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PMID: 17569856 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

The Release 5.1 annotation of Drosophila melanogaster heterochromatin.

Science (New York, N.Y.) ·Vol. 316 ·No. 5831 ·2007-06-15 ·Pages 1586-91

Smith CD, Shu S, Mungall CJ, Karpen GH

Abstract

The repetitive DNA that constitutes most of the heterochromatic regions of metazoan genomes has hindered the comprehensive analysis of gene content and other functions. We have generated a detailed computational and manual annotation of 24 megabases of heterochromatic sequence in the Release 5 Drosophila melanogaster genome sequence. The heterochromatin contains a minimum of 230 to 254 protein-coding genes, which are conserved in other Drosophilids and more diverged species, as well as 32 pseudogenes and 13 noncoding RNAs. Improved methods revealed that more than 77% of this heterochromatin sequence, including introns and intergenic regions, is composed of fragmented and nested transposable elements and other repeated DNAs. Drosophila heterochromatin contains "islands" of highly conserved genes embedded in these "oceans" of complex repeats, which may require special expression and splicing mechanisms.

MeSH Terms
Animals Chromosome Mapping Computational Biology Conserved Sequence DNA Transposable Elements DNA, Complementary Drosophila/genetics Drosophila Proteins/genetics Drosophila melanogaster/genetics Exons Expressed Sequence Tags Genes, Insect Genome Heterochromatin/genetics Insecta/genetics Introns Pseudogenes RNA, Untranslated/genetics Repetitive Sequences, Nucleic Acid Retroelements Sequence Analysis, DNA
Chemicals
DNA Transposable Elements DNA, Complementary Drosophila Proteins Heterochromatin RNA, Untranslated Retroelements
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Smith Christopher D
Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.
Shu Shengqiang
Mungall Christopher J
Karpen Gary H
References (25)
25 references, click to expand
  1. Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements.
    Genetics. 2005 Jun;170(2):661-74 PMID: 15802507
  2. Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains.
    Genome Biol. 2006;7(2):R15 PMID: 16507169
  3. Biological function of unannotated transcription during the early development of Drosophila melanogaster.
    Nat Genet. 2006 Oct;38(10):1151-8 PMID: 16951679
  4. Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera).
    Genome Res. 2006 Nov;16(11):1404-13 PMID: 17065610
  5. The chemoreceptor superfamily in the honey bee, Apis mellifera: expansion of the odorant, but not gustatory, receptor family.
    Genome Res. 2006 Nov;16(11):1395-403 PMID: 17065611
  6. Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome.
    Genome Biol. 2006;7(11):R112 PMID: 17134480
  7. Improved repeat identification and masking in Dipterans.
    Gene. 2007 Mar 1;389(1):1-9 PMID: 17137733
  8. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.
    Cell. 2007 Mar 23;128(6):1089-103 PMID: 17346786
  9. Sequence finishing and mapping of Drosophila melanogaster heterochromatin.
    Science. 2007 Jun 15;316(5831):1625-8 PMID: 17569867
  10. Heterochromatin: silence is golden.
    Curr Biol. 2003 Dec 2;13(23):R895-8 PMID: 14654010
  11. Initial sequencing and analysis of the human genome.
    Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
  12. Mega-introns in the dynein gene DhDhc7(Y) on the heterochromatic Y chromosome give rise to the giant threads loops in primary spermatocytes of Drosophila hydei.
    Genetics. 2000 Feb;154(2):759-69 PMID: 10655227
  13. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
  14. The sequence of the human genome.
    Science. 2001 Feb 16;291(5507):1304-51 PMID: 11181995
  15. Inparanoid: a comprehensive database of eukaryotic orthologs.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D476-80 PMID: 15608241
  16. FlyBase: genes and gene models.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D390-5 PMID: 15608223
  17. Tandem repeats finder: a program to analyze DNA sequences.
    Nucleic Acids Res. 1999 Jan 15;27(2):573-80 PMID: 9862982
  18. Estimating metazoan divergence times with a molecular clock.
    Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6536-41 PMID: 15084738
  19. An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.
    Genome Biol. 2003;5(1):R3 PMID: 14709175
  20. A genome-wide survey of human pseudogenes.
    Genome Res. 2003 Dec;13(12):2559-67 PMID: 14656963
  21. Identification of pseudogenes in the Drosophila melanogaster genome.
    Nucleic Acids Res. 2003 Feb 1;31(3):1033-7 PMID: 12560500
  22. Heterochromatic sequences in a Drosophila whole-genome shotgun assembly.
    Genome Biol. 2002;3(12):RESEARCH0085 PMID: 12537574
  23. Determining centromere identity: cyclical stories and forking paths.
    Nat Rev Genet. 2001 Aug;2(8):584-96 PMID: 11483983
  24. Apollo: a sequence annotation editor.
    Genome Biol. 2002;3(12):RESEARCH0082 PMID: 12537571
  25. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.
    Genome Biol. 2002;3(12):RESEARCH0084 PMID: 12537573
Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
DOI
10.1126/science.1139815
Published
2007-06-15
Pages
1586-91
Language
English
Region
United States
NLM ID
0404511
PMCID
PMC2819280
Subset
IM
Grants
NHGRI NIH HHS · U54 HG004028 · United States
NHGRI NIH HHS · R01-HG000747 · United States
NHGRI NIH HHS · P41 HG000739-15 · United States
NHGRI NIH HHS · U54 HG004028-01 · United States
NHGRI NIH HHS · R01 HG000747 · United States
NHGRI NIH HHS · R01 HG000747-16 · United States
Corrections
ErratumIn
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External Links
PubMed source DOI: 10.1126/science.1139815 PMC Full Text View journal details
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