Identifying Nuclear Matrix-Attached DNA Across the Genome.
Experimental 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. J. Cell. Physiol. 232: 1295-1305, 2017. © 2016 Wiley Periodicals, Inc.
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
Jason R
JR
Dobson
Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.
Deli
D
Hong
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
A Rasim
AR
Barutcu
Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.
Hai
H
Wu
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
Anthony N
AN
Imbalzano
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts.|Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.
Jane B
JB
Lian
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts.|Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.
Janet L
JL
Stein
Departments of Orthopedic Surgery and Biochemistry & Molecular Biology, Mayo Clinic, Rochester, Minnesota.
Andre J
AJ
van Wijnen
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
Jeffrey A
JA
Nickerson
Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts.|Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.
Gary S
GS
Stein
D001943:Breast Neoplasms / Q000235:genetics; D002460:Cell Line; D002843:Chromatin / Q000378:metabolism; D003432:Cross-Linking Reagents / Q000378:metabolism; D004247:DNA / Q000378:metabolism*; D005260:Female; D005455:Fluorescent Antibody Technique; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006657:Histones / Q000378:metabolism; D006801:Humans; D045170:Matrix Attachment Regions / Q000235:genetics*; D015530:Nuclear Matrix / Q000378:metabolism*; D016366:Open Reading Frames / Q000235:genetics; D015203:Reproducibility of Results
D002843:Chromatin; D003432:Cross-Linking Reagents; D006657:Histones; D004247:DNA