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Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):E4428-37. doi: 10.1073/pnas.1507253112. Epub 2015 Jul 27.

MIR retrotransposon sequences provide insulators to the human genome.

Author information

1
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332;
2
Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), 28029 Madrid, Spain;
3
Centro Andaluz de Biología del Desarrollo CSIC-Universidad Pablo de Olavide (UPO), 41013 Sevilla, Spain;
4
Aelan Cell Technologies, Inc., San Francisco, CA 94107;
5
School of Biology, Georgia Institute of Technology, Atlanta, GA 30332; PanAmerican Bioinformatics Institute, Santa Marta, Magdalena, Colombia king.jordan@biology.gatech.edu.

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.

KEYWORDS:

chromatin; gene regulation; genomics; insulators; transposable elements

PMID:
26216945
PMCID:
PMC4538669
DOI:
10.1073/pnas.1507253112
[Indexed for MEDLINE]
Free PMC Article

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