title: Genome-wide mapping of matrix attachment regions in Drosophila melanogaster.
abstract: BACKGROUND
  Eukaryotic genome acquires functionality upon proper packaging within the nucleus. This process is facilitated by the structural framework of Nuclear Matrix, a nucleo-proteinaceous meshwork. Matrix Attachment Regions (MARs) in the genome serve as anchoring sites to this framework.
  
  
  RESULTS
  Here we report direct sequencing of the MAR preparation from Drosophila melanogaster embryos and identify >7350 MARs. This amounts to ~2.5% of the fly genome and often coincide with AT rich non-coding regions. We find significant association of MARs with the origins of replication, transcription start sites, paused RNA Polymerase II sites and exons, but not introns, of highly expressed genes. We also identified sequence motifs and repeats that constitute MARs.
  
  
  CONCLUSIONS
  Our data reveal the contact points of genome to the nuclear architecture and provide a link between nuclear functions and genomic packaging.
authors.forename: Rashmi U
authors.initials: RU
authors.lastname: Pathak
authors.forename: Arumugam
authors.initials: A
authors.lastname: Srinivasan
authors.affiliation: Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500 007, India. mishra@ccmb.res.in.
authors.forename: Rakesh K
authors.initials: RK
authors.lastname: Mishra
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D059006:Chromosomes, Insect; D019295:Computational Biology / Q000379:methods; D004257:DNA Polymerase II / Q000378:metabolism; D004251:DNA Transposable Elements; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D017344:Genes, Insect; D049750:Genome, Insect; D023281:Genomics; D045170:Matrix Attachment Regions; D005810:Multigene Family; D015530:Nuclear Matrix / Q000378:metabolism; D059372:Nucleotide Motifs; D056510:Position-Specific Scoring Matrices; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements; D004257:DNA Polymerase II