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PMID: 16365385 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Transposon-free regions in mammalian genomes.

Genome research ·Vol. 16 ·No. 2 ·2006-02-00 ·Pages 164-72

Simons C, Pheasant M, Makunin IV, Mattick JS

Abstract

Despite the presence of over 3 million transposons separated on average by approximately 500 bp, the human and mouse genomes each contain almost 1000 transposon-free regions (TFRs) over 10 kb in length. The majority of human TFRs correlate with orthologous TFRs in the mouse, despite the fact that most transposons are lineage specific. Many human TFRs also overlap with orthologous TFRs in the marsupial opossum, indicating that these regions have remained refractory to transposon insertion for long evolutionary periods. Over 90% of the bases covered by TFRs are noncoding, much of which is not highly conserved. Most TFRs are not associated with unusual nucleotide composition, but are significantly associated with genes encoding developmental regulators, suggesting that they represent extended regions of regulatory information that are largely unable to tolerate insertions, a conclusion difficult to reconcile with current conceptions of gene regulation.

MeSH Terms
Animals DNA Transposable Elements/genetics Evolution, Molecular Gene Expression Regulation, Developmental/genetics Genome, Human/genetics Humans Mice Opossums/embryology,genetics
Chemicals
DNA Transposable Elements
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Simons Cas
ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane QLD 4072, Australia.
Pheasant Michael
Makunin Igor V
Mattick John S
References (40)
40 references, click to expand
  1. Comparative analyses of multi-species sequences from targeted genomic regions.
    Nature. 2003 Aug 14;424(6950):788-93 PMID: 12917688
  2. A comprehensive transcript map of the mouse Gnas imprinted complex.
    Genome Res. 2003 Jun;13(6B):1410-5 PMID: 12819140
  3. Hox cluster duplications and the opportunity for evolutionary novelties.
    Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):14603-6 PMID: 14638945
  4. The microRNA Registry.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11 PMID: 14681370
  5. The Gene Ontology (GO) database and informatics resource.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61 PMID: 14681407
  6. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6 PMID: 14681408
  7. RTCGD: retroviral tagged cancer gene database.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D523-7 PMID: 14681473
  8. Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are frequently functional.
    Genome Res. 2004 Mar;14(3):367-72 PMID: 14962988
  9. The regulatory content of intergenic DNA shapes genome architecture.
    Genome Biol. 2004;5(4):R25 PMID: 15059258
  10. NUMTs in sequenced eukaryotic genomes.
    Mol Biol Evol. 2004 Jun;21(6):1081-4 PMID: 15014143
  11. Ultraconserved elements in the human genome.
    Science. 2004 May 28;304(5675):1321-5 PMID: 15131266
  12. Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
    PLoS Biol. 2004 Jun;2(6):e162 PMID: 15103394
  13. Phylogenetic footprint analysis of IGF2 in extant mammals.
    Genome Res. 2004 Sep;14(9):1726-32 PMID: 15342558
  14. Evidence for turnover of functional noncoding DNA in mammalian genome evolution.
    Genomics. 2004 Nov;84(5):806-13 PMID: 15475259
  15. Finishing the euchromatic sequence of the human genome.
    Nature. 2004 Oct 21;431(7011):931-45 PMID: 15496913
  16. Assessment of inhomogeneities in an E. coli physical map.
    Nucleic Acids Res. 1991 Aug 11;19(15):4241-6 PMID: 1870978
  17. Genome sequence of the nematode C. elegans: a platform for investigating biology.
    Science. 1998 Dec 11;282(5396):2012-8 PMID: 9851916
  18. Tandem repeats finder: a program to analyze DNA sequences.
    Nucleic Acids Res. 1999 Jan 15;27(2):573-80 PMID: 9862982
  19. Evolution and functional classification of vertebrate gene deserts.
    Genome Res. 2005 Jan;15(1):137-45 PMID: 15590943
  20. Genomic maps and comparative analysis of histone modifications in human and mouse.
    Cell. 2005 Jan 28;120(2):169-81 PMID: 15680324
  21. Mathematics/computation. Accelerating networks.
    Science. 2005 Feb 11;307(5711):856-8 PMID: 15705831
  22. Small regulatory RNAs in mammals.
    Hum Mol Genet. 2005 Apr 15;14 Spec No 1:R121-32 PMID: 15809264
  23. Clustering and conservation patterns of human microRNAs.
    Nucleic Acids Res. 2005;33(8):2697-706 PMID: 15891114
  24. Distribution and intensity of constraint in mammalian genomic sequence.
    Genome Res. 2005 Jul;15(7):901-13 PMID: 15965027
  25. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res. 2005 Aug;15(8):1034-50 PMID: 16024819
  26. Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences.
    Hum Mol Genet. 2005 Sep 1;14(17):2533-46 PMID: 16037065
  27. Evidence for evolutionarily conserved secondary structure in the H19 tumor suppressor RNA.
    Nucleic Acids Res. 2000 Mar 1;28(5):1221-7 PMID: 10666466
  28. SINE retroposons can be used in vivo as nucleation centers for de novo methylation.
    Mol Cell Biol. 2000 May;20(10):3434-41 PMID: 10779333
  29. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization.
    Proc Natl Acad Sci U S A. 2000 Dec 19;97(26):14311-6 PMID: 11106375
  30. Initial sequencing and analysis of the human genome.
    Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
  31. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.
    Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):327-32 PMID: 11756672
  32. Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.
    Genome Res. 2002 Jun;12(6):894-908 PMID: 12045143
  33. Comparative sequence analysis of the INS-IGF2-H19 gene cluster in pigs.
    Mamm Genome. 2002 Jul;13(7):388-98 PMID: 12140686
  34. Initial sequencing and comparative analysis of the mouse genome.
    Nature. 2002 Dec 5;420(6915):520-62 PMID: 12466850
  35. The UCSC Genome Browser Database.
    Nucleic Acids Res. 2003 Jan 1;31(1):51-4 PMID: 12519945
  36. Human-mouse alignments with BLASTZ.
    Genome Res. 2003 Jan;13(1):103-7 PMID: 12529312
  37. Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar.
    Curr Opin Struct Biol. 2003 Feb;13(1):40-8 PMID: 12581658
  38. An enhancer-titration effect induces digit-specific regulatory alleles of the HoxD cluster.
    Dev Biol. 2003 Apr 15;256(2):212-20 PMID: 12679098
  39. Genomic clocks and evolutionary timescales.
    Trends Genet. 2003 Apr;19(4):200-6 PMID: 12683973
  40. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.
    Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9 PMID: 14500911
Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.4624306
Published
2006-02-00
Epub
2005-00-19
Pages
164-72
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC1361711
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.4624306 PMC Full Text View journal details
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