Microplate-based platform for combined chromatin and DNA methylation immunoprecipitation assays

BMC Molecular Biology

Volumn 12, Issue , 2011, Pages

  Yu, Jingjing ^a   Feng, Qinghua ^a   Ruan, Yusong ^a   Komers, Radko ^b   Kiviat, Nancy ^a   Bomsztyk, Karol ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE; PROTEIN;

ANIMAL TISSUE; ARTICLE; BINDING SITE; CELL CULTURE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CONTROLLED STUDY; DIABETIC NEPHROPATHY; DNA DETERMINATION; DNA METHYLATION; FEMALE; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN TISSUE; IMMUNOPRECIPITATION; IN VIVO STUDY; MALE; MICROCHIP ANALYSIS; MICROPLATE BASED IMMUNOPRECIPITATION; MOUSE; NEOPLASM; NONHUMAN; PROTEIN DNA INTERACTION; ANIMAL; C57BL MOUSE; CELL LINE; CHROMATIN; EVALUATION; GENETICS; HIGH THROUGHPUT SCREENING; INSTRUMENTATION; METABOLISM; METHODOLOGY;

ANIMALS; CELL LINE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA; DNA METHYLATION; HIGH-THROUGHPUT SCREENING ASSAYS; HUMANS; MALE; MICE; MICE, INBRED C57BL; PROTEINS;

EID: 81255128238     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-12-49     Document Type: Article

References (63)

1. Sharma S, Kelly TK, Jones PA. Epigenetics in cancer. Carcinogenesis 2010, 31:27-36.
2. Heiser LM, Wang NJ, Talcott CL, Laderoute KR, Knapp M, Guan Y, Hu Z, Ziyad S, Weber BL, Laquerre S, et al. Integrated analysis of breast cancer cell lines reveals unique signaling pathways. Genome Biol 2009, 10:R31.
3. Lund AH, van Lohuizen M. Epigenetics and cancer. Genes Dev 2004, 18:2315-2335.
4. Villeneuve LM, Natarajan R. The role of epigenetics in the pathology of diabetic complications. Am J Physiol Renal Physiol 2010, 299:F14-25.
5. El-Osta A, Brasacchio D, Yao D, Pocai A, Jones PL, Roeder RG, Cooper ME, Brownlee M. Transient high glucose causes persistent epigenetic changes and altered gene expression during subsequent normoglycemia. J Exp Med 2008, 205:2409-2417.
6. Hang CT, Yang J, Han P, Cheng HL, Shang C, Ashley E, Zhou B, Chang CP. Chromatin regulation by Brg1 underlies heart muscle development and disease. Nature 2010, 466:62-67.
7. Fraga MF, Esteller M. Epigenetics and aging: the targets and the marks. Trends Genet 2007, 23:413-418.
8. Li B, Carey M, Workman JL. The role of chromatin during transcription. Cell 2007, 128:707-719.
9. Kouzarides T. Chromatin modifications and their function. Cell 2007, 128:693-705.
10. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462:315-322.
11. Gronbaek K, Hother C, Jones PA. Epigenetic changes in cancer. Apmis 2007, 115:1039-1059.
12. Laird PW. The power and the promise of DNA methylation markers. Nat Rev Cancer 2003, 3:253-266.
13. Patra SK, Patra A, Rizzi F, Ghosh TC, Bettuzzi S. Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development. Cancer Metastasis Rev 2008, 27:315-334.
14. Choi JK, Bae JB, Lyu J, Kim TY, Kim YJ. Nucleosome deposition and DNA methylation at coding region boundaries. Genome Biol 2009, 10:R89.
15. Choi JK. Contrasting chromatin organization of CpG islands and exons in the human genome. Genome Biol 2010, 11:R70.
16. Bender CM, Gonzalgo ML, Gonzales FA, Nguyen CT, Robertson KD, Jones PA. Roles of cell division and gene transcription in the methylation of CpG islands. Mol Cell Biol 1999, 19:6690-6698.
17. Pomraning KR, Smith KM, Freitag M. Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 2009, 47:142-150.
18. Sorensen AL, Collas P. Immunoprecipitation of methylated DNA. Methods Mol Biol 2009, 567:249-262.
19. Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV, Laird PW. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 2000, 28:E32.
20. Ushijima T, Morimura K, Hosoya Y, Okonogi H, Tatematsu M, Sugimura T, Nagao M. Establishment of methylation-sensitive-representational difference analysis and isolation of hypo- and hypermethylated genomic fragments in mouse liver tumors. Proc Natl Acad Sci USA 1997, 94:2284-2289.
21. Jacinto FV, Ballestar E, Esteller M. Methyl-DNA immunoprecipitation (MeDIP): Hunting down the DNA methylome. Biotechniques 2008, 44:35-42.
22. Wysocka J, Swigut T, Milne TA, Dou Y, Zhang X, Burlingame AL, Roeder RG, Brivanlou AH, Allis CD. WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development. Cell 2005, 121:859-872.
23. Fischle W, Tseng BS, Dormann HL, Ueberheide BM, Garcia BA, Shabanowitz J, Hunt DF, Funabiki H, Allis CD. Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature 2005, 438:1116-1122.
24. Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell 2007, 128:669-681.
25. Garcia BA, Shabanowitz J, Hunt DF. Characterization of histones and their post-translational modifications by mass spectrometry. Curr Opin Chem Biol 2007, 11:66-73.
26. Trojer P, Reinberg D. Histone lysine demethylases and their impact on epigenetics. Cell 2006, 125:213-217.
27. Clayton AL, Hazzalin CA, Mahadevan LC. Enhanced histone acetylation and transcription: a dynamic perspective. Mol Cell 2006, 23:289-296.
28. Thiagalingam S, Cheng KH, Lee HJ, Mineva N, Thiagalingam A, Ponte JF. Histone deacetylases: unique players in shaping the epigenetic histone code. Ann N Y Acad Sci 2003, 983:84-100.
29. Hirota T, Lipp JJ, Toh BH, Peters JM. Histone H3 serine 10 phosphorylation by Aurora B causes HP1 dissociation from heterochromatin. Nature 2005, 438:1176-1180.
30. He Z, Cho YY, Ma WY, Choi HS, Bode AM, Dong Z. Regulation of ultraviolet B-induced phosphorylation of histone H3 at serine 10 by Fyn kinase. J Biol Chem 2005, 280:2446-2454.
31. Bennett D. Transcriptional control by chromosome-associated protein phosphatase-1. Biochem Soc Trans 2005, 33:1444-1446.
32. Edmunds JW, Mahadevan LC. Cell signaling. Protein kinases seek close encounters with active genes. Science 2006, 313:449-451.
33. Mikula M, Bomsztyk K. Direct recruitment of ERK cascade components to inducible genes is regulated by the heterogeneous nuclear ribonucleoprotein (HnRNP) K. J Biol Chem 2011, 286:9763-9775.
34. Pokholok DK, Zeitlinger J, Hannett NM, Reynolds DB, Young RA. Activated signal transduction kinases frequently occupy target genes. Science 2006, 313:533-536.
35. Bungard D, Fuerth BJ, Zeng PY, Faubert B, Mass NL, Viollet B, Carling D, Thompson CB, Jones RG, Berger SL. Signaling Kinase AMPK Activates Stress-Promoted Transcription via Histone H2B Phosphorylation. Science 2010, 329:1201-1205.
36. Nelson JD, Leboeuf RC, Bomsztyk K. Direct recruitment of insulin receptor and ERK signaling cascade to insulin-inducible gene loci. Diabetes 2011, 60:127-137.
37. Trinkle-Mulcahy L, Andersen J, Lam YW, Moorhead G, Mann M, Lamond AI. Repo-Man recruits PP1 gamma to chromatin and is essential for cell viability. J Cell Biol 2006, 172:679-692.
38. Moorhead GB, Trinkle-Mulcahy L, Ulke-Lemee A. Emerging roles of nuclear protein phosphatases. Nat Rev Mol Cell Biol 2007, 8:234-244.
39. Orlando V, Strutt H, Paro R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 1997, 11:205-214.
40. Solomon MJ, Varshavsky A. Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures. Proc Natl Acad Sci USA 1985, 82:6470-6474.
41. O'Neill LP, Turner BM. Immunoprecipitation of chromatin. Methods Enzymol 1996, 274:189-197.
42. Cedar H, Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 2009, 10:295-304.
43. Sova P, Feng Q, Geiss G, Wood T, Strauss R, Rudolf V, Lieber A, Kiviat N. Discovery of novel methylation biomarkers in cervical carcinoma by global demethylation and microarray analysis. Cancer Epidemiol Biomarkers Prev 2006, 15:114-123.
44. Zheng S, Noonan WT, Metreveli NS, Coventry S, Kralik PM, Carlson EC, Epstein PN. Development of late-stage diabetic nephropathy in OVE26 diabetic mice. Diabetes 2004, 53:3248-3257.
45. Gletsu NA, Field CJ, Clandinin MT. Obese mice have higher insulin receptor levels in the hepatocyte cell nucleus following insulin stimulation in vivo with an oral glucose meal. Biochim Biophys Acta 1999, 1454:251-260.
46. Nelson JD, Denisenko O, Bomsztyk K. Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat Protoc 2006, 1:179-185.
47. Flanagin S, Nelson JD, Castner DG, Denisenko O, Bomsztyk K. Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events. Nucleic Acids Res 2008, 36:e17.
48. Nelson J, Denisenko O, Bomsztyk K. Profiling RNA polymerase II using the fast chromatin immunoprecipitation method. Methods Mol Biol 2011, 703:219-234.
49. Feng Q, Hawes SE, Stern JE, Wiens L, Lu H, Dong ZM, Jordan CD, Kiviat NB, Vesselle H. DNA methylation in tumor and matched normal tissues from non-small cell lung cancer patients. Cancer Epidemiol Biomarkers Prev 2008, 17:645-654.
50. Yang AS, Estecio MR, Doshi K, Kondo Y, Tajara EH, Issa JP. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 2004, 32:e38.
51. Feng Q, Stern JE, Hawes SE, Lu H, Jiang M, Kiviat NB. DNA methylation changes in normal liver tissues and hepatocellular carcinoma with different viral infection. Exp Mol Pathol 2010, 88:287-292.
52. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011, 144:646-674.
53. Brosius FC, Alpers CE, Bottinger EP, Breyer MD, Coffman TM, Gurley SB, Harris RC, Kakoki M, Kretzler M, Leiter EH, et al. Mouse models of diabetic nephropathy. J Am Soc Nephrol 2009, 20:2503-2512.
54. Sun G, Reddy MA, Yuan H, Lanting L, Kato M, Natarajan R. Epigenetic histone methylation modulates fibrotic gene expression. J Am Soc Nephrol 2010, 21:2069-2080.
55. Sayyed SG, Gaikwad AB, Lichtnekert J, Kulkarni O, Eulberg D, Klussmann S, Tikoo K, Anders HJ. Progressive glomerulosclerosis in type 2 diabetes is associated with renal histone H3K9 and H3K23 acetylation, H3K4 dimethylation and phosphorylation at serine 10. Nephrol Dial Transplant 2010, 25:1811-1817.
56. Villeneuve LM, Reddy MA, Natarajan R. Epigenetics: deciphering its role in diabetes and its chronic complications. Clin Exp Pharmacol Physiol 2011, 38:401-409.
57. Tesch GH. MCP-1/CCL2: a new diagnostic marker and therapeutic target for progressive renal injury in diabetic nephropathy. Am J Physiol Renal Physiol 2008, 294:F697-701.
58. Kanamori H, Matsubara T, Mima A, Sumi E, Nagai K, Takahashi T, Abe H, Iehara N, Fukatsu A, Okamoto H, et al. Inhibition of MCP-1/CCR2 pathway ameliorates the development of diabetic nephropathy. Biochem Biophys Res Commun 2007, 360:772-777.
59. Hudkins KL, Pichaiwong W, Wietecha T, Kowalewska J, Banas MC, Spencer MW, Muhlfeld A, Koelling M, Pippin JW, Shankland SJ, et al. BTBR Ob/Ob mutant mice model progressive diabetic nephropathy. J Am Soc Nephrol 2010, 21:1533-1542.
60. Vogelmann SU, Nelson WJ, Myers BD, Lemley KV. Urinary excretion of viable podocytes in health and renal disease. Am J Physiol Renal Physiol 2003, 285:F40-48.
61. Lao K, Xu NL, Straus NA. Whole genome amplification using single-primer PCR. Biotechnol J 2008, 3:378-382.
62. Aker M, Bomsztyk K, Emery DW. POLY(ADP-RIBOSE) polymerase-1 (Parp-1) contributes to the barrier function of a vertebrate chromatin insulator. J Biol Chem 2010, 285:37589-37597.
63. Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 2011, 473:43-49.