Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine.

Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

Original Publication: London : BioMed Central, [2000-

Cattle/*embryology ; Cattle/*genetics ; DNA Methylation/*genetics ; Embryo, Mammalian/*embryology ; Embryo, Mammalian/*metabolism ; Genomics/*methods; Animals ; Chromosome Mapping ; Consensus Sequence/genetics ; CpG Islands/genetics ; DNA-Cytosine Methylases/metabolism ; Deoxyribonuclease HpaII/metabolism ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; Repetitive Sequences, Nucleic Acid/genetics

Background: It was recently established that changes in methylation during development are dynamic and involve both methylation and demethylation processes. Yet, which genomic sites are changing and what are the contributions of methylation (5mC) and hydroxymethylation (5hmC) to this epigenetic remodeling is still unknown. When studying early development, options for methylation profiling are limited by the unavailability of sufficient DNA material from these scarce samples and limitations are aggravated in non-model species due to the lack of technological platforms. We therefore sought to obtain a representation of differentially 5mC or 5hmC loci during bovine early embryo stages through the use of three complementary methods, based on selective methyl-sensitive restriction and enrichment by ligation-mediated PCR or on subtractive hybridization. Using these strategies, libraries of putative methylation and hydroxymethylated sites were generated from Day-7 and Day-12 bovine embryos.
Results: Over 1.2 million sequencing reads were analyzed, resulting in 151,501 contigs, of which 69,136 were uniquely positioned on the genome. A total of 101,461 putative methylated sites were identified. The output of the three methods differed in genomic coverage as well as in the nature of the identified sites. The classical MspI/HpaII combination of restriction enzymes targeted CpG islands whereas the other methods covered 5mC and 5hmC sites outside of these regions. Data analysis suggests a transition of these methylation marks between Day-7 and Day-12 embryos in specific classes of repeat-containing elements.
Conclusions: Our combined strategy offers a genomic map of the distribution of cytosine methylation/hydroxymethylation during early bovine embryo development. These results support the hypothesis of a regulatory phase of hypomethylation in repeat sequences during early embryogenesis.

Biochem Biophys Res Commun. 2011 Jul 22;411(1):40-3. (PMID: 21703242)
Curr Biol. 2000 Apr 20;10(8):475-8. (PMID: 10801417)
BMC Bioinformatics. 2006 Feb 22;7:85. (PMID: 16504059)
BMC Genomics. 2011 May 11;12(1):231. (PMID: 21569359)
Genome Biol. 2009;10(4):R42. (PMID: 19393038)
Nat Genet. 2011 Jun 26;43(8):811-4. (PMID: 21706000)
Genome Res. 2002 Apr;12(4):656-64. (PMID: 11932250)
Hum Reprod. 2011 Sep;26(9):2576-85. (PMID: 21685140)
Cell Reprogram. 2010 Feb;12(1):33-42. (PMID: 20132011)
Biochem J. 1972 Feb;126(4):781-90. (PMID: 4538516)
Nature. 2012 Mar 28;484(7394):339-44. (PMID: 22456710)
Curr Opin Genet Dev. 2003 Dec;13(6):562-8. (PMID: 14638315)
Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2284-9. (PMID: 9122186)
Mol Cell. 2011 May 20;42(4):451-64. (PMID: 21514197)
Nature. 2011 May 19;473(7347):394-7. (PMID: 21552279)
BMC Genomics. 2007 Nov 13;8:416. (PMID: 17997864)
Nucleic Acids Res. 2010 Oct;38(19):e181. (PMID: 20685817)
Mol Reprod Dev. 2010 Feb;77(2):105-13. (PMID: 19921744)
Mol Reprod Dev. 2010 Jan;77(1):69-75. (PMID: 19743475)
Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):210-223. (PMID: 20836023)
J Mol Biol. 1978 Jan 5;118(1):27-47. (PMID: 625056)
Science. 1993 Feb 12;259(5097):946-51. (PMID: 8438152)
Mamm Genome. 2007 May;18(5):287-99. (PMID: 17588189)
Biol Reprod. 2004 Jul;71(1):217-23. (PMID: 15028629)
Genomics. 2008 Mar;91(3):267-73. (PMID: 18226492)
Science. 2011 Sep 2;333(6047):1303-7. (PMID: 21817016)
Hum Mol Genet. 2001 Dec 1;10(25):2917-31. (PMID: 11741835)
Methods. 2010 Nov;52(3):232-6. (PMID: 20542119)
Anim Sci J. 2011 Aug;82(4):523-30. (PMID: 21794009)
Nature. 2000 Feb 3;403(6769):501-2. (PMID: 10676950)
Cytogenet Genome Res. 2005;110(1-4):462-7. (PMID: 16093699)
Methods Mol Biol. 2009;507:117-30. (PMID: 18987811)
Nat Biotechnol. 2010 Oct;28(10):1097-105. (PMID: 20852635)
Nature. 2007 May 24;447(7143):425-32. (PMID: 17522676)
Methods Mol Biol. 2009;507:77-87. (PMID: 18987808)
FEBS Lett. 2009 Jun 5;583(11):1713-20. (PMID: 19376112)
Nature. 2010 Aug 26;466(7310):1129-33. (PMID: 20639862)
Nat Protoc. 2012 Oct;7(10):1897-908. (PMID: 23018193)
BMC Dev Biol. 2008 Feb 11;8:14. (PMID: 18261243)
Bioinformatics. 2010 Oct 1;26(19):2460-1. (PMID: 20709691)
Nature. 2010 Dec 9;468(7325):839-43. (PMID: 21057493)
Nucleic Acids Res. 2011 Apr;39(8):e55. (PMID: 21300643)
Cloning Stem Cells. 2004;6(2):133-9. (PMID: 15268787)
Nucleic Acids Res. 2012 Sep 1;40(17):8255-65. (PMID: 22730288)
Nucleic Acids Res. 2010 Jan;38(Database issue):D234-6. (PMID: 19846593)
Genome Res. 2009 Jun;19(6):959-66. (PMID: 19273618)
Science. 2009 May 15;324(5929):930-5. (PMID: 19372391)
Nat Protoc. 2012 Oct;7(10):1909-17. (PMID: 23018194)
Nucleic Acids Res. 2004 Aug 09;32(14):4100-8. (PMID: 15302911)
Nat Commun. 2011;2:241. (PMID: 21407207)
Science. 2012 May 18;336(6083):934-7. (PMID: 22539555)
Lancet. 1999 Nov 6;354(9190):1579-85. (PMID: 10560671)
Reproduction. 2009 Feb;137(2):245-57. (PMID: 18987256)
Nat Biotechnol. 2011 Jan;29(1):68-72. (PMID: 21151123)
Science. 2010 Oct 29;330(6004):622-7. (PMID: 21030646)
J Biol Chem. 2005 Nov 25;280(47):39594-600. (PMID: 16188882)
Nucleic Acids Res. 2010 Jun;38(11):e125. (PMID: 20371518)
Science. 2011 Oct 14;334(6053):194. (PMID: 21940858)
Epigenomics. 2010 Oct;2(5):639-55. (PMID: 22122049)
Cell Reprogram. 2010 Apr;12(2):175-81. (PMID: 20677931)
Genome Biol. 2011 Jun 20;12(6):R54. (PMID: 21689397)
Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23. (PMID: 22086951)
J Biol Chem. 2011 May 27;286(21):18347-53. (PMID: 21454628)
Methods Mol Biol. 2001;181:113-32. (PMID: 12843445)
Biochem Biophys Res Commun. 1988 Mar 30;151(3):1173-9. (PMID: 3355548)
Epigenetics. 2006 Jul-Sep;1(3):146-52. (PMID: 17965615)
Nucleic Acids Res. 2006 Jan 20;34(2):528-42. (PMID: 16428248)
Genome Res. 2006 Aug;16(8):1046-55. (PMID: 16809668)
Cell Reprogram. 2010 Feb;12(1):15-22. (PMID: 19780699)
Nucleic Acids Res. 1984 Mar 26;12(6):2807-22. (PMID: 6324127)
Nature. 2011 May 19;473(7347):398-402. (PMID: 21460836)
Bioinformatics. 2010 Mar 15;26(6):841-2. (PMID: 20110278)
Nucleic Acids Res. 2006 Feb 09;34(3):e19. (PMID: 16473842)
BMC Bioinformatics. 2011 Jan 26;12:35. (PMID: 21269502)
Epigenomics. 2009 Dec;1(2):331-45. (PMID: 20526417)
Epigenetics. 2012 Feb;7(2):131-6. (PMID: 22395461)
Birth Defects Res A Clin Mol Teratol. 2011 Aug;91(8):652-65. (PMID: 21425433)
Am J Reprod Immunol. 2010 Oct;64(4):255-64. (PMID: 20528833)

EC 2.1.1.- (DNA modification methylase HpaII)
EC 2.1.1.- (DNA-Cytosine Methylases)
EC 3.1.21.- (Deoxyribonuclease HpaII)

Date Created: 20130619 Date Completed: 20131030 Latest Revision: 20211021

20231215

PMC3689598

10.1186/1471-2164-14-406

23773395