ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/008/SRR4346778/SRR4346778_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/007/SRR4346777/SRR4346777_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/006/SRR4346776/SRR4346776_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/005/SRR4346775/SRR4346775_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/004/SRR4346774/SRR4346774_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/000/SRR4346770/SRR4346770_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/009/SRR4346769/SRR4346769_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/008/SRR4346768/SRR4346768_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/003/SRR4346763/SRR4346763_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/006/SRR4346776/SRR4346776_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/004/SRR4346774/SRR4346774_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/004/SRR4346764/SRR4346764_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/005/SRR4346775/SRR4346775_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/001/SRR4346771/SRR4346771_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/002/SRR4346772/SRR4346772_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/003/SRR4346773/SRR4346773_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/008/SRR4346768/SRR4346768_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/007/SRR4346767/SRR4346767_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/006/SRR4346766/SRR4346766_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/008/SRR4346778/SRR4346778_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/005/SRR4346765/SRR4346765_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/007/SRR4346777/SRR4346777_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/007/SRR4346767/SRR4346767_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/001/SRR4346771/SRR4346771_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/000/SRR4346770/SRR4346770_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/003/SRR4346773/SRR4346773_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/002/SRR4346772/SRR4346772_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/006/SRR4346766/SRR4346766_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/003/SRR4346763/SRR4346763_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/005/SRR4346765/SRR4346765_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/009/SRR4346769/SRR4346769_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR434/004/SRR4346764/SRR4346764_1.fastq.gzprimary200OKGenomicsBiochemistry, University of Vermonthttps://www.ebi.ac.uk/ena/browser/view/PRJNA345501Homo 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: ChIP-seq of 3 histone modifications in 2 cell lines with 2 replicatesENAfalseHomo sapiensIdentifying Nuclear Matrix–attached DNA across the Genome (ChIP-seq)2025-09-242016-10-07PRJNA345501GSE87662960627627025