title: A significant fraction of conserved noncoding DNA in human and mouse consists of predicted matrix attachment regions.
abstract: Noncoding DNA in the human-mouse orthologous intergenic regions contains "islands" of conserved sequences, the functions of which remain largely unknown. We hypothesized that some of these regions might be matrix-scaffold attachment regions, MARs (or S/MARs). MARs comprise one of the few classes of eukaryotic noncoding DNA with an experimentally characterized function, being involved in the attachment of chromatin to the nuclear matrix, chromatin remodeling and transcription regulation. To test our hypothesis, we analyzed the co-occurrence of predicted MARs with highly conserved noncoding DNA regions in human-mouse genomic alignments. We found that 11% of the conserved noncoding DNA consists of predicted MARs. Conversely, more than half of the predicted MARs co-occur with one or more independently identified conserved sequence blocks. An excess of conserved predicted MARs is seen in intergenic regions preceding 5' ends of genes, suggesting that these MARs are primarily involved in transcriptional control.
authors.affiliation: Institute of Molecular Evolutionary Genetics and Dept of Biology, Pennsylvania State University, 328 Mueller Lab, University Park, PA 16802, USA.
authors.forename: Galina V
authors.initials: GV
authors.lastname: Glazko
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.forename: Igor B
authors.initials: IB
authors.lastname: Rogozin
authors.forename: Svetlana A
authors.initials: SA
authors.lastname: Shabalina
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002843:Chromatin / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence / Q000235:genetics*; D004264:DNA Topoisomerases, Type I / Q000235:genetics; D004250:DNA Topoisomerases, Type II / Q000235:genetics; D021901:DNA, Intergenic / Q000032:analysis / Q000235:genetics*; D030541:Databases, Genetic; D006801:Humans; D007136:Immunoglobulins / Q000235:genetics; D051379:Mice; D008969:Molecular Sequence Data; D015530:Nuclear Matrix / Q000235:genetics / Q000378:metabolism*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D002843:Chromatin; D021901:DNA, Intergenic; C014609:IgK; D007136:Immunoglobulins; D004264:DNA Topoisomerases, Type I; D004250:DNA Topoisomerases, Type II