Epigenetics of Muscle- and Brain-Specific Expression of KLHL Family Genes
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Abstract
KLHL and the related KBTBD genes encode components of the Cullin-E3 ubiquitin ligase complex and typically target tissue-specific proteins for degradation, thereby affecting differentiation, homeostasis, metabolism, cell signaling, and the oxidative stress response. Despite their importance in cell function and disease (especially, KLHL40, KLHL41, KBTBD13, KEAP1, and ENC1), previous studies of epigenetic factors that affect transcription were predominantly limited to promoter DNA methylation. Using diverse tissue and cell culture whole-genome profiles, we examined 17 KLHL or KBTBD genes preferentially expressed in skeletal muscle or brain to identify tissue-specific enhancer and promoter chromatin, open chromatin (DNaseI hypersensitivity), and DNA hypomethylation. Sixteen of the 17 genes displayed muscle- or brain-specific enhancer chromatin in their gene bodies, and most exhibited specific intergenic enhancer chromatin as well. Seven genes were embedded in super-enhancers (particularly strong, tissue-specific clusters of enhancers). The enhancer chromatin regions typically displayed foci of DNA hypomethylation at peaks of open chromatin. In addition, we found evidence for an intragenic enhancer in one gene upregulating expression of its neighboring gene, specifically for KLHL40/HHATL and KLHL38/FBXO32 gene pairs. Many KLHL/KBTBD genes had tissue-specific promoter chromatin at their 5′ ends, but surprisingly, two (KBTBD11 and KLHL31) had constitutively unmethylated promoter chromatin in their 3′ exons that overlaps a retrotransposed KLHL gene. Our findings demonstrate the importance of expanding epigenetic analyses beyond the 5′ ends of genes in studies of normal and abnormal gene regulation.
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KLHL40 and KLHL41 are clearest examples of ligases with tissue-specific expression in skeletal muscle.
“Among the clearest examples of ligases with tissue-specific expression are kelch-like family member 40 (KLHL40) and KLHL41 in skeletal muscle145”
From PROTAC targeted protein degraders: the past is prologue (2022) · cites this paper as [145]
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- Authors
- Ehrlich, K. C., Baribault, C., & Ehrlich, M.
- Affiliations
- Tulane University (US)
- Corresponding author
- Ehrlich, Melanie
- Venue
- International Journal of Molecular Sciences
- Publisher
- MDPI AG
- Published
- 2020-11-09
- Volume
- 21
- Issue
- 21
- Pages
- 8394
- ISSN
- 1422-0067 (ISSN-L)
- PMC
- PMC7672584
- OpenAlex
- W3093026272
- Cited by
- 35
- References
- 78
- Citations by year
- 2026: 5 · 2025: 9 · 2024: 5 · 2023: 6 · 2022: 6 · 2021: 3 · 2020: 1
- FWCI
- 1.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- International Journal of Molecular Sciences (publishedVersion, cc-by)
- Preprints.org (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (NS04885)
- Tulane Cancer Center (none)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- tissue-specific gene expression, skeletal muscle, brain, super-enhancers, DNA hypomethylation, open chromatin, DNase I hypersensitivity, promoter chromatin, intragenic enhancers, retrotransposition, gene expression regulation
- MeSH terms
- Adult, Aged, Brain, Cells, Cultured, Child, Preschool, Chromatin, Enhancer Elements, Genetic, Exons, Female, Gene Expression Regulation, Humans, Male, Middle Aged, Muscle Proteins, Promoter Regions, Genetic, Transcription, Genetic, Up-Regulation, Muscle, Skeletal, DNA Methylation, Epigenesis, Genetic, Adaptor Proteins, Signal Transducing, Epigenomics
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