MIR retrotransposon sequences provide insulators to the human genome

Abstract

Insulators are regulatory elements that help to organize eukaryotic chromatin via enhancer-blocking and chromatin barrier activity. Although there are several examples of transposable element (TE)-derived insulators, the contribution of TEs to human insulators has not been systematically explored. Mammalian-wide interspersed repeats (MIRs) are a conserved family of TEs that have substantial regulatory capacity and share sequence characteristics with tRNA-related insulators. We sought to evaluate whether MIRs can serve as insulators in the human genome. We applied a bioinformatic screen using genome sequence and functional genomic data from CD4 + T cells to identify a set of 1,178 predicted MIR insulators genome-wide. These predicted MIR insulators were computationally tested to serve as chromatin barriers and regulators of gene expression in CD4 + T cells. The activity of predicted MIR insulators was experimentally validated using in vitro and in vivo enhancer-blocking assays. MIR insulators are enriched around genes of the T-cell receptor pathway and reside at T-cell-specific boundaries of repressive and active chromatin. A total of 58% of the MIR insulators predicted here show evidence of T-cell-specific chromatin barrier and gene regulatory activity. MIR insulators appear to be CCCTC-binding factor (CTCF) independent and show a distinct local chromatin environment with marked peaks for RNA Pol III and a number of histone modifications, suggesting that MIR insulators recruit transcriptional complexes and chromatin modifying enzymes in situ to help establish chromatin and regulatory domains in the human genome. The provisioning of insulators by MIRs across the human genome suggests a specific mechanism by which TE sequences can be used to modulate gene regulatory networks.

Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire

“…Furthermore, caution must be exercised when interpreting the results of loss-of-function studies on lncRNAs due to the complex nature of their activities at the transcriptional and post-transcriptional levels (Bassett et al, 2014). Finally, while other retrotransposons have been exapted into both enhancers and insulators in humans (Jjingo et al, 2014; Wang et al, 2015) LTR-derived insulators have not been identified to date. Future investigations into these and related questions will further our understanding of the extent to which mammalian genomes have harnessed the latent regulatory potential of LTRs to control tissue-specific gene expression.…”

Regulatory activities of transposable elements: from conflicts to benefits

“…Such sequences serve to partition the genome into domains of active or inactive transcription ranging in size from 100 kb to 1 Mb, often by preventing the spread of heterochromatin 45 . Several studies showed that many TEs, in particular SINEs, harbour binding sites for factors such as CTCF or TFIIIC that confer insulator activity and organize nuclear architecture 46–48 . A subset of these TEs appear to play roles in the three-dimensional organization of the genome by functioning as ‘anchors’ that serve to isolate regions of active transcription.…”

Towards a predictive model of chromatin 3D organization

“…Additionally, tRNA genes and SINE elements are also enriched at TAD borders [2], suggesting that TFIIIC, which binds to these sequences, may also be involved in mediating long range interactions [10, 35]. Furthermore, tRNA-like Mammalian-wide Interspersed Repeat (MIR) elements were recently characterized as a new group of sequences in the human genome that possess canonical insulator activity, are close to TAD borders, and appear to be CTCF-independent, suggesting the existence of proteins that bind these sequences with an architectural function [36]. These results suggest that Znf143, YY1, and TFIIIC along with its interaction partner the condensin II complex, may function as new architectural proteins in the mammalian genome but additional functional studies are required to verify their involvement in organizing chromatin contacts.…”