Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

Nature Methods

Volumn 3, Issue 7, 2006, Pages 511-518

  Sabo, Peter J ^a   Kuehn, Michael S ^a   Thurman, Robert ^a   Johnson, Brett E ^a   Johnson, Ericka M ^a   Cao, Hua ^a   Yu, Man ^a   Rosenzweig, Elizabeth ^a   Goldy, Jeff ^a   Haydock, Andrew ^a   Weaver, Molly ^a   Shafer, Anthony ^a   Lee, Kristin ^a   Neri, Fidencio ^a   Humbert, Richard ^a   Singer, Michael A ^b   Richmond, Todd A ^b   Dorschner, Michael O ^a   McArthur, Michael ^c   Hawrylycz, Michael ^d   Green, Roland D ^b   Navas, Patrick A ^a   Noble, William S ^a   Stamatoyannopoulos, John A ^a   more..

^a UNIVERSITY OF WASHINGTON   (United States)

^b Roche NimbleGen Inc   (United States)

^c JOHN INNES CENTRE   (United Kingdom)

^d ALLEN INSTITUTE FOR BRAIN SCIENCE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; DEOXYRIBONUCLEASE I; DNA FRAGMENT;

ARTICLE; CHROMATIN; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA MICROARRAY; DNA SEQUENCE; ENZYME ACTIVE SITE; GENE LOCATION; GENE MAPPING; GENETIC REGULATION; HUMAN; HUMAN CELL; IN VIVO STUDY; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; TRANSCRIPTION INITIATION;

CHROMATIN; DEOXYRIBONUCLEASE I; GENOME; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 33745416080     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth890     Document Type: Article

References (29)

1. Felsenfeld, G. Chromatin as an essential part of the transcriptional mechanism. Nature 355, 219-224 (1992).
2. Felsenfeld, G. & Groudine, M. Controlling the double helix. Nature 421, 448-453 (2003).
3. Wu, C. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase. Nature 286, 854-860 (1980).
4. Keene, M.A., Corces, V., Lowenhaupt, K. & Elgin, S.C. DNase I hypersensitive sites in Drosophila chromatin occur at the 5′ ends of regions of transcription. Proc. Natl. Acad. Sci. USA 78, 143-146 (1981).
5. McGhee, J.D., Wood, W.I., Dolan, M., Engel, J.D. & Felsenfeld, G. A 200 base pair region at the 5′ end of the chicken adult β-globin gene is accessible to nuclease digestion. Cell 27, 45-55 (1981).
6. Gross, D.S. & Garrard, W.T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159-197 (1988).
7. Li, Q., Peterson, K.R., Fang, X. & Stamatoyannopoulos, G. Locus control regions. Blood 100, 3077-3086 (2002).
8. Weintraub, H. & Groudine, M. Chromosomal subunits in active genes have an altered conformation. Science 193, 848-856 (1976).
9. Felsenfeld, G. et al. Chromatin boundaries and chromatin domains. Cold Spring Harb. Symp. Quant. Biol. 69, 245-250 (2004).
10. Sproul, D., Gilbert, N. & Bickmore, W.A. The role of chromatin structure in regulating the expression of clustered genes. Nat. Rev. Genet. 6, 775-781 (2005).
11. The Encode Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636-640 (2004).
12. Elgin, S.C. The formation and function of DNase I hypersensitive sites in the process of gene activation. J. Biol. Chem. 263, 19259-19262 (1988).
13. Dorschner, M.O. et al. High-throughput localization of functional elements by quantitative chromatin profiling. Nat. Methods 1, 219-225 (2004).
14. Lee, G.R., Fields, P.E., Griffin, T.J. & Flavell, R.A. Regulation of the Th2 cytokine locus by a locus control region. Immunity 19, 145-153 (2003).
15. Lee, G.R., Spilianakis, C.G. & Flavell, R.A. Hypersensitive site 7 of the TH2 locus control region is essential for expressing TH2 cytokine genes and for long-range intrachromosomal interactions. Nat. Immunol. 6, 42-48 (2005).
16. Loots, G.G. et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science 288, 136-140 (2000).
17. Ansel, K.M. et al. Deletion of a conserved Il4 silencer impairs T helper type 1-mediated immunity. Nat. Immunol. 5, 1251-1259 (2004).
18. Smale, S.T. & Kadonaga, J.T. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72, 449-479 (2003).
19. West, A.G. & Fraser, P. Remote control of gene transcription. Hum. Mol. Genet. 14 (Spec. No. 1), R101-111 (2005).
20. Yelin, R. et al. Widespread occurrence of antisense transcription in the human genome. Nat. Biotechnol. 21, 379-386 (2003).
21. Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509 (2004).
22. Katayama, S. et al. Antisense transcription in the mammalian transcriptome. Science 309, 1564-1566 (2005).
23. Hinrichs, A.S. et al. The UCSC Genome Browser Database: Update 2006. Nucleic Acids Res. 34, D590-D598 (2006).
24. Percival, D.B. Wavelet methods for time series analysis (Cambridge University Press, Cambridge, 2000).
25. Korenberg, J.R. et al. Down syndrome phenotypes: The consequences of chromosomal imbalance. Proc. Natl. Acad. Sci. USA 91, 4997-5001 (1994).
26. Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
27. Sabo, P.J. et al. Discovery of functional noncoding elements by digital analysis of chromatin structure. Proc. Natl. Acad. Sci. USA 101, 16837-16842 (2004).
28. Sabo, P.J. et al. Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc. Natl. Acad. Sci. USA 101, 4537-4542 (2004).
29. McArthur, M., Gerum, S. & Stamatoyannopoulos, G. Quantification of DNaseI-sensitivity by real-time PCR: Quantitative analysis of DNaseI-hypersensitivity of the mouse beta-globin LCR. J. Mol. Biol. 313, 27-34 (2001).