Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros

Abstract

C2H2 zinc fingers are found in several key transcriptional regulators in the immune system. However, these proteins usually contain more fingers than are needed for sequence-specific DNA binding, which suggests that different fingers regulate different genes and functions. Here we found that mice lacking finger 1 or finger 4 of Ikaros exhibited distinct subsets of the hematological defects of Ikaros-null mice. Most notably, the two fingers controlled different stages of lymphopoiesis, and finger 4 was selectively required for tumor suppression. The distinct defects support the hypothesis that only a small number of genes that are targets of Ikaros are critical for each of its biological functions. The subcategorization of functions and target genes by mutagenesis of individual zinc fingers will facilitate efforts to understand how zinc-finger transcription factors regulate development, immunity and disease.

This is a preview of subscription content

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Adult B cells are present in mice with germline deletion of Ikzf1 exons encoding zinc-finger 1 or 4.
Figure 2: B cell development is disrupted at different stages in Ikzf1ΔF1/ΔF1 and Ikzf1ΔF4/ΔF4 mice.
Figure 3: Selective thymocyte and fetal phenotypes in Ikzf1ΔF1/ΔF1 and Ikzf1ΔF4/ΔF4 mice.
Figure 4: Differences in the binding of Ikaros to DNA in Ikzf1ΔF1/ΔF1 and Ikzf1ΔF4/ΔF4 thymocytes.
Figure 5: Deregulation of distinct sets of genes in Ikzf1ΔF1/ΔF1 and Ikzf1ΔF4/ΔF4 DP thymocytes.
Figure 6: Ikzf1ΔF4/ΔF4 mice develop spontaneous thymic lymphoma but Ikzf1ΔF1/ΔF1 mice do not.
Figure 7: Selective synergy between BCR-ABL and the Ikzf1ΔF4/ΔF4 mutation in vitro and in vivo.

Accession codes

Primary accessions

Gene Expression Omnibus

References

  1. Wang, J.H. et al. Selective defects in the development of the fetal and adult lymphoid system in mice with an Ikaros null mutation. Immunity 5, 537–549 (1996).

    CAS  PubMed  Google Scholar 

  2. Georgopoulos, K. Haematopoietic cell-fate decisions, chromatin regulation and ikaros. Nat. Rev. Immunol. 2, 162–174 (2002).

    CAS  PubMed  Google Scholar 

  3. Yoshida, T., Ng, S.Y. & Georgopoulos, K. Awakening lineage potential by Ikaros-mediated transcriptional priming. Curr. Opin. Immunol. 22, 154–160 (2010).

    CAS  PubMed  Google Scholar 

  4. Yoshida, T., Ng, S.Y., Zuniga-Pflucker, J.C. & Georgopoulos, K. Early hematopoietic lineage restrictions directed by Ikaros. Nat. Immunol. 7, 382–391 (2006).

    CAS  PubMed  Google Scholar 

  5. Kirstetter, P., Thomas, M., Dierich, A., Kastner, P. & Chan, S. Ikaros is critical for B cell differentiation and function. Eur. J. Immunol. 32, 720–730 (2002).

    CAS  PubMed  Google Scholar 

  6. Thompson, E.C. et al. Ikaros DNA-binding proteins as integral components of B cell developmental-stage-specific regulatory circuits. Immunity 26, 335–344 (2007).

    CAS  PubMed  Google Scholar 

  7. Reynaud, D. et al. Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros. Nat. Immunol. 9, 927–936 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Trageser, D. et al. Pre-B cell receptor-mediated cell cycle arrest in Philadelphia chromosome-positive acute lymphoblastic leukemia requires IKAROS function. J. Exp. Med. 206, 1739–1753 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Ma, S. et al. Ikaros and Aiolos inhibit pre-B-cell proliferation by directly suppressing c-Myc expression. Mol. Cell Biol. 30, 4149–4158 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Winandy, S., Wu, P. & Georgopoulos, K. A dominant mutation in the Ikaros gene leads to rapid development of leukemia and lymphoma. Cell 83, 289–299 (1995).

    CAS  PubMed  Google Scholar 

  11. Dumortier, A. et al. Notch activation is an early and critical event during T-cell leukemogenesis in Ikaros-deficient mice. Mol. Cell Biol. 26, 209–220 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Mullighan, C.G. et al. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 453, 110–114 (2008).

    CAS  PubMed  Google Scholar 

  13. Mullighan, C.G. et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N. Engl. J. Med. 360, 470–480 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Kim, J. et al. Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity 10, 345–355 (1999).

    CAS  PubMed  Google Scholar 

  15. Sridharan, R. & Smale, S.T. Predominant interaction of both Ikaros and Helios with the NuRD complex in immature thymocytes. J. Biol. Chem. 282, 30227–30238 (2007).

    CAS  PubMed  Google Scholar 

  16. Zhang, J. et al. Harnessing of the nucleosome-remodeling-deacetylase complex controls lymphocyte development and prevents leukemogenesis. Nat. Immunol. 13, 86–94 (2011).

    PubMed  PubMed Central  Google Scholar 

  17. Harker, N. et al. The CD8α gene locus is regulated by the Ikaros family of proteins. Mol. Cell 10, 1403–1415 (2002).

    CAS  PubMed  Google Scholar 

  18. Naito, T., Gomez-Del Arco, P., Williams, C.J. & Georgopoulos, K. Antagonistic interactions between Ikaros and the chromatin remodeler Mi-2β determine silencer activity and Cd4 gene expression. Immunity 27, 723–734 (2007).

    CAS  PubMed  Google Scholar 

  19. Gomez-del Arco, P. et al. Alternative promoter usage at the Notch1 locus supports ligand-independent signaling in T cell development and leukemogenesis. Immunity 33, 685–698 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Ng, S.Y., Yoshida, T., Zhang, J. & Georgopoulos, K. Genome-wide lineage-specific transcriptional networks underscore Ikaros-dependent lymphoid priming in hematopoietic stem cells. Immunity 30, 493–507 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. John, L.B. & Ward, A.C. The Ikaros gene family: transcriptional regulators of hematopoiesis and immunity. Mol. Immunol. 48, 1272–1278 (2011).

    CAS  PubMed  Google Scholar 

  22. Sun, L., Liu, A. & Georgopoulos, K. Zinc finger-mediated protein interactions modulate Ikaros activity, a molecular control of lymphocyte development. EMBO J. 15, 5358–5369 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. Trinh, L.A. et al. Down-regulation of TDT transcription in CD4+CD8+ thymocytes by Ikaros proteins in direct competition with an Ets activator. Genes Dev. 15, 1817–1832 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. McCarty, A.S., Kleiger, G., Eisenberg, D. & Smale, S.T. Selective dimerization of a C2H2 zinc finger subfamily. Mol. Cell 11, 459–470 (2003).

    CAS  PubMed  Google Scholar 

  25. Tupler, R., Perini, G. & Green, M.R. Expressing the human genome. Nature 409, 832–833 (2001).

    CAS  PubMed  Google Scholar 

  26. Ravasi, T. et al. Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome Res. 13, 1430–1442 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Klug, A. The discovery of zinc fingers and their applications in gene regulation and genome manipulation. Annu. Rev. Biochem. 79, 213–231 (2010).

    CAS  PubMed  Google Scholar 

  28. Wolfe, S.A., Nekludova, L. & Pabo, C.O. DNA recognition by Cys2His2 zinc finger proteins. Annu. Rev. Biophys. Biomol. Struct. 29, 183–212 (2000).

    CAS  PubMed  Google Scholar 

  29. Molnar, A. & Georgopoulos, K. The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins. Mol. Cell Biol. 14, 8292–8303 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Cobb, B.S. et al. Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding. Genes Dev. 14, 2146–2160 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Koipally, J., Heller, E.J., Seavitt, J.R. & Georgopoulos, K. Unconventional potentiation of gene expression by Ikaros. J. Biol. Chem. 277, 13007–13015 (2002).

    CAS  PubMed  Google Scholar 

  32. Hahm, K. et al. Helios, a T cell-restricted Ikaros family member that quantitatively associates with Ikaros at centromeric heterochromatin. Genes Dev. 12, 782–796 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Payne, K.J. et al. Ikaros isoform x is selectively expressed in myeloid differentiation. J. Immunol. 170, 3091–3098 (2003).

    CAS  PubMed  Google Scholar 

  34. Miller, J., McLachlan, A.D. & Klug, A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 4, 1609–1614 (1985).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Shastry, B.S. Transcription factor IIIA (TFIIIA) in the second decade. J. Cell Sci. 109, 535–539 (1996).

    CAS  PubMed  Google Scholar 

  36. Filippova, G.N. et al. An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol. Cell Biol. 16, 2802–2813 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Ohlsson, R., Renkawitz, R. & Lobanenkov, V. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet. 17, 520–527 (2001).

    CAS  PubMed  Google Scholar 

  38. Renda, M. et al. Critical DNA binding interactions of the insulator protein CTCF: a small number of zinc fingers mediate strong binding, and a single finger-DNA interaction controls binding at imprinted loci. J. Biol. Chem. 282, 33336–33345 (2007).

    CAS  PubMed  Google Scholar 

  39. Nurmemmedov, E., Yengo, R.K., Uysal, H., Karlsson, R. & Thunnissen, M.M. New insights into DNA-binding behavior of Wilms tumor protein (WT1)–a dual study. Biophys. Chem. 145, 116–125 (2009).

    CAS  PubMed  Google Scholar 

  40. Nakahashi, H. et al. A genome-wide map of CTCF multivalency redefines the CTCF code. Cell Rep. 3, 1678–1689 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Hardy, R.R., Carmack, C.E., Shinton, S.A., Kemp, J.D. & Hayakawa, K. Resolution and characterization of pro-B and pre-pro-B cell stages in normal mouse bone marrow. J. Exp. Med. 173, 1213–1225 (1991).

    CAS  PubMed  Google Scholar 

  42. Rolink, A., Grawunder, U., Winkler, T.H., Karasuyama, H. & Melchers, F. IL-2 receptor α chain (CD25, TAC) expression defines a crucial stage in pre-B cell development. Int. Immunol. 6, 1257–1264 (1994).

    CAS  PubMed  Google Scholar 

  43. Rothenberg, E.V., Moore, J.E. & Yui, M.A. Launching the T-cell-lineage developmental programme. Nat. Rev. Immunol. 8, 9–21 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Randall, T.D., Carragher, D.M. & Rangel-Moreno, J. Development of secondary lymphoid organs. Annu. Rev. Immunol. 26, 627–650 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Juric, D. et al. Differential gene expression patterns and interaction networks in BCR-ABL-positive and -negative adult acute lymphoblastic leukemias. J. Clin. Oncol. 25, 1341–1349 (2007).

    CAS  PubMed  Google Scholar 

  46. Lu, Q. delta-Catenin dysregulation in cancer: interactions with E-cadherin and beyond. J. Pathol. 222, 119–123 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Wang, H. et al. The role of Crk/Dock180/Rac1 pathway in the malignant behavior of human ovarian cancer cell SKOV3. Tumour Biol. 31, 59–67 (2010).

    PubMed  Google Scholar 

  48. Perentes, J.Y. et al. Cancer cell-associated MT1-MMP promotes blood vessel invasion and distant metastasis in triple-negative mammary tumors. Cancer Res. 71, 4527–4538 (2011).

    CAS  PubMed  Google Scholar 

  49. Marcais, A. et al. Genetic inactivation of Ikaros is a rare event in human T-ALL. Leuk. Res. 34, 426–429 (2010).

    CAS  PubMed  Google Scholar 

  50. Wong, S. et al. Sole BCR-ABL inhibition is insufficient to eliminate all myeloproliferative disorder cell populations. Proc. Natl. Acad. Sci. USA 101, 17456–17461 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  51. Papathanasiou, P. et al. Widespread failure of hematolymphoid differentiation caused by a recessive niche-filling allele of the Ikaros transcription factor. Immunity 19, 131–144 (2003).

    CAS  PubMed  Google Scholar 

  52. Lickwar, C.R., Mueller, F., Hanlon, S.W., McNally, J.G. & Lieb, J.D. Genome-wide protein-DNA binding dynamics suggest a molecular clutch for transcription factor function. Nature 484, 251–255 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Virely, C. et al. Haploinsufficiency of the IKZF1 (IKAROS) tumor suppressor gene cooperates with BCR-ABL in a transgenic model of acute lymphoblastic leukemia. Leukemia 24, 1200–1204 (2010).

    CAS  PubMed  Google Scholar 

  54. Sun, Z. et al. Requirement for RORgamma in thymocyte survival and lymphoid organ development. Science 288, 2369–2373 (2000).

    CAS  PubMed  Google Scholar 

  55. Montecino-Rodriguez, E., Leathers, H. & Dorshkind, K. Identification of a B-1 B cell-specified progenitor. Nat. Immunol. 7, 293–301 (2006).

    CAS  PubMed  Google Scholar 

  56. Aliahmad, P., de la Torre, B. & Kaye, J. Shared dependence on the DNA-binding factor TOX for the development of lymphoid tissue-inducer cell and NK cell lineages. Nat. Immunol. 11, 945–952 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  57. Pandya-Jones, A. & Black, D.L. Co-transcriptional splicing of constitutive and alternative exons. RNA 15, 1896–1908 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Nagalakshmi, U., Waern, K. & Snyder, M. RNA-Seq: a method for comprehensive transcriptome analysis. Curr. Protoc. Mol. Biol. 89, 4.11.1–4.11.13 (2010).

    Google Scholar 

  59. Giardine, B. et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 15, 1451–1455 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Blankenberg, D. et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. 89, 19.10.1–19–10–21 (2010).

    Google Scholar 

  62. Fujita, P.A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876–D882 (2010).

    PubMed  PubMed Central  Google Scholar 

  63. Goecks, J., Nekrutenko, A. & Taylor, J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86 (2010).

    PubMed  PubMed Central  Google Scholar 

  64. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).

    CAS  PubMed  Google Scholar 

  66. Anders, S. & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. Eisen, M.B., Spellman, P.T., Brown, P.O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95, 14863–14868 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. de Hoon, M.J., Imoto, S., Nolan, J. & Miyano, S. Open source clustering software. Bioinformatics 20, 1453–1454 (2004).

    CAS  PubMed  Google Scholar 

  69. Saldana, A.J. Java Treeview - extensible visualization of microarray data. Bioinformatics 20, 3246–3248 (2004).

    Google Scholar 

  70. Thomas, P.D. et al. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 34, W645–W650 (2006).

    PubMed  PubMed Central  Google Scholar 

  71. O'Geen, H., Frietze, S. & Farnham, P.J. Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods Mol. Biol. 649, 437–455 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    PubMed  PubMed Central  Google Scholar 

  73. Blahnik, K.R. et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 38, e13 (2010).

    PubMed  Google Scholar 

  74. Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Bailey, T.L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202–W208 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank P. Aliahmad, D. Bhatt, K. Dorshkind, C. Li and E. Montecino-Rodriguez for advice and/or critical reading of the manuscript; the Division of Laboratory Animal Medicine of the University of California, Los Angeles, for ongoing care of mice; and H. Mak, T. Jacob, C. Garcia, J. Flores and J. Lorenzano for assistance with the mouse colony. ChIP-seq and RNA-Seq libraries were sequenced at the Epigenome Data Production Facility of the University of Southern California, and the Broad Stem Cell Research Center High Throughput Sequencing Core of the University of California, Los Angeles. Supported by the US National Institutes of Health (RO1DK043726 to S.T.S. and U54HG004558 to P.J.F.). O.N.W. is an Investigator of the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

Authors

Contributions

H.S., J.M., T.L.A., S.F., D.C., S.E.W. and G.W.L. designed and did experiments and analyzed data; S.J.B. provided intellectual input and experimental advice; P.J.F., O.N.W. and S.T.S. supervised research and analyzed data; and H.S. and S.T.S. wrote the manuscript.

Corresponding author

Correspondence to Stephen T Smale.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Tables 1–2 (PDF 6921 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Schjerven, H., McLaughlin, J., Arenzana, T. et al. Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol 14, 1073–1083 (2013). https://doi.org/10.1038/ni.2707

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ni.2707

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing