A method to study the epigenetic chromatin states of rare hematopoietic stem and progenitor cells; Minichip-chip

Biological Procedures Online

Volumn 12, Issue 1, 2010, Pages 1-17

  Weishaupt, Holger ^a   Attema, Joanne L ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Epigenetic regulation; Histone modifications; Lineage commitment; Microarray technology; Miniaturized chromatin immunoprecipitation assays; Stem and progenitor cells

Indexed keywords

FORMALDEHYDE; HISTONE;

ANIMAL CELL; ARTICLE; BIOINFORMATICS; CELL DIFFERENTIATION; CELL FUNCTION; CELL POPULATION; CELL SUSPENSION; CELL VIABILITY; CHEMICAL MODIFICATION; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CONTROLLED STUDY; DROSOPHILA; EPIGENETICS; GENE EXPRESSION; HEMATOPOIETIC STEM CELL; MOLECULAR DYNAMICS; MOUSE; NEMATODE; NONHUMAN; POLYMERASE CHAIN REACTION; PROGENY; PROTEIN EXPRESSION; ZEBRA FISH;

MURINAE;

EID: 78649892923     PISSN: 14809222     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12575-010-9031-y     Document Type: Article

References (41)

1. Zardo G, Cimino G, Nervi C (2008) Epigenetic plasticity of chromatin in embryonic and hematopoietic stem/progenitor cells: therapeutic potential of cell reprogramming. Leukemia 22 (8):1503-18
2. Collas P (2008) Epigenetic states in stem cells. Biochimica et biophysica acta, Oct 25
3. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A (2009) An operational definition ofepigenetics. Genes Dev 23(7):781-3
4. Fraser P, Bickmore W (2007) Nuclear organization of the genome and the potential for gene regulation. Nature 447(7143):413-7
5. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389(6648):251-60
6. Li B, Carey M, Workman JL (2007) The role of chromatin during transcription. Cell 128(4):707-19
7. Bassett A, Cooper S, Wu C, Travers A (2009) The folding and unfolding of eukaryotic chromatin. Curr Opin Genet Dev 19 (2):159-65
8. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128(4):669-81
9. Cedar H, Bergman Y (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10 (5):295-304
10. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16(1):6-21
11. Jones PA, Takai D (2001) The role of DNA methylation in mammalian epigenetics. Science 293(5532):1068-70
12. Kouzarides T (2007) Chromatin modifications and their function. Cell 128(4):693-705
13. Mendenhall EM, Bernstein BE (2008) Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev 18(2):109-15
14. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41-5
15. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S et al (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40(7):897-903
16. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129(4):823-37
17. Boyer LA, Mathur D, Jaenisch R (2006) Molecular control of pluripotency Curr Opin Genet Dev 16(5):455-62
18. Meshorer E, Misteli T (2006) Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol, May 17.
19. Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P et al (2008) Dissecting direct reprogramming through integrative genomic analysis. Nature 454(7200):49-55
20. Schones DE, Zhao K (2008) Genome-wide approaches to studying chromatin modifications. Nat Rev Genet 9(3):179-91
21. Kuo MH, Allis CD (1999) In vivo cross-linking and immunopre-cipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 19(3):425-33
22. Das PM, Ramachandran K, van Wert J, Singal R (2004) Chromatin immunoprecipitation assay Biotechniques 37(6):961-9
23. Barski A, Zhao K (2009) Genomic location analysis by ChIP-Seq. J Cell Biochem 107(1):11-8
24. Kim TH, Barrera LO, Ren B (2007) ChIP-chip for genome-wide analysis of protein binding in mammalian cells. Curr Protoc Mol Biol. Jul;Chapter 21:Unit 21 13
25. Maynard ND, Chen J, Stuart RK, Fan JB, Ren B (2008) Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nat Methods 5(4):307-9
26. Acevedo LG, Iniguez AL, Holster HL, Zhang X, Green R, Farnham PJ (2007) Genome-scale ChIP-chip analysis using 10, 000 human cells. Biotechniques 43(6):791-7
27. Dahl JA, Reiner AH, Collas P (2009) Fast genomic muChIP-chip from 1, 000 cells. Genome biology 10(2):R13
28. Weishaupt H, Sigvardsson M, Attema JL (2009) Epigenetic chromatin states uniquely define the developmental plasticity of murine hematopoietic stem cells. Blood. Nov 3
29. Kiel MJ, Yilmaz OH, Iwashita T, Yilmaz OH, Terhorst C, Morrison SJ (2005) SLAM family receptors distinguish hemato-poietic stem and progenitor cells and reveal endothelial niches for stem cells. Cell 121(7):1109-21
30. Attema JL, Papathanasiou P, Forsberg EC, Xu J, Smale ST, Weissman IL (2007) Epigenetic characterization of hemato-poietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc Natl Acad Sci USA 104 (30):12371-6
31. Dahl JA, Collas P (2007) Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay unravels epigenetic dynam-ics ofdevelopmentally regulated genes in human carcinoma cells. Stem Cells, Feb 1
32. Attema JL, Pronk CJ, Norddahl GL, Nygren JM, Bryder D (2009) Hematopoietic stem cell ageing is uncoupled from p16(INK4A)-mediated senescence. Oncogene, Apr 27
33. Dahl JA, Collas P (2008) A rapid micro chromatin immunopre-cipitation assay (microChIP). Nature protocols 3(6):1032-45
34. Dahl JA, Collas P (2009) muChIP: chromatin immunoprecip-itation for small cell numbers. Methods Mol Biol 567:59-74
35. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ et al (2005) Genomic maps and comparative analysis ofhistone modifications in human and mouse. Cell 120 (2):169-81
36. Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD et al (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39(3):311-8
37. Peng S, Alekseyenko AA, Larschan E, Kuroda MI, Park PJ (2007) Normalization and experimental design for ChIP-chip data. BMC Bioinformatics 8:219
38. Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK et al (2007) Model-based analysis of two-color arrays (MA2C). Genome biology 8(8):R178
39. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S et al (2007) Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array-and sequencing-based technologies. Genome Res 17 (6):898-909
40. Bolstad BM, Irizarry RA, Astrand M, Speed TP (2003) A comparison of normalization methods for high density oligonu-cleotide array data based on variance and bias. Bioinformatics 19 (2):185-93
41. Dahl JA, Collas P (2007) Q2ChIP, a quick and quantitative chromatin immunoprecipitation assay, unravels epigenetic dynam-ics ofdevelopmentally regulated genes in human carcinoma cells. Stem Cells 25(4):1037-46