Erythroid-induced commitment of K562 cells results in clusters of differentially expressed genes enriched for specific transcription regulatory elements

Physiological Genomics

Volumn 19, Issue , 2005, Pages 117-130

  Addya, Sankar ^a   Keller, Margaret A ^a   Delgrosso, Kathleen ^a   Ponte, Christine M ^a   Vadigepalli, Rajanikanth ^a   Gonye, Gregory E ^a   Surrey, Saul ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

Cell differentiation; Gene expression profiling; Hemin; Transcription regulatory elements

Indexed keywords

HEMIN; TRANSCRIPTOME;

ALGORITHM; ARTICLE; CELL STRAIN K 562; COMPUTER PROGRAM; CONTROLLED STUDY; DNA FLANKING REGION; DNA MICROARRAY; ERYTHROID CELL; GENE CLUSTER; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSCRIPTION REGULATION; UNINDEXED SEQUENCE;

5' FLANKING REGION; CELL DIFFERENTIATION; CLUSTER ANALYSIS; ERYTHROCYTES; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HEMIN; HUMANS; K562 CELLS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGULATORY SEQUENCES, NUCLEIC ACID; REPRODUCIBILITY OF RESULTS; RESPONSE ELEMENTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; TIME FACTORS; TRANSCRIPTION, GENETIC;

EID: 11144330111     PISSN: 15312267     EISSN: None     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00028.2004     Document Type: Article

References (60)

1. Adachi K, Zhao Y, and Surrey S. Effects of heme addition on formation of stable human globin chains and hemoglobin subunit assembly in a cell-free system. Arch Biochem Biophys 413: 99-106, 2003.
2. Anwar A, Siegel D, Kepa JK, and Ross D. Interaction of the molecular chaperone Hsp70 with human NAD(P)H:quinone oxidoreductase 1. J Biol Chem 277: 14060-14067, 2002.
3. Applied Biosystems. Relative Quantitation of Gene Expression. User bulletin no. 2, ABI PRISM 7700 Sequence Detection System. Applied Biosystems, 1997.
4. Atweh GF, DeSimone J, Saunthararajah Y, Fathallah H, Weinberg RS, Nagel RL, Fabry ME, and Adams RJ. Hemoglobinopathies. Hematology (Am Soc Hematol Educ Program): 14-39, 2003.
5. Benz EJ Jr, Murnane MJ, Tonkonow BL, Berman BW, Mazur EM, Cavallesco C, Jenko T, Snyder EL, Forget BG, and Hoffman R. Embryonic-fetal erythroid characteristics of a human leukemic cell line. Proc Natl Acad Sci USA 77: 3509-3513, 1980.
6. Bieker JJ. Isolation, genomic structure, and expression of human erythroid Kruppel-like factor (EKLF). DNA Cell Biol 15: 347-352, 1996.
7. Brand M, Ranish JA, Kummer NT, Hamilton J, Igarashi K, Francastel C, Chi TH, Crabtree GR, Aebersold R, and Groudine M. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol 1: 73-80, 2004.
8. Bunn HF and Forget BG. Hemoglobin: Molecular, Genetic and Clinical Aspects. Philadelphia: Saunders, 1986.
9. Burton GR, Guan Y, Nagarajan R, and McGehee RE Jr. Microarray analysis of gene expression during early adipocyte differentiation. Gene 293: 21-31, 2002.
10. Costa RH, Kalinichenko VV, Holterman AX, and Wang X. Transcription factors in liver development, differentiation, and regeneration. Hepatology 38: 1331-1347, 2003.
11. Davidson E. Gene activity in early development. In: RNA Sequence Complexity and Structural Gene Transcription in Early Embryos (2nd ed.). New York: Academic, 1976, p. 189-236.
12. Denk A, Wirth T, and Baumann B. NF-kappaB transcription factors: critical regulators of hematopoiesis and neuronal survival. Cytokine Growth Factor Rev 11: 303-320, 2000.
13. Duan Z, Stamatoyannopoulos G, and Li Q. Role of NF-Y in in vivo regulation of the γ-globin gene. Mol Cell Biol 21: 3083-3095, 2001.
14. Dziak R. Evidence for a role of MCM (mini-chromosome maintenance)5 in transcriptional repression of sub-telomeric and Ty-proximal genes in Saccharomyces cerevisiae. J Biol Chem 278: 27372-27381, 2003.
15. Elagib KE, Racke FK, Mogass M, Khetawat R, Delehanty LL, and Goldfarb AN. RUNX1 and GATA-1 coexpression and cooperation in megakaryocytic differentiation. Blood 101: 4333-4341, 2003.
16. Elkon R, Linhart C, Sharan R, Shamir R, and Shiloh Y. Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res 13: 773-780, 2003.
17. Fadigan A and Dailey HA. Inhibition of ferrochelatase during differentiation of murine erythroleukaemia cells. Biochem J 243: 419-424, 1987.
18. Firulli AB. A HANDful of questions: the molecular biology of the heart and neural crest derivatives (HAND)-subclass of basic helix-loop-helix transcription factors. Gene 312: 27-40, 2003.
19. Forget BG. Molecular basis of hereditary persistence of fetal hemoglobin. Ann NY Acad Sci 850: 38-44, 1998.
20. Gianni AM, Presta M, Polli E, Peschle C, Lettieri F, Saglio G, Comi P, Giglioni B, and Ottolenghi S. Preferential induction of fetal versus embryonic globin chains in human leukemic cell lines. Leuk Res 6: 155-163, 1982.
21. Gui CY and Dean A. A major role for the TATA box in recruitment of chromatin modifying complexes to a globin gene promoter. Proc Natl Acad Sci USA 100: 7009-7014, 2003.
22. Han AP, Yu C, Lu L, Fujiwara Y, Browne C, Chin G, Fleming M, Leboulch P, Orkin SH, and Chen JJ. Heme-regulated eIF2alpha kinase (HRI) is required for translational regulation and survival of erythroid precursors in iron deficiency. EMBO J 20: 6909-6918, 2001.
23. Igarashi K, Hoshino H, Muto A, Suwabe N, Nishikawa S, Nakauchi H, and Yamamoto M. Multivalent DNA binding complex generated by small Maf and Bach1 as a possible biochemical basis for beta-globin locus control region complex. J Biol Chem 273: 11783-11790, 1998.
24. Kalousova A, Benes V, Paces J, Paces V, and Kozmik Z. DNA binding and transactivating properties of the paired and homeobox protein Pax4. Biochem Biophys Res Commun 259: 510-518, 1999.
25. Keefer JR, Schneidereith TA, Mays AC, Purvis SH, Dover GJ. Differential regulation of Hb F induction in K562 cells and human CD34+ erythrocyte cultures: the possible role of cyclic nucleotide dependent signaling pathways (Abstract). Blood 102: 267, 2003.
26. Kobayashi A, Yamagiwa H, Hoshino H, Muto A, Sato K, Morita M, Hayashi N, Yamamoto M, and Igarashi K. A combinatorial code for gene expression generated by transcription factor Bach2 and MAZR (MAZ-related factor) through the BTB/POZ domain. Mol Cell Biol 20: 1733-1746, 2000.
27. Koury MJ, Sawyer ST, and Brandt SJ. New insights into erythropoiesis. Curr Opin Hematol 9: 93-100, 2002.
28. Lampronti I, Bianchi N, Borgatti M, Fibach E, Prus E, and Gambari R. Accumulation of gamma-globin mRNA in human erythroid cells treated with angelicin. Eur J Haematol 3: 189-95, 2003.
29. Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, and Siani-Rose MA. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86, 2003.
30. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, and Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680, 1996.
31. Lozzio CB and Lozzio BB. Human chronic myelogenous leukemia cell-line with positive Philadelphia chromosome. Blood 45: 321-334, 1975.
32. Lumelsky NL and Forget BG. Negative regulation of globin gene expression during megakaryocytic differentiation of a human erythroleukemic cell line. Mol Cell Biol 11: 3528-3536, 1991.
33. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, Kloos DU, Land S, Lewicki-Potapov B, Michael H, Munch R, Reuter I, Rotert S, Saxel H, Scheer M, Thiele S, and Wingender E. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31: 374-378, 2003.
34. Mora-Garcia P, Cheng J, Crans-Vargas HN, Countouriotis A, Shankar D, and Sakamoto KM. Transcriptional regulators and myelopoiesis: the role of serum response factor and CREB as targets of cytokine signaling. Stem Cells 21: 123-130, 2003.
35. Murnane MJ, Phipps PM, and Denekamp DS. Expression and induction of cathepsins B and D in K562 cells. Exp Hematol 16: 33-37, 1988.
36. Muto A, Tashiro S, Tsuchiya H, Kume A, Kanno M, Ito E, Yamamoto M, and Igarashi K. Activation of Maf/AP-1 repressor Bach2 by oxidative stress promotes apoptosis and its interaction with promyelocytic leukemia nuclear bodies. J Biol Chem 277: 20724-20733, 2002.
37. Niitsu N, Yamamoto-Yamaguchi Y, Miyoshi H, Shimizu K, Ohki M, Umeda M, and Honma Y. AML1a but not AML1b inhibits erythroid differentiation induced by sodium butyrate and enhances the megakaryocytic differentiation of K562 leukemia cells. Cell Growth Differ 8: 319-326, 1997.
38. Ogawa K, Sun J, Taketani S, Nakajima O, Nishitani C, Sassa S, Hayashi N, Yamamoto M, Shibahara S, Fujita H, and Igarashi K. Heme mediates derepression of Maf recognition element through direct binding to transcription repressor Bach1. EMBO J 20: 2835-2843, 2001.
39. Ohashi K, Naruto M, Nakaki T, and Sano E. Identification of interleukin-8 converting enzyme as cathepsin L. Biochim Biophys Acta 1649: 30-39, 2003.
40. Osawa M, Yamaguchi T, Nakamura Y, Kaneko S, Onodera M, Sawada K, Jegalian A, Wu H, Nakauchi H, and Iwama A. Erythroid expansion mediated by the Gfi-1B zinc finger protein: role in normal hematopoiesis. Blood 100: 2769-2777, 2002.
41. Pace BS, Qian XH, Sangerman J, Ofori-Acquah SF, Baliga BS, Han J, and Critz SD. p38 MAP kinase activation mediates gamma-globin gene induction in erythroid progenitors. Exp Hematol 11: 1089-1096, 2003.
42. Papayannopoulou T, Nakamoto B, Kurachi S, and Nelson R. Analysis of the erythroid phenotype of HEL cells: clonal variation and the effect of inducers. Blood 70: 1764-1772, 1987.
43. Pettiford SM and Herbst R. The protein tyrosine phosphatase HePTP regulates nuclear translocation of ERK2 and can modulate megakaryocytic differentiation of K562 cells. Leukemia 17: 366-378, 2003.
44. Plonczynski M, Hardy CL, Safaya S, Harrell A, McCoy L, Brinson A, Agwarangbo L, and Steinberg MH. Induction of globin synthesis in K562 cells is associated with differential expression of transcription factor genes. Blood Cells Mol Dis 25: 156-165, 1999.
45. Reddy RK, Mao C, Baumeister P, Austin RC, Kaufman RJ, and Lee AS. Endoplasmic reticulum chaperone protein GRP78 protects cells from apoptosis induced by topoisomerase inhibitors: role of ATP binding site in suppression of caspase-7 activation. J Biol Chem 278: 20915-20924, 2003.
46. Richon V, Rifkind R, and Marks P. Differentiation of murine erythroleukemia cells (friend cells). In: Cell Biology: A Laboratory Handbook, edited by Celis JC. London: Academic, 1994, p. 213-217.
47. Rutherford TR, Clegg JB, and Weatherall DJ. K562 human leukaemic cells synthesise embryonic haemoglobin in response to haemin. Nature 280: 164-165, 1979.
48. Schultheis B, Carapeti-Marootian M, Hochhaus A, Weisser A, Goldman JM, and Melo JV. Overexpression of SOCS-2 in advanced stages of chronic myeloid leukemia: possible inadequacy of a negative feedback mechanism. Blood 99: 1766-1775, 2002.
49. Shinozawa I, Inokuchi K, Wakabayashi I, and Dan K. Disturbed expression of the anti-apoptosis gene, survivin, and EPR-1 in hematological malignancies. Leuk Res 24: 965-970, 2000.
50. Smith RD, Malley JD, and Schechter AN. Quantitative analysis of globin gene induction in single human erythroleukemic cells. Nucleic Acids Res 28: 4998-5004, 2000.
51. Stamatoyannopoulos G and Nienhuis AW. Hemoglobin switching. In: The Molecular Basis of Blood Disease, edited by Stamatoyannopoulos G, Nienhuis AW, Majerus PW, and Varmus H. Philadelphia: Saunders, 1994, p. 107.
52. Tahara T, Sun J, Nakanishi K, Yamamoto M, Mori H, Saito T, Fujita H, Igarashi K, and Taketani S. Heme positively regulates the expression of beta-globin at the locus control region via the transcriptional factor Bach1 in erythroid cells. J Biol Chem 7: 5480-54877, 2004.
53. Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, and Golub TR. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96: 2907-2912, 1999.
54. Vadigepalli R, Chakravarthula P, Zak DE, Schwaber JS, and Gonye GE. PAINT: a promoter analysis and interaction network generation tool for gene regulatory network identification. OMICS 7: 235-252, 2003.
55. Vieira SA, Deininger MW, Sorour A, Sinclair P, Foroni L, Goldman JM, and Melo JV. Transcription factor BACH2 is transcriptionally regulated by the BCR/ABL oncogene. Genes Chromosomes Cancer 32: 353-363, 2001.
56. Warren LA and Rothenberg EV. Regulatory coding of lymphoid lineage choice by hematopoietic transcription factors. Curr Opin Immunol 15: 166-175, 2003.
57. Xiao H, Palhan V, Yang Y, and Roeder R. TIP30 has an intrinsic kinase activity required for up-regulation of a subset of apoptotic genes. EMBO J 19: 956-963, 2000.
58. Yamada Y, Warren AJ, Dobson C, Forster A, Pannell R, and Rabbitts TH. The T cell leukemia LIM protein Lmo2 is necessary for adult mouse hematopoiesis. Proc Natl Acad Sci USA 95: 3890-3895, 1998.
59. Zafarana G, Rottier R, Grosveld F, and Philipsen S. Erythroid overexpression of C/EBPγ in transgenic mice affects γ-globin expression and fetal liver erythropoiesis. EMBO J 19: 5856-5863, 2000.
60. Zhou W, Clouston DR, Wang X, Cerruti L, Cunningham JM, and Jane SM. Induction of human fetal globin gene expression by a novel erythroid factor, NF-E4. Mol Cell Biol 20: 7662-7672, 2000.