Regulatory interdependence of myeloid transcription factors revealed by matrix RNAi analysis

Genome Biology

Volumn 10, Issue 11, 2009, Pages

  Tomaru, Yasuhiro ^a,b   Simon, Christophe ^a   Forrest, Alistair R R ^a,c   Miura, Hisashi ^a,b   Kubosaki, Atsutaka ^a   Hayashizaki, Yoshihide ^a,b   Suzuki, Masanori ^a,b  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

^c GRIFFITH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

MIXED LINEAGE LEUKEMIA PROTEIN; PHORBOL 13 ACETATE 12 MYRISTATE; PROTEIN MYB; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MLLT3; UNCLASSIFIED DRUG;

ARTICLE; CELL CYCLE; CELL DIFFERENTIATION; CELL TYPE; CONTROLLED STUDY; DOWN REGULATION; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; MONOCYTE; QUALITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA INTERFERENCE; TRANSCRIPTION REGULATION; UPREGULATION; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETIC TRANSCRIPTION; GENETIC TRANSFECTION; GENETICS; METABOLISM;

CELL DIFFERENTIATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; HUMANS; MODELS, BIOLOGICAL; MODELS, GENETIC; MONOCYTES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE; RNA, SMALL INTERFERING; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 76249130293     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-11-r121     Document Type: Article

References (42)

1. Nilsson R, Bajic VB, Suzuki H, di Bernardo D, Bjorkegren J, Katayama S, Reid JF, Sweet MJ, Gariboldi M, Carninci P, Hayashizaki Y, Hume DA, Tegner J, Ravasi T. Transcriptional network dynamics in macrophage activation. Genomics 2006, 88:133-142. 10.1016/j.ygeno.2006.03.022, 16698233.
2. Loh YH, Wu Q, Chew JL, Vega VB, Zhang W, Chen X, Bourque G, George J, Leong B, Liu J, Wong KY, Sung KW, Lee CW, Zhao XD, Chiu KP, Lipovich L, Kuznetsov VA, Robson P, Stanton LW, Wei CL, Ruan Y, Lim B, Ng HH. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006, 38:431-440. 10.1038/ng1760, 16518401.
3. Zeitlinger J, Zinzen RP, Stark A, Kellis M, Zhang H, Young RA, Levine M. Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo. Genes Dev 2007, 21:385-390. 10.1101/gad.1509607, 1804326, 17322397.
4. Tomaru Y, Kondo S, Suzuki M, Hayashizaki Y. A comprehensive search for HNF-3alpha-regulated genes in mouse hepatoma cells by 60 K cDNA microarray and chromatin immunoprecipitation/PCR analysis. Biochem Biophys Res Commun 2003, 310:667-674. 10.1016/j.bbrc.2003.08.148, 14521963.
5. Nakanishi M, Tomaru Y, Miura H, Hayashizaki Y, Suzuki M. Identification of transcriptional regulatory cascades in retinoic acid-induced growth arrest of HepG2 cells. Nucleic Acids Res 2008, 36:3443-3454. 10.1093/nar/gkn066, 2425469, 18445634.
6. Tanaka T, Tomaru Y, Nomura Y, Miura H, Suzuki M, Hayashizaki Y. Comprehensive search for HNF-1beta-regulated genes in mouse hepatoma cells perturbed by transcription regulatory factor-targeted RNAi. Nucleic Acids Res 2004, 32:2740-2750. 10.1093/nar/gkh597, 419602, 15148361.
7. Tomaru Y, Nakanishi M, Miura H, Kimura Y, Ohkawa H, Ohta Y, Hayashizaki Y, Suzuki M. Identification of an inter-transcription factor regulatory network in human hepatoma cells by Matrix RNAi. Nucleic Acids Res 2009, 37:1049-1060. 10.1093/nar/gkn1028, 2651797, 19129217.
8. Sato M, Taniguchi T, Tanaka N. The interferon system and interferon regulatory factor transcription factors - studies from gene knockout mice. Cytokine Growth Factor Rev 2001, 12:133-142. 10.1016/S1359-6101(00)00032-0, 11325597.
9. Shivdasani RA, Fujiwara Y, McDevitt MA, Orkin SH. A lineage-selective knockout establishes the critical role of transcription factor GATA-1 in megakaryocyte growth and platelet development. EMBO J 1997, 16:3965-3973. 10.1093/emboj/16.13.3965, 1170020, 9233806.
10. Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman WW. Identification of conserved regulatory elements by comparative genome analysis. J Biol 2003, 2:13. 10.1186/1475-4924-2-13, 193685, 12760745.
11. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4:651-657. 10.1038/nmeth1068, 17558387.
12. Balaji S, Iyer LM, Babu MM, Aravind L. Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?. Trends Genet 2008, 24:319-323. 10.1016/j.tig.2008.04.006, 2768723, 18514968.
13. Zhang X, Odom DT, Koo SH, Conkright MD, Canettieri G, Best J, Chen H, Jenner R, Herbolsheimer E, Jacobsen E, Kadam S, Ecker JR, Emerson B, Hogenesch JB, Unterman T, Young RA, Montminy M. Genome-wide analysis of cAMP-response element binding protein occupancy, phosphorylation, and target gene activation in human tissues. Proc Natl Acad Sci USA 2005, 102:4459-4464. 10.1073/pnas.0501076102, 555478, 15753290.
14. Miura H, Tomaru Y, Nakanishi M, Kondo S, Hayashizaki Y, Suzuki M. Identification of DNA regions and a set of transcriptional regulatory factors involved in transcriptional regulation of several human liver-enriched transcription factor genes. Nucleic Acids Res 2009, 37:778-792. 10.1093/nar/gkn978, 2647325, 19074951.
15. Tsuchiya S, Yamabe M, Yamaguchi Y, Kobayashi Y, Konno T, Tada K. Establishment and characterization of a human acute monocytic leukemia cell line (THP-1). Int J Cancer 1980, 26:171-176. 10.1002/ijc.2910260208, 6970727.
16. Lacraz S, Dayer JM, Nicod L, Welgus HG. 1,25-dihydroxyvitamin D3 dissociates production of interstitial collagenase and 92-kDa gelatinase in human mononuclear phagocytes. J Biol Chem 1994, 269:6485-6490.
17. Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, 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, Chalk AM, et al. FANTOM Consortium The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 2009, 41:553-562. 10.1038/ng.375, 19377474, FANTOM Consortium.
18. Gitter A, Siegfried Z, Klutstein M, Fornes O, Oliva B, Simon I, Bar-Joseph Z. Backup in gene regulatory networks explains differences between binding and knockout results. Mol Syst Biol 2009, 5:276. 10.1038/msb.2009.33, 2710864, 19536199.
19. Kraus J, Borner C, Hollt V. Distinct palindromic extensions of the 5'-TTC...GAA-3' motif allow STAT6 binding in vivo. FASEB J 2003, 17:304-306.
20. GenBank: CR595360. , http://www.ncbi.nlm.nih.gov/nuccore/50476167
21. Weisz A, Marx P, Sharf R, Appella E, Driggers PH, Ozato K, Levi BZ. Human interferon consensus sequence binding protein is a negative regulator of enhancer elements common to interferon-inducible genes. J Biol Chem 1992, 267:25589-25596.
22. Norton JD. ID helix-loop-helix proteins in cell growth, differentiation and tumorigenesis. J Cell Sci 2000, 113:3897-3905.
23. Odero MD, Zeleznik-Le NJ, Chinwalla V, Rowley JD. Cytogenetic and molecular analysis of the acute monocytic leukemia cell line THP-1 with an MLL-AF9 translocation. Genes Chromosomes Cancer 2000, 29:333-338. 10.1002/1098-2264(2000)9999:9999<::AID-GCC1040>3.0.CO;2-Z, 11066077.
24. Kawagoe H, Kawagoe R, Sano K. Targeted down-regulation of MLL-AF9 with antisense oligodeoxyribonucleotide reduces the expression of the HOXA7 and -A10 genes and induces apoptosis in a human leukemia cell line, THP-1. Leukemia 2001, 15:1743-1749.
25. Buske C, Feuring-Buske M, Antonchuk J, Rosten P, Hogge DE, Eaves CJ, Humphries RK. Overexpression of HOXA10 perturbs human lymphomyelopoiesis in vitro and in vivo. Blood 2001, 97:2286-2292. 10.1182/blood.V97.8.2286, 11290589.
26. Thorsteinsdottir U, Sauvageau G, Hough MR, Dragowska W, Lansdorp PM, Lawrence HJ, Largman C, Humphries RK. Overexpression of HOXA10 in murine hematopoietic cells perturbs both myeloid and lymphoid differentiation and leads to acute myeloid leukemia. Mol Cell Biol 1997, 17:495-505. 231774, 8972230.
27. Taketani T, Taki T, Ono R, Kobayashi Y, Ida K, Hayashi Y. The chromosome translocation t(7;11)(p15;p15) in acute myeloid leukemia results in fusion of the NUP98 gene with a HOXA cluster gene, HOXA13, but not HOXA9. Genes Chromosomes Cancer 2002, 34:437-443. 10.1002/gcc.10077, 12112533.
28. Kelly LM, Englmeier U, Lafon I, Sieweke MH, Graf T. MafB is an inducer of monocytic differentiation. EMBO J 2000, 19:1987-1997. 10.1093/emboj/19.9.1987, 305687, 10790365.
29. Tillmanns S, Otto C, Jaffray E, Du Roure C, Bakri Y, Vanhille L, Sarrazin S, Hay RT, Sieweke MH. SUMO modification regulates MafB-driven macrophage differentiation by enabling Myb-dependent transcriptional repression. Mol Cell Biol 2007, 27:5554-5564. 10.1128/MCB.01811-06, 1952098, 17548468.
30. Perry P, Sauer S, Billon N, Richardson WD, Spivakov M, Warnes G, Livesey FJ, Merkenschlager M, Fisher AG, Azuara V. A dynamic switch in the replication timing of key regulator genes in embryonic stem cells upon neural induction. Cell Cycle 2004, 3:1645-1650.
31. Chen Q, Ross AC. Retinoic acid regulates cell cycle progression and cell differentiation in human monocytic THP-1 cells. Exp Cell Res 2004, 297:68-81. 10.1016/j.yexcr.2004.02.017, 15194426.
32. Lulli V, Romania P, Morsilli O, Gabbianelli M, Pagliuca A, Mazzeo S, Testa U, Peschle C, Marziali G. Overexpression of Ets-1 in human hematopoietic progenitor cells blocks erythroid and promotes megakaryocytic differentiation. Cell Death Differ 2006, 13:1064-1074. 10.1038/sj.cdd.4401811, 16294212.
33. Levine M, Tjian R. Transcription regulation and animal diversity. Nature 2003, 424:147-151. 10.1038/nature01763, 12853946.
34. Ernst P, Smale ST. Combinatorial regulation of transcription. I: General aspects of transcriptional control. Immunity 1995, 2:311-319. 10.1016/1074-7613(95)90139-6, 7719936.
35. Hemmi H, Breitman TR. Induction of functional differentiation of a human monocytic leukemia cell line (THP-1) by retinoic acid and cholera toxin. Jpn J Cancer Res 1985, 76:345-351.
36. Dawson MI, Elstner E, Kizaki M, Chen DL, Pakkala S, Kerner B, Koeffler HP. Myeloid differentiation mediated through retinoic acid receptor/retinoic × receptor (RXR) not RXR/RXR pathway. Blood 1994, 84:446-452.
37. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408. 10.1006/meth.2001.1262, 11846609.
38. Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100:9440-9445. 10.1073/pnas.1530509100, 170937, 12883005.
39. Q-VALUE. , http://genomics.princeton.edu/storeylab/qvalue/
40. R: a Language and Environment for Statistical Computing. , http://www.R-project.org
41. GNP. , http://genomenetwork.nig.ac.jp/index_e.html
42. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13:2498-2504. 10.1101/gr.1239303, 403769, 14597658.