Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation

• Published in: Cell reports (Cambridge) 2020-03, Vol.30 (10), p.3296-3311.e5
• Main Authors: Lu, J. Yuyang, Shao, Wen, Chang, Lei, Yin, Yafei, Li, Tong, Zhang, Hui, Hong, Yantao, Percharde, Michelle, Guo, Lerui, Wu, Zhongyang, Liu, Lichao, Liu, Wei, Yan, Pixi, Ramalho-Santos, Miguel, Sun, Yujie, Shen, Xiaohua
• Format: Article
• Language: English
• Subjects: Animals; B1 or Alu; Base Sequence; Cell Nucleolus - genetics; Chromatin - metabolism; Embryonic Development - genetics; Embryonic Stem Cells - metabolism; Embryonic Stem Cells - ultrastructure; Gene Expression Regulation, Developmental; gene function; Gene Ontology; gene silencing; Genome; HEK293 Cells; Humans; K562 Cells; L1 RNA; low-complexity repeats; Mice; Models, Genetic; Nuclear Lamina - genetics; Nucleolin; nucleolus and lamina-associated domains; Phosphoproteins - genetics; Phosphoproteins - metabolism; regulation and expression; repetitive elements; Repetitive Sequences, Nucleic Acid - genetics; RNA - genetics; RNA-Binding Proteins - genetics; RNA-Binding Proteins - metabolism; SINE; Transcription, Genetic
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2020.02.048

Repetitive elements are abundantly distributed in mammalian genomes. Here, we reveal a striking association between repeat subtypes and gene function. SINE, L1, and low-complexity repeats demarcate distinct functional categories of genes and may dictate the time and level of gene expression by providing binding sites for different regulatory proteins. Importantly, imaging and sequencing analysis show that L1 repeats sequester a large set of genes with specialized functions in nucleolus- and lamina-associated inactive domains that are depleted of SINE repeats. In addition, L1 transcripts bind extensively to its DNA in embryonic stem cells (ESCs). Depletion of L1 RNA in ESCs leads to relocation of L1-enriched chromosomal segments from inactive domains to the nuclear interior and de-repression of L1-associated genes. These results demonstrate a role of L1 DNA and RNA in gene silencing and suggest a general theme of genomic repeats in orchestrating the function, regulation, and expression of their host genes. [Display omitted] •SINE, L1, and low-complexity repeats barcode genes with distinct functions•Genomic repeats dictate the time and level of gene expression during development•L1-enriched genes are sequestered in the inactive NAD/LAD domains for silencing•L1 RNA promotes the nuclear localization and repression of L1-enriched genes Lu et al. report a striking association between genomic repeats and gene regulation and demonstrate a key role of L1 repeat RNA in sequestering L1-rich sequences and associated genes in inactive domains for silencing, revealing a general theme of repeat sequences in shaping gene regulatory networks within their host genome.