Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique

Nucleic Acids Research

Volumn 35, Issue 8, 2007, Pages

  Follows, George A ^a   Janes, Mary E ^a   Vallier, Ludovic ^a   Green, Anthony R ^a   Gottgens, Berthold ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE I; DNA;

ARTICLE; CELL CULTURE; CELL STRAIN K 562; CONTROLLED STUDY; DNA LIBRARY; DNA MICROARRAY; EMBRYONIC STEM CELL; GENE AMPLIFICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; HUMAN; HUMAN CELL; LEUKEMIA; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; SOUTHERN BLOTTING; TRANSCRIPTION REGULATION; CHEMISTRY; CHROMOSOME MAP; EVALUATION; GENE LIBRARY; GENETICS; METHODOLOGY; POLYMERASE CHAIN REACTION; REGULATORY SEQUENCE; T CELL LEUKEMIA;

BLOTTING, SOUTHERN; CELLS, CULTURED; CHROMOSOME MAPPING; DEOXYRIBONUCLEASE I; DNA; EMBRYONIC STEM CELLS; GENOMIC LIBRARY; HUMANS; K562 CELLS; LEUKEMIA, T-CELL, ACUTE; POLYMERASE CHAIN REACTION; REGULATORY SEQUENCES, NUCLEIC ACID;

EID: 34250348746     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm108     Document Type: Article

References (33)

1. Follows,G.A., Tagoh,H., Lefevre,P., Hodge,D., Morgan,G.J. and Bonifer,C. (2003) Epigenetic consequences of AML1-ETO action at the human c-FMS locus. EMBO J., 22, 2798-2809.
2. Vyas,P., Vickers,M.A., Simmons,D.L., Ayyub,H., Craddock,C.F. and Higgs,D.R. (1992) Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. Cell, 69, 781-793.
3. Sawada,S., Scarborough,J.D., Killeen,N. and Littman,D.R. (1994) A lineage-specific transcriptional silencer regulates CD4 gene expression during T lymphocyte development. Cell, 77, 917-929.
4. Ansel,K.M., Greenwald,R.J., Agarwal,S., Bassing,C.H., Monticelli,S.,Interlandi J., Djuretic,I.M., Lee,D.U., Sharpe,A.H. et al. (2004) Deletion of a conserved Il4 silencer impairs T helper type 1-mediated immunity. Nat. Immunol., 5, 1251-1259.
5. Mutskov,V.J., Farrell,C.M., Wade,P.A., Wolffe,A.P. and Felsenfeld,G. (2002) The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation. Genes Dev., 16, 1540-1554.
6. Chung,J.H., Whiteley,M. and Felsenfeld,G. (1993) A 5′ element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell, 74, 505-514.
7. Crawford,G.E., Davis,S., Scacheri,P.C., Renaud,G., Halawi,M.J., Erdos,M.R., Green,R., Meltzer,P.S., Wolfsberg,T.G. et al. (2006) DNase-chip: A high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat. Methods, 3, 503-509.
8. Crawford,G.E., Holt,I.E., Mullikin J.C., Tai,D., 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. USA, 101, 992-997.
9. Crawford,G.E., Holt,I.E., Whittle J., Webb,B.D., Tai,D., Davis,S., Margulies,E.H., Chen,Y., Bernat,J.A. et al. (2006) Genomewide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res., 16, 123-131.
10. Dorschner,M.O., Hawrylycz,M., Humbert,R., Wallace,J.C., Shafer,A., Kawamoto J., Mack J., Hall,R., Goldy,J. et al. (2004) High-throughput localization of functional elements by quantitative chromatin profiling. Nat. Methods, 1, 219-225.
11. Follows,G.A., Dhami,P., Gottgens,B., Bruce,A.W., Campbell,P.J., Dillon,S.C., Smith,A.M., Koch,C., Donaldson,I.J. et al. (2006) Identifying gene regulatory elements by genomic microarray mapping of DNasel hypersensitive sites. Genome Res., 16, 1310-1319.
12. Sabo,P.J., Humbert,R., Hawrylycz,M., Wallace,J.C., Dorschner,M.O., McArthur,M. and Stamatoyannopoulos,J.A. (2004) Genome-wide identification of DNasel hypersensitive sites using active chromatin sequence libraries. Proc. Natl. Acad. Sci. USA, 101, 4537-4542.
13. Sabo,P.J., Kuehn,M.S., Thurman,R., Johnson,B.E., Johnson,E.M., Cao,H., Yu,M., Rosenzweig,E., Goldy,J. et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods, 3, 511-518.
14. Aplan,P.D., Lombardi,D.P. and Kirsch,I.R. (1991) Structural characterization of SIL, a gene frequently disrupted in T-cell acute lymphoblastic leukemia. Mol. Cell. Biol., 11, 5462-5469.
15. Robb,L., Lyons, I., Li,R., Hartley,L., Kontgen,F., Harvey,R.P., Metcalf,D. and Begley,C.G. (1995) Absence of yolk sac hematopoiesis from mice with a targeted disruption of the scl gene. Proc. Natl. Acad. Sci. USA, 92, 7075-7079.
16. van Eekelen J.A., Bradley,C.K., Gothert,J.R., Robb,L., Elefanty,A.G., Begley,C.G. and Harvey,A.R. (2003) Expression pattern of the stem cell leukaemia gene in the CNS of the embryonic and adult mouse. Neuroscience, 122, 421-436.
17. Drake,C.J., Brandt,S.J., Trusk,T.C. and Little,C.D. (1997) TAL1/SCL is expressed in endothelial progenitor cells/angioblasts and defines a dorsal-to-ventral gradient of vasculogenesis. Dev. Biol., 192 17-30.
18. Gering,M., Rodaway,A.R., Gottgens,B., Patient,R.K. and Green,A.R. (1998) The SCL gene specifies haemangioblast development from early mesoderm. EMBO J., 17, 4029-4045.
19. Begley,C.G., Robb,L., Rockman,S., Visvader J., Bockamp,E.O., Chan,Y.S. and Green,A.R. (1994) Structure of the gene encoding the murine SCL protein. Gene, 138, 93-99.
20. Bockamp,E.O., McLaughlin,F., Murrell,A. and Green,A.R. (1994) Transcription factors and the regulation of haemopoiesis: Lessons from GATA and SCL proteins. Bioessays, 16, 481-488.
21. Bockamp, E.O., McLaughlin,F., Murrell,A.M., Gottgens,B., Robb,L., Begley,C.G. and Green,A.R. (1995) Lineage-restricted regulation of the murine SCL/TAL-1 promoter. Blood, 86, 1502-1514.
22. Bockamp,E.O., McLaughlin,F., Gottgens,B., Murrell,A.M., Elefanty,A.G. and Green,A.R.(1997) Distinct mechanisms direct SCL/tal-1 expression in erythroid cells and CD34 positive primitive myeloid cells. J. Biol. Chem., 272, 8781-8790.
23. Gottgens,B., McLaughlin,F., Bockamp,E.O., Fordham,J.L., Begley,C.G., Kosmopoulos,K., Elefanty,A.G. and Green,A.R. (1997) Transcription of the SCL gene in erythroid and CD34 positive primitive myeloid cells is controlled by a complex network of lineage-restricted chromatin-dependent and chromatin-independent regulatory elements. Oncogene, 15, 2419-2428.
24. Sanchez,M., Gottgens,B., Sinclair,A.M., Stanley,M., Begley,C.G., Hunter,S. and Green,A.R. (1999) An SCL 3′ enhancer targets developing endothelium together with embryonic and adult haematopoietic progenitors. Development, 126, 3891-3904.
25. Sinclair,A.M., Gottgens,B., Barton,L.M., Stanley,M.L., Pardanaud,L., Klaine,M., Gering,M., Bahn,S., Sanchez,M. et al. (1999) Distinct 5′ SCL enhancers direct transcription to developing brain, spinal cord, and endothelium: Neural expression is mediated by GATA factor binding sites. Dev. Biol., 209, 128-142.
26. Gottgens,B., Barton,L.M., Gilbert,J.G., Bench,A.J., Sanchez,M.J., Bahn,S., Mistry,S., Grafham,D., McMurray,A. et al. (2000) Analysis of vertebrate SCL loci identifies conserved enhancers. Nat. Biotechnol., 18, 181-186.
27. Gottgens,B., Barton,L.M., Chapman,M.A., Sinclair A.M., Knudsen,B., Grafham,D., Gilbert,J.G., Rogers,J., Bentley,D.R. et al. (2002) Transcriptional regulation of the stem cell leukemia gene (SCL)-comparative analysis of five vertebrate SCL loci. Genome Res. 12, 749-759.
28. Delabesse,E., Ogilvy,S., Chapman,M.A., Piltz,S.G., Gottgens,B. and Green,A.R. (2005) Transcriptional regulation of the SCL locus: identification of an enhancer that targets the primitive erythroid lineage in vivo. Mol. Cell. Biol., 25, 5215-5225.
29. Silberstein,L., Sanchez,M.J., Socolovsky,M., Liu,Y., Hoffman,G., Kinston,S., Piltz,S., Bowen,M., Gambardella,L. et al. (2005) Transgenic analysis of the SCL + 19 stem cell enhancer in adult and embryonic haematopoietic and endothelial cells. Stem Cells.
30. Gottgens,B., Nastos,A., Kinston,S., Piltz,S., Delabesse,E.C., Stanley,M., Sanchez,M.J., Ciau-Uitz,A., Patient,R. et al. (2002) Establishing the transcriptional programme for blood: The SCL stem cell enhancer is regulated by a multiprotein complex containing Ets and GATA factors. EMBO J., 21, 3039-3050.
31. Gottgens,B., Broccardo,C., Sanchez,M.J., Deveaux,S., Murphy,G., Gothert,J.R., Kotsopoulou,E., Kinston,S., Delaney,L. et al. (2004) The scl + 18/19 stem cell enhancer is not required for hematopoiesis: identification of a 5′ bifunctional hematopoietic-endothelial enhancer bound by Fli-1 and Elf-1. Mol. Cell. Biol., 24, 1870-1883.
32. Chung,Y.S., Zhang,W.J., Arentson.E., Kingsley,P.D., Palis J. and Choi,K. (2002) Lineage analysis of the hemangioblast as defined by FLK1 and SCL expression. Development, 129, 5511-5520.
33. Vallier,L., Alexander,M. and Pedersen,R.A. (2005) Activin/Nodal and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells. J. Cell Sci., 118, 4495-4509.