MARome

MARome maps Scaffold and Matrix Attachment Regions (S/MARs) across the human genome, providing genome-wide coordinates and annotations to study chromatin domain organization, gene regulation, and retroviral integration.

Key Features:

• Genome-wide S/MAR coordinates: Non-redundant S/MAR coordinates derived from analysis of ChIP-Seq data from 14 distinct S/MAR binding proteins.
• S/MAR attribute annotation: Per-region annotations include S/MAR length, inter-SMAR lengths (indicative of chromatin loop sizes), nucleotide repeats, motif abundance, chromosomal distribution, and genomic context.
• Retroviral integration enrichment: Annotation and analysis identify S/MARs as hotspots for retroviral integration, including enrichment for HIV and HTLV integration sites.
• Cross-resource integration: S/MAR coordinates and annotations are cross-referenced with the UCSC Genome Browser, Ensembl, and NCBI-Gene.

Scientific Applications:

• Chromatin architecture mapping: Use inter-SMAR lengths and S/MAR distributions to infer chromatin loop sizes and domain boundaries.
• Gene regulation studies: Investigate the influence of S/MARs on gene expression based on genomic context and motif abundance.
• Retroviral integration studies: Analyze integration site preferences and enrichment for retroviruses such as HIV and HTLV at S/MARs.
• Disease and phenotype research: Correlate S/MAR organization and distribution with phenotypic outcomes and disease mechanisms.

Methodology:

ChIP-Seq data from 14 distinct S/MAR binding proteins were analyzed to generate a non-redundant dataset of S/MAR coordinates and to compute region attributes (length, inter-SMAR lengths, nucleotide repeats, motif abundance, chromosomal distribution, genomic context), with results cross-referenced to UCSC Genome Browser, Ensembl, and NCBI-Gene.