ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/005/SRR4348285/SRR4348285_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/004/SRR4348284/SRR4348284_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/008/SRR4348288/SRR4348288_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/000/SRR4348290/SRR4348290_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/007/SRR4348287/SRR4348287_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/009/SRR4348289/SRR4348289_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/006/SRR4348286/SRR4348286_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/004/SRR4348284/SRR4348284_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/001/SRR4348291/SRR4348291_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/005/SRR4348285/SRR4348285_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/008/SRR4348288/SRR4348288_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/001/SRR4348291/SRR4348291_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/006/SRR4348286/SRR4348286_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/007/SRR4348287/SRR4348287_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/000/SRR4348290/SRR4348290_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/009/SRR4348289/SRR4348289_1.fastq.gzprimaryOK200GenomicsBiochemistry, University of Vermonthttps://www.ebi.ac.uk/ena/browser/view/PRJNA345506Homo sapiensxref:PubMed:27627025Experimental approaches to define the relationship between gene expression and nuclear matrix attachment regions (MARs) have given contrasting and method-specific results. We have developed a next generation sequencing strategy to identify MARs across the human genome (MAR-Seq). The method is based on crosslinking chromatin to its nuclear matrix attachment sites to minimize changes during biochemical processing. We used this method to compare nuclear matrix organization in MCF-10A mammary epithelial-like cells and MDA-MB-231 breast cancer cells and evaluated the results in the context of global gene expression (array analysis) and positional enrichment of gene-regulatory histone modifications (ChIP-Seq). In the normal-like cells, nuclear matrix–attached DNA was enriched in expressed genes, while in the breast cancer cells, it was enriched in non-expressed genes. In both cell lines, the chromatin modifications that mark transcriptional activation or repression were appropriately associated with gene expression. Using this new MAR-Seq approach, we provide the first genome-wide characterization of nuclear matrix attachment in mammalian cells and reveal that the nuclear matrix–associated genome is highly cell-context dependent. Overall design: MAR-seq, nuclear matrix associated DNA and digested background for 2 cell lines with 2 replicatesENAfalseHomo sapiensIdentifying Nuclear Matrix–attached DNA across the Genome (MAR-seq)2025-09-242016-10-07PRJNA345506GSE87667960627627025