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Genomic imprinting of the metabolic regulator gene Klf14 is regulated by a paternal sub-TAD anchored at Mest [4C-seq]

ABSTRACT: KLF14 acts as a master regulator of gene expression in adipose tissue and variants at the human KLF14 gene show reproducible association with type 2 diabetes and metabolic syndrome. Risk alleles are only pathological when maternally inherited, consistent with the observation that KLF14/Klf14 is a maternally-expressed imprinted gene in human and mouse. However, how genomic imprinting is regulated at this important locus is currently unknown. In both species, KLF14/Klf14 is located ~200 kb away from the paternally expressed imprinted gene MEST/Mest, regulated by a maternal gametic differentially methylated region (gDMR) at its promoter. Although the Klf14 promoter is unmethylated in most tissues, maternally-inherited DNA methylation marks are paradoxically required for Klf14 expression. Here, we show that Mest and Klf14 reside within the same topologically associating domain (TAD) in embryonic stem cells (ESCs), defined by biallelic CTCF binding at the boundaries. Using allele-specific 4C-seq, we show that CTCF binding to the unmethylated Mest gDMR generates a paternal allele-specific sub-TAD encompassing Klf14. CRISPR-Cas9 deletions of the paternal Mest promoter region in ESCs and in vivo in mutant mice result in loss of Mest expression and acquisition of biallelic expression at Klf14. By analyzing epigenetic marks and chromatin looping in the Klf14-expressing pituitary cells, we identify a putative enhancer element shared by Mest and Klf14, providing a mechanistic model for the regulation of Klf14 imprinting. This work defines a new role for the Mest maternally methylated gDMR, revealing that it exerts long-range effects via allele-specific modulation of TAD structures and acts as an imprinting control region in the regulation of Klf14 imprinting.

ORGANISM(S): Mus musculus

PROVIDER: GSE207164 | GEO | 2026/09/06

REPOSITORIES: GEO

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Project description:<p>Cardiac fibrosis, characterized by excessive extracellular matrix (ECM) deposition in the myocardium, is a critical target for heart disease treatments. Pw1 (paternally expressed gene 3) is an imprinted gene expressed from the paternally allele, and de novo purine biosynthesis (DNPB) is a crucial pathway for nucleotide synthesis. However, the roles of PW1 and DNPB in ECM production by cardiac fibroblasts during myocardial ischemia are not yet understood. To induce myocardial damage, we performed left anterior descending coronary artery ligation. We generated Pw1CreER-2A-eGFP and Pw12A-CreER knock-in mouse lines to evaluate the expression of the two Pw1 alleles in normal and injured hearts. Bisulfite sequencing was employed to analyze the DNA methylation of the Pw1 imprinting control region. We identified the phosphoribosylformylglycinamidine synthase (Pfas) gene, encoding the DNPB enzyme PFAS, as a direct target of PW1 using chromatin immunoprecipitation sequencing and real-time quantitative polymerase chain reaction. The role of DNPB in ECM production and cardiac fibrosis post-injury was examined in vitro using cultured cardiac fibroblasts and in vivo with Pfas-deficient mice. Our study demonstrates that myocardial infarction reduces DNA methylation at the imprinting control region of the maternally imprinted gene Pw1, triggering a switch from monoallelic imprinting to biallelic expression of Pw1 in cardiac fibroblasts. In activated cardiac fibroblasts, increased Pw1 expression promotes purine biosynthesis and induces ECM production by transcriptionally activating the DNPB factor Pfas. Notably, we identified that DNPB is essential for ECM production in activated fibroblasts and that loss of Pfas in fibroblasts limits cardiac fibrosis and improves heart function after heart injury. This study reveals that post-injury, the imprinting of Pw1 is disrupted, highlighting a novel role for the downstream DNPB pathway in cardiac fibrogenesis. Targeting DNPB presents a promising therapeutic strategy for improving cardiac repair following injury.</p>

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Genomic imprinting of the metabolic regulator gene Klf14 is regulated by a paternal sub-TAD anchored at Mest [4C-seq]

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