Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families
Abstract
:1. Introduction
2. Results
2.1. The SkM-Related Genes and Their Gene Families Chosen for Epigenetic Analysis
2.2. LRRC Genes that are Preferentially Expressed in SkM Display Muscle-Associated Enhancers or Super-Enhancers Containing Hypomethylated DNA Regions
2.3. Preferential Expression of OSBPL6 and OSBPL11 in SkM was Associated with SkM-Specific Enhancer Chromatin Mostly within the Gene Body or Upstream
2.4. Nine of the 18 ASB Genes Display SkM or SkM/Heart Preferential Expression that was Associated with Loss of DNA Methylation in or Adjacent to the Promoter
2.5. SkM-Associated Genes in the TMEM Family Exhibited SkM-Specific Intragenic, Intergenic, or Neighboring-Gene Enhancer Chromatin
2.6. Related Sequences of the Proteins Encoded by Some of the Studied SkM or SkM/Heart Genes Suggest Functional Similarities
3. Discussion
4. Materials and Methods
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Epigenetic Patterns Associated with SkM | ASB Family (9 Genes) | LRRC Family (6 Genes) | OSBPL Family (2 Genes) | TMEM Family (4 Genes) |
---|---|---|---|---|
Prom chrom assoc with expression in SkM | ASB2, 4, 5, 10, 11, 15 | LRRC2, 14Bb, 20, 30, 38,39 | none | TMEM52, 233 |
SkM-assoc prom DNA hypometh | ASB4, 5, 10, 11, 12, 15 | LRRC30, 39 | none | none |
constit LMR at TSS | ASB2, 8, 16 | LRRC2, 14B, 20, 38 | OSBPL11 | none |
CpG island at prom | ASB8 | LRRC14B, 20, 38 | OSBPL6, 11 | TMEM38A, 38B, 52 |
Super-enhancer | ASB2,5, 8, 11 | LRRC14B, 20, 38 | none | TMEM52 |
SkM enh chrom in adjacent gene | ASB2, 8, 10, 16 | LRRC14B, 39 | none | TMEM52; 38A |
Intragenic enhancer chrom | ASB2, 4, 5, 8, 10, 11, 12, 15, 16 | LRRC2, 14B, 20, 38, 39 | OSBPL6, 11 | TMEM38A, 38B, 52, 233 |
Intergenic proximal enh chrom | ASB2, 5, 8, 10, 12, 15, 16 | LRRC14B, 30, 38 | OSBPL11 | TMEM52 |
Intergenic distal enh chrom | ASB2, 4, 10, 15, 16 | LRRC14B, 30 | OSBPL11 | TMEM38A, 38B, 233 |
DNA hypometh in SkM-assoc enh chrom | ASB2, 5, 10, 11, 12, 15, 16 | LRRC2, 14B, 20, 30, 38, 39 | OSBPL6, 11 | TMEM38A, 38B, 52, 233 |
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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://doi.org/10.3390/epigenomes4010001
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://doi.org/10.3390/epigenomes4010001
Chicago/Turabian StyleEhrlich, Kenneth C., Michelle Lacey, and Melanie Ehrlich. 2020. "Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families" Epigenomes 4, no. 1: 1. https://doi.org/10.3390/epigenomes4010001
APA StyleEhrlich, K. C., Lacey, M., & Ehrlich, M. (2020). Epigenetics of Skeletal Muscle-Associated Genes in the ASB, LRRC, TMEM, and OSBPL Gene Families. Epigenomes, 4(1), 1. https://doi.org/10.3390/epigenomes4010001