Thorvaldsen Joanne L, Juan Aimee M, Lan Yemin, Krapp Christopher, Bartolomei Marisa S
University of Pennsylvania Perelman School of Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Philadelphia, Pennsylvania, United States of America.
PLoS Genet. 2025 Aug 29;21(8):e1011834. doi: 10.1371/journal.pgen.1011834. eCollection 2025 Aug.
Precise, monoallelic expression of imprinted genes is governed by cis regulatory elements called imprinting control regions (ICRs) and enhancer-promoter (E-P) interactions shaped by local chromatin architecture. The Igf2/H19 locus employs allele-specific CTCF binding at the ICR to instruct enhancer accessibility to maternal H19 and paternal Igf2 promoters. Here, we investigate the CTCF-bound centrally conserved domain (CCD), intergenic to H19 and Igf2, and an adjacent widely expressed lncRNA. Using transgenic mice, deletion alleles reinforced CCD as a neonatal muscle-specific repressor of maternal Igf2. However, deletion of the abutting lncRNA did not affect Igf2 levels. Unexpectedly, in adult skeletal muscle where Igf2 is normally repressed, absence of CCD resulted in remarkable, high-level activation of Igf2 from both parental alleles. Through multimodal chromatin analyses, we identified a conserved putative adult skeletal muscle enhancer (PaSME) insulated between chromatin domains at ICR and CCD. We propose that removal of CCD allows PaSME to drive robust abnormal Igf2 activation on both alleles in adult skeletal muscle. Thus, we uncover CCD as a developmental biallelic muscle-specific repressor, adding a new layer of architectural regulation to the extensively studied Igf2/H19 locus.
印记基因的精确单等位基因表达受称为印记控制区（ICR）的顺式调控元件以及由局部染色质结构塑造的增强子-启动子（E-P）相互作用的支配。Igf2/H19基因座在ICR处采用等位基因特异性CTCF结合，以指导增强子对母本H19和父本Igf2启动子的可及性。在此，我们研究了位于H19和Igf2基因之间的CTCF结合的中央保守结构域（CCD）以及一个相邻的广泛表达的长链非编码RNA。利用转基因小鼠进行研究，缺失等位基因强化了CCD作为母本Igf2的新生儿肌肉特异性抑制因子的作用。然而，缺失相邻的长链非编码RNA并不影响Igf2的水平。出乎意料的是，在正常情况下Igf2受到抑制的成年骨骼肌中，缺失CCD导致来自双亲等位基因的Igf2显著高水平激活。通过多模态染色质分析，我们在ICR和CCD的染色质结构域之间鉴定出一个保守的假定成年骨骼肌增强子（PaSME）。我们提出，去除CCD会使PaSME在成年骨骼肌中驱动两个等位基因上的Igf2发生强烈的异常激活。因此，我们发现CCD是一种发育性双等位基因肌肉特异性抑制因子，为广泛研究的Igf2/H19基因座增添了一层新的结构调控。
