Mapping of scaffold/matrix attachment regions in human genome: a data mining exercise

Abstract

Scaffold/matrix attachment regions (S/MARs) are DNA elements that serve to compartmentalize the chromatin into structural and functional domains. These elements are involved in control of gene expression which governs the phenotype and also plays role in disease biology. Therefore, genome-wide understanding of these elements holds great therapeutic promise. Several attempts have been made toward identification of S/MARs in genomes of various organisms including human. However, a comprehensive genome-wide map of human S/MARs is yet not available. Toward this objective, ChIP-Seq data of 14 S/MAR binding proteins were analyzed and the binding site coordinates of these proteins were used to prepare a non-redundant S/MAR dataset of human genome. Along with co-ordinate (location) details of S/MARs, the dataset also revealed details of S/MAR features, namely, length, inter-SMAR length (the chromatin loop size), nucleotide repeats, motif abundance, chromosomal distribution and genomic context. S/MARs identified in present study and their subsequent analysis also suggests that these elements act as hotspots for integration of retroviruses. Therefore, these data will help toward better understanding of genome functioning and designing effective anti-viral therapeutics. In order to facilitate user friendly browsing and retrieval of the data obtained in present study, a web interface, MARome (http://bioinfo.net.in/MARome), has been developed.

TADs enriched in histone H1.2 strongly overlap with the B compartment, inaccessible chromatin, and AT‐rich Giemsa bands

“…Because of their AT richness, it was initially proposed that S/MARs were present densely within dark G bands [30]. Mapping of human S/MARs using ChIP‐seq data of 14 S/MAR binding proteins was recently achieved [31]. These sites were confirmed to contain the previously described features including AT richness.…”

“…(G–I) Abundance of H1 variants at retroviral integration sites and S/MAR protein binding sites. Average, input‐subtracted ChIP‐seq signal of H1.2 and H1X around the center of S/MARs sites (mapped in [31]) (G), HIV‐1 integration sites (H), or around the center of the S/MAR binding protein sites indicated (I).…”

DNA sequence-dependent positioning of the linker histone in a nucleosome: a single-pair FRET study

“…These two arginines protrude into the characteristically narrow minor groove of the A-tract. A-tract regions, which are abundantly present in S/MAR (scaffold/matrix attachment regions) (58) and satellite sequences (26), are known to have the narrowest minor groove, and hence have a high density of negative charges. Moreover, A-tracts complementary to deoxy-uracils would have very similar minor groove widths to A-tracts complementary to thymines.…”

piggyBac-Based Non-Viral In Vivo Gene Delivery Useful for Production of Genetically Modified Animals and Organs

“…Matrix attachment regions (MARs) are cis-acting DNA elements and known to act as epigenetic regulatory sequences that increase gene expression [95]. Ley et al [96] demonstrated that incorporation of human MAR 1-68 in a PB transposon cassette was beneficial for reduced silencing effects and caused increased transgene expression in cultured cells.…”