Ataei Lamisa, Zhang Juan, Monis Simon, Giemza Krystyna, Mittal Kirti, Yang Joshua, Shimomura Mayu, McStay Brian, Wilson Michael D, Ramalho-Santos Miguel
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5T 3H7, Canada.
Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
Genes Dev. 2025 Feb 3;39(3-4):280-298. doi: 10.1101/gad.351979.124.
The nucleolus is a major subnuclear compartment where ribosomal DNA (rDNA) is transcribed and ribosomes are assembled. In addition, recent studies have shown that the nucleolus is a dynamic organizer of chromatin architecture that modulates developmental gene expression. rDNA gene units are assembled into arrays located in the p-arms of five human acrocentric chromosomes. Distal junctions (DJs) are ∼400 kb sequences adjacent to rDNA arrays that are thought to anchor them at the nucleolus, although the underlying regulatory elements remain unclear. Here we show that DJs display a dynamic chromosome conformation profile in human embryonic stem cells (hESCs). We identified a primate-specific, full-length insertion of the retrotransposon long interspersed nuclear element 1 (LINE1) in a conserved position across all human DJs. This DJ-LINE1 locus interacts with specific regions of the DJ and is upregulated in naïve hESCs. CRISPR-based deletion and interference approaches revealed that DJ-LINE1 contributes to nucleolar positioning of the DJs. Moreover, we found that the expression of DJ-LINE1 is required for maintenance of the structure and transcriptional output of the nucleolus in hESCs. Silencing of DJ-LINE1 leads to loss of self-renewal, disruption of the landscape of chromatin accessibility, and derepression of earlier developmental programs in naïve hESCs. This work uncovers specific LINE1 elements with a fundamental role in nucleolar organization in hESCs and provides new insights into how the nucleolus functions as a key genome-organizing hub.
核仁是一个主要的亚核区室，核糖体DNA（rDNA）在此处进行转录，核糖体在此处组装。此外，最近的研究表明，核仁是染色质结构的动态组织者，可调节发育基因的表达。rDNA基因单位组装成阵列，位于五条人类近端着丝粒染色体的短臂上。远端连接（DJs）是与rDNA阵列相邻的约400 kb序列，尽管其潜在的调控元件尚不清楚，但人们认为这些序列可将rDNA阵列锚定在核仁上。在这里，我们表明DJs在人类胚胎干细胞（hESCs）中呈现出动态的染色体构象图谱。我们在所有人类DJs的保守位置鉴定出一种灵长类特异性的逆转录转座子长散在核元件1（LINE1）的全长插入。这个DJ-LINE1位点与DJ的特定区域相互作用，并在原始hESCs中上调。基于CRISPR的缺失和干扰方法表明，DJ-LINE1有助于DJs在核仁中的定位。此外，我们发现DJ-LINE1的表达对于维持hESCs中核仁的结构和转录输出是必需的。沉默DJ-LINE1会导致原始hESCs丧失自我更新能力、染色质可及性景观的破坏以及早期发育程序的去抑制。这项工作揭示了在hESCs核仁组织中起基本作用的特定LINE1元件，并为核仁如何作为关键的基因组组织中心发挥作用提供了新的见解。
