Genom, Hlth Sci Ctr, New Orleans, LA 70112 USA
[2] Tulane Univ, Dept Math, New Orleans, LA 70118 USA
[3] Tulane Univ, Tulane Canc Ctr, Hlth Sci Ctr, New Orleans, LA 70112 USA
基金
美国国家卫生研究院;
关键词
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; DNA METHYLATION; ANKYRIN REPEAT; SUPER-ENHANCERS; PROTEIN FAMILY; TRIC-B; DIFFERENTIATION; CHANNELS; MOUSE; MYOD; HYPOMETHYLATION;
D O I
10.3390/epigenomes4010001
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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.
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页数:22
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