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.

Figure 1.

Validation of dataset by determining presence of S/MAR-associated features. (A) Abundance (in percentage) of seven S/MAR features including OriC, TG richness, curved DNA, kinked DNA, Topo II site, AT richness and MRS in the dataset. (B) Venn diagram depicting number of S/MAR sequences having one or more features.

Figure 2.

Length distribution of S/MARs and chromatin loops. (A) Length of S/MARs (in bp) was plotted against their occurrence. (B) Inter-S/MAR distance or chromatin loop size (in Kb) was plotted against their occurrence.

Figure 3.

Distribution of S/MARs on human chromosomes. (A) Visualization of S/MARs on all human chromosomes. (B) Number of S/MARs present on each human chromosome. (C) Gene density and S/MAR density correlation graph for each human chromosome.

Figure 4.

Genomic context of S/MARs: (A) Percentage distribution of S/MARs in different genomic regions. (B) Distance of S/MARs from the TSS of nearest downstream gene versus S/MAR count.

Figure 5.

Functional classification of S/MAR associated genes. (A) Classification of genes based on gene ontology; Biological Processes. (B) Classification of genes based on their involvement in different pathways.

Figure 6.

Repeats and motifs present in S/MAR sequences. (A) Graphical representation for number of various mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats present in S/MARs. (B) Occurrence of 12 abundant nucleotide repeats in S/MAR sequences. (C) Three most abundant motifs as identified by MEME-ChIP program in the S/MARs. (D) Graphical representation of abundance of the identified motifs. (E) Abundance of various repeats in S/MAR dataset.

Figure 7.

Experimental validation of S/MAR sequences by nuclear matrix DNA PCR. Matrix-DNA preparation: M; Semi-quantitative PCR for positive controls: P1-P5; (A), negative controls: N1 and N2 (B) and randomly selected 30 S/MAR sequences (C–E).

Figure 8.

Correlation between S/MARs and retrovirus integration sites. (A) Distance of HIV integration sites from the nearest upstream and downstream S/MARs plotted against their count. (B) Distance of HTLV integration sites from the nearest upstream and downstream S/MARs plotted against their count.