NA-Seq: A Discovery Tool for the Analysis of Chromatin Structure and Dynamics during Differentiation

Developmental Cell

Volumn 16, Issue 3, 2009, Pages 466-481

  Gargiulo, Gaetano ^a   Levy, Samuel ^b   Bucci, Gabriele ^a   Romanenghi, Mauro ^a   Fornasari, Lorenzo ^c   Beeson, Karen Y ^b   Goldberg, Susanne M ^b   Cesaroni, Matteo ^a   Ballarini, Marco ^c   Santoro, Fabio ^c   Bezman, Natalie ^d   Frigè, Gianmaria ^a   Gregory, Philip D ^d   Holmes, Michael C ^d   Strausberg, Robert L ^b   Pelicci, Pier Giuseppe ^a   Urnov, Fyodor D ^d   Minucci, Saverio ^a,e  

^a EUROPEAN INSTITUTE OF ONCOLOGY   (Italy)

^b J CRAIG VENTER INSTITUTE   (United States)

^c Genextra Group   (Italy)

^d SANGAMO BIOSCIENCES INC   (United States)

^e UNIVERSITY OF MILAN   (Italy)

Author keywords

DEVBIO; DNA

Indexed keywords

CD34 ANTIGEN; HISTONE; TRANSCRIPTION FACTOR;

ANALYTIC METHOD; ARTICLE; BONE MARROW CELL; CELL DIFFERENTIATION; CELL MATURATION; CHROMATIN STRUCTURE; CHROMOSOME ANALYSIS; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; GENE EXPRESSION REGULATION; GENETIC REGULATION; MULTIPOTENT STEM CELL; NUCLEASE ACCESSIBLE SITE SEQUENCING; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN PROCESSING;

ANTIGENS, CD34; CELL DIFFERENTIATION; CELLS, CULTURED; CHROMATIN; DNA RESTRICTION ENZYMES; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME-WIDE ASSOCIATION STUDY; HEMATOPOIETIC STEM CELLS; HISTONES; HUMANS; MYELOPOIESIS; TRANSCRIPTION FACTORS;

EID: 61749088375     PISSN: 15345807     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.devcel.2009.02.002     Document Type: Article

References (60)

1. Almer A., and Horz W. Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast. EMBO J. 5 (1986) 2681-2687
2. Archer T.K., Lefebvre P., Wolford R.G., and Hager G.L. Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science 255 (1992) 1573-1576
3. Attema J.L., Papathanasiou P., Forsberg E.C., Xu J., Smale S.T., and Weissman I.L. Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis. Proc. Natl. Acad. Sci. USA 104 (2007) 12371-12376
4. Ballas N., Grunseich C., Lu D.D., Speh J.C., and Mandel G. REST and its corepressors mediate plasticity of neuronal gene chromatin throughout neurogenesis. Cell 121 (2005) 645-657
5. Barski A., Cuddapah S., Cui K., Roh T., Schones D., Wang Z., Wei G., Chepelev I., and Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 129 (2007) 823-837
6. Bejerano G., Pheasant M., Makunin I., Stephen S., Kent W.J., Mattick J.S., and Haussler D. Ultraconserved elements in the human genome. Science 304 (2004) 1321-1325
7. Bernstein B., Mikkelsen T., Xie X., Kamal M., Huebert D.J., Cuff J., Fry B., Meissner A., Wernig M., Plath K., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
8. Bernstein B., Meissner A., and Lander E. The mammalian epigenome. Cell 128 (2007) 669-681
9. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 16 (2002) 6-21
10. Bottardi S., Aumont A., Grosveld F., and Milot E. Developmental stage-specific epigenetic control of human β-globin gene expression is potentiated in hematopoietic progenitor cells prior to their transcriptional activation. Blood 102 (2003) 3989-3997
11. Boyle A.P., Davis S., Shulha H.P., Meltzer P., Margulies E.H., Weng Z., Furey T.S., and Crawford G.E. High-resolution mapping and characterization of open chromatin across the genome. Cell 132 (2008) 311-322
12. Boyle A.P., Davis S., Shulha H.P., Meltzer P., Margulies E.H., Weng Z., Furey T.S., and Crawford G.E. High-resolution mapping and characterization of open chromatin across the genome. Cell 132 (2008) 311-322
13. Bracken A.P., Dietrich N., Pasini D., Hansen K.H., and Helin K. Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev. 20 (2006) 1123-1136
14. Carroll J., Meyer C., Song J., Li W., Geistlinger T., Eeckhoute J., Brodsky A., Keeton E., Fertuck K., Hall G., et al. Genome-wide analysis of estrogen receptor binding sites. Nat. Genet. 38 (2006) 1289-1297
15. Chen L., Decerbo J., and Carmichael G. Alu element-mediated gene silencing. EMBO J. 27 (2008) 1694-1705
16. Chen X., Xu H., Yuan P., Fang F., Huss M., Vega V., Wong E., Orlov Y.L., Zhang W., Jiang J., et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133 (2008) 1106-1117
17. Crawford G.E., Holt I.E., Mullikin J.C., Tai D., Blakesley R., Bouffard G., Young A., Masiello C., Green E.D., Wolfsberg T.G., and Collins F.S. Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc. Natl. Acad. Sci. USA 101 (2004) 992-997
18. Crawford G.E., Holt I.E., Whittle J., Webb B.D., Tai D., Davis S., Margulies E.H., Chen Y., Bernat J.A., Ginsburg D., et al. Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 16 (2006) 123-131
19. Cui K., Zang C., Roh T., Schones D., Childs R.W., Peng W., and Zhao K. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4 (2009) 80-93
20. Di Croce L., Raker V.A., Corsaro M., Fazi F., Fanelli M., Faretta M., Fuks F., Lo Coco F., Kouzarides T., Nervi C., et al. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science 295 (2002) 1079-1082
21. Elgin S.C. The formation and function of DNase I hypersensitive sites in the process of gene activation. J. Biol. Chem. 263 (1988) 19259-19262
22. ENCODE Project Consortium, Birney E., Stamatoyannopoulos J., Dutta A., Guigó R., Gingeras T., Margulies E., Weng Z., Snyder M., Dermitzakis E., Thurman R.E., et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447 (2007) 799-816
23. Farkash-Amar S., Lipson D., Polten A., Goren A., Helmstetter C., Yakhini Z., and Simon I. Global organization of replication time zones of the mouse genome. Genome Res. 18 (2008) 1562-1570
24. Fraser P., and Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature 447 (2007) 413-417
25. Gargiulo G., and Minucci S. Epigenomic profiling of cancer cells. Int. J. Biochem. Cell Biol. 41 (2009) 127-135
26. Giresi P., Kim J., McDaniell R.M., Iyer V., and Lieb J. FAIRE (formaldehyde-assisted isolation of regulatory elements) isolates active regulatory elements from human chromatin. Genome Res. 17 (2007) 877-885
27. Guccione E., Martinato F., Finocchiaro G., Luzi L., Tizzoni L., Dall' Olio V., Zardo G., Nervi C., Bernard L., and Amati B. Myc-binding-site recognition in the human genome is determined by chromatin context. Nat. Cell Biol. 8 (2006) 764-770
28. Guenther M.G., Levine S.S., Boyer L.A., Jaenisch R., and Young R.A. A chromatin landmark and transcription initiation at most promoters in human cells. Cell 130 (2007) 77-88
29. Hebbes T.R., Clayton A.L., Thorne A.W., and Crane-Robinson C. Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken β-globin chromosomal domain. EMBO J. 13 (1994) 1823-1830
30. Heintzman N., Stuart R., Hon G., Fu Y., Ching C., Hawkins R., Barrera L., Van Calcar S., Qu C., Ching K., et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39 (2007) 311-318
31. Jäger R., Werling U., Rimpf S., Jacob A., and Schorle H. Transcription factor AP-2γ stimulates proliferation and apoptosis and impairs differentiation in a transgenic model. Mol. Cancer Res. 1 (2003) 921-929
32. Johnson D.S., Mortazavi A., Myers R., and Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502
33. Kim T., Abdullaev Z.K., Smith A.D., Ching K., Loukinov D.I., Green R., Zhang M., Lobanenkov V.V., and Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128 (2007) 1231-1245
34. Kosak S., Scalzo D., Alworth S., Li F., Palmer S., Enver T., Lee J.S., and Groudine M. Coordinate gene regulation during hematopoiesis is related to genomic organization. PLoS Biol. 5 (2007) e309
35. Laperriere D., Wang T.T., White J.H., and Mader S. Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics 8 (2007) 23
36. Lawson G.M., Knoll B.J., March C.J., Woo S.L., Tsai M.J., and O'Malley B.W. Definition of 5′ and 3′ structural boundaries of the chromatin domain containing the ovalbumin multigene family. J. Biol. Chem. 257 (1982) 1501-1507
37. Levy S., and Hannenhalli S. Identification of transcription factor binding sites in the human genome sequence. Mamm. Genome 13 (2002) 510-514
38. Li X., Macarthur S., Bourgon R., Nix D., Pollard D., Iyer V., Hechmer A., Simirenko L., Stapleton M., Hendriks C., et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 6 (2008) e27
39. Löffler H., Rastetter J., Haferlach T., Heilmeyer L., and Begemann H. Atlas of Clinical Hematology. Sixth Edition (2004), Springer, Berlin
40. Loo S., and Rine J. Silencers and domains of generalized repression. Science 264 (1994) 1768-1771
41. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., Berka J., Braverman M.S., Chen Y.J., Chen Z., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437 (2005) 376-380 Erratum: (2006). Nature 441, 120
42. Matys V., Fricke E., Geffers R., Gossling E., Haubrock M., Hehl R., Hornischer K., Karas D., Kel A.E., Kel-Margoulis O.V., et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31 (2003) 374-378
43. McArthur M., Gerum S., and Stamatoyannopoulos G. Quantification of DNaseI-sensitivity by real-time PCR: quantitative analysis of DNaseI-hypersensitivity of the mouse β-globin LCR. J. Mol. Biol. 313 (2001) 27-34
44. Morrison S.J., Uchida N., and Weissman I.L. The biology of hematopoietic stem cells. Annu. Rev. Cell Dev. Biol. 11 (1995) 35-71
45. Orford K., Kharchenko P., Lai W., Dao M.C., Worhunsky D.J., Ferro A., Janzen V., Park P.J., and Scadden D.T. Differential H3K4 methylation identifies developmentally poised hematopoietic genes. Dev. Cell 14 (2008) 798-809
46. Pan G., Tian S., Nie J., Yang C., Ruotti V., Wei H., Jonsdottir G.A., Stewart R., and Thomson J.A. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1 (2007) 299-312
47. Piacibello W., Sanavio F., Severino A., Danè A., Gammaitoni L., Fagioli F., Perissinotto E., Cavalloni G., Kollet O., Lapidot T., and Aglietta M. Engraftment in nonobese diabetic severe combined immunodeficient mice of human CD34(+) cord blood cells after ex vivo expansion: evidence for the amplification and self-renewal of repopulating stem cells. Blood 93 (1999) 3736-3749
48. Pingoud A., and Jeltsch A. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29 (2001) 3705-3727
49. Rosenbauer F., and Tenen D. Transcription factors in myeloid development: balancing differentiation with transformation. Nat. Rev. Immunol. 7 (2007) 105-117
50. Schones D., Cui K., Cuddapah S., Roh T., Barski A., Wang Z., Wei G., and Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell 132 (2008) 887-898
51. Spilianakis C., Lalioti M.D., Town T., Lee G., and Flavell R. Interchromosomal associations between alternatively expressed loci. Nature 435 (2005) 637-645
52. Steidl U., Steidl C., Ebralidze A., Chapuy B., Han H.J., Will B., Rosenbauer F., Becker A., Wagner K., Koschmieder S., et al. A distal single nucleotide polymorphism alters long-range regulation of the PU.1 gene in acute myeloid leukemia. J. Clin. Invest. 117 (2007) 2611-2620
53. Takizawa T., Meaburn K.J., and Misteli T. The meaning of gene positioning. Cell 135 (2008) 9-13
54. Tazi J., and Bird A. Alternative chromatin structure at CpG islands. Cell 60 (1990) 909-920
55. Turner B. Chromatin and Gene Regulation: Mechanisms in Epigenetics (2001), Blackwell Science, Oxford
56. Visel A., Minovitsky S., Dubchak I., and Pennacchio L.A. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res. 35 (2007) D88-D92
57. Wang Z., Zang C., Rosenfeld J., Schones D., Barski A., Cuddapah S., Cui K., Roh T., Peng W., Zhang M., and Zhao K. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40 (2008) 897-903
58. Weintraub H., and Groudine M. Chromosomal subunits in active genes have an altered conformation. Science 193 (1976) 848-856
59. Wu C. The 5′ ends of Drosophila heat shock genes in chromatin are hypersensitive to DNase I. Nature 286 (1980) 854-860
60. Xi H., Shulha H.P., Lin J., Vales T.R., Fu Y., Bodine D.M., McKay R.D., Chenoweth J.G., Tesar P.J., Furey T.S., et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 3 (2007) e136