Transcriptomics: Unravelling the biology of transcription factors and chromatin remodelers during development and differentiation

Seminars in Cell and Developmental Biology

Volumn 20, Issue 7, 2009, Pages 835-841

  Brien, Gerard L ^a   Bracken, Adrian P ^a  

^a ADELAIDE AND MEATH HOSPITAL   (Ireland)

Author keywords

Chromatin immunoprecipitation; Development; Differentiation; Polycomb; Transcription factor Chromatin remodeler

Indexed keywords

EMBRYONIC ECTODERM DEVELOPMENT PROTEIN; GA BINDING PROTEIN; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; HEPATOCYTE NUCLEAR FACTOR 3BETA; HISTONE; KRUPPEL LIKE FACTOR 4; MYC PROTEIN; MYOCYTE ENHANCER FACTOR 2; MYOD PROTEIN; MYOGENIN; NUCLEAR RECEPTOR DAX 1; NUCLEIC ACID BINDING PROTEIN; OCTAMER TRANSCRIPTION FACTOR 4; POLYCOMB GROUP PROTEIN; PROTEIN P53; PROTEIN P63; PROTEIN P73; STAT1 PROTEIN; STAT3 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR E2F; TRANSCRIPTION FACTOR ELF 1; TRANSCRIPTION FACTOR ETS 1; TRANSCRIPTION FACTOR FOXP3; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR PAX6; TRANSCRIPTION FACTOR RUNX1; TRANSCRIPTION FACTOR SOX2; TRANSCRIPTION FACTOR SOX4; TRITHORAX GROUP PROTEIN; UNCLASSIFIED DRUG;

CELL CYCLE REGULATION; CELL DIFFERENTIATION; CELL FATE; CELL MATURATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CHROMATIN IMMUNOPRECIPITATION; EMBRYONIC STEM CELL; GENE EXPRESSION; GENE REGULATORY NETWORK; HUMAN; NONHUMAN; PLURIPOTENT STEM CELL; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN FUNCTION; REVIEW; TRANSCRIPTOMICS;

MAMMALIA;

EID: 70349332451     PISSN: 10849521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.semcdb.2009.07.010     Document Type: Review

References (69)

1. Arnold S.J., and Robertson E.J. Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo. Nat Rev Mol Cell Biol 10 (2009) 91-103
2. Rosenbauer F., and Tenen D.G. Transcription factors in myeloid development: balancing differentiation with transformation. Nat Rev Immunol 7 (2007) 105-117
3. Orkin S.H., and Zon L.I. Hematopoiesis: an evolving paradigm for stem cell biology. Cell 132 (2008) 631-644
4. Myatt S.S., and Lam E.W. The emerging roles of forkhead box (Fox) proteins in cancer. Nat Rev Cancer 7 (2007) 847-859
5. Robson E.J., He S.J., and Eccles M.R. A PANorama of PAX genes in cancer and development. Nat Rev Cancer 6 (2006) 52-62
6. Kouros-Mehr H., Kim J.W., Bechis S.K., and Werb Z. GATA-3 and the regulation of the mammary luminal cell fate. Curr Opin Cell Biol 20 (2008) 164-170
7. Cedar H., and Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10 (2009) 295-304
8. Sparmann A., and van Lohuizen M. Polycomb silencers control cell fate, development and cancer. Nat Rev Cancer 6 (2006) 846-856
9. Ren B., Robert F., Wyrick J.J., Aparicio O., Jennings E.G., Simon I., et al. Genome-wide location and function of DNA binding proteins. Science 290 (2000) 2306-2309
10. Wang Z., Gerstein M., and Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10 (2009) 57-63
11. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125 (2006) 301-313
12. Kim J., Chu J., Shen X., Wang J., and Orkin S.H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132 (2008) 1049-1061
13. Jaenisch R., and Young R. Stem cells, the molecular circuitry of pluripotency and nuclear reprogramming. Cell 132 (2008) 567-582
14. Ivanova N., Dobrin R., Lu R., Kotenko I., Levorse J., DeCoste C., et al. Dissecting self-renewal in stem cells with RNA interference. Nature 442 (2006) 533-538
15. Boyer L.A., Lee T.I., Cole M.F., Johnstone S.E., Levine S.S., Zucker J.P., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122 (2005) 947-956
16. Kidder B.L., Yang J., and Palmer S. Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells. PLoS ONE 3 (2008) e3932
17. Chen X., Xu H., Yuan P., Fang F., Huss M., Vega V.B., et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133 (2008) 1106-1117
18. Yang J., Chai L., Fowles T.C., Alipio Z., Xu D., Fink L.M., et al. Genome-wide analysis reveals Sall4 to be a major regulator of pluripotency in murine-embryonic stem cells. Proc Natl Acad Sci USA 105 (2008) 19756-19761
19. Cole M.F., Johnstone S.E., Newman J.J., Kagey M.H., and Young R.A. Tcf3 is an integral component of the core regulatory circuitry of embryonic stem cells. Genes Dev 22 (2008) 746-755
20. Yuan H., Corbi N., Basilico C., and Dailey L. Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev 9 (1995) 2635-2645
21. Nishimoto M., Fukushima A., Okuda A., and Muramatsu M. The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2. Mol Cell Biol 19 (1999) 5453-5465
22. Botquin V., Hess H., Fuhrmann G., Anastassiadis C., Gross M.K., Vriend G., et al. New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2. Genes Dev 12 (1998) 2073-2090
23. Loh Y.H., Wu Q., Chew J.L., Vega V.B., Zhang W., Chen X., et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 38 (2006) 431-440
24. Marson A., Levine S.S., Cole M.F., Frampton G.M., Brambrink T., Johnstone S., et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134 (2008) 521-533
25. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458 (2009) 223-227
26. Hombria J.C., and Lovegrove B. Beyond homeosis-HOX function in morphogenesis and organogenesis. Differentiation 71 (2003) 461-476
27. Babu M.M., Luscombe N.M., Aravind L., Gerstein M., and Teichmann S.A. Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14 (2004) 283-291
28. Sansom S.N., Griffiths D.S., Faedo A., Kleinjan D.J., Ruan Y., Smith J., et al. The level of the transcription factor Pax6 is essential for controlling the balance between neural stem cell self-renewal and neurogenesis. PLoS Genet 5 (2009) e1000511
29. Nielsen R., Pedersen T.A., Hagenbeek D., Moulos P., Siersbaek R., Megens E., et al. Genome-wide profiling of PPARgamma:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis. Genes Dev 22 (2008) 2953-2967
30. Lefterova M.I., Zhang Y., Steger D.J., Schupp M., Schug J., Cristancho A., et al. PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 22 (2008) 2941-2952
31. Rosen E.D., Walkey C.J., Puigserver P., and Spiegelman B.M. Transcriptional regulation of adipogenesis. Genes Dev 14 (2000) 1293-1307
32. Zheng Y., Josefowicz S.Z., Kas A., Chu T.T., Gavin M.A., and Rudensky A.Y. Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells. Nature 445 (2007) 936-940
33. Blais A., Tsikitis M., Acosta-Alvear D., Sharan R., Kluger Y., and Dynlacht B.D. An initial blueprint for myogenic differentiation. Genes Dev 19 (2005) 553-569
34. Wilson N.K., Miranda-Saavedra D., Kinston S., Bonadies N., Foster S.D., Calero-Nieto F., et al. The transcriptional programme controlled by the stem cell leukaemia gene Scl/Tal1 during early embryonic haematopoietic development. Blood (2009)
35. Robertson A.G., Bilenky M., Tam A., Zhao Y., Zeng T., Thiessen N., et al. Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding. Genome Res 18 (2008) 1906-1917
36. Carroll J.S., Liu X.S., Brodsky A.S., Li W., Meyer C.A., Szary A.J., et al. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 122 (2005) 33-43
37. Pietersen A.M., and van Lohuizen M. Stem cell regulation by polycomb repressors: postponing commitment. Curr Opin Cell Biol 20 (2008) 201-207
38. 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
39. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441 (2006) 349-353
40. Negre N., Hennetin J., Sun L.V., Lavrov S., Bellis M., White K.P., et al. Chromosomal distribution of PcG proteins during Drosophila development. PLoS Biol 4 (2006) e170
41. Schwartz Y.B., Kahn T.G., Nix D.A., Li X.Y., Bourgon R., Biggin M., et al. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 38 (2006) 700-705
42. Tolhuis B., de Wit E., Muijrers I., Teunissen H., Talhout W., van Steensel B., et al. Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat Genet 38 (2006) 694-699
43. Pasini D., Bracken A.P., Hansen J.B., Capillo M., and Helin K. The polycomb group protein Suz12 is required for embryonic stem cell differentiation. Mol Cell Biol 27 (2007) 3769-3779
44. Mohn F., Weber M., Rebhan M., Roloff T.C., Richter J., Stadler M.B., et al. Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 30 (2008) 755-766
45. Schuettengruber B., Chourrout D., Vervoort M., Leblanc B., and Cavalli G. Genome regulation by polycomb and trithorax proteins. Cell 128 (2007) 735-745
46. Guenther M.G., Lawton L.N., Rozovskaia T., Frampton G.M., Levine S.S., Volkert T.L., et al. Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia. Genes Dev 22 (2008) 3403-3408
47. Pan G., Tian S., Nie J., Yang C., Ruotti V., Wei H., et al. Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1 (2007) 299-312
48. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125 (2006) 315-326
49. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448 (2007) 553-560
50. 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
51. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA (2009)
52. Weissman I.L., and Shizuru J.A. The origins of the identification and isolation of hematopoietic stem cells, and their capability to induce donor-specific transplantation tolerance and treat autoimmune diseases. Blood 112 (2008) 3543-3553
53. O'Neill L.P., VerMilyea M.D., and Turner B.M. Epigenetic characterization of the early embryo with a chromatin immunoprecipitation protocol applicable to small cell populations. Nat Genet 38 (2006) 835-841
54. Acevedo L.G., Iniguez A.L., Holster H.L., Zhang X., Green R., and Farnham P.J. Genome-scale ChIP-chip analysis using 10,000 human cells. Biotechniques 43 (2007) 791-797
55. Dahl J.A., and Collas P. A rapid micro chromatin immunoprecipitation assay (microChIP). Nat Protoc 3 (2008) 1032-1045
56. Zhang X., Guo C., Chen Y., Shulha H.P., Schnetz M.P., LaFramboise T., et al. Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies. Nat Methods 5 (2008) 163-165
57. Guccione E., Martinato F., Finocchiaro G., Luzi L., Tizzoni L., Dall' Olio V., et al. Myc-binding-site recognition in the human genome is determined by chromatin context. Nat Cell Biol 8 (2006) 764-770
58. Ren B., Cam H., Takahashi Y., Volkert T., Terragni J., Young R.A., et al. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev 16 (2002) 245-256
59. Hollenhorst P.C., Shah A.A., Hopkins C., and Graves B.J. Genome-wide analyses reveal properties of redundant and specific promoter occupancy within the ETS gene family. Genes Dev 21 (2007) 1882-1894
60. Carroll J.S., Meyer C.A., Song J., Li W., Geistlinger T.R., Eeckhoute J., et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 38 (2006) 1289-1297
61. Lupien M., Eeckhoute J., Meyer C.A., Wang Q., Zhang Y., Li W., et al. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132 (2008) 958-970
62. Smeenk L., van Heeringen S.J., Koeppel M., van Driel M.A., Bartels S.J., Akkers R.C., et al. Characterization of genome-wide p53-binding sites upon stress response. Nucleic Acids Res 36 (2008) 3639-3654
63. Wei C.L., Wu Q., Vega V.B., Chiu K.P., Ng P., Zhang T., et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 124 (2006) 207-219
64. Vigano M.A., Lamartine J., Testoni B., Merico D., Alotto D., Castagnoli C., et al. New p63 targets in keratinocytes identified by a genome-wide approach. EMBO J 25 (2006) 5105-5116
65. Johnson D.S., Mortazavi A., Myers R.M., and Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502
66. Gekas C., Rhodes K.E., Gereige L.M., Helgadottir H., Ferrari R., Kurdistani S.K., et al. Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis. Blood 113 (2009) 3461-3471
67. Scharer C.D., McCabe C.D., Ali-Seyed M., Berger M.F., Bulyk M.L., and Moreno C.S. Genome-wide promoter analysis of the SOX4 transcriptional network in prostate cancer cells. Cancer Res 69 (2009) 709-717
68. Robertson G., Hirst M., Bainbridge M., Bilenky M., Zhao Y., Zeng T., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4 (2007) 651-657
69. Acosta-Alvear D., Zhou Y., Blais A., Tsikitis M., Lents N.H., Arias C., et al. XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks. Mol Cell 27 (2007) 53-66