Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation

Genome Biology

Volumn 10, Issue 4, 2009, Pages

  Kubosaki, Atsutaka ^a   Tomaru, Yasuhiro ^a,b   Tagami, Michihira ^a   Arner, Erik ^a   Miura, Hisashi ^a,b   Suzuki, Takahiro ^a,b   Suzuki, Masanori ^a,b   Suzuki, Harukazu ^a   Hayashizaki, Yoshihide ^a,b  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; EARLY GROWTH RESPONSE FACTOR 1; EARLY GROWTH RESPONSE FACTOR 2; EARLY GROWTH RESPONSE FACTOR 3; MESSENGER RNA; PHORBOL 13 ACETATE 12 MYRISTATE; WT1 PROTEIN; EGR1 PROTEIN, HUMAN; HISTONE; LYSINE; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR SP1;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CELL DIFFERENTIATION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CPG ISLAND; DOWN REGULATION; ENZYME ACTIVATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; GENOME; GENOME ANALYSIS; HUMAN; HUMAN CELL; IN VIVO STUDY; MONOCYTE; PROMOTER REGION; SEQUENCE ANALYSIS; UPREGULATION; ACETYLATION; CELL LINE; CYTOLOGY; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETIC TRANSFECTION; GENETICS; HUMAN GENOME; METABOLISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; WESTERN BLOTTING;

ACETYLATION; BINDING SITES; BLOTTING, WESTERN; CELL DIFFERENTIATION; CELL LINE; CHROMATIN IMMUNOPRECIPITATION; CPG ISLANDS; EARLY GROWTH RESPONSE PROTEIN 1; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENOME, HUMAN; HISTONES; HUMANS; LYSINE; MONOCYTES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, SMALL INTERFERING; SP1 TRANSCRIPTION FACTOR; TETRADECANOYLPHORBOL ACETATE; TRANSFECTION;

EID: 65549156703     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-4-r41     Document Type: Article

References (48)

1. Takahashi K Yamanaka S Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126:663-676. 10.1016/j.cell.2006.07.024 16904174
2. Fahmy RG Dass CR Sun LQ Chesterman CN Khachigian LM Transcription factor Egr-1 supports FGF-dependent angiogenesis during neovascularization and tumor growth. Nat Med 2003, 9:1026-1032. 10.1038/nm905 12872165
3. Jouvert P Revel MO Lazaris A Aunis D Langley K Zwiller J Activation of the cGMP pathway in dopaminergic structures reduces cocaine-induced EGR-1 expression and locomotor activity. J Neurosci 2004, 24:10716-10725. 10.1523/JNEUROSCI.1398-04.2004 15564589
4. Sayasith K Brown KA Lussier JG Doré M Sirois J Characterization of bovine early growth response factor-1 and its gonadotropin-dependent regulation in ovarian follicles prior to ovulation. J Mol Endocrinol 2006, 37:239-250. 10.1677/jme.1.02078 17032742
5. Wong DL Tai TC Wong-Faull DC Claycomb R Kvetnansky R Genetic mechanisms for adrenergic control during stress. Ann N Y Acad Sci 2004, 1018:387-397. 10.1196/annals.1296.048 15240394
6. McMullen MR Pritchard MT Wang Q Millward CA Croniger CM Nagy LE Early growth response-1 transcription factor is essential for ethanol-induced fatty liver injury in mice. Gastroenterology 2005, 128:2066-2076. 1959407 15940638 10.1053/j.gastro.2005.02.065
7. Fahmy RG Dass CR Sun LQ Chesterman CN Khachigian LM Transcription factor Egr-1 supports FGF-dependent angiogenesis during neovascularization and tumor growth. Nat Med 2003, 9:1026-1032. 10.1038/nm905 12872165
8. Davis S Bozon B Laroche S How necessary is the activation of the immediate early gene zif268 in synaptic plasticity and learning? Behav Brain Res 2003, 142:17-30. 10.1016/S0166-4328(02)00421-7 12798262
9. Fu M Zhu X Zhang J Liang J Lin Y Zhao L Ehrengruber MU Chen YE Egr-1 target genes in human endothelial cells identified by microarray analysis. Gene 2003, 315:33-41. 10.1016/S0378-1119(03)00730-3 14557062
10. Zeng XR Sun Y Wenger L Cheung HS Basic calcium phosphate crystal-induced Egr-1 expression stimulates mitogenesis in human fibroblasts. Biochem Biophys Res Commun 2005, 330:658-664. 10.1016/j.bbrc.2005.03.036 15809048
11. Nguyen HQ Hoffman-Liebermann B Liebermann DA The zinc finger transcription factor Egr-1 is essential for and restricts differentiation along the macrophage lineage. Cell 1993, 72:197-209. 10.1016/0092-8674(93)90660-I 7678779
12. Gibbs JD Liebermann DA Hoffman B Egr-1 abrogates the E2F-1 block in terminal myeloid differentiation and suppresses leukemia. Oncogene 2008, 27:98-106. 10.1038/sj.onc.1210627 17599039
13. Shafarenko M Liebermann DA Hoffman B Egr-1 abrogates the block imparted by c-Myc on terminal M1 myeloid differentiation. Blood 2005, 106:871-878. 1895156 15840692 10.1182/blood-2004-08-3056
14. The FANTOM Consortium Suzuki H Forrest A Van Nimwegen E Daub C Balwierz P Irvine K Lassman T Ravasi T Hasegawa Y de Hoon M Katayama S Schroder K Carninci P Tomaru Y Kanamori-Katayama M Kubosaki A Akalin A Ando Y Arner E Asada M Asahara H Bailey T Bajic VB Bauer D Beckhouse AG Bertin N Björkegren J Brombacher F Bulger E, et al The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 2009.
15. GNP http://genomenetwork.nig.ac.jp/index_e.html
16. Kharbanda S Nakamura T Stone R Hass R Bernstein S Datta R Sukhatme VP Kufe D Expression of the early growth response 1 and 2 zinc finger genes during induction of monocytic differentiation. J Clin Invest 1991, 88:571-577. 295388 1864967 10.1172/JCI115341
17. Guha M O'Connell MA Pawlinski R Hollis A McGovern P Yan SF Stern D Mackman N Lipopolysaccharide activation of the MEK-ERK1/2 pathway in human monocytic cells mediates tissue factor and tumor necrosis factor alpha expression by inducing Elk-1 phosphorylation and Egr-1 expression. Blood 2001, 98:1429-1439. 10.1182/blood.V98.5.1429 11520792
18. Kumbrink J Gerlinger M Johnson JP Egr-1 induces the expression of its corepressor nab2 by activation of the nab2 promoter thereby establishing a negative feedback loop. J Biol Chem 2005, 280:42785-42793. 10.1074/ jbc.M511079200 16260776
19. Bain G Cravatt CB Loomans C Alberola-Ila J Hendrick SM Murre C Regulation of the helix-loop-helix proteins, E2A and Id3, by the Ras-ERK MAPK cascade. Nat Immunol 2001, 2:165-171. 10.1038/84273 11175815
20. Minc E de Coppet P Masson P Thiery L Dutertre S Amor-Gueret M Jaulin C The human copper-zinc superoxide dismutase gene (SOD1) proximal promoter is regulated by Sp1, Egr-1, and WT1 via non-canonical binding sites. J Biol Chem 1999, 274:503-509. 10.1074/jbc.274.1.503 9867871
21. Mora-López F Pedreño-Horrillo N Delgado-Pérez L Brieva JA Campos-Caro A Transcription of PRDM1, the master regulator for plasma cell differentiation, depends on an SP1/SP3/EGR-1 GC-box. Eur J Immunol 2008, 38:2316-2324. 10.1002/eji.200737861 18604866
22. MEME: Submission Form http://meme.sdsc.edu/meme/cgi-bin/meme.cgi
23. Kodzius R Kojima M Nishiyori H Nakamura M Fukuda S Tagami M Sasaki D Imamura K Kai C Harbers M Hayashizaki Y Carninci P CAGE: Cap analysis of gene expression. Nat Methods 2006, 3:211-222. 10.1038/nmeth0306-211 16489339
24. Beissbarth T Speed TP GOstat: Find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004, 20:1464-1465. 10.1093/bioinformatics/bth088 14962934
25. GOstat by Tim Beissbarth http://gostat.wehi.edu.au/
26. Raychowdhury R Schäfer G Fleming J Rosewicz S Wiedenmann B Wang TC Höcker M Interaction of early growth response protein 1 (Egr-1), specificity protein 1 (Sp1), and cyclic adenosine 3′5′-monophosphate response element binding protein (CREB) at a proximal response element is critical for gastrin-dependent activation of the chromogranin A promoter. Mol Endocrinol 2002, 16:2802-2818. 10.1210/me.2001-0292 12456801
27. Gustincich S Sandelin A Plessy C Katayama S Simone R Lazarevic D Hayashizaki Y Carninci P The complexity of the mammalian transcriptome. J Physiol 2006, 575:321-332. 1819450 16857706 10.1113/ jphysiol.2006.115568
28. Carlone DL Skalnik DG CpG binding protein is crucial for early embryonic development. Mol Cell Biol 2001, 21:7601-7606. 99931 11604496 10.1128/ MCB.21.22.7601-7606.2001
29. Strathdee G Sim A Brown R Control of gene expression by CpG island methylation in normal cells. Biochem Soc Trans 2004, 32:913-915. 10.1042/ BST0320916 15506922
30. Ogishima T Shiina H Breault JE Terashima M Honda S Enokida H Urakami S Tokizane T Kawakami T Ribeiro-Filho LA Fujime M Kane CJ Carroll PR Igawa M Dahiya R Promoter CpG hypomethylation and transcription factor EGR1 hyperactivate heparanase expression in bladder cancer. Oncogene 2005, 24:6765-6772. 10.1038/sj.onc.1208811 16007175
31. Fukada T Tonks NK The reciprocal role of Egr-1 and Sp family proteins in regulation of the PTP1B promoter in response to the p210 Bcr-Abl oncoprotein-tyrosine kinase. J Biol Chem 2001, 276:25512-25519. 10.1074/ jbc.M101354200 11316810
32. Li X Nie S Chang C Qiu T Cao X Smads oppose Hox transcriptional activities. Exp Cell Res 2006, 312:854-864. 10.1016/j.yexcr.2005.12.002 16405960
33. Majello B De Luca P Lania L Sp3 is a bifunctional transcription regulator with modular independent activation and repression domains. J Biol Chem 1997, 272:4021-4026. 10.1074/jbc.272.7.4021 9020109
34. Gibbs JD Liebermann DA Hoffman B Egr-1 abrogates the E2F-1 block in terminal myeloid differentiation and suppresses leukemia. Oncogene 2008, 27:98-106. 10.1038/sj.onc.1210627 17599039
35. Shafarenko M Liebermann DA Hoffman B Egr-1 abrogates the block imparted by c-Myc on terminal M1 myeloid differentiation. Blood 2005, 106:871-878. 1895156 15840692 10.1182/blood-2004-08-3056
36. Thiel G Kaufmann K Magin A Lietz M Bach K Cramer M The human transcriptional repressor protein NAB1: Expression and biological activity. Biochim Biophys Acta 2000, 1493:289-301. 11018254
37. Houston P Campbell CJ Svaren J Milbrandt J Braddock M The transcriptional corepressor NAB2 blocks Egr-1-mediated growth factor activation and angiogenesis. Biochem Biophys Res Commun 2001, 283:480-486. 10.1006/bbrc.2001.4810 11327726
38. Srinivasan R Mager GM Ward RM Mayer J Svaren J NAB2 represses transcription by interacting with the CHD4 subunit of the nucleosome remodeling and deacetylase (NuRD) complex. J Biol Chem 2006, 281:15129-15137. 10.1074/jbc.M600775200 16574654
39. Arora S Wang Y Jia Z Vardar-Sengul S Munawar A Doctor KS Birrer M McClelland M Adamson E Mercola D Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip. Genome Biol 9:R166. 2614498 19032775 10.1186/ gb-2008-9-11-r166
40. Lee SL Tourtellotte LC Wesselschmidt RL Milbrandt J Growth and differentiation proceeds normally in cells deficient in the immediate early gene NGFI-A. J Biol Chem 1995, 270:9971-9977. 10.1074/ jbc.270.17.9971 7730380
41. Topilko P Schneider-maunoury S Levi G Trembleau A Gourdji D Driancourt MA Rao CV Charnay P Multiple pituitary and ovarian defects in Krox-24 (NGFI-A, Egr-1)-targeted mice. Mol Endocrinol 1998, 12:107-122. 10.1210/ me.12.1.107 9440815
42. Joes MW Errington ML French PJ Fine A Bliss TV Garel S Charnay P Bozon B Laroche S Davis S A requirement for the immediate early gene Zif268 in the expression of late LTP and long-term memories. Nat Neurosci 2001, 4:289-296. 10.1038/85138 11224546
43. Wei F Xu ZC Qu Z Milbrandt J Zhuo M Role of EGR1 in hippocampal synaptic enhancement induced by tetanic stimulation and amputation. J Cell Biol 2000, 149:1325-1334. 2175137 10871275 10.1083/jcb.149.7.1325
44. Laslo P spooner CJ Warmflash A Lancki DW Lee HJ Sciammas R Gantner BN Dinner AR Singh H Multilineage transcriptional priming and determination of alternate hematopoietic cell fates. Cell 2006, 126:755-766. 10.1016/ j.cell.2006.06.052 16923394
45. Carter JH Tourtellotte WG Early growth response transcriptional regulators are dispensable for macrophage differentiation. J Immunol 2007, 178:3038-3047. 17312150
46. Rossi D Cozzio A Flechsig E Klein MA Rülicke T Aguzzi A Weissmann C Onset of ataxia and Purkinje cell loss in PrP null mice inversely correlated with Dpl level in brain. EMBO J 2001, 20:694-702. 145426 11179214 10.1093/emboj/20.4.694
47. Boyer LA Lee TI Cole MF Johnstone SE Levine SS Zucker JP Guenther MG Kumar RM Murray HL Jenner RG Gifford DK Melton DA Jaenisch R Young RA Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122:947-956. 10.1016/j.cell.2005.08.020 16153702
48. The Vmatch large scale sequence analysis software http://www.vmatch.de