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PMID: 20584328 Published · ppublish English Journal Article

Estimating enrichment of repetitive elements from high-throughput sequence data.

Genome biology ·Vol. 11 ·No. 6 ·2010-00-00 ·Pages R69

Day DS, Luquette LJ, Park PJ, Kharchenko PV

Abstract

We describe computational methods for analysis of repetitive elements from short-read sequencing data, and apply them to study histone modifications associated with the repetitive elements in human and mouse cells. Our results demonstrate that while accurate enrichment estimates can be obtained for individual repeat types and small sets of repeat instances, there are distinct combinatorial patterns of chromatin marks associated with major annotated repeat families, including H3K27me3/H3K9me3 differences among the endogenous retroviral element classes.

MeSH Terms
Animals Base Sequence CD4-Positive T-Lymphocytes/metabolism Cell Line Databases, Nucleic Acid Embryo, Mammalian/cytology Fibroblasts/metabolism High-Throughput Screening Assays/methods Histones/metabolism Humans Mice Phylogeny Protein Processing, Post-Translational Repetitive Sequences, Nucleic Acid/genetics Sequence Analysis, DNA/methods
Chemicals
Histones
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Day Daniel S
Harvard-MIT Health Sciences and Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
Luquette Lovelace J
Park Peter J
Kharchenko Peter V
References (43)
43 references, click to expand
  1. Fast and accurate short read alignment with Burrows-Wheeler transform.
    Bioinformatics. 2009 Jul 15;25(14):1754-60 PMID: 19451168
  2. High-resolution mapping of copy-number alterations with massively parallel sequencing.
    Nat Methods. 2009 Jan;6(1):99-103 PMID: 19043412
  3. Repbase Update, a database of eukaryotic repetitive elements.
    Cytogenet Genome Res. 2005;110(1-4):462-7 PMID: 16093699
  4. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin.
    Curr Biol. 2003 Jul 15;13(14):1192-200 PMID: 12867029
  5. Mouse centric and pericentric satellite repeats form distinct functional heterochromatin.
    J Cell Biol. 2004 Aug 16;166(4):493-505 PMID: 15302854
  6. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains.
    Nature. 2007 Aug 30;448(7157):1050-3 PMID: 17660834
  7. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53.
    Proc Natl Acad Sci U S A. 2007 Nov 20;104(47):18613-8 PMID: 18003932
  8. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease.
    Trends Genet. 2007 Jul;23(7):326-33 PMID: 17524519
  9. Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements.
    Mol Cell Biol. 2002 Jan;22(2):480-91 PMID: 11756544
  10. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity.
    EMBO J. 2008 Oct 22;27(20):2691-701 PMID: 18818693
  11. Transposable elements and host genome evolution.
    Trends Ecol Evol. 2000 Mar;15(3):95-99 PMID: 10675923
  12. Role of endogenous retroviruses in autoimmune diseases.
    Infect Dis Clin North Am. 2006 Dec;20(4):913-29 PMID: 17118296
  13. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
    Nature. 2007 Jun 14;447(7146):799-816 PMID: 17571346
  14. Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects.
    Cell. 2002 Feb 22;108(4):489-500 PMID: 11909520
  15. An integrated software system for analyzing ChIP-chip and ChIP-seq data.
    Nat Biotechnol. 2008 Nov;26(11):1293-300 PMID: 18978777
  16. Preferential epigenetic suppression of the autonomous MusD over the nonautonomous ETn mouse retrotransposons.
    Mol Cell Biol. 2009 May;29(9):2456-68 PMID: 19273603
  17. Evolution of the mammalian transcription factor binding repertoire via transposable elements.
    Genome Res. 2008 Nov;18(11):1752-62 PMID: 18682548
  18. ChIP-seq: advantages and challenges of a maturing technology.
    Nat Rev Genet. 2009 Oct;10(10):669-80 PMID: 19736561
  19. Transposable elements and the evolution of regulatory networks.
    Nat Rev Genet. 2008 May;9(5):397-405 PMID: 18368054
  20. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
    Nature. 2007 Aug 2;448(7153):553-60 PMID: 17603471
  21. Determination of enriched histone modifications in non-genic portions of the human genome.
    BMC Genomics. 2009 Mar 31;10:143 PMID: 19335899
  22. Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells.
    J Biol Chem. 2003 Jul 25;278(30):27658-62 PMID: 12724318
  23. RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos.
    Dev Biol. 2004 May 1;269(1):276-85 PMID: 15081373
  24. Design and analysis of ChIP-seq experiments for DNA-binding proteins.
    Nat Biotechnol. 2008 Dec;26(12):1351-9 PMID: 19029915
  25. Retroelement distributions in the human genome: variations associated with age and proximity to genes.
    Genome Res. 2002 Oct;12(10):1483-95 PMID: 12368240
  26. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.
    Nat Biotechnol. 2009 Jan;27(1):66-75 PMID: 19122651
  27. Activation and transposition of endogenous retroviral elements in hypomethylation induced tumors in mice.
    Oncogene. 2008 Jan 10;27(3):404-8 PMID: 17621273
  28. Keeping active endogenous retroviral-like elements in check: the epigenetic perspective.
    Cell Mol Life Sci. 2008 Nov;65(21):3329-47 PMID: 18818875
  29. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain.
    Nature. 2001 Mar 1;410(6824):120-4 PMID: 11242054
  30. Transposable elements and the epigenetic regulation of the genome.
    Nat Rev Genet. 2007 Apr;8(4):272-85 PMID: 17363976
  31. Confidence intervals for a ratio of two independent binomial proportions.
    Stat Med. 2008 Nov 20;27(26):5497-508 PMID: 18781560
  32. SeqMap: mapping massive amount of oligonucleotides to the genome.
    Bioinformatics. 2008 Oct 15;24(20):2395-6 PMID: 18697769
  33. Unlocking the secrets of the genome.
    Nature. 2009 Jun 18;459(7249):927-30 PMID: 19536255
  34. High-resolution profiling of histone methylations in the human genome.
    Cell. 2007 May 18;129(4):823-37 PMID: 17512414
  35. The profile of repeat-associated histone lysine methylation states in the mouse epigenome.
    EMBO J. 2005 Feb 23;24(4):800-12 PMID: 15678104
  36. Loss of the Suv39h histone methyltransferases impairs mammalian heterochromatin and genome stability.
    Cell. 2001 Nov 2;107(3):323-37 PMID: 11701123
  37. Model-based analysis of ChIP-Seq (MACS).
    Genome Biol. 2008;9(9):R137 PMID: 18798982
  38. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.
    Cell. 2008 Jun 13;133(6):1106-17 PMID: 18555785
  39. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation.
    Nat Genet. 1998 Oct;20(2):116-7 PMID: 9771701
  40. Initial sequencing and analysis of the human genome.
    Nature. 2001 Feb 15;409(6822):860-921 PMID: 11237011
  41. Polycomb complexes repress developmental regulators in murine embryonic stem cells.
    Nature. 2006 May 18;441(7091):349-53 PMID: 16625203
  42. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin.
    Mol Cell. 2003 Dec;12(6):1577-89 PMID: 14690609
  43. Initial sequencing and comparative analysis of the mouse genome.
    Nature. 2002 Dec 5;420(6915):520-62 PMID: 12466850
Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2010-11-6-r69
Published
2010-00-00
Epub
2010-00-28
Pages
R69
Language
English
Region
England
NLM ID
100960660
PMCID
PMC2911117
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2010-11-6-r69 PMC Full Text View journal details
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