Hosny El Said Nadine, Abdrabou Wael, Mahmood Syed Raza, Venit Tomas, Idaghdour Youssef, Percipalle Piergiorgio
Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), PO Box 129188, Abu Dhabi, United Arab Emirates.
Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), PO Box 129188, Abu Dhabi, United Arab Emirates.
Nucleic Acids Res. 2025 Apr 10;53(7). doi: 10.1093/nar/gkaf280.
Nuclear actin mediates enhancer-dependent transcriptional regulation at compartment level, playing critical roles in 3D genome organization. In β-actin depleted cells, H3K27 acetylation is enhanced, directly affecting enhancer-dependent transcriptional regulation and gene expression changes during compartment-switching. Here, we report these mechanisms are influenced by the long non-coding RNA (lncRNA) Meg3. Bulk RNA-seq analysis and qPCR on wild-type (WT), heterozygous (HET), and β-actin knockout (KO) mouse embryonic fibroblasts (MEFs) show that β-actin depletion significantly alters expression of several lncRNAs, including Meg3. Results from ChIRP-seq, ChIRP-MS, and fRIP-qPCR revealed that in β-actin KO cells, Meg3 becomes enriched and binds to H3K27 acetylation marks within gene regulatory regions. By integrating RNA-seq, H3K27 acetylation ChIP-seq, ATAC-seq, and HiC-seq data through activity by contact (ABC) analysis, we discovered Meg3 binding disrupts promoter-enhancer interactions in β-actin KO cells. These results, combined with metabolomics in WT, HET, and β-actin KO MEFs, show Meg3 binding to regulatory regions at sites of increased H3K27 acetylation impairs the expression of genes involved in the synthesis of chondroitin, heparan, dermatan sulfate, and phospholipases. We propose that in β-actin KO cells Meg3 binds to H3K27 acetylation levels. This interferes with promoter-enhancer interactions, disrupts genome organization, and downregulates gene expression and key metabolic pathways.
核肌动蛋白在区室水平介导增强子依赖性转录调控，在三维基因组组织中发挥关键作用。在β-肌动蛋白缺失的细胞中，H3K27乙酰化增强，直接影响区室转换过程中增强子依赖性转录调控和基因表达变化。在此，我们报告这些机制受长链非编码RNA（lncRNA）Meg3的影响。对野生型（WT）、杂合子（HET）和β-肌动蛋白敲除（KO）小鼠胚胎成纤维细胞（MEF）进行的大量RNA测序分析和qPCR显示，β-肌动蛋白缺失显著改变了包括Meg3在内的几种lncRNA的表达。ChIRP-seq、ChIRP-MS和fRIP-qPCR结果表明，在β-肌动蛋白KO细胞中，Meg3富集并与基因调控区域内的H3K27乙酰化标记结合。通过活性接触（ABC）分析整合RNA-seq、H3K27乙酰化ChIP-seq、ATAC-seq和HiC-seq数据，我们发现Meg3结合破坏了β-肌动蛋白KO细胞中的启动子-增强子相互作用。这些结果与WT、HET和β-肌动蛋白KO MEF中的代谢组学相结合，表明Meg3在H3K27乙酰化增加的位点与调控区域结合，损害了参与硫酸软骨素、硫酸乙酰肝素、硫酸皮肤素和磷脂酶合成的基因的表达。我们提出，在β-肌动蛋白KO细胞中，Meg3与H3K27乙酰化水平结合。这会干扰启动子-增强子相互作用，破坏基因组组织，并下调基因表达和关键代谢途径。
