MIR retrotransposon sequences provide insulators to the human genome

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.This work was supported by an Alfred P. Sloan Research Fellowship in Computational and Evolutionary Molecular Biology (BR-4839 to J.W. and I.K.J.); a Georgia Tech Integrative BioSystems Institute pilot program grant (to J.W. and I.K.J.); the Spanish Ministry of Science and Innovation (BIO2009-1297 and BIO2012-39980 to L.M., and BFU2010-14839 and CSD2007-00008 to J.L.G.-S); and by Junta de Andalucía (CVI-3488 to J.L.G.-S.). E.M. was supported by Centro de Investigación Biomédica en Red de Enfermedades Raras, Instituto de Salud Carlos III and D.S. was supported by a PhD fellowship from La Caixa program.Peer Reviewe