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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. [ABSTRACT FROM AUTHOR]

A typical eukaryotic genome harbors a rich variety of repetitive elements. The most abundant are retrotransposons, mobile retroelements that utilize reverse transcriptase and an RNA intermediate to relocate to a new location within the cellular genomes. A vast majority of the repetitive mammalian genome content has originated from the retrotransposition of SINE (100-300 bp short interspersed nuclear elements that are derived from the structural 7SL RNA or tRNA), LINE (7kb long interspersed nuclear element), and LTR (2-3 kb long terminal repeats) transposable element superfamilies. Broadly labeled as 'evolutionary junkyard' or 'fossils', this enigmatic 'dark matter' of the genome possesses many yet to be discovered properties. [ABSTRACT FROM AUTHOR]

Motivation: Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is widely used in biological research. ChIP-seq experiments yield many ambiguous tags that can be mapped with equal probability to multiple genomic sites. Such ambiguous tags are typically eliminated from consideration resulting in a potential loss of important biological information.Results: We have developed a Gibbs sampling-based algorithm for the genomic mapping of ambiguous sequence tags. Our algorithm relies on the local genomic tag context to guide the mapping of ambiguous tags. The Gibbs sampling procedure we use simultaneously maps ambiguous tags and updates the probabilities used to infer correct tag map positions. We show that our algorithm is able to correctly map more ambiguous tags than existing mapping methods. Our approach is also able to uncover mapped genomic sites from highly repetitive sequences that can not be detected based on unique tags alone, including transposable elements, segmental duplications and peri-centromeric regions. This mapping approach should prove to be useful for increasing biological knowledge on the too often neglected repetitive genomic regions.Availability: http://esbg.gatech.edu/jordan/software/mapContact: king.jordan@biology.gatech.eduSupplementary Information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]

One way to modulate transcription is by partitioning the chromatin fiber within the nucleus into the active or inactive domains through the establishment of higher-order chromatin structure. Such subdivision of chromatin implies the existence of insulators and boundaries that delimit differentially regulated chromosomal loci. Recently published data on transcriptional interference from the repeated component of the genome fits the classic definition of insulator/boundary activity. This review discusses the phenomena of transcriptional interference and raises the question about functionality of genomic “junk” along with the need to stimulate a dialogue on how we would define the insulators and boundaries in the light of contemporary data. Rule 19 (a) (Boundaries) “Before the toss, the umpires shall agree the boundary of the field of play with both captains. The boundary shall, if possible, be marked along its whole length” Rules of Cricket [Copyright &y& Elsevier]