151
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Vradii D, Wagner S, Doan DN, Nickerson JA, Montecino M, Lian JB, Stein JL, van Wijnen AJ, Imbalzano AN, Stein GS. Brg1, the ATPase subunit of the SWI/SNF chromatin remodeling complex, is required for myeloid differentiation to granulocytes. J Cell Physiol 2005; 206:112-8. [PMID: 15965950 DOI: 10.1002/jcp.20432] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Many mammalian SWI/SNF complexes use Brahma-related gene 1 (Brg1) as a catalytic subunit to remodel nucleosomes for transcription regulation. In several mesenchymal cells and tissues, expression of a defective Brg1 protein negates the normal activity of the SWI/SNF complex and delays or blocks differentiation. To investigate the role of SWI/SNF complexes during myelopoiesis, we stably expressed a dominant negative (dn) Brg1 mutant in the myeloid lineage. Forced expression of dnBrg1 in IL-3-dependent murine 32Dcl3 myeloid progenitor cells results in a profound delay in the granulocyte-colony stimulating factor (G-CSF) induced granulocytic maturation. These cells also exhibit a significant decrease in the expression of both CD11b and Gr-1 surface receptors, which are normally upregulated during granulopoiesis, and show sustained expression of myeloperoxidase, which is synthesized primarily during the promyelocytic (blast) stage of myeloid development. Thus, dnBrg1 expression causes a developmental block at the promyelocytic/metamyelocytic stage of myeloid differentiation. Our findings indicate that the normal chromatin remodeling function of Brg1 is necessary for the G-CSF dependent differentiation of myeloid cells towards the granulocytic lineage. This dependency on Brg1 may reflect a stringent requirement for chromatin remodeling at a critical stage of hematopoietic cell maturation.
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Affiliation(s)
- Diana Vradii
- Department of Cell Biology and Cancer Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655-0106, USA
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152
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de la Serna IL, Ohkawa Y, Berkes CA, Bergstrom DA, Dacwag CS, Tapscott SJ, Imbalzano AN. MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a stable DNA-bound complex. Mol Cell Biol 2005; 25:3997-4009. [PMID: 15870273 PMCID: PMC1087700 DOI: 10.1128/mcb.25.10.3997-4009.2005] [Citation(s) in RCA: 228] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The activation of muscle-specific gene expression requires the coordinated action of muscle regulatory proteins and chromatin-remodeling enzymes. Microarray analysis performed in the presence or absence of a dominant-negative BRG1 ATPase demonstrated that approximately one-third of MyoD-induced genes were highly dependent on SWI/SNF enzymes. To understand the mechanism of activation, we performed chromatin immunoprecipitations analyzing the myogenin promoter. We found that H4 hyperacetylation preceded Brg1 binding in a MyoD-dependent manner but that MyoD binding occurred subsequent to H4 modification and Brg1 interaction. In the absence of functional SWI/SNF enzymes, muscle regulatory proteins did not bind to the myogenin promoter, thereby providing evidence for SWI/SNF-dependent activator binding. We observed that the homeodomain factor Pbx1, which cooperates with MyoD to stimulate myogenin expression, is constitutively bound to the myogenin promoter in a SWI/SNF-independent manner, suggesting a two-step mechanism in which MyoD initially interacts indirectly with the myogenin promoter and attracts chromatin-remodeling enzymes, which then facilitate direct binding by MyoD and other regulatory proteins.
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Affiliation(s)
- Ivana L de la Serna
- University of Massachusetts Medical School, Department of Cell Biology, 55 Lake Avenue North, Worcester, MA 01655, USA
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153
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Link KA, Burd CJ, Williams E, Marshall T, Rosson G, Henry E, Weissman B, Knudsen KE. BAF57 governs androgen receptor action and androgen-dependent proliferation through SWI/SNF. Mol Cell Biol 2005; 25:2200-15. [PMID: 15743818 PMCID: PMC1061596 DOI: 10.1128/mcb.25.6.2200-2215.2005] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Androgen receptor (AR) activity is required for prostate cancer development and progression. Thus, there is a major impetus to understand the regulation of AR action. We and others have previously shown that AR transactivation potential is dependent on the presence of an active SWI/SNF chromatin remodeling complex. However, the mechanisms underlying SWI/SNF regulation of the AR remained unsolved. We show here that the BAF57 subunit, an accessory component of the remodeling complex, is a critical regulator of AR function. We show that BAF57 is expressed in the luminal epithelia of the prostate and is required for AR-dependent transactivation in prostatic adenocarcinoma cells. Our data reveal that BAF57 can directly bind to the AR and is recruited to endogenous AR targets upon ligand activation. Loss of BAF57 or inhibition of BAF57 function severely compromised AR activity, as observed with both exogenous and endogenous AR targets. Rescue of BAF57 function restored AR activity, thus demonstrating a specific requirement of BAF57 for AR activity. This action of BAF57 proved to be dependent on SWI/SNF ATPase function. BAF57 has previously been implicated in nuclear receptor coactivator function, and we show that, although BAF57 facilitated coactivator activity, only a selected subset required BAF57 for coactivator function. Lastly, we demonstrate that both BAF57 and BRM are required for the proliferation of AR-dependent prostatic adenocarcinoma cells. In summary, these findings identify BAF57 as a critical modulator of the AR that is capable of altering AR activity, coactivator function, and AR-dependent proliferation.
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Affiliation(s)
- Kevin A Link
- Department of Cell Biology, Vontz Center for Molecular Studies, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0521, USA
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154
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Abstract
Ikaros plays a key role in lymphocyte development and homeostasis by both potentiating and repressing gene expression. Here we show that Ikaros interacts with components of the SUMO pathway and is SUMOylated in vivo. Two SUMOylation sites are identified on Ikaros whose simultaneous modification results in a loss of Ikaros' repression function. Ikaros SUMOylation disrupts its participation in both histone deacetylase (HDAC)-dependent and HDAC-independent repression but does not influence its nuclear localization into pericentromeric heterochromatin. These studies reveal a new dynamic way by which Ikaros-mediated gene repression is controlled by SUMOylation.
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Affiliation(s)
- Pablo Gómez-del Arco
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
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155
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Abstract
T cell development is guided by a complex set of transcription factors that act recursively, in different combinations, at each of the developmental choice points from T-lineage specification to peripheral T cell specialization. This review describes the modes of action of the major T-lineage-defining transcription factors and the signal pathways that activate them during intrathymic differentiation from pluripotent precursors. Roles of Notch and its effector RBPSuh (CSL), GATA-3, E2A/HEB and Id proteins, c-Myb, TCF-1, and members of the Runx, Ets, and Ikaros families are critical. Less known transcription factors that are newly recognized as being required for T cell development at particular checkpoints are also described. The transcriptional regulation of T cell development is contrasted with that of B cell development, in terms of their different degrees of overlap with the stem-cell program and the different roles of key transcription factors in gene regulatory networks leading to lineage commitment.
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Affiliation(s)
- Ellen V Rothenberg
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA.
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156
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Hill DA, de la Serna IL, Veal TM, Imbalzano AN. BRCA1 interacts with dominant negative SWI/SNF enzymes without affecting homologous recombination or radiation-induced gene activation of p21 or Mdm2. J Cell Biochem 2005; 91:987-98. [PMID: 15034933 DOI: 10.1002/jcb.20003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BRCA1 is a tumor suppressor gene linked to familial breast and ovarian cancer. The BRCA1 protein has been implicated in a diverse set of cellular functions, including activation of gene expression by the p53 tumor suppressor and control of homologous recombination (HR) during DNA repair. Prior reports have demonstrated that BRCA1 can exist in cells in a complex with the BRG1-based SWI/SNF ATP-dependent chromatin remodeling enzymes and that SWI/SNF components contribute to p53-mediated gene activation. To investigate the link between SWI/SNF function and BRCA1 mediated effects on p53-mediated gene activation and on mechanisms of homologous recombination, we have utilized mammalian cells that inducibly express an ATPase-deficient, dominant negative SWI/SNF enzymes. Mutant SWI/SNF ATPases retain the ability to interact with BRCA1 in cells. We report that expression of dominant negative SWI/SNF enzymes does not affect p53-mediated induction of the p21 cyclin dependent kinase inhibitor or the Mdm2 E3 ubiquitin ligase that regulates p53 in cells exposed to UV or gamma irradiation. Similarly, integration of a reporter that monitors homologous recombination by gene conversion into these cells demonstrated no change in the recombination rate in the absence of functional SWI/SNF enzyme. We conclude that the SWI/SNF chromatin remodeling enzymes may contribute to but are not required for these processes.
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Affiliation(s)
- David A Hill
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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157
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Sato T, Ohno SI, Hayashi T, Sato C, Kohu K, Satake M, Habu S. Dual Functions of Runx Proteins for Reactivating CD8 and Silencing CD4 at the Commitment Process into CD8 Thymocytes. Immunity 2005; 22:317-28. [PMID: 15780989 DOI: 10.1016/j.immuni.2005.01.012] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2004] [Revised: 01/24/2005] [Accepted: 01/26/2005] [Indexed: 11/19/2022]
Abstract
To understand how CD8 expression is regulated during the transition process from CD4+8+ (CD4 and CD8 double positive, DP) to CD4-8+ (CD8 single positive, CD8SP) cells in the thymus, the involvement of Runx proteins in the alteration of chromatin configuration was investigated. Using the chromatin immunoprecipitation assay, we first demonstrated that Runx proteins bind to the stage-specific CD8 enhancer, as well as the CD4 silencer, in CD8SP thymocytes. Among Runx family members, Runx3 expression was initiated in DP thymocytes receiving a positive selection signal and increased in concert with differentiation to the CD8SP stage. Furthermore, reactivation of the CD8 gene, as well as CD4 silencing, was suppressed in positively selected thymocytes of Runx dominant-negative transgenic mice. These results suggest that Runx proteins, especially Runx3, are involved in lineage specification of CD8 T cells and provide important information for understanding the mechanism for the mutually exclusive expression of coreceptors in mature thymocytes.
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Affiliation(s)
- Takehito Sato
- Department of Immunology, Tokai University School of Medicine, Boseidai, Isehara, Kanagawa 259-1193, Japan
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158
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Feik N, Bilic I, Tinhofer J, Unger B, Littman DR, Ellmeier W. Functional and Molecular Analysis of the Double-Positive Stage-Specific CD8 Enhancer E8III during Thymocyte Development. THE JOURNAL OF IMMUNOLOGY 2005; 174:1513-24. [PMID: 15661911 DOI: 10.4049/jimmunol.174.3.1513] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Several developmental stage-, subset-, and lineage-specific Cd8 cis-regulatory regions have been identified. These include the E8(III) enhancer, which directs expression in double-positive (DP) thymocytes, and E8(II), which is active in DP cells and CD8(+) T cells. Using a transgenic reporter expression assay, we identified a 285-bp core fragment of the E8(III) enhancer that retains activity in DP thymocytes. In vitro characterization of the core enhancer revealed five regulatory elements that are required for full enhancer activity, suggesting that multiple factors contribute to the developmental stage-specific activity. Furthermore, deletion of E8(III) in the mouse germline showed that this enhancer is required for nonvariegated expression of CD8 in DP thymocytes when E8(II) is also deleted. These results indicate that E8(III) is one of the cis-elements that contribute to the activation of the Cd8a and Cd8b gene complex during T cell development.
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Affiliation(s)
- Nicholas Feik
- Institute of Immunology, Medical University Vienna, Vienna, Austria
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159
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Wang Z, Zhai W, Richardson JA, Olson EN, Meneses JJ, Firpo MT, Kang C, Skarnes WC, Tjian R. Polybromo protein BAF180 functions in mammalian cardiac chamber maturation. Genes Dev 2004; 18:3106-16. [PMID: 15601824 PMCID: PMC535920 DOI: 10.1101/gad.1238104] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Accepted: 10/12/2004] [Indexed: 11/24/2022]
Abstract
BAF and PBAF are two related mammalian chromatin remodeling complexes essential for gene expression and development. PBAF, but not BAF, is able to potentiate transcriptional activation in vitro mediated by nuclear receptors, such as RXRalpha, VDR, and PPARgamma. Here we show that the ablation of PBAF-specific subunit BAF180 in mouse embryos results in severe hypoplastic ventricle development and trophoblast placental defects, similar to those found in mice lacking RXRalpha and PPARgamma. Embryonic aggregation analyses reveal that in contrast to PPARgamma-deficient mice, the heart defects are likely a direct result of BAF180 ablation, rather than an indirect consequence of trophoblast placental defects. We identified potential target genes for BAF180 in heart development, such as S100A13 as well as retinoic acid (RA)-induced targets RARbeta2 and CRABPII. Importantly, BAF180 is recruited to the promoter of these target genes and BAF180 deficiency affects the RA response for CRABPII and RARbeta2. These studies reveal unique functions of PBAF in cardiac chamber maturation.
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Affiliation(s)
- Zhong Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204, USA
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160
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Abstract
Chromatin structure dictates whether DNA templates are accessible to nuclear proteins; therefore, it is tightly regulated. To reconfigure chromatin, cells often mobilize 'chromatin-remodelling complexes' that use energy to disrupt histone-DNA contacts. BAF complexes, which are related to the yeast SWI-SNF complex, are the prototypical mammalian chromatin-remodelling complexes. In the past few years, studies have revealed the crucial and diverse roles of BAF complexes in the regulation of the immune system - from lymphocyte development to immune responses. This review surveys these advances, highlighting the general insights these studies provide into the modes of action of BAF complexes, and it concludes with a discussion of some of the key opportunities and challenges in this field.
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Affiliation(s)
- Tian Chi
- Section of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
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161
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Sif S. ATP-dependent nucleosome remodeling complexes: enzymes tailored to deal with chromatin. J Cell Biochem 2004; 91:1087-98. [PMID: 15048866 DOI: 10.1002/jcb.20005] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromatin remodeling complexes play a central role in the control of nuclear processes that utilize genomic DNA as a template including transcription, replication, recombination, and repair. Modulation of chromatin structure is mediated by a wide variety of enzymes which can affect nucleosome stability by either disrupting histone-DNA contacts or by covalently modifying histones and/or DNA. Although the biochemical properties of most chromatin-modifying enzymes have been well characterized and links between histone and DNA-modifying enzymes and ATP-dependent chromatin remodeling complexes have been established, the importance of their concerted action has just begun to emerge. As more and more genes are examined, new rules are being established about their transcriptional regulation, and it is becoming clear that diverse mechanisms are used to modify chromatin and either promote or hinder accessibility to DNA and histones. Moreover, the involvement of ATP-dependent chromatin remodelers in transcriptional regulation of cyclin genes and the association of misregulated expression of chromatin remodeling subunits with many cancers highlight the importance of chromatin remodeling complexes in the control of cell growth and proliferation.
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Affiliation(s)
- Saïd Sif
- Department of Molecular and Cellular Biochemistry, College of Medicine and Public Health, The Ohio State University, Columbus, Ohio 43210, USA.
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162
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Yui MA, Rothenberg EV. Deranged Early T Cell Development in Immunodeficient Strains of Nonobese Diabetic Mice. THE JOURNAL OF IMMUNOLOGY 2004; 173:5381-91. [PMID: 15494484 DOI: 10.4049/jimmunol.173.9.5381] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
NOD mice exhibit defects in T cell functions that have been postulated to contribute to diabetes susceptibility in this strain. However, early T cell development in NOD mice has been largely unexplored. NOD mice with the scid mutation and Rag1 deficiency were analyzed for pre-T cell development in the NOD genetic background. These strains reveal an age-dependent, programmed breakdown in beta selection checkpoint enforcement. At 5-8 wk of age, even in the absence of TCRbeta expression, CD4+ and CD4+CD8+ blasts appear spontaneously. However, these breakthrough cells fail to restore normal thymic cellularity. The breakthrough phenotype is recessive in hybrid (NODxB6)F1-scid and -Rag1null mice. The breakthrough cells show a mosaic phenotype with respect to components of the beta selection program. They mimic normal beta selection by up-regulating germline TCR-Calpha transcripts, CD2, and Bcl-xL and down-regulating Bcl-2. However, they fail to down-regulate transcription factors HEB-alt and Hes1 and initially express aberrantly high levels of Spi-B, c-kit (CD117), and IL-7Ralpha. Other genes examined distinguish this form of breakthrough from previously reported models. Some of the abnormalities appear first in a cohort of postnatal thymocytes as early as the double-negative 2/double-negative 3 transitional stage. Thus, our results reveal an NOD genetic defect in T cell developmental programming and checkpoint control that permits a subset of the normal outcomes of pre-TCR signaling to proceed even in the absence of TCRbeta rearrangement. Furthermore, this breakthrough may initiate thymic lymphomagenesis that occurs with high frequency in both NOD-scid and -Rag1null mice.
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MESH Headings
- Aging/genetics
- Aging/immunology
- Animals
- CD2 Antigens/biosynthesis
- CD2 Antigens/genetics
- CD4 Antigens/biosynthesis
- Cell Cycle/genetics
- Cell Cycle/immunology
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Cell Division/genetics
- Cell Division/immunology
- Gene Expression Regulation/immunology
- Genes, RAG-1
- Genes, Recessive
- Genes, T-Cell Receptor alpha
- Lymphopenia/genetics
- Lymphopenia/immunology
- Lymphopenia/pathology
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Knockout
- Mice, SCID
- Mice, Transgenic
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/biosynthesis
- Proto-Oncogene Proteins c-kit/biosynthesis
- Receptors, Interleukin-7/biosynthesis
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- T-Lymphocyte Subsets/pathology
- Thymus Gland/immunology
- Thymus Gland/metabolism
- Thymus Gland/pathology
- Transcription, Genetic
- Up-Regulation/immunology
- bcl-X Protein
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Affiliation(s)
- Mary A Yui
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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163
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Bosselut R. CD4/CD8-lineage differentiation in the thymus: from nuclear effectors to membrane signals. Nat Rev Immunol 2004; 4:529-40. [PMID: 15229472 DOI: 10.1038/nri1392] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Rémy Bosselut
- Laboratory of Immune Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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164
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Williams CJ, Naito T, Arco PGD, Seavitt JR, Cashman SM, De Souza B, Qi X, Keables P, Von Andrian UH, Georgopoulos K. The chromatin remodeler Mi-2beta is required for CD4 expression and T cell development. Immunity 2004; 20:719-33. [PMID: 15189737 DOI: 10.1016/j.immuni.2004.05.005] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2003] [Revised: 03/09/2004] [Accepted: 04/14/2004] [Indexed: 11/20/2022]
Abstract
Changes in chromatin structure underlie the activation or silencing of genes during development. The chromatin remodeler Mi-2beta is highly expressed in thymocytes and is presumed to be a transcriptional repressor because of its presence in the nucleosome remodeling deacetylase (NuRD) complex. Using conditional inactivation, we show that Mi-2beta is required at several steps during T cell development: for differentiation of beta selected immature thymocytes, for developmental expression of CD4, and for cell divisions in mature T cells. We further show that Mi-2beta plays a direct role in promoting CD4 gene expression. Mi-2beta associates with the CD4 enhancer as well as the E box binding protein HEB and the histone acetyltransferase (HAT) p300, enabling their recruitment to the CD4 enhancer and causing histone H3-hyperacetylation to this regulatory region. These findings provide important insights into the regulation of CD4 expression during T cell development and define a role for Mi-2beta in gene activation.
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Affiliation(s)
- Christine J Williams
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
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165
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Abstract
Runx family proteins have the potential for either activating or suppressing gene expression in a context-dependent manner. There are several mechanisms by which transcriptional repression can occur. A wide range of locus inactivation, that is often called gene silencing, is thought to be achieved by chromatin modifications. Recently, Runx family proteins were found to have an essential role in either temporal transcriptional repression or irreversible epigenetic silencing at the CD4 locus through binding to a CD4 silencer at different stages of development. These findings link Runx function to epigenetic gene regulation, and shed new light on the mechanisms by which Runx represses target gene expression.
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Affiliation(s)
- Ichiro Taniuchi
- Laboratory for Transcriptional Regulation, RIKEN Research Center for Allergy and Immunology, Yokohama 230-0045, Japan.
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166
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Längst G, Becker PB. Nucleosome remodeling: one mechanism, many phenomena? ACTA ACUST UNITED AC 2004; 1677:58-63. [PMID: 15020046 DOI: 10.1016/j.bbaexp.2003.10.011] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2003] [Accepted: 10/14/2003] [Indexed: 11/18/2022]
Abstract
The term 'nucleosome remodeling' subsumes a large number of energy-dependent alterations of canonical nucleosome structure, catalyzed by dedicated ATPases in large multiprotein complexes. The importance of these factors for gene regulation and other processes with chromatin substrate have emerged from genetic studies. Mechanistic analyses of nucleosome remodeling by different enzymes provided a diverse, almost confusing phenomenology of ATP-dependent derangement of nucleosomes in vitro, suggesting that different remodeling machines follow different strategies to disrupt histone-DNA interactions. This review explores the alternative possibility that the rich phenomenology of nucleosome remodeling may be brought about by variations of one basic remodeling reaction.
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Affiliation(s)
- Gernot Längst
- Adolf-Butenandt-Institut, Molekularbiologie, Ludwig-Maximilians-University Munchen, Schillerstrasse 44, D-80336 Munich, Germany
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167
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Aliahmad P, O'Flaherty E, Han P, Goularte OD, Wilkinson B, Satake M, Molkentin JD, Kaye J. TOX provides a link between calcineurin activation and CD8 lineage commitment. ACTA ACUST UNITED AC 2004; 199:1089-99. [PMID: 15078895 PMCID: PMC2211890 DOI: 10.1084/jem.20040051] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
T cell development is dependent on the integration of multiple signaling pathways, although few links between signaling cascades and downstream nuclear factors that play a role in thymocyte differentiation have been identified. We show here that expression of the HMG box protein TOX is sufficient to induce changes in coreceptor gene expression associated with β-selection, including CD8 gene demethylation. TOX expression is also sufficient to initiate positive selection to the CD8 lineage in the absence of MHC–TCR interactions. TOX-mediated positive selection is associated with up-regulation of Runx3, implicating CD4 silencing in the process. Interestingly, a strong T cell receptor–mediated signal can modify this cell fate. We further demonstrate that up-regulation of TOX in double positive thymocytes is calcineurin dependent, linking this critical signaling pathway to nuclear changes during positive selection.
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Affiliation(s)
- Parinaz Aliahmad
- Department of Immunology IMM-8, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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168
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Zamoyska R, Lovatt M. Signalling in T-lymphocyte development: integration of signalling pathways is the key. Curr Opin Immunol 2004; 16:191-6. [PMID: 15023412 DOI: 10.1016/j.coi.2004.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
alpha beta T-cell development is restricted to the thymus. Interactions between developing lymphocytes and the thymic stroma, together with bone-marrow-derived monocytes and dendritic cells, are critical for proper development of the T-cell lineage. The developmental sequence through which T-cell progenitors pass on their way to maturity is well established, and can be followed by the sequential acquisition and/or removal of cell surface molecules. Using the combination of modern genetic manipulations, such as transgenesis, gene ablation (knockouts) and targeted mutagenesis (knock-ins), with the ever-improving conditional and inducible manipulation of gene expression, we are beginning to gain an understanding of how intercellular interactions can be relayed via intracellular signalling cascades to bring about nuclear re-organisation and the differentiated mature CD4(+) and CD8(+) subpopulations.
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Affiliation(s)
- Rose Zamoyska
- Molecular Immunology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.
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169
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Kioussis D. Shh! Shh! It's, oh, so quiet. Nat Immunol 2004; 5:353-4. [PMID: 15052261 DOI: 10.1038/ni0404-353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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170
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Bonaldi T, Längst G, Strohner R, Becker PB, Bianchi ME. The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. EMBO J 2004. [PMID: 12486007 DOI: 10.1093/embo/cdf692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Nucleosome remodelling complexes CHRAC and ACF contribute to chromatin dynamics by converting chemical energy into sliding of histone octamers on DNA. Their shared ATPase subunit ISWI binds DNA at the sites of entry into the nucleosome. A prevalent model assumes that DNA distortions catalysed by ISWI are converted into relocation of DNA relative to a histone octamer. HMGB1, one of the most abundant nuclear non-histone proteins, binds with preference to distorted DNA. We have now found that transient interaction of HMGB1 with nucleosomal linker DNA overlapping ISWI-binding sites enhances the ability of ACF to bind nucleosomal DNA and accelerates the sliding activity of limiting concentrations of remodelling factor. By contrast, an HMGB1 mutant with increased binding affinity was inhibitory. These observations are consistent with a role for HMGB1 as a DNA chaperone facilitating the rate-limiting DNA distortion during nucleosome remodelling.
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Affiliation(s)
- Tiziana Bonaldi
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany
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171
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Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. ACTA ACUST UNITED AC 2004; 198:1937-49. [PMID: 14676303 PMCID: PMC2194157 DOI: 10.1084/jem.20030714] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mammalian SWI–SNF-related complexes use brahma-related gene 1 (Brg1) as a catalytic subunit to remodel nucleosomes and regulate transcription. Recent biochemical data has linked Brg1 function to genes important for T lymphocyte differentiation. To investigate the role of SWI–SNF-related complexes in this lineage, we ablated Brg1 function in T lymphocytes. T cell–specific Brg1-deficient mice showed profound thymic abnormalities, CD4 derepression at the double negative (DN; CD4− CD8−) stage, and a developmental block at the DN to double positive (CD4+ CD8+) transition. 5′-bromo-2′-deoxyuridine incorporation and annexin V staining establish a role for Brg1 complexes in the regulation of thymocyte cell proliferation and survival. This Brg1-dependent cell survival is specific for developing thymocytes as indicated by the presence of Brg1-deficient mature T lymphocytes that have escaped the developmental block in the thymus. However, reductions in peripheral T cell populations lead to immunodeficiency and compromised health of mutant mice. These results highlight the importance of chromatin-remodeling complexes at different stages in the development of a mammalian cell lineage.
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Affiliation(s)
- Thomas C Gebuhr
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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172
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Zheng P, Patel B, McMenamin M, Paprocki AM, Schramm RD, Nagl NG, Wilsker D, Wang X, Moran E, Latham KE. Expression of genes encoding chromatin regulatory factors in developing rhesus monkey oocytes and preimplantation stage embryos: possible roles in genome activation. Biol Reprod 2004; 70:1419-27. [PMID: 14724134 DOI: 10.1095/biolreprod.103.023796] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
One of the most critical events of preimplantation development is the successful activation of gene transcription. Both the timing and the array of genes activated must be controlled. The ability to regulate gene transcription appears to be reduced just prior to the time of the major genome activation event, and changes in chromatin structure appear essential for establishing this ability. Major molecules that modulate chromatin structure are the linker and core histones, enzymes that modify histones, and a wide variety of other factors that associate with DNA and mediate either repressive or activating changes. Among the latter are chromatin accessibility complexes, SWI/SNF complexes, and the YY1 protein and its associated factors. Detailed information about the expression and regulation of these factors in preimplantation stage embryos has not been published for any species. In order to ascertain which of these factors may participate in chromatin remodeling, genome activation, and DNA replication during early primate embryogenesis, we determined the temporal expression patterns of mRNA encoding these factors. Our data identify the predominant members of these different functional classes of factors expressed in oocytes and embryos, and reveal patterns of expression distinct from those patterns seen in somatic cells. Among each of four classes of mRNAs examined, some mRNAs were expressed predominantly in the oocyte, with these largely giving way to others expressed stage specifically in the embryo. This transition may be part of a global mechanism underlying the transition from maternal to embryonic control of development, wherein the oocyte program is silenced and an embryonic pattern of gene expression becomes established. Possible roles for these mRNAs in chromatin remodeling, genome activation, DNA replication, cell lineage determination, and nuclear reprogramming are discussed.
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Affiliation(s)
- Ping Zheng
- The Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania 19140, USA
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173
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Chromosomal HMG-box proteins. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/s0167-7306(03)39005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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174
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Taniuchi I, Ellmeier W, Littman DR. The CD4/CD8 lineage choice: new insights into epigenetic regulation during T cell development. Adv Immunol 2004; 83:55-89. [PMID: 15135628 DOI: 10.1016/s0065-2776(04)83002-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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175
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von Boehmer H. Selection of the T-Cell Repertoire: Receptor-Controlled Checkpoints in T-Cell Development. Adv Immunol 2004; 84:201-38. [PMID: 15246254 DOI: 10.1016/s0065-2776(04)84006-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Harald von Boehmer
- Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts USA
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176
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Brand M, Ranish JA, Kummer NT, Hamilton J, Igarashi K, Francastel C, Chi TH, Crabtree GR, Aebersold R, Groudine M. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol 2003; 11:73-80. [PMID: 14718926 DOI: 10.1038/nsmb713] [Citation(s) in RCA: 161] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2003] [Accepted: 11/17/2003] [Indexed: 01/30/2023]
Abstract
During erythroid differentiation, beta-globin gene expression is regulated by the locus control region (LCR). The transcription factor NF-E2p18/MafK binds within this region and is essential for beta-globin expression in murine erythroleukemia (MEL) cells. Here we use the isotope-coded affinity tag (ICAT) technique of quantitative mass spectrometry to compare proteins interacting with NF-E2p18/MafK during differentiation. Our results define MafK as a 'dual-function' molecule that shifts from a repressive to an activating mode during erythroid differentiation. The exchange of MafK dimerization partner from Bach1 to NF-E2p45 is a key step in the switch from the repressed to the active state. This shift is associated with changes in the interaction of MafK with co-repressors and co-activators. Thus, our results suggest that in addition to its role as a cis-acting activator of beta-globin gene expression in differentiated erythroid cells, the LCR also promotes an active repression of beta-globin transcription in committed cells before terminal differentiation.
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Affiliation(s)
- Marjorie Brand
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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177
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Guidi CJ, Veal TM, Jones SN, Imbalzano AN. Transcriptional compensation for loss of an allele of the Ini1 tumor suppressor. J Biol Chem 2003; 279:4180-5. [PMID: 14630919 DOI: 10.1074/jbc.m312043200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gene encoding INI1, a component of the mammalian SWI/SNF ATP-dependent chromatin remodeling enzymes, has been classified as a tumor suppressor in humans. Gene-targeting experiments confirmed that Ini1 also functions as a tumor suppressor in mice. Although Ini1-null mice are embryonic lethal, 15-30% of mice heterozygous for Ini1 presented with poorly differentiated tumors with variable rhabdoid features. All tumors examined showed loss of heterozygosity at the Ini1 locus. We report here that cells and tissues heterozygous for the Ini1 tumor suppressor express levels of Ini1 protein and message roughly equivalent to the levels observed in wild type counterparts. Compensation of Ini1 is mediated by an increase in the rate of transcription from the Ini1 promoter. Moreover, when Ini1 is expressed exogenously, transcription from the endogenous promoter is reduced, suggesting that Ini1 levels are tightly regulated. This is the first report describing transcriptional compensation for haploinsufficiency of a tumor suppressor gene.
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Affiliation(s)
- Cynthia J Guidi
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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178
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Chi Y, Senyuk V, Chakraborty S, Nucifora G. EVI1 promotes cell proliferation by interacting with BRG1 and blocking the repression of BRG1 on E2F1 activity. J Biol Chem 2003; 278:49806-11. [PMID: 14555651 DOI: 10.1074/jbc.m309645200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
EVI1 is a complex protein required for embryogenesis and inappropriately expressed in many types of human myeloid leukemia. Earlier we showed that the forced expression of EVI1 in murine hematopoietic precursor cells leads to their abnormal differentiation and increased proliferation. In this report, we show that EVI1 physically interacts with BRG1 and its functional homolog BRM in mammalian cells. We found that the C terminus of EVI1 interacts strongly with BRG1 and that the central and C-terminal regions of BRG1 are involved in EVI1-BRG1 interaction. Using reporter gene assays, we demonstrate that EVI1 activates the E2F1 promoter in NIH3T3 cells but not in BRG1-negative SW13 cells. Ectopic expression of BRG1 is able to repress the E2F1 promoter in vector-transfected SW13 cells but not in EVI1-transfected SW13 cells. Finally, we show that EVI1 up-regulates cell proliferation in BRG1-positive 32Dcl3 cells but not in BRG1-negative SW13 cells. Taken together, these data support the hypothesis that the interaction with BRG1 is important for up-regulation of cell-growth by EVI1.
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Affiliation(s)
- Yiqing Chi
- Department of Pathology and The Cancer Center, University of Illinois, Chicago, Illinois 60607, USA
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179
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Barlev NA, Emelyanov AV, Castagnino P, Zegerman P, Bannister AJ, Sepulveda MA, Robert F, Tora L, Kouzarides T, Birshtein BK, Berger SL. A novel human Ada2 homologue functions with Gcn5 or Brg1 to coactivate transcription. Mol Cell Biol 2003; 23:6944-57. [PMID: 12972612 PMCID: PMC193946 DOI: 10.1128/mcb.23.19.6944-6957.2003] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In yeast, the transcriptional adaptor yeast Ada2 (yAda2) is a part of the multicomponent SAGA complex, which possesses histone acetyltransferase activity through action of the yGcn5 catalytic enzyme. yAda2, among several SAGA proteins, serves to recruit SAGA to genes via interactions with promoter-bound transcription factors. Here we report identification of a new human Ada2 homologue, hAda2beta. Ada2beta differs both biochemically and functionally from the previously characterized hAda2alpha, which is a stable component of the human PCAF (human Gcn5 homologue) acetylase complex. Ada2beta, relative to Ada2alpha, interacted selectively, although not stably, with the Gcn5-containing histone acetylation complex TFTC/STAGA. In addition, Ada2beta interacted with Baf57 (a component of the human Swi/Snf complex) in a yeast two-hybrid screen and associated with human Swi/Snf in vitro. In functional assays, hAda2beta (but not Ada2alpha), working in concert with Gcn5 (but not PCAF) or Brg1 (the catalytic component of hSwi/Snf complex), increased transcription via the B-cell-specific transcription factor Pax5/BSAP. These findings support the view that Gcn5 and PCAF have distinct roles in vivo and suggest a new mechanism of coactivator function, in which a single adaptor protein (Ada2beta) can coordinate targeting of both histone acetylation and chromatin remodeling activities.
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Affiliation(s)
- Nickolai A Barlev
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
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180
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Fitzpatrick DR, Wilson CB. Methylation and demethylation in the regulation of genes, cells, and responses in the immune system. Clin Immunol 2003; 109:37-45. [PMID: 14585274 DOI: 10.1016/s1521-6616(03)00205-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA methylation is a focus of epigenetic research in the immune system. This overview begins with a synopsis of the players and processes involved in DNA methylation, demethylation, methyl-CpG-recognition, histone modification, and chromatin remodeling. The role of these mechanisms in immune responses, with a focus on T lymphocytes, is then reviewed. There is evidence for epigenetic regulation of several key immune processes including thymocyte development, antigen presentation, differentiation, cytokine expression, effector function, and memory. DNA methylation contributes, along with other epigenetic mechanisms, to the establishment of transcriptional thresholds that vary between genes and T cell types. The immune system is a fertile field for studies of epigenetic regulation of cell fate and function.
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Affiliation(s)
- David R Fitzpatrick
- Immunological Systems Department, Amgen Inc, 51 University St, Seattle, WA 98101, USA.
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181
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Koyama AH, Adachi A, Irie H. Physiological significance of apoptosis during animal virus infection. Int Rev Immunol 2003; 22:341-59. [PMID: 12959749 DOI: 10.1080/08830180305210] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Apoptosis has been considered to be a host defense mechanism against viral infection in multicellular organisms. This is based on the findings that apoptogenic mutants of insect viruses cannot grow because infected host cells die by apoptosis. This suggests that the apoptotic response of host cells has a deleterious effect on virus infection. Thus, apoptosis is an important host defense mechanism that is capable of inhibiting viral replication during infection. However, in vitro studies indicated that apoptosis alone does not provide the same protection against viral infection in animal cells as it does in the insect cells. Still, most animal viruses have acquired a strategy to overcome host cell apoptosis. In addition, a varying degree of necrosis usually accompanies apoptosis, suggesting a possible contribution of necrosis to the host reactions against virus. To understand the physiological significance of apoptosis during animal virus infection, we have characterized viral growth and the cellular responses against virus infection in a wide variety of virus-cell interaction systems. Mainly based on our own works, we discuss the nature of apoptosis in the animal virus infection and verify its role as a host defense mechanism against virus infection.
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Affiliation(s)
- A Hajime Koyama
- Department of Virology, The University of Tokushima Graduate School of Medicine, Tokushima 770-8503, Japan.
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182
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Chi TH, Wan M, Lee PP, Akashi K, Metzger D, Chambon P, Wilson CB, Crabtree GR. Sequential roles of Brg, the ATPase subunit of BAF chromatin remodeling complexes, in thymocyte development. Immunity 2003; 19:169-82. [PMID: 12932351 DOI: 10.1016/s1074-7613(03)00199-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
T cells develop through distinct stages directed by a series of signals. We explored the roles of SWI/SNF-like BAF chromatin remodeling complexes in this process by progressive deletion of the ATPase subunit, Brg, through successive stages of early T cell development. Brg-deficient cells were blocked at each of the developmental transitions examined. Bcl-xL overexpression suppressed cell death without relieving the developmental blockades, leading to the accumulation of Brg-deleted cells that were unexpectedly cell cycle arrested. These defects resulted partly from the disruptions of pre-TCR and potentially Wnt signaling pathways controlling the expression of genes such as c-Kit and c-Myc critical for continued development. Our studies indicate that BAF complexes dynamically remodel chromatin to propel sequential developmental transitions in response to external signals.
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Affiliation(s)
- Tian H Chi
- Departments of Pathology and Developmental Biology, Howard Hughes Medical Institute, Stanford University Medical School, Palo Alto, California 94305, USA
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183
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Clevers H. Thymocyte development: drama without Brahma. Immunity 2003; 19:157-8. [PMID: 12932348 DOI: 10.1016/s1074-7613(03)00213-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Hans Clevers
- Hubrecht Laboratory, Center for Biomedical Genetics, Utrecht, The Netherlands
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184
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Abstract
Cell identity is determined by selective gene activation and by the maintenance of other regulated genes in a silent state. Although activation mechanisms have been dissected in considerable depth, great strides towards an understanding of the molecular control of gene silencing have been made only recently. Molecular hallmarks of silent chromatin and proteins involved in its assembly and maintenance have been identified through genetic, cytological and biochemical studies in a variety of organisms. Immunologists are now beginning to use this knowledge to elucidate mechanisms underlying cell fate decisions and key developmental steps. This review surveys the current knowledge of gene silencing, with an emphasis on studies in lymphocytes that are advancing our general understanding of silencing mechanisms during development.
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Affiliation(s)
- Stephen T Smale
- Howard Hughes Medical Institute and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095-1662, USA.
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185
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Abstract
Antigen and cytokine receptor signals act in synergy to direct the differentiation of CD4+ T cells. These signals initiate reciprocal activation and silencing of the interferon-gamma (IFN-gamma) and interleukin 4 (IL-4) cytokine gene loci, changes that are heritably maintained in the resulting T helper type 1 (T(H)1) or T(H)2 cells and their progeny. Early, unpolarized transcription and chromatin remodeling of the poised cytokine genes of naive T cells is followed by consolidation and spreading of epigenetic changes and the establishment of self-reinforcing transcription factor networks. Recent studies have begun to elucidate the molecular mechanisms that establish and maintain polarized cytokine gene expression, and thus the cellular identity of differentiated helper T cells.
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Affiliation(s)
- K Mark Ansel
- Center for Blood Research, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
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186
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Szerlong H, Saha A, Cairns BR. The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J 2003; 22:3175-87. [PMID: 12805231 PMCID: PMC162148 DOI: 10.1093/emboj/cdg296] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2002] [Revised: 04/28/2003] [Accepted: 04/28/2003] [Indexed: 11/12/2022] Open
Abstract
Nuclear actin-related proteins (ARPs) are essential components of chromatin remodeling and modifying complexes, but their functions and relationship to actin remain elusive. The yeast SWI/SNF and RSC complexes contain Arp7 and Arp9, and are shown to form a stable heterodimer with the properties of a functional module. Arp7 and Arp9 rely on their actin-related regions for heterodimerization, and their unique C-termini cooperate for assembly into RSC. We suggest that regulated ARP-ARP (and possibly ARP-beta-actin) heterodimerization might be a conserved feature of chromatin complexes. A RSC complex lacking Arp7/9 was isolated that displays robust nucleosome remodeling activity, suggesting a separate essential role for ARPs in the regulation of chromatin structure. A screen for suppressors of arp mutations yielded the DNA bending architectural transcription factor Nhp6, which interacts with RSC complex physically and functionally and shows facilitated binding to nucleosomes by RSC. We propose that Arp7/9 dimers function with DNA bending proteins to facilitate proper chromatin architecture and complex- complex interactions.
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Affiliation(s)
- Heather Szerlong
- Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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187
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Abstract
One hallmark of ATP-dependent remodeling complexes is the ability to make nucleosomal DNA accessible to regulatory factors. We have compared two prominent human ATP-dependent remodelers, BRG1 from the SWI/SNF family and SNF2h from the ISWI family, for their abilities to make a spectrum of nucleosomal sites accessible. By measuring rates of remodeling at seven different sites on a mononucleosome and at six different sites on the central nucleosome of a trinucleosome, we have found that BRG1 opens centrally located sites more than an order of magnitude better than SNF2h. We provide evidence that this capability of BRG1 is caused by its ability to create DNA loops on the surface of a nucleosome, even when that nucleosome is constrained by adjacent nucleosomes. This specialized ability to make central sites accessible should allow SWI/SNF family complexes to facilitate binding of nuclear factors in chromatin environments where adjacent nucleosomes might otherwise constrain mobility.
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Affiliation(s)
- Hua-Ying Fan
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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188
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Wilson CB, Uittenbogaart CH, Mathis DJ. Immunology at Asilomar: from molecules to mice. Nat Immunol 2003; 4:300-2. [PMID: 12660724 DOI: 10.1038/ni0403-300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Christopher B Wilson
- University of Washington, Department of Immunology, Box 357650, Seattle, WA 98195, USA
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189
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Abstract
Members of the Swi/Snf family of chromatin-remodeling complexes play critical roles in transcriptional control. Recent studies have made significant advances in our understanding of the fundamental aspects of Swi/Snf complexes, including the roles of specific subunits, the repression of transcription, and the mechanism of remodeling. In addition, new findings also indicate an important role for the Swi/Snf-related complex, RSC, in controlling gene expression.
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Affiliation(s)
- Joseph A Martens
- Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA
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190
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Abstract
CD4 and CD8 genes are integral indicators of T-cell lineage commitment. New insights into the control of expression of these genes have come from recent reports implicating chromatin-remodelling factors in their regulation.
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Affiliation(s)
- Rose Zamoyska
- Division of Molecular Immunology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.
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191
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Travers AA. Priming the nucleosome: a role for HMGB proteins? EMBO Rep 2003; 4:131-6. [PMID: 12612600 PMCID: PMC1315838 DOI: 10.1038/sj.embor.embor741] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2002] [Accepted: 12/20/2002] [Indexed: 11/09/2022] Open
Abstract
The high-mobility-group B (HMGB) chromosomal proteins are characterized by the HMG box, a DNA-binding domain that both introduces a tight bend into DNA and binds preferentially to a variety of distorted DNA structures. The HMGB proteins seem to act primarily as architectural facilitators in the manipulation of nucleoprotein complexes; for example, in the assembly of complexes involved in recombination and transcription. Recent genetic and biochemical evidence suggests that these proteins can facilitate nucleosome remodelling. One mechanism by which HMGB proteins could prime the nucleosome for migration is to loosen the wrapped DNA and so enhance accessibility to chromatin-remodelling complexes and possibly also to transcription factors. By constraining a tight loop of untwisted DNA at the edge of a nucleosome, an HMGB protein could induce movements in the contacts between certain core histones that would result in an overall change in nucleosome structure.
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Affiliation(s)
- Andrew A Travers
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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192
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Kadam S, Emerson BM. Transcriptional specificity of human SWI/SNF BRG1 and BRM chromatin remodeling complexes. Mol Cell 2003; 11:377-89. [PMID: 12620226 DOI: 10.1016/s1097-2765(03)00034-0] [Citation(s) in RCA: 267] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mammalian SWI/SNF chromatin remodeling complexes are involved in critical aspects of cellular growth and genomic stability. Each complex contains one of two highly homologous ATPases, BRG1 and BRM, yet little is known about their specialized functions. We show that BRG1and BRM associate with different promoters during cellular proliferation and differentiation, and in response to specific signaling pathways by preferential interaction with certain classes of transcription factors. BRG1 binds to zinc finger proteins through a unique N-terminal domain that is not present in BRM. BRM interacts with two ankyrin repeat proteins that are critical components of Notch signal transduction. Thus, BRG1 and BRM complexes may direct distinct cellular processes by recruitment to specific promoters through protein-protein interactions that are unique to each ATPase.
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Affiliation(s)
- Shilpa Kadam
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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193
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Chi T, Yan Z, Xue Y, Wang W. Purification and functional analysis of the mammalian SWI/SNF-family of chromatin-remodeling complexes. Methods Enzymol 2003; 377:299-316. [PMID: 14979033 DOI: 10.1016/s0076-6879(03)77018-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tianhuai Chi
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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194
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Bonaldi T, Längst G, Strohner R, Becker PB, Bianchi ME. The DNA chaperone HMGB1 facilitates ACF/CHRAC-dependent nucleosome sliding. EMBO J 2002; 21:6865-73. [PMID: 12486007 PMCID: PMC139112 DOI: 10.1093/emboj/cdf692] [Citation(s) in RCA: 204] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2002] [Revised: 10/11/2002] [Accepted: 11/05/2002] [Indexed: 11/14/2022] Open
Abstract
Nucleosome remodelling complexes CHRAC and ACF contribute to chromatin dynamics by converting chemical energy into sliding of histone octamers on DNA. Their shared ATPase subunit ISWI binds DNA at the sites of entry into the nucleosome. A prevalent model assumes that DNA distortions catalysed by ISWI are converted into relocation of DNA relative to a histone octamer. HMGB1, one of the most abundant nuclear non-histone proteins, binds with preference to distorted DNA. We have now found that transient interaction of HMGB1 with nucleosomal linker DNA overlapping ISWI-binding sites enhances the ability of ACF to bind nucleosomal DNA and accelerates the sliding activity of limiting concentrations of remodelling factor. By contrast, an HMGB1 mutant with increased binding affinity was inhibitory. These observations are consistent with a role for HMGB1 as a DNA chaperone facilitating the rate-limiting DNA distortion during nucleosome remodelling.
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Affiliation(s)
- Tiziana Bonaldi
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany,
DIBIT, San Raffaele Scientific Institute and Università Vita Salute San Raffaele, Via Olgettina 58, 4, I-20132 Milano, Italy Corresponding author e-mail: T.Bonaldi and G.Längst contributed equally to this work
| | | | | | - Peter B. Becker
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany,
DIBIT, San Raffaele Scientific Institute and Università Vita Salute San Raffaele, Via Olgettina 58, 4, I-20132 Milano, Italy Corresponding author e-mail: T.Bonaldi and G.Längst contributed equally to this work
| | - Marco E. Bianchi
- Adolf-Butenandt Institut, Molekularbiologie, Schillerstrasse 44, D-80336 München, Germany,
DIBIT, San Raffaele Scientific Institute and Università Vita Salute San Raffaele, Via Olgettina 58, 4, I-20132 Milano, Italy Corresponding author e-mail: T.Bonaldi and G.Längst contributed equally to this work
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195
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Harker N, Naito T, Cortes M, Hostert A, Hirschberg S, Tolaini M, Roderick K, Georgopoulos K, Kioussis D. The CD8alpha gene locus is regulated by the Ikaros family of proteins. Mol Cell 2002; 10:1403-15. [PMID: 12504015 DOI: 10.1016/s1097-2765(02)00711-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ikaros family members are important regulatory factors in lymphocyte development. Here we show that Ikaros may play an important role in CD4 versus CD8 lineage commitment decisions by demonstrating: (1) that it binds to regulatory elements in the endogenous CD8alpha locus in vivo using thymocyte chromatin immunoprecipitations, (2) that Ikaros suppresses position effect variegation of transgenes driven by CD8 regulatory elements, and (3) that mice with reduced levels of Ikaros and Aiolos show an apparent increase in CD4 populations with immature phenotype, i.e., cells that failed to activate the CD8alpha gene locus. We propose that Ikaros family members function as activators of the CD8alpha gene locus and that their associated activities are critical for appropriate chromatin remodeling transitions during thymocyte differentiation and lineage commitment.
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Affiliation(s)
- Nicola Harker
- Division of Molecular Immunology, National Institute for Medical Research, Medical Research Council, NW7 1AA, London, United Kingdom
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196
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Kioussis D, Ellmeier W. Chromatin and CD4, CD8A and CD8B gene expression during thymic differentiation. Nat Rev Immunol 2002; 2:909-19. [PMID: 12461564 DOI: 10.1038/nri952] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The regulation of gene expression during thymocyte development provides an ideal experimental system to study lineage-commitment processes. In particular, expression of the CD4, CD8A and CD8B genes seems to correlate well with the cell-fate decisions that are taken by thymocytes, and elucidating the molecular mechanisms that underlie the differential expression of these genes could reveal key events in differentiation processes. Here, we review examples of how gene cis elements (such as promoters, enhancers and locus control regions) and trans elements (such as transcription factors, chromatin-remodelling complexes and histone-modification enzymes) come together to orchestrate a finely tuned sequence of events that results in the complex pattern of CD4, CD8A and CD8B gene expression that is observed during thymocyte development.
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Affiliation(s)
- Dimitris Kioussis
- Division of Molecular Immunology, National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.
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197
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Taniuchi I, Osato M, Egawa T, Sunshine MJ, Bae SC, Komori T, Ito Y, Littman DR. Differential requirements for Runx proteins in CD4 repression and epigenetic silencing during T lymphocyte development. Cell 2002; 111:621-33. [PMID: 12464175 DOI: 10.1016/s0092-8674(02)01111-x] [Citation(s) in RCA: 600] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
T lymphocytes differentiate in discrete stages within the thymus. Immature thymocytes lacking CD4 and CD8 coreceptors differentiate into double-positive cells (CD4(+)CD8(+)), which are selected to become either CD4(+)CD8(-)helper cells or CD4(-)CD8(+) cytotoxic cells. A stage-specific transcriptional silencer regulates expression of CD4 in both immature and CD4(-)CD8(+) thymocytes. We show here that binding sites for Runt domain transcription factors are essential for CD4 silencer function at both stages, and that different Runx family members are required to fulfill unique functions at each stage. Runx1 is required for active repression in CD4(-)CD8(-) thymocytes whereas Runx3 is required for establishing epigenetic silencing in cytotoxic lineage thymocytes. Runx3-deficient cytotoxic T cells, but not helper cells, have defective responses to antigen, suggesting that Runx proteins have critical functions in lineage specification and homeostasis of CD8-lineage T lymphocytes.
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Affiliation(s)
- Ichiro Taniuchi
- Howard Hughes Medical Institute, Molecular Pathogenesis Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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198
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Taniuchi I, Sunshine MJ, Festenstein R, Littman DR. Evidence for distinct CD4 silencer functions at different stages of thymocyte differentiation. Mol Cell 2002; 10:1083-96. [PMID: 12453416 DOI: 10.1016/s1097-2765(02)00735-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
An intronic silencer within the CD4 gene is the critical cis regulatory element for T cell subset-specific expression of CD4. We have combined transfection studies with gene targeting in mice to identify several key sequences within the silencer core that are required for gene silencing during thymocyte development. In mice, mutations in individual sites resulted in variegated, but heritable, derepression of CD4 in mature CD8(+) T lymphocytes, whereas compound mutations resulted in full derepression. These results indicate that there is partial redundancy in recruiting a chromatin remodeling machinery that results in epigenetic silencing. Mutations in single sites also resulted in partial derepression of CD4 in immature double-negative thymocytes, but there was no apparent variegation. These findings suggest two distinct modes of CD4 silencer function at different developmental stages: active repression in CD4(-)CD8(-) thymocytes, in which silencing must be reversible, and epigenetic gene silencing upon differentiation to the CD8(+) cytotoxic T cell lineage.
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Affiliation(s)
- Ichiro Taniuchi
- Howard Hughes Medical Institute, Molecular Pathogenesis Program, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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199
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Roberts CWM, Leroux MM, Fleming MD, Orkin SH. Highly penetrant, rapid tumorigenesis through conditional inversion of the tumor suppressor gene Snf5. Cancer Cell 2002; 2:415-25. [PMID: 12450796 DOI: 10.1016/s1535-6108(02)00185-x] [Citation(s) in RCA: 232] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent data suggest the SWI/SNF chromatin remodeling complex may also act as a tumor suppressor. Utilizing a reversibly inactivating conditional allele, we demonstrate that loss of Snf5/Ini1/Baf47/SmarcB1, a core subunit of SWI/SNF, results in highly penetrant cancer predisposition with 100% of mice developing mature CD8(+) T cell lymphoma or rare rhabdoid tumors with a median onset of only 11 weeks. Notably, while loss of Snf5 predisposes to aggressive cancers, it is also required for survival of virtually all nonmalignant cells in vivo. Reversible gene targeting demonstrates a critical and specific role for Snf5 in tumor suppression, provides a novel system in which to explore the genetic pathways involved in tumor suppression by Swi/Snf, and should be of wide use in evaluating other essential tumor suppressor genes.
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Affiliation(s)
- Charles W M Roberts
- Division of Hematology-Oncology, Dana-Farber Cancer Institute and Children's Hospital, Department of Pediatrics, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA 02115, USA
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200
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Battaglioli E, Andrés ME, Rose DW, Chenoweth JG, Rosenfeld MG, Anderson ME, Mandel G. REST repression of neuronal genes requires components of the hSWI.SNF complex. J Biol Chem 2002; 277:41038-45. [PMID: 12192000 DOI: 10.1074/jbc.m205691200] [Citation(s) in RCA: 158] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A function of the transcription factor REST is to block the expression of neuronal phenotypic traits in non-neuronal cells. Previous studies have shown that REST-mediated repression requires histone deacetylase activity and that recruitment of deacetylases is mediated by two co-repressors, Sin3A and CoREST. In this study, we show that a repressor domain in CoREST interacts with BRG1-associated factor (BAF) 57, a component of the hSWI.SNF complex. In vivo, BAF57 occupies the neuronal sodium channel gene (Nav1.2) promoter, and targeting to this gene requires REST. In addition to BAF57, the ATPase BRG1 and BAF170, other members of the hSWI.SNF complex, are also present in the REST.CoREST repressor complex. Microinjection of specific antibodies against BRG1, BAF57, or BAF170 into Rat1 fibroblasts relieves repression of RE1 reporter genes. Together, our data suggest that ATP-dependent chromatin remodeling, as well as histone deacetylation, is needed for REST-mediated repression.
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Affiliation(s)
- Elena Battaglioli
- Department of Neurobiology and Behavior, Howard Hughes Medical Institute, State University of New York, Stony Brook, NY 11794, USA
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