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

Abstract

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.

Interconnection between molecular regulators in LMNA related muscular dystrophy

“…Downregulation of the Wnt signaling pathway, as well as the concentration of repressive chromatin marks in the differentiated state of mutants, could have influenced downstream effectors such as, transcription factors and cofactors. In line with this, we detected significant downregulation of the following transcription factors (mentioned in Figure 7), which directly or indirectly affect muscle differentiation in mutants, as indicated by a plethora of evidences : MEF2A (Kaushal et al 1994), MEF2C (Lin et al 1997), Rb1 (Novitch et al 1996, Schneider et al1994), Tead 4 (Benhaddou et al 2012), Asb5 (Ehrlich et al 2020), Asb 15 (Tee et al 2010), Bcl6 (Kumagai et al 1999), NR4A1 (Pan et al2019), Gli (Lin et al 2014), Nfatc2 (Armand et al2008), Clock (Andrewset al 2010).According to earlier studies, downregulated transcription factors are critical components of numerous signaling pathways, several of which were shown to be dysregulated in our investigation. Future study into how these pathways interact through co-ordinated molecular interactions will provide a clearer picture of the defective differentiation programme in lamin A-associated muscular dystrophy.…”

Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes

“…The intergenic and intragenic enhancer chromatin usually contained foci of DNA hypomethylation. Tissue-specific enhancer chromatin was more common than tissue-specific promoter chromatin, as has been found for some other gene families [16]. About half of these genes displayed SkM-or brain-associated Promoter-enhancer interactions that boost transcription initiation are mediated by looping of the enhancer to its target promoter, which may facilitate their sharing of bound TFs and cis-acting short-lived ncRNAs [36].…”

“…The most dramatic enhancer cooperation is seen in super-enhancers, which are large structures consisting of clusters of neighboring enhancers (or enhancers and promoters) that strongly upregulate expression of differentiation-related genes [27], including SkM-associated genes [15,16]. Seven of the 17 SkM-or brainassociated KLHL family genes exhibited expression-linked super-enhancers (Table 3).…”

“…The importance of having normal levels of expression of KLHL family genes is supported by siRNA knockdown or overexpression studies in which decreases or increases in protein levels of the KLHL family genes impacted normal cellular function (e.g., for KLHL40, KLHL41, KEAP1, ENC1 and KBTBD11 [30,[63][64][65][66]). Chromatin and DNA epigenetics are frequently involved in setting or maintaining gene expression levels [4,16,62]. In addition, fine-tuning of RNA abundance by downregulation at the post-transcriptional level is often mediated by miRNAs.…”

“…For quantitation of cell culture RNA-seq data, we determined the signal for each gene from ENCODE data [24] and from our analyses with Cufflinks [69,70]. For comparisons of RNA levels in myoblasts and myotubes, we used our previously generated data [16].…”