Majumdar Sudeshna, Bammidi Lakshmi Sowjanya, Naik Hemant C, Manhas Avinchal, Baro Runumi, Kalita Akash, Naskar Amlan Jyoti, Nidharshan Sundarraj, Bariha Girija S, Notani Dimple, Gayen Srimonta
Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore-560012, India.
Functional Genomics and Bioinformatics Unit, The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore 560064, India.
Genome Res. 2025 Sep 2;35(9):1992-2010. doi: 10.1101/gr.279822.124.
long noncoding RNA is the master regulator of the X-Chromosome inactivation (XCI) process. is expressed from the inactive X and coats the inactive X to facilitate XCI. -regulation of expression remains poorly understood in the context of maintenance of XCI. Here, we have explored the role of the upstream sequences (∼6 kb) lying between and in the regulation of and XCI in mouse extra-embryonic endoderm stem cells (XEN), which represent the maintenance phase of imprinted XCI. Here, we show that the deletion of this upstream sequence in the inactive X leads to the upregulation of expression accompanied by the dispersal of the cloud. Notably, we find the loss of enrichment of repressive marks such as H3K27me3, H4K20me1, and MacroH2A, except that of H2AK119ub, in dispersed nuclei. However, X-linked genes remain silent despite dispersal and loss of enrichment of repressive marks. Notably, we find that many autosomal genes, including cohesin , are dysregulated in -upstream-deleted cells. Additionally, we demonstrate that -upstream deletion leads to alterations of topological contacts of the locus with its upstream positive regulator and across the inactive X and autosomes. Finally, we show genome-wide alterations of the occupancy of architectural proteins CTCF/RAD21, including at many loci of the inactive X such as the upstream regions and the locus, which is critical for maintaining inactive X conformation. Taken together, we demonstrate that the upstream sequence imparts a multifaceted role in genome regulation beyond the XCI.
长链非编码RNA是X染色体失活（XCI）过程的主要调节因子。它从失活的X染色体上表达，并覆盖在失活的X染色体上以促进XCI。在XCI维持的背景下，其表达的调控仍知之甚少。在这里，我们探索了位于[具体基因名称1]和[具体基因名称2]之间的[具体基因名称1]上游序列（约6 kb）在小鼠胚外内胚层干细胞（XEN）中对[具体基因名称1]和XCI的调控作用，XEN代表印记XCI的维持阶段。在这里，我们表明，在失活的X染色体上删除该[具体基因名称1]上游序列会导致[具体基因名称1]表达上调，并伴随着[具体基因名称1]云的分散。值得注意的是，我们发现在分散的[具体基因名称1]细胞核中，除了H2AK119ub外，抑制性标记如H3K27me3、H4K20me1和MacroH2A的富集减少。然而，尽管[具体基因名称1]分散且抑制性标记富集减少，X连锁基因仍然保持沉默。值得注意的是，我们发现许多常染色体基因，包括黏连蛋白[具体基因名称3]，在[具体基因名称1]上游缺失的细胞中表达失调。此外，我们证明[具体基因名称1]上游缺失会导致[具体基因名称1]基因座与其上游正调控因子[具体基因名称4]以及跨失活的X染色体和常染色体的拓扑接触发生改变。最后，我们展示了全基因组范围内结构蛋白CTCF/RAD21占据情况的改变，包括在失活的X染色体的许多位点，如[具体基因名称1]上游区域和[具体基因名称1]基因座，这对于维持失活的X染色体构象至关重要。综上所述，我们证明[具体基因名称1]上游序列在基因组调控中除了XCI之外还发挥着多方面的作用。
