title: Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays.
abstract: BACKGROUND
  The processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP) and methylated DNA (MeDIP) represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription.
  
  
  RESULTS
  To allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease.
  
  
  CONCLUSIONS
  The high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation to pursue mechanistic, functional and diagnostic information at genes of interest in health and disease.
authors.affiliation: UW Medicine Lake Union, University of Washington, Seattle, WA 98109, USA.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Yu
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Feng
authors.forename: Yusong
authors.initials: Y
authors.lastname: Ruan
authors.forename: Radko
authors.initials: R
authors.lastname: Komers
authors.forename: Nancy
authors.initials: N
authors.lastname: Kiviat
authors.forename: Karol
authors.initials: K
authors.lastname: Bomsztyk
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000295:instrumentation / Q000379:methods*; D004247:DNA / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D011506:Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D002843:Chromatin; D011506:Proteins; D004247:DNA
references.citation: Biochem Soc Trans. 2005 Dec;33(Pt 6):1444-6
references.pmid: 16246142
references.citation: Am J Physiol Renal Physiol. 2010 Jul;299(1):F14-25
references.pmid: 20462972
references.citation: Mol Cell. 2006 Aug 4;23(3):289-96
references.pmid: 16885019
references.citation: Carcinogenesis. 2010 Jan;31(1):27-36
references.pmid: 19752007
references.citation: Diabetes. 2004 Dec;53(12):3248-57
references.pmid: 15561957
references.citation: Nat Rev Cancer. 2003 Apr;3(4):253-66
references.pmid: 12671664
references.citation: Nature. 2009 Nov 19;462(7271):315-22
references.pmid: 19829295
references.citation: Nature. 2011 May 5;473(7345):43-9
references.pmid: 21441907
references.citation: Exp Mol Pathol. 2010 Apr;88(2):287-92
references.pmid: 20079733
references.citation: J Am Soc Nephrol. 2010 Dec;21(12):2069-80
references.pmid: 20930066
references.citation: Nucleic Acids Res. 2004 Feb 18;32(3):e38
references.pmid: 14973332
references.citation: Cell. 2007 Feb 23;128(4):707-19
references.pmid: 17320508
references.citation: Cell. 2007 Feb 23;128(4):693-705
references.pmid: 17320507
references.citation: Clin Exp Pharmacol Physiol. 2011 Jul;38(7):451-9
references.pmid: 21309809
references.citation: Nat Rev Genet. 2009 May;10(5):295-304
references.pmid: 19308066
references.citation: Methods Mol Biol. 2009;567:249-62
references.pmid: 19588097
references.citation: Cancer Epidemiol Biomarkers Prev. 2008 Mar;17(3):645-54
references.pmid: 18349282
references.citation: Proc Natl Acad Sci U S A. 1997 Mar 18;94(6):2284-9
references.pmid: 9122186
references.citation: Cell. 2011 Mar 4;144(5):646-74
references.pmid: 21376230
references.citation: Nat Rev Mol Cell Biol. 2007 Mar;8(3):234-44
references.pmid: 17318227
references.citation: Science. 2010 Sep 3;329(5996):1201-5
references.pmid: 20647423
references.citation: Nat Protoc. 2006;1(1):179-85
references.pmid: 17406230
references.citation: APMIS. 2007 Oct;115(10):1039-59
references.pmid: 18042143
references.citation: J Cell Biol. 2006 Feb 27;172(5):679-92
references.pmid: 16492807
references.citation: Nucleic Acids Res. 2008 Feb;36(3):e17
references.pmid: 18203739
references.citation: Methods. 2009 Mar;47(3):142-50
references.pmid: 18950712
references.citation: Biotechnol J. 2008 Mar;3(3):378-82
references.pmid: 18293327
references.citation: Nephrol Dial Transplant. 2010 Jun;25(6):1811-7
references.pmid: 20067909
references.citation: Cancer Metastasis Rev. 2008 Jun;27(2):315-34
references.pmid: 18246412
references.citation: Biochem Biophys Res Commun. 2007 Sep 7;360(4):772-7
references.pmid: 17631861
references.citation: Genome Biol. 2010;11(7):R70
references.pmid: 20602769
references.citation: J Biol Chem. 2010 Nov 26;285(48):37589-97
references.pmid: 20876582
references.citation: Nature. 2005 Dec 22;438(7071):1116-22
references.pmid: 16222246
references.citation: Cell. 2006 Apr 21;125(2):213-7
references.pmid: 16630806
references.citation: Nucleic Acids Res. 2000 Apr 15;28(8):E32
references.pmid: 10734209
references.citation: J Exp Med. 2008 Sep 29;205(10):2409-17
references.pmid: 18809715
references.citation: Mol Cell Biol. 1999 Oct;19(10):6690-8
references.pmid: 10490608
references.citation: Methods Mol Biol. 2011;703:219-34
references.pmid: 21125493
references.citation: Am J Physiol Renal Physiol. 2008 Apr;294(4):F697-701
references.pmid: 18272603
references.citation: Curr Opin Chem Biol. 2007 Feb;11(1):66-73
references.pmid: 17157550
references.citation: J Am Soc Nephrol. 2009 Dec;20(12):2503-12
references.pmid: 19729434
references.citation: Am J Physiol Renal Physiol. 2003 Jul;285(1):F40-8
references.pmid: 12631553
references.citation: Nature. 2005 Dec 22;438(7071):1176-80
references.pmid: 16222244
references.citation: Cell. 2005 Jun 17;121(6):859-72
references.pmid: 15960974
references.citation: Cancer Epidemiol Biomarkers Prev. 2006 Jan;15(1):114-23
references.pmid: 16434596
references.citation: Trends Genet. 2007 Aug;23(8):413-8
references.pmid: 17559965
references.citation: Proc Natl Acad Sci U S A. 1985 Oct;82(19):6470-4
references.pmid: 2995966
references.citation: Cell. 2007 Feb 23;128(4):669-81
references.pmid: 17320505
references.citation: J Biol Chem. 2011 Mar 18;286(11):9763-75
references.pmid: 21233203
references.citation: Genes Dev. 2004 Oct 1;18(19):2315-35
references.pmid: 15466484
references.citation: Ann N Y Acad Sci. 2003 Mar;983:84-100
references.pmid: 12724214
references.citation: Genome Biol. 2009;10(9):R89
references.pmid: 19723310
references.citation: J Biol Chem. 2005 Jan 28;280(4):2446-54
references.pmid: 15537652
references.citation: Methods Enzymol. 1996;274:189-97
references.pmid: 8902805
references.citation: Biochim Biophys Acta. 1999 Aug 30;1454(3):251-60
references.pmid: 10452959
references.citation: Nature. 2010 Jul 1;466(7302):62-7
references.pmid: 20596014
references.citation: Diabetes. 2011 Jan;60(1):127-37
references.pmid: 20929976
references.citation: Genome Biol. 2009;10(3):R31
references.pmid: 19317917
references.citation: Methods. 1997 Feb;11(2):205-14
references.pmid: 8993033
references.citation: Biotechniques. 2008 Jan;44(1):35, 37, 39 passim
references.pmid: 18254377
references.citation: J Am Soc Nephrol. 2010 Sep;21(9):1533-42
references.pmid: 20634301
references.citation: Science. 2006 Jul 28;313(5786):449-51
references.pmid: 16873633
references.citation: Science. 2006 Jul 28;313(5786):533-6
references.pmid: 16873666