title: Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains.
abstract: BACKGROUND
  Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago.
  
  
  RESULTS
  Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms (273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4 %).
  
  
  CONCLUSIONS
  Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.
authors.affiliation: Biology Department, Washington University, St Louis, MO 63130, USA. libbyslawson@gmail.com
authors.forename: Elizabeth E
authors.initials: EE
authors.lastname: Slawson
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Shaffer
authors.forename: Colin D
authors.initials: CD
authors.lastname: Malone
authors.forename: Wilson
authors.initials: W
authors.lastname: Leung
authors.forename: Elmer
authors.initials: E
authors.lastname: Kellmann
authors.forename: Rachel B
authors.initials: RB
authors.lastname: Shevchek
authors.forename: Carolyn A
authors.initials: CA
authors.lastname: Craig
authors.forename: Seth M
authors.initials: SM
authors.lastname: Bloom
authors.forename: James
authors.initials: J
authors.lastname: Bogenpohl
authors.forename: James
authors.initials: J
authors.lastname: Dee
authors.forename: Emiko T A
authors.initials: ET
authors.lastname: Morimoto
authors.forename: Jenny
authors.initials: J
authors.lastname: Myoung
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Nett
authors.forename: Fatih
authors.initials: F
authors.lastname: Ozsolak
authors.forename: Mindy E
authors.initials: ME
authors.lastname: Tittiger
authors.forename: Andrea
authors.initials: A
authors.lastname: Zeug
authors.forename: Mary-Lou
authors.initials: ML
authors.lastname: Pardue
authors.forename: Jeremy
authors.initials: J
authors.lastname: Buhler
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Sarah C R
authors.initials: SC
authors.lastname: Elgin
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004247:DNA / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics*; D020224:Expressed Sequence Tags; D016678:Genome; D006570:Heterochromatin / Q000235:genetics*; D017403:In Situ Hybridization; D008957:Models, Genetic; D015233:Models, Statistical; D034622:RNA Interference; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements / Q000235:genetics; D018709:Statistics, Nonparametric
chemical_list: D004251:DNA Transposable Elements; D029721:Drosophila Proteins; D006570:Heterochromatin; D018626:Retroelements; D004247:DNA