Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics
10.1038/nsmb713
Crossref journal-article
Springer Science and Business Media LLC
Nature Structural & Molecular Biology (297)
Bibliography

Brand, M., Ranish, J. A., Kummer, N. T., Hamilton, J., Igarashi, K., Francastel, C., Chi, T. H., Crabtree, G. R., Aebersold, R., & Groudine, M. (2003). Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nature Structural & Molecular Biology, 11(1), 73–80.

Authors 10
  1. Marjorie Brand (first)
  2. Jeffrey A Ranish (additional)
  3. Nicolas T Kummer (additional)
  4. Joan Hamilton (additional)
  5. Kazuhiko Igarashi (additional)
  6. Claire Francastel (additional)
  7. Tian H Chi (additional)
  8. Gerald R Crabtree (additional)
  9. Ruedi Aebersold (additional)
  10. Mark Groudine (additional)
References 71 Referenced 172
  1. Forrester, W.C. et al. A deletion of the human β-globin locus activation region causes a major alteration in chromatin structure and replication across the entire β-globin locus. Genes Dev. 4, 1637–1649 (1990). (10.1101/gad.4.10.1637) / Genes Dev. by WC Forrester (1990)
  2. Fraser, P. & Grosveld, F. Locus control regions, chromatin activation and transcription. Curr. Opin. Cell Biol. 10, 361–365 (1998). (10.1016/S0955-0674(98)80012-4) / Curr. Opin. Cell Biol. by P Fraser (1998)
  3. Epner, E. et al. The β-globin LCR is not necessary for an open chromatin structure or developmentally regulated transcription of the native mouse β-globin locus. Mol. Cell 2, 447–455 (1998). (10.1016/S1097-2765(00)80144-6) / Mol. Cell by E Epner (1998)
  4. Reik, A. et al. The locus control region is necessary for gene expression in the human β-globin locus but not the maintenance of an open chromatin structure in erythroid cells. Mol. Cell. Biol. 18, 5992–6000 (1998). (10.1128/MCB.18.10.5992) / Mol. Cell. Biol. by A Reik (1998)
  5. Bender, M.A., Bulger, M., Close, J. & Groudine, M. β-globin gene switching and DNase I sensitivity of the endogenous β-globin locus in mice do not require the locus control region. Mol. Cell 5, 387–393 (2000). (10.1016/S1097-2765(00)80433-5) / Mol. Cell by MA Bender (2000)
  6. Bulger, M. et al. A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse β-globin locus. Mol. Cell. Biol. 23, 5234–5244 (2003). (10.1128/MCB.23.15.5234-5244.2003) / Mol. Cell. Biol. by M Bulger (2003)
  7. Orkin, S.H. Transcription factors and hematopoietic development. J. Biol. Chem. 270, 4955–4958 (1995). (10.1074/jbc.270.10.4955) / J. Biol. Chem. by SH Orkin (1995)
  8. Hardison, R. et al. Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights. Gene 205, 73–94 (1997). (10.1016/S0378-1119(97)00474-5) / Gene by R Hardison (1997)
  9. Armstrong, J.A. & Emerson, B.M. Transcription of chromatin: these are complex times. Curr. Opin. Genet. Dev. 8, 165–172 (1998). (10.1016/S0959-437X(98)80137-8) / Curr. Opin. Genet. Dev. by JA Armstrong (1998)
  10. Levings, P.P. & Bungert, J. The human β-globin locus control region. Eur. J. Biochem. 269, 1589–1599 (2002). (10.1046/j.1432-1327.2002.02797.x) / Eur. J. Biochem. by PP Levings (2002)
  11. Liu, D. et al. Dissection of the enhancer activity of β-globin 5′ DNase I-hypersensitive site 2 in transgenic mice. Proc. Natl. Acad. Sci. USA 89, 3899–3903 (1992). (10.1073/pnas.89.9.3899) / Proc. Natl. Acad. Sci. USA by D Liu (1992)
  12. Ney, P.A., Sorrentino, B.P., McDonagh, K.T. & Nienhuis, A.W. Tandem AP-1-binding sites within the human β-globin dominant control region function as an inducible enhancer in erythroid cells. Genes Dev. 4, 993–1006 (1990). (10.1101/gad.4.6.993) / Genes Dev. by PA Ney (1990)
  13. Sorrentino, B.P., Ney, P.A. & Nienhuis, A.W. Localization and characterization of the DNase I-hypersensitive site II (HS II) enhancer. A critical regulatory element within the β-globin locus-activating region. Ann. NY Acad. Sci. 612, 141–151 (1990). (10.1111/j.1749-6632.1990.tb24300.x) / Ann. NY Acad. Sci. by BP Sorrentino (1990)
  14. Talbot, D., Philipsen, S., Fraser, P. & Grosveld, F. Detailed analysis of the site 3 region of the human β-globin dominant control region. EMBO J. 9, 2169–2177 (1990). (10.1002/j.1460-2075.1990.tb07386.x) / EMBO J. by D Talbot (1990)
  15. Gong, Q.H., McDowell, J.C. & Dean, A. Essential role of NF-E2 in remodeling of chromatin structure and transcriptional activation of the epsilon-globin gene in vivo by 5′ hypersensitive site 2 of the β-globin locus control region. Mol. Cell. Biol. 16, 6055–6064 (1996). (10.1128/MCB.16.11.6055) / Mol. Cell. Biol. by QH Gong (1996)
  16. Strauss, E.C., Andrews, N.C., Higgs, D.R. & Orkin, S.H. In vivo footprinting of the human α-globin locus upstream regulatory element by guanine and adenine ligation-mediated polymerase chain reaction. Mol. Cell. Biol. 12, 2135–2142 (1992). (10.1128/MCB.12.5.2135) / Mol. Cell. Biol. by EC Strauss (1992)
  17. Moi, P. & Kan, Y.W. Synergistic enhancement of globin gene expression by activator protein-1-like proteins. Proc. Natl. Acad. Sci. USA 87, 9000–9004 (1990). (10.1073/pnas.87.22.9000) / Proc. Natl. Acad. Sci. USA by P Moi (1990)
  18. Moon, A.M. & Ley, T.J. Functional properties of the β-globin locus control region in K562 erythroleukemia cells. Blood 77, 2272–2284 (1991). (10.1182/blood.V77.10.2272.2272) / Blood by AM Moon (1991)
  19. Mignotte, V., Wall, L., deBoer, E., Grosveld, F. & Romeo, P.H. Two tissue-specific factors bind the erythroid promoter of the human porphobilinogen deaminase gene. Nucleic Acids Res. 17, 37–54 (1989). (10.1093/nar/17.1.37) / Nucleic Acids Res. by V Mignotte (1989)
  20. Andrews, N.C., Erdjument-Bromage, H., Davidson, M.B., Tempst, P. & Orkin, S.H. Erythroid transcription factor NF-E2 is a haematopoietic-specific basic-leucine zipper protein. Nature 362, 722–728 (1993). (10.1038/362722a0) / Nature by NC Andrews (1993)
  21. Andrews, N.C. et al. The ubiquitous subunit of erythroid transcription factor NF-E2 is a small basic-leucine zipper protein related to the v-maf oncogene. Proc. Natl. Acad. Sci. USA 90, 11488–11492 (1993). (10.1073/pnas.90.24.11488) / Proc. Natl. Acad. Sci. USA by NC Andrews (1993)
  22. Igarashi, K. et al. Regulation of transcription by dimerization of erythroid factor NF-E2 p45 with small Maf proteins. Nature 367, 568–572 (1994). (10.1038/367568a0) / Nature by K Igarashi (1994)
  23. Andrews, N.C. The NF-E2 transcription factor. Int. J. Biochem. Cell Biol. 30, 429–432 (1998). (10.1016/S1357-2725(97)00135-0) / Int. J. Biochem. Cell Biol. by NC Andrews (1998)
  24. Gygi, S.P. et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994–999 (1999). (10.1038/13690) / Nat. Biotechnol. by SP Gygi (1999)
  25. Tao, W.A. & Aebersold, R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr. Opin. Biotechnol. 14, 110–118 (2003). (10.1016/S0958-1669(02)00018-6) / Curr. Opin. Biotechnol. by WA Tao (2003)
  26. Ranish, J.A. et al. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 33, 349–355 (2003). (10.1038/ng1101) / Nat. Genet. by JA Ranish (2003)
  27. Kotkow, K.J. & Orkin, S.H. Dependence of globin gene expression in mouse erythroleukemia cells on the NF-E2 heterodimer. Mol. Cell. Biol. 15, 4640–4647 (1995). (10.1128/MCB.15.8.4640) / Mol. Cell. Biol. by KJ Kotkow (1995)
  28. Igarashi, K., Itoh, K., Hayashi, N., Nishizawa, M. & Yamamoto, M. Conditional expression of the ubiquitous transcription factor MafK induces erythroleukemia cell differentiation. Proc. Natl. Acad. Sci. USA 92, 7445–7449 (1995). (10.1073/pnas.92.16.7445) / Proc. Natl. Acad. Sci. USA by K Igarashi (1995)
  29. Francastel, C., Poindessous-Jazat, V., Augery-Bourget, Y. & Robert-Lezenes, J. NF-E2p18/mafK is required in DMSO-induced differentiation of Friend erythroleukemia cells by enhancing NF-E2 activity. Leukemia 11, 273–280 (1997). (10.1038/sj.leu.2400552) / Leukemia by C Francastel (1997)
  30. Motohashi, H., Shavit, J.A., Igarashi, K., Yamamoto, M. & Engel, J.D. The world according to Maf. Nucleic Acids Res. 25, 2953–2959 (1997). (10.1093/nar/25.15.2953) / Nucleic Acids Res. by H Motohashi (1997)
  31. Friend, C., Scher, W., Holland, J.G. & Sato, T. Hemoglobin synthesis in murine virus-induced leukemic cells in vitro: stimulation of erythroid differentiation by dimethyl sulfoxide. Proc. Natl. Acad. Sci. USA 68, 378–382 (1971). (10.1073/pnas.68.2.378) / Proc. Natl. Acad. Sci. USA by C Friend (1971)
  32. Tsiftsoglou, A.S. & Wong, W. Molecular and cellular mechanisms of leukemic hemopoietic cell differentiation: an analysis of the Friend system. Anticancer Res. 5, 81–99 (1985). / Anticancer Res. by AS Tsiftsoglou (1985)
  33. Sawado, T., Igarashi, K. & Groudine, M. Activation of β-major globin gene transcription is associated with recruitment of NF-E2 to the β-globin LCR and gene promoter. Proc. Natl. Acad. Sci. USA 98, 10226–10231 (2001). (10.1073/pnas.181344198) / Proc. Natl. Acad. Sci. USA by T Sawado (2001)
  34. Dignam, J.D., Lebovitz, R.M. & Roeder, R.G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 11, 1475–1489 (1983). (10.1093/nar/11.5.1475) / Nucleic Acids Res. by JD Dignam (1983)
  35. Han, D.K., Eng, J., Zhou, H. & Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19, 946–951 (2001). (10.1038/nbt1001-946) / Nat. Biotechnol. by DK Han (2001)
  36. Eng, J.K., McCormack, A.L. & Yates, J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in protein databases. J. Am. Soc. Mass Spectrom. 5, 976–989 (1994). (10.1016/1044-0305(94)80016-2) / J. Am. Soc. Mass Spectrom. by JK Eng (1994)
  37. Keller, A., Nesvizhskii, A.I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383–5392 (2002). (10.1021/ac025747h) / Anal. Chem. by A Keller (2002)
  38. Nesvizhskii, A.I., Keller, A., Kolker, E. & Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646–4658 (2003). (10.1021/ac0341261) / Anal. Chem. by AI Nesvizhskii (2003)
  39. Oyake, T. et al. Bach proteins belong to a novel family of BTB-basic leucine zipper transcription factors that interact with MafK and regulate transcription through the NF-E2 site. Mol. Cell. Biol. 16, 6083–6095 (1996). (10.1128/MCB.16.11.6083) / Mol. Cell. Biol. by T Oyake (1996)
  40. Sawado, T., Halow, J., Bender, M.A. & Groudine, M. The β-globin locus control region (LCR) functions primarily by enhancing the transition from transcription initiation to elongation. Genes Dev. 17, 1009–1018 (2003). (10.1101/gad.1072303) / Genes Dev. by T Sawado (2003)
  41. Leach, K.M. et al. Characterization of the human β-globin downstream promoter region. Nucleic Acids Res. 31, 1292–1301 (2003). (10.1093/nar/gkg209) / Nucleic Acids Res. by KM Leach (2003)
  42. Feng, Q. & Zhang, Y. The NuRD complex: linking histone modification to nucleosome remodeling. Curr. Top. Microbiol. Immunol. 274, 269–290 (2003). / Curr. Top. Microbiol. Immunol. by Q Feng (2003)
  43. Knoepfler, P.S. & Eisenman, R.N. Sin meets NuRD and other tails of repression. Cell 99, 447–450 (1999). (10.1016/S0092-8674(00)81531-7) / Cell by PS Knoepfler (1999)
  44. Olave, I.A., Reck-Peterson, S.L. & Crabtree, G.R. Nuclear actin and actin-related proteins in chromatin remodeling. Annu. Rev. Biochem. 71, 755–781 (2002). (10.1146/annurev.biochem.71.110601.135507) / Annu. Rev. Biochem. by IA Olave (2002)
  45. Armstrong, J.A., Bieker, J.J. & Emerson, B.M. A SWI/SNF-related chromatin remodeling complex, E-RC1, is required for tissue-specific transcriptional regulation by EKLF in vitro. Cell 95, 93–104 (1998). (10.1016/S0092-8674(00)81785-7) / Cell by JA Armstrong (1998)
  46. Chi, T.H. et al. Reciprocal regulation of CD4/CD8 expression by SWI/SNF-like BAF complexes. Nature 418, 195–199 (2002). (10.1038/nature00876) / Nature by TH Chi (2002)
  47. Lachner, M., O'Carroll, D., Rea, S., Mechtler, K. & Jenuwein, T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410, 116–120 (2001). (10.1038/35065132) / Nature by M Lachner (2001)
  48. Ryan, R.F. et al. KAP-1 corepressor protein interacts and colocalizes with heterochromatic and euchromatic HP1 proteins: a potential role for Kruppel-associated box-zinc finger proteins in heterochromatin-mediated gene silencing. Mol. Cell. Biol. 19, 4366–4378 (1999). (10.1128/MCB.19.6.4366) / Mol. Cell. Biol. by RF Ryan (1999)
  49. Lechner, M.S., Begg, G.E., Speicher, D.W. & Rauscher, F.J. 3rd. Molecular determinants for targeting heterochromatin protein 1-mediated gene silencing: direct chromoshadow domain-KAP-1 corepressor interaction is essential. Mol. Cell. Biol. 20, 6449–6465 (2000). (10.1128/MCB.20.17.6449-6465.2000) / Mol. Cell. Biol. by MS Lechner (2000)
  50. Vassallo, M.F. & Tanese, N. Isoform-specific interaction of HP1 with human TAFII130. Proc. Natl. Acad. Sci. USA 99, 5919–5924 (2002). (10.1073/pnas.092025499) / Proc. Natl. Acad. Sci. USA by MF Vassallo (2002)
  51. Kanemaki, M. et al. TIP49b, a new RuvB-like DNA helicase, is included in a complex together with another RuvB-like DNA helicase, TIP49a. J. Biol. Chem. 274, 22437–22444 (1999). (10.1074/jbc.274.32.22437) / J. Biol. Chem. by M Kanemaki (1999)
  52. Wood, M.A., McMahon, S.B. & Cole, M.D. An ATPase/helicase complex is an essential cofactor for oncogenic transformation by c-Myc. Mol. Cell 5, 321–330 (2000). (10.1016/S1097-2765(00)80427-X) / Mol. Cell by MA Wood (2000)
  53. Cheng, X., Reginato, M.J., Andrews, N.C. & Lazar, M.A. The transcriptional integrator CREB-binding protein mediates positive cross talk between nuclear hormone receptors and the hematopoietic bZip protein p45/NF-E2. Mol. Cell. Biol. 17, 1407–1416 (1997). (10.1128/MCB.17.3.1407) / Mol. Cell. Biol. by X Cheng (1997)
  54. Chen, C.J., Deng, Z., Kim, A.Y., Blobel, G.A. & Lieberman, P.M. Stimulation of CREB binding protein nucleosomal histone acetyltransferase activity by a class of transcriptional activators. Mol. Cell. Biol. 21, 476–487 (2001). (10.1128/MCB.21.2.476-487.2001) / Mol. Cell. Biol. by CJ Chen (2001)
  55. Wadman, I.A. et al. The LIM-only protein Lmo2 is a bridging molecule assembling an erythroid, DNA-binding complex which includes the TAL1, E47, GATA-1 and Ldb1/NLI proteins. EMBO J. 16, 3145–3157 (1997). (10.1093/emboj/16.11.3145) / EMBO J. by IA Wadman (1997)
  56. Xu, Z., Huang, S., Chang, L.S., Agulnick, A.D. & Brandt, S.J. Identification of a TAL1 target gene reveals a positive role for the LIM domain-binding protein Ldb1 in erythroid gene expression and differentiation. Mol. Cell. Biol. 23, 7585–7599 (2003). (10.1128/MCB.23.21.7585-7599.2003) / Mol. Cell. Biol. by Z Xu (2003)
  57. Ge, H., Si, Y. & Roeder, R.G. Isolation of cDNAs encoding novel transcription coactivators p52 and p75 reveals an alternate regulatory mechanism of transcriptional activation. EMBO J. 17, 6723–6729 (1998). (10.1093/emboj/17.22.6723) / EMBO J. by H Ge (1998)
  58. Westermarck, J. et al. The DEXD/H-box RNA helicase RHII/Gu is a co-factor for c-Jun-activated transcription. EMBO J. 21, 451–460 (2002). (10.1093/emboj/21.3.451) / EMBO J. by J Westermarck (2002)
  59. Igarashi, K. et al. Multivalent DNA binding complex generated by small Maf and Bach1 as a possible biochemical basis for β-globin locus control region complex. J. Biol. Chem. 273, 11783–11790 (1998). (10.1074/jbc.273.19.11783) / J. Biol. Chem. by K Igarashi (1998)
  60. Yoshida, C. et al. Long range interaction of cis-DNA elements mediated by architectural transcription factor Bach1. Genes Cells 4, 643–655 (1999). (10.1046/j.1365-2443.1999.00291.x) / Genes Cells by C Yoshida (1999)
  61. Motohashi, H., O'Connor, T., Katsuoka, F., Engel, J.D. & Yamamoto, M. Integration and diversity of the regulatory network composed of Maf and CNC families of transcription factors. Gene 294, 1–12 (2002). (10.1016/S0378-1119(02)00788-6) / Gene by H Motohashi (2002)
  62. Johnson, K.D., Christensen, H.M., Zhao, B. & Bresnick, E.H. Distinct mechanisms control RNA polymerase II recruitment to a tissue-specific locus control region and a downstream promoter. Mol. Cell 8, 465–471 (2001). (10.1016/S1097-2765(01)00309-4) / Mol. Cell by KD Johnson (2001)
  63. Bulger, M., Sawado, T., Schubeler, D. & Groudine, M. ChIPs of the β-globin locus: unraveling gene regulation within an active domain. Curr. Opin. Genet. Dev. 12, 170–177 (2002). (10.1016/S0959-437X(02)00283-6) / Curr. Opin. Genet. Dev. by M Bulger (2002)
  64. Hung, H.L., Kim, A.Y., Hong, W., Radowski, C. & Blobel, G.A. Stimulation of NF-E2 DNA binding by CREB-binding protein (CBP)-mediated acetylation. J. Biol. Chem. 276, 10715–10721 (2001). (10.1074/jbc.M007846200) / J. Biol. Chem. by HL Hung (2001)
  65. Benezra, R., Cantor, C.R. & Axel, R. Nucleosomes are phased along the mouse β-major globin gene in erythroid and nonerythroid cells. Cell 44, 697–704 (1986). (10.1016/0092-8674(86)90835-4) / Cell by R Benezra (1986)
  66. Ogawa, K. et al. Heme mediates derepression of Maf recognition element through direct binding to transcription repressor Bach1. EMBO J. 20, 2835–2843 (2001). (10.1093/emboj/20.11.2835) / EMBO J. by K Ogawa (2001)
  67. Grandori, C., Cowley, S.M., James, L.P. & Eisenman, R.N. The Myc/Max/Mad network and the transcriptional control of cell behavior. Annu. Rev. Cell. Dev. Biol. 16, 653–699 (2000). (10.1146/annurev.cellbio.16.1.653) / Annu. Rev. Cell. Dev. Biol. by C Grandori (2000)
  68. Khavari, P.A., Peterson, C.L., Tamkun, J.W., Mendel, D.B. & Crabtree, G.R. BRG1 contains a conserved domain of the SWI2/SNF2 family necessary for normal mitotic growth and transcription. Nature 366, 170–174 (1993). (10.1038/366170a0) / Nature by PA Khavari (1993)
  69. Nielsen, A.L. et al. Interaction with members of the heterochromatin protein 1 (HP1) family and histone deacetylation are differentially involved in transcriptional silencing by members of the TIF1 family. EMBO J. 18, 6385–6395 (1999). (10.1093/emboj/18.22.6385) / EMBO J. by AL Nielsen (1999)
  70. Griffin, T.J. et al. Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae. Mol. Cell. Proteomics 1, 323–333 (2002). (10.1074/mcp.M200001-MCP200) / Mol. Cell. Proteomics by TJ Griffin (2002)
  71. Soutoglou, E. & Talianidis, I. Coordination of PIC assembly and chromatin remodeling during differentiation-induced gene activation. Science 295, 1901–1904 (2002). (10.1126/science.1068356) / Science by E Soutoglou (2002)
Dates
Type When
Created 21 years, 8 months ago (Dec. 29, 2003, 12:51 p.m.)
Deposited 2 years, 3 months ago (May 19, 2023, 12:52 a.m.)
Indexed 1 month ago (Aug. 2, 2025, 1:24 a.m.)
Issued 21 years, 8 months ago (Dec. 29, 2003)
Published 21 years, 8 months ago (Dec. 29, 2003)
Published Online 21 years, 8 months ago (Dec. 29, 2003)
Published Print 21 years, 8 months ago (Jan. 1, 2004)
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@article{Brand_2003, title={Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics}, volume={11}, ISSN={1545-9985}, url={http://dx.doi.org/10.1038/nsmb713}, DOI={10.1038/nsmb713}, number={1}, journal={Nature Structural & Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Brand, Marjorie and Ranish, Jeffrey A and Kummer, Nicolas T and Hamilton, Joan and Igarashi, Kazuhiko and Francastel, Claire and Chi, Tian H and Crabtree, Gerald R and Aebersold, Ruedi and Groudine, Mark}, year={2003}, month=dec, pages={73–80} }