Mammalian genomes harbor a large number of transposable elements (TEs) and their remnants. Most TEs are incapable of retrotransposition. Although most TEs are epigenetically repressed, transcriptional silencing is partially released to permit developmental or tissue-specific expression of TEs. Some TEs have also evolved as cis-regulatory elements (CREs), enabling them to recruit host-encoded transcription factors. Understanding the contribution of TEs in the regulation of the mammalian genome is an active area of research. Previously, the noncoding long terminal repeat (LTR) part of the endogenous retrovirus (ERV) families has been shown to function as enhancers. We show that new LTR families and the promoter region of LINE1 (L1) are enriched with H4K16ac and H3K122ac and the chromatin features associated with active enhancers. Depletion of MSL complex and H4K16ac levels leads to a significant reduction in the expression of L1 and ERV/LTRs. We demonstrate that H4K16ac regulates TE transcription by maintaining a permissive chromatin structure. Furthermore, CRISPR-based perturbation of candidate TEs led to the downregulation of genes in cis. We conclude that H4K16ac and H3K122ac regulate a significant portion of the mammalian genome by opening local chromatin structure and transcriptional activity at TEs.

Mammalian genomes harbor abundant transposable elements (TEs) and their remnants, with numerous epigenetic repression mechanisms enacted to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, and cancers, although the epigenetic factors contributing to the transcription of TEs have yet to be fully elucidated. Here, we demonstrate that the male-specific lethal (MSL)-complex-mediated histone H4 acetylation at lysine 16 (H4K16ac) is enriched at TEs in human embryonic stem cells (hESCs) and cancer cells. This in turn activates transcription of subsets of full-length long interspersed nuclear elements (LINE1s, L1s) and endogenous retrovirus (ERV) long terminal repeats (LTRs). Furthermore, we show that the H4K16ac-marked L1 and LTR subfamilies display enhancer-like functions and are enriched in genomic locations with chromatin features associated with active enhancers. Importantly, such regions often reside at boundaries of topologically associated domains and loop with genes. CRISPR-based epigenetic perturbation and genetic deletion of L1s reveal that H4K16ac-marked L1s and LTRs regulate the expression of genes in cis. Overall, TEs enriched with H4K16ac contribute to the cis-regulatory landscape at specific genomic locations by maintaining an active chromatin landscape at TEs.

The genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood. We sequenced 63 whole genomes from 21 ID probands and their unaffected parents. In addition, we analysed 30 previously sequenced genomes from exome-negative ID probands. We found that regulatory DNMs were selectively enriched in fetal brain-specific enhancers as compared with adult brain enhancers. DNM-containing enhancers were associated with genes that show preferential expression in the prefrontal cortex. Furthermore, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1,OLFM1, andPOU3F3). Most of the DNMs from ID probands showed allele-specific enhancer activity when tested using luciferase assay. Using CRISPR-mediated mutation and editing of epigenomic marks, we show that DNMs at regulatory elements affect the expression of putative target genes. Our results, therefore, provide new evidence to indicate that DNMs in fetal brain-specific enhancers play an essential role in the aetiology of ID.

The genetic aetiology of a major fraction of patients with intellectual disability (ID) remains unknown. De novo mutations (DNMs) in protein-coding genes explain up to 40% of cases, but the potential role of regulatory DNMs is still poorly understood. We sequenced 63 whole genomes from 21 ID probands and their unaffected parents (trio). Additionally, we analysed 30 previously sequenced genomes from exome-negative ID probands. We found that regulatory DNMs were selectively enriched in fetal brain-specific and human-gained enhancers. DNM-containing enhancers were associated with genes that show preferential expression in the pre-frontal cortex, have been previously implicated in ID or related disorders, and exhibit intolerance to loss of function mutations. Moreover, we found that highly interacting regulatory regions from intermediate progenitor cells of the developing human cortex were strongly enriched for ID DNMs. Furthermore, we identified recurrently mutated enhancer clusters that regulate genes involved in nervous system development (CSMD1, OLFM1, and POU3F3). The majority of the DNMs from ID probands showed allele-specific enhancer activity when tested using luciferase assay. Using CRISPR-mediated mutation and editing of epigenomic marks, we show that regulatory elements harbouring DNMs indeed function as enhancers and DNMs at regulatory elements affect the expression of putative target genes. Our results, therefore, provide new evidence to indicate that DNMs in fetal brain-specific enhancers play an essential role in the aetiology of ID.