Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

Genome Research

Volumn 16, Issue 1, 2006, Pages 123-131

  Crawford, Gregory E ^a   Holt, Ingeborg E ^a   Whittle, James ^a   Webb, Bryn D ^a   Tai, Denise ^a   Davis, Sean ^a   Margulies, Elliott H ^a   Chen, YiDong ^a   Bernat, John A ^b   Ginsburg, David ^b   Zhou, Daixing ^c   Luo, Shujun ^c   Vasicek, Thomas J ^c   Daly, Mark J ^d   Wolfsberg, Tyra G ^a   Collins, Francis S ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c Solexa Inc   (United States)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE;

ARTICLE; B LYMPHOCYTE; CD4 LYMPHOCYTE COUNT; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL FUNCTION; CELL LINE; CELL SPECIFICITY; CELL TYPE; CHROMATIN STRUCTURE; DNA FLANKING REGION; DNA LIBRARY; ENDOTHELIUM CELL; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE MAPPING; GENE SEQUENCE; GENOME; GENOME ANALYSIS; HELA CELL; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN CELL; HYPERSENSITIVITY REACTION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; T LYMPHOCYTE; UMBILICAL VEIN;

CELL DIFFERENTIATION; CHROMATIN; CHROMOSOME MAPPING; DEOXYRIBONUCLEASE I; ENDOTHELIAL CELLS; GENOME, HUMAN; GENOMIC LIBRARY; GENOMICS; HELA CELLS; HEPATOCYTES; HUMANS; LYMPHOCYTES; ORGAN SPECIFICITY; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SEQUENCE ANALYSIS, DNA; SEQUENCE TAGGED SITES; UMBILICAL VEINS;

EID: 30044449116     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4074106     Document Type: Article

References (24)

1. Barnett, V. and Lewis, T. 1998. Outliers in statistical data. John Wiley and Sons, West Sussex, UK.
2. Brenner, S., Johnson, M., Bridgham, J., Golda, G., Lloyd, D.H., Johnson, D., Luo, S., McCurdy, S., Foy, M., Ewan, M., et al. 2000. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays. Nat. Biotechnol. 18: 630-634.
3. Collins, F.S., Green, E.D., Guttmacher, A.E., and Guyer, M.S. 2003. A vision for the future of genomics research. Nature 422: 835-847.
4. Crawford, G.E., Holt, I.E., Mullikin, J.C., Tai, D., National Institutes of Health Intramural Sequencing, Blakesley, R., Bouffard, G., Young, A., Masiello, C., Green, E.D., et al. 2004. Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc. Natl. Acad. Sci. 101: 992-997.
5. The Encode Consortium. 2004. The ENCODE (Encyclopedia of DNA Elements) Project. Science 306: 636-640.
6. Gross, D.S. and Garrard, W.T. 1988. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57: 159-197.
7. Hebbes, T.R., Thorne, A.W., Clayton, A.L., and Crane-Robinson, C. 1992. Histone acetylation and globin gene switching. Nucleic Acids Res. 20: 1017-1022.
8. Hewish, D. 1977. Features of the structure of replicating and non-replicating chromatin in chicken erythroblasts. Nucleic Acids Res. 4: 1881-1890.
9. Irizarry, R.A., Bolstad, B.M., Collin, F., Cope, L.M., Hobbs, B., and Speed, T.P. 2003. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31: e15.
10. Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., et al. 2003. The UCSC Genome Browser Database. Nucleic Acids Res. 31: 51-54.
11. Kim, T.H., Barrera, L.O., Qu, C., Van Calcar, S., Trinklein, N.D., Cooper, S.J., Luna, R.M., Glass, C.K., Rosenfeld, M.G., Myers, R.M., et al. 2005. Direct isolation and identification of promoters in the human genome. Genome Res. 15: 830-839.
12. Margulies, E.H., Blanchette, M., Haussler, D., and Green, E.D. 2003. Identification and characterization of multi-species conserved sequences. Genome Res. 13: 2507-2518.
13. McArthur, M., Gerum, S., and Stamatoyannopoulos, G. 2001. Quantification of DNaseI-sensitivity by real-time PCR: Quantitative analysis of DNaseI-hypersensitivity of the mouse β-globin LCR. J. Mol. Biol. 313: 27-34.
14. Rozen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 132: 365-386.
15. Sabo, P.J., Humbert, R., Hawrylycz, M., Wallace, J.C., Dorschner, M.O., McArthur, M., and Stamatoyannopoulos, J.A. 2004. Genome-wide identification of DNaseI hypersensitive sites using active chromatin sequence libraries. Proc. Natl. Acad. Sci. 101: 4537-4542.
16. Schneider, R., Bannister, A.J., Myers, F.A., Thorne, A.W., Crane-Robinson, C., and Kouzarides, T. 2004. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nat. Cell Biol. 6: 73-77.
17. Su, A.I., Cooke, M.P., Ching, K.A., Hakak, Y., Walker, J.R., Wiltshire, T., Orth, A.P., Vega, R.G., Sapinoso, L.M., Moqrich, A., et al. 2002. Large-scale analysis of the human and mouse transcriptomes. Proc. Natl. Acad. Sci. 99: 4465-4470.
18. Trinklein, N.D., Aldred, S.J., Saldanha, A.J., and Myers, R.M. 2003. Identification and functional analysis of human transcriptional promoters. Genome Res. 13: 308-312.
19. Wu, C., Wong, Y.C., and Elgin, S.C. 1979. The chromatin structure of specific genes, II: Disruption of chromatin structure during gene activity. Cell 16: 807-814.
20. http://genome.ucsc.edu/ENCODE/; UCSC genome browser for ENCODE regions
21. http://genome.ucsc.edu/; UCSC genome browser
22. http://www.ncbi.nlm.nih.gov/geo; Gene Expression Omnibus
23. http://www.bioconductor.org; Bioconductor
24. http://research.nhgri.nih.gov/DNaseHS/; List of DNase HS sites described in this paper