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Giudice FS, Pinto DS, Nör JE, Squarize CH, Castilho RM. Inhibition of histone deacetylase impacts cancer stem cells and induces epithelial-mesenchyme transition of head and neck cancer. PLoS One 2013; 8:e58672. [PMID: 23527004 PMCID: PMC3603970 DOI: 10.1371/journal.pone.0058672] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 02/05/2013] [Indexed: 12/30/2022] Open
Abstract
The genome is organized and packed into the nucleus through interactions with core histone proteins. Emerging evidence suggests that tumors are highly responsive to epigenetic alterations that induce chromatin-based events and dynamically influence tumor behavior. We examined chromatin organization in head and neck squamous cell carcinoma (HNSCC) using acetylation levels of histone 3 as a marker of chromatin compaction. Compared to control oral keratinocytes, we found that HNSCC cells are hypoacetylated and that microenvironmental cues (e.g., microvasculature endothelial cells) induce tumor acetylation. Furthermore, we found that chemical inhibition of histone deacetylases (HDAC) reduces the number of cancer stem cells (CSC) and inhibits clonogenic sphere formation. Paradoxically, inhibition of HDAC also induced epithelial-mesenchymal transition (EMT) in HNSCC cells, accumulation of BMI-1, an oncogene associated with tumor aggressiveness, and expression of the vimentin mesenchymal marker. Importantly, we observed co-expression of vimentin and acetylated histone 3 at the invasion front of human HNSCC tumor tissues. Collectively, these findings suggest that environmental cues, such as endothelial cell-secreted factors, modulate tumor plasticity by limiting the population of CSC and inducing EMT. Therefore, inhibition of HDAC may constitute a novel strategy to disrupt the population of CSC in head and neck tumors to create a homogeneous population of cancer cells with biologically defined signatures and predictable behavior.
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Affiliation(s)
- Fernanda S. Giudice
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Decio S. Pinto
- Department of Oral Pathology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Jacques E. Nör
- Department of Cariology, Restorative Sciences and Endodontics, School of Dentistry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
| | - Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, Michigan, United States of America
- * E-mail:
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BRG1 is required for formation of senescence-associated heterochromatin foci induced by oncogenic RAS or BRCA1 loss. Mol Cell Biol 2013; 33:1819-29. [PMID: 23438604 DOI: 10.1128/mcb.01744-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cellular senescence is an important tumor suppression mechanism. We have previously reported that both oncogene-induced dissociation of BRCA1 from chromatin and BRCA1 knockdown itself drive senescence by promoting formation of senescence-associated heterochromatin foci (SAHF). However, the molecular mechanism by which BRCA1 regulates SAHF formation and senescence is unclear. BRG1 is a chromatin-remodeling factor that interacts with BRCA1 and pRB. Here we show that BRG1 is required for SAHF formation and senescence induced by oncogenic RAS or BRCA1 loss. The interaction between BRG1 and BRCA1 is disrupted during senescence. This correlates with an increased level of chromatin-associated BRG1 in senescent cells. BRG1 knockdown suppresses the formation of SAHF and senescence, while it has no effect on BRCA1 chromatin dissociation induced by oncogenic RAS, indicating that BRG1 functions downstream of BRCA1 chromatin dissociation. Furthermore, BRG1 knockdown inhibits SAHF formation and senescence induced by BRCA1 knockdown. Conversely, BRG1 overexpression drives SAHF formation and senescence in a DNA damage-independent manner. This effect depends upon BRG1's chromatin-remodeling activity as well as the interaction between BRG1 and pRB. Indeed, the interaction between BRG1 and pRB is enhanced during senescence. Chromatin immunoprecipitation analysis revealed that BRG1's association with the human CDKN2A and CDKN1A gene promoters was enhanced during senescence induced by oncogenic RAS or BRCA1 knockdown. Consistently, knockdown of pRB, p21(CIP1), and p16(INK4a), but not p53, suppressed SAHF formation induced by BRG1. Together, these studies reveal the molecular underpinning by which BRG1 acts downstream of BRCA1 to promote SAHF formation and senescence.
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53
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The WSTF-ISWI chromatin remodeling complex transiently associates with the human inactive X chromosome during late S-phase prior to BRCA1 and γ-H2AX. PLoS One 2012; 7:e50023. [PMID: 23166813 PMCID: PMC3498190 DOI: 10.1371/journal.pone.0050023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 10/16/2012] [Indexed: 01/08/2023] Open
Abstract
Replicating the genome prior to each somatic cell division not only requires precise duplication of the genetic information, but also accurately reestablishing the epigenetic signatures that instruct how the genetic material is to be interpreted in the daughter cells. The mammalian inactive X chromosome (Xi), which is faithfully inherited in a silent state in each daughter cell, provides an excellent model of epigenetic regulation. While much is known about the early stages of X chromosome inactivation, much less is understood with regards to retaining the Xi chromatin through somatic cell division. Here we report that the WSTF-ISWI chromatin remodeling complex (WICH) associates with the Xi during late S-phase as the Xi DNA is replicated. Elevated levels of WICH at the Xi is restricted to late S-phase and appears before BRCA1 and γ-H2A.X. The sequential appearance of WICH and BRCA1/γ-H2A.X implicate each as performing important but distinct roles in the maturation and maintenance of heterochromatin at the Xi.
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54
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Holwerda S, de Laat W. Chromatin loops, gene positioning, and gene expression. Front Genet 2012; 3:217. [PMID: 23087710 PMCID: PMC3473233 DOI: 10.3389/fgene.2012.00217] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/01/2012] [Indexed: 01/09/2023] Open
Abstract
Technological developments and intense research over the last years have led to a better understanding of the 3D structure of the genome and its influence on genome function inside the cell nucleus. We will summarize topological studies performed on four model gene loci: the α- and β-globin gene loci, the antigen receptor loci, the imprinted H19-Igf2 locus and the Hox gene clusters. Collectively, these studies show that regulatory DNA sequences physically contact genes to control their transcription. Proteins set up the 3D configuration of the genome and we will discuss the roles of the key structural organizers CTCF and cohesin, the nuclear lamina and the transcription machinery. Finally, genes adopt non-random positions in the nuclear interior. We will review studies on gene positioning and propose that cell-specific genome conformations can juxtapose a regulatory sequence on one chromosome to a responsive gene on another chromosome to cause altered gene expression in subpopulations of cells.
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Affiliation(s)
- Sjoerd Holwerda
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht Utrecht, Netherlands
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55
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Blackford JA, Guo C, Zhu R, Dougherty EJ, Chow CC, Simons SS. Identification of location and kinetically defined mechanism of cofactors and reporter genes in the cascade of steroid-regulated transactivation. J Biol Chem 2012; 287:40982-95. [PMID: 23055525 DOI: 10.1074/jbc.m112.414805] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A currently obscure area of steroid hormone action is where the component factors, including receptor and reporter gene, act. The DNA binding of factors can be precisely defined, but the location and timing of factor binding and action are usually not equivalent. These questions are addressed for several factors (e.g. glucocorticoid receptor (GR), reporter, TIF2, NCoR, NELF-A, sSMRT, and STAMP) using our recently developed competition assay. This assay reveals both the kinetically defined mechanism of factor action and where the above factors act relative to both each other and the equilibrium equivalent to the rate-limiting step, which we call the concentration limiting step (CLS). The utility of this competition assay would be greatly increased if the position of the CLS is invariant and if the factor acting at the CLS is known. Here we report that the exogenous GREtkLUC reporter acts at the CLS as an accelerator for gene induction by GRs in U2OS cells. This mechanism of reporter function at the CLS persists with different reporters, factors, receptors, and cell types. We, therefore, propose that the reporter gene always acts at the CLS during gene induction and constitutes a landmark around which one can order the actions of all other factors. Current data suggest that how and where GR and the short form of SMRT act is also constant. These results validate a novel and rational methodology for identifying distally acting factors that would be attractive targets for pharmaceutical intervention in the treatment of diseases involving GR-regulated genes.
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Affiliation(s)
- John A Blackford
- Steroid Hormones Section, Laboratory of Endocrinology and Receptor Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, USA
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56
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Bunting SF, Callen E, Kozak ML, Kim JM, Wong N, Lopez-Contreras AJ, Ludwig T, Baer R, Faryabi RB, Malhowski A, Chen HT, Fernandez-Capetillo O, D’Andrea A, Nussenzweig A. BRCA1 functions independently of homologous recombination in DNA interstrand crosslink repair. Mol Cell 2012; 46:125-35. [PMID: 22445484 PMCID: PMC3340543 DOI: 10.1016/j.molcel.2012.02.015] [Citation(s) in RCA: 215] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 01/13/2012] [Accepted: 02/10/2012] [Indexed: 11/23/2022]
Abstract
Brca1 is required for DNA repair by homologous recombination (HR) and normal embryonic development. Here we report that deletion of the DNA damage response factor 53BP1 overcomes embryonic lethality in Brca1-nullizygous mice and rescues HR deficiency, as measured by hypersensitivity to polyADP-ribose polymerase (PARP) inhibition. However, Brca1,53BP1 double-deficient cells are hypersensitive to DNA interstrand crosslinks (ICLs), indicating that BRCA1 has an additional role in DNA crosslink repair that is distinct from HR. Disruption of the nonhomologous end-joining (NHEJ) factor, Ku, promotes DNA repair in Brca1-deficient cells; however deletion of either Ku or 53BP1 exacerbates genomic instability in cells lacking FANCD2, a mediator of the Fanconi anemia pathway for ICL repair. BRCA1 therefore has two separate roles in ICL repair that can be modulated by manipulating NHEJ, whereas FANCD2 provides a key activity that cannot be bypassed by ablation of 53BP1 or Ku.
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Affiliation(s)
- Samuel F Bunting
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
| | - Marina L Kozak
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
| | - Jung-Min Kim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
| | | | - Thomas Ludwig
- Institute for Cancer Genetics, Columbia University Medical Center, Irving Cancer Research Center, Rm. 503A, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Richard Baer
- Institute for Cancer Genetics, Columbia University Medical Center, Irving Cancer Research Center, Rm. 503A, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Robert B Faryabi
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
| | - Amy Malhowski
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
| | - Hua-Tang Chen
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
| | | | - Alan D’Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 1108, Bethesda, MD 20892, USA
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57
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A new non-catalytic role for ubiquitin ligase RNF8 in unfolding higher-order chromatin structure. EMBO J 2012; 31:2511-27. [PMID: 22531782 DOI: 10.1038/emboj.2012.104] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Accepted: 03/23/2012] [Indexed: 11/08/2022] Open
Abstract
The ubiquitin ligases RNF8 and RNF168 orchestrate DNA damage signalling through the ubiquitylation of histone H2A and the recruitment of downstream repair factors. Here, we demonstrate that RNF8, but not RNF168 or the canonical H2A ubiquitin ligase RNF2, mediates extensive chromatin decondensation. Our data show that CHD4, the catalytic subunit of the NuRD complex, interacts with RNF8 and is essential for RNF8-mediated chromatin unfolding. The chromatin remodelling activity of CHD4 promotes efficient ubiquitin conjugation and assembly of RNF168 and BRCA1 at DNA double-strand breaks. Interestingly, RNF8-mediated recruitment of CHD4 and subsequent chromatin remodelling were independent of the ubiquitin-ligase activity of RNF8, but involved a non-canonical interaction with the forkhead-associated (FHA) domain. Our study reveals a new mechanism of chromatin remodelling-assisted ubiquitylation, which involves the cooperation between CHD4 and RNF8 to create a local chromatin environment that is permissive to the assembly of checkpoint and repair machineries at DNA lesions.
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58
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Luijsterburg MS, Lindh M, Acs K, Vrouwe MG, Pines A, van Attikum H, Mullenders LH, Dantuma NP. DDB2 promotes chromatin decondensation at UV-induced DNA damage. ACTA ACUST UNITED AC 2012; 197:267-81. [PMID: 22492724 PMCID: PMC3328393 DOI: 10.1083/jcb.201106074] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In addition to its role in DNA lesion recognition, the damaged DNA-binding protein DDB2 elicits unfolding of large-scale chromatin structure independently of the CRL4 ubiquitin ligase complex. Nucleotide excision repair (NER) is the principal pathway that removes helix-distorting deoxyribonucleic acid (DNA) damage from the mammalian genome. Recognition of DNA lesions by xeroderma pigmentosum group C (XPC) protein in chromatin is stimulated by the damaged DNA-binding protein 2 (DDB2), which is part of a CUL4A–RING ubiquitin ligase (CRL4) complex. In this paper, we report a new function of DDB2 in modulating chromatin structure at DNA lesions. We show that DDB2 elicits unfolding of large-scale chromatin structure independently of the CRL4 ubiquitin ligase complex. Our data reveal a marked adenosine triphosphate (ATP)–dependent reduction in the density of core histones in chromatin containing UV-induced DNA lesions, which strictly required functional DDB2 and involved the activity of poly(adenosine diphosphate [ADP]–ribose) polymerase 1. Finally, we show that lesion recognition by XPC, but not DDB2, was strongly reduced in ATP-depleted cells and was regulated by the steady-state levels of poly(ADP-ribose) chains.
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Affiliation(s)
- Martijn S Luijsterburg
- Department of Cell and Molecular Biology, Karolinska Institutet, S-17177 Stockholm, Sweden.
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59
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Tu Z, Aird KM, Bitler BG, Nicodemus JP, Beeharry N, Xia B, Yen TJ, Zhang R. Oncogenic RAS regulates BRIP1 expression to induce dissociation of BRCA1 from chromatin, inhibit DNA repair, and promote senescence. Dev Cell 2011; 21:1077-91. [PMID: 22137763 DOI: 10.1016/j.devcel.2011.10.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 06/29/2011] [Accepted: 10/11/2011] [Indexed: 12/16/2022]
Abstract
Here, we report a cell-intrinsic mechanism by which oncogenic RAS promotes senescence while predisposing cells to senescence bypass by allowing for secondary hits. We show that oncogenic RAS inactivates the BRCA1 DNA repair complex by dissociating BRCA1 from chromatin. This event precedes senescence-associated cell cycle exit and coincides with the accumulation of DNA damage. Downregulation of BRIP1, a physiological partner of BRCA1 in the DNA repair pathway, triggers BRCA1 chromatin dissociation. Conversely, ectopic BRIP1 rescues BRCA1 chromatin dissociation and suppresses RAS-induced senescence and the DNA damage response. Significantly, cells undergoing senescence do not exhibit a BRCA1-dependent DNA repair response when exposed to DNA damage. Overall, our study provides a molecular basis by which oncogenic RAS promotes senescence. Because DNA damage has the potential to produce additional "hits" that promote senescence bypass, our findings may also suggest one way a small minority of cells might bypass senescence and contribute to cancer development.
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Affiliation(s)
- Zhigang Tu
- Women's Cancer Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, USA
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60
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Establishment of a Technology Detecting The Large Scale Chromatin Relaxation Based on GFP Fluorescence Imaging*. PROG BIOCHEM BIOPHYS 2011. [DOI: 10.3724/sp.j.1206.2010.00642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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61
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Proia TA, Keller PJ, Gupta PB, Klebba I, Jones AD, Sedic M, Gilmore H, Tung N, Naber SP, Schnitt S, Lander ES, Kuperwasser C. Genetic predisposition directs breast cancer phenotype by dictating progenitor cell fate. Cell Stem Cell 2011; 8:149-63. [PMID: 21295272 DOI: 10.1016/j.stem.2010.12.007] [Citation(s) in RCA: 286] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 08/19/2010] [Accepted: 11/30/2010] [Indexed: 01/27/2023]
Abstract
Women with inherited mutations in the BRCA1 gene have increased risk of developing breast cancer but also exhibit a predisposition for the development of aggressive basal-like breast tumors. We report here that breast epithelial cells derived from patients harboring deleterious mutations in BRCA1 (BRCA1(mut /+) give rise to tumors with increased basal differentiation relative to cells from BRCA1+/+ patients. Molecular analysis of disease-free breast tissues from BRCA1(mut /+) patients revealed defects in progenitor cell lineage commitment even before cancer incidence. Moreover, we discovered that the transcriptional repressor Slug is an important functional suppressor of human breast progenitor cell lineage commitment and differentiation and that it is aberrantly expressed in BRCA1(mut /+) tissues. Slug expression is necessary for increased basal-like phenotypes prior to and after neoplastic transformation. These findings demonstrate that the genetic background of patient populations, in addition to affecting incidence rates, significantly impacts progenitor cell fate commitment and, therefore, tumor phenotype.
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Affiliation(s)
- Theresa A Proia
- Department of Anatomy & Cellular Biology, Sackler School of Biomedical Research, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
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62
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Abstract
The fractal globule is a compact polymer state that emerges during polymer condensation as a result of topological constraints which prevent one region of the chain from passing across another one. This long-lived intermediate state was introduced in 1988 (Grosberg et al. 1988) and has not been observed in experiments or simulations until recently (Lieberman-Aiden et al. 2009). Recent characterization of human chromatin using a novel chromosome conformational capture technique brought the fractal globule into the spotlight as a structural model of human chromosome on the scale of up to 10 Mb (Lieberman-Aiden et al. 2009). Here, we present the concept of the fractal globule, comparing it to other states of a polymer and focusing on its properties relevant for the biophysics of chromatin. We then discuss properties of the fractal globule that make it an attractive model for chromatin organization inside a cell. Next, we connect the fractal globule to recent studies that emphasize topological constraints as a primary factor driving formation of chromosomal territories. We discuss how theoretical predictions, made on the basis of the fractal globule model, can be tested experimentally. Finally, we discuss whether fractal globule architecture can be relevant for chromatin packing in other organisms such as yeast and bacteria.
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Affiliation(s)
- Leonid A Mirny
- Harvard-MIT Division of Health Sciences and Technology, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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63
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Nechaev S, Adelman K. Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1809:34-45. [PMID: 21081187 DOI: 10.1016/j.bbagrm.2010.11.001] [Citation(s) in RCA: 202] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Revised: 11/06/2010] [Accepted: 11/09/2010] [Indexed: 01/12/2023]
Abstract
Proper regulation of gene expression is essential for the differentiation, development and survival of all cells and organisms. Recent work demonstrates that transcription of many genes, including key developmental and stimulus-responsive genes, is regulated after the initiation step, by pausing of RNA polymerase II during elongation through the promoter-proximal region. Thus, there is great interest in better understanding the events that follow transcription initiation and the ways in which the efficiency of early elongation can be modulated to impact expression of these highly regulated genes. Here we describe our current understanding of the steps involved in the transition from an unstable initially transcribing complex into a highly stable and processive elongation complex. We also discuss the interplay between factors that affect early transcript elongation and the potential physiological consequences for genes that are regulated through transcriptional pausing.
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Affiliation(s)
- Sergei Nechaev
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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64
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Wong PG, Glozak MA, Cao TV, Vaziri C, Seto E, Alexandrow M. Chromatin unfolding by Cdt1 regulates MCM loading via opposing functions of HBO1 and HDAC11-geminin. Cell Cycle 2010; 9:4351-63. [PMID: 20980834 DOI: 10.4161/cc.9.21.13596] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The efficiency of metazoan origins of DNA replication is known to be enhanced by histone acetylation near origins. Although this correlates with increased MCM recruitment, the mechanism by which such acetylation regulates MCM loading is unknown. We show here that Cdt1 induces large-scale chromatin decondensation that is required for MCM recruitment. This process occurs in G₁, is suppressed by Geminin, and requires HBO1 HAT activity and histone H4 modifications. HDAC11, which binds Cdt1 and replication origins during S-phase, potently inhibits Cdt1-induced chromatin unfolding and re-replication, suppresses MCM loading and binds Cdt1 more efficiently in the presence of Geminin. We also demonstrate that chromatin at endogenous origins is more accessible in G₁ relative to S-phase. These results provide evidence that histone acetylation promotes MCM loading via enhanced chromatin accessibility. This process is regulated positively by Cdt1 and HBO1 in G₁ and repressed by Geminin-HDAC11 association with Cdt1 in S-phase, and represents a novel form of replication licensing control.
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Affiliation(s)
- Philip G Wong
- Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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65
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Zou W, Yang Y, Wu Y, Sun L, Chi Y, Wu W, Yun X, Xie J, Gu J. Negative role of trihydrophobin 1 in breast cancer growth and migration. Cancer Sci 2010; 101:2156-62. [PMID: 20735431 PMCID: PMC11158160 DOI: 10.1111/j.1349-7006.2010.01656.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Trihydrophobin 1 (TH1) is a member of the negative elongation factor complex, which is involved in transcriptional pausing. Although the negative elongation factor complex attenuates the estrogen receptor α-mediated transcription, little is known about the relationship between TH1 and tumor progression. Here, we report that the protein level of TH1 was negatively correlated with the aggressiveness of human breast cancer. Immunohistochemical analysis revealed that TH1 expression in clinical stage III-IV primary breast cancer tissues was statistically significantly lower than that in stage I-II breast tissues (P < 0.01), and especially inversely associated with lymph node metastasis (P < 0.001). Furthermore, we showed that overexpression of TH1 in MDA-MB-231 breast cancer cells inhibited, and knockdown of TH1 in MCF-7 cells enhanced, cell proliferation and migratory ability. Moreover, upregulation of TH1 in MDA-MB-231 cells resulted in the decrease of cyclin D1, β-catenin, and ERK activity, and the increase of p21. In contrast, knockdown of TH1 in MCF-7 cells enhanced the expression of cyclin D1 and β-catenin, increased the activity of ERK, and downregulated the expression of p21. Additionally, overexpression of TH1 in MDA-MB-231 cells prevented. However, knockdown of TH1 in MCF-7 cells induced a number of molecular and cellular alterations associated with epithelial-mesenchymal transition. Taken together, our results suggest that TH1 might play an important role in regulation of proliferation and invasion in human breast cancer, and could be a potential target for human breast cancer treatment.
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Affiliation(s)
- Weiying Zou
- Gene Research Center, Key Laboratory of Glycoconjugate Research, Ministry of Public Health, Shanghai Medical College of Fudan University, Shanghai, China
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66
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Kitchen NS, Schoenherr CJ. Sumoylation modulates a domain in CTCF that activates transcription and decondenses chromatin. J Cell Biochem 2010; 111:665-75. [DOI: 10.1002/jcb.22751] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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67
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Thakar A, Parvin JD, Zlatanova J. BRCA1/BARD1 E3 ubiquitin ligase can modify histones H2A and H2B in the nucleosome particle. J Biomol Struct Dyn 2010; 27:399-406. [PMID: 19916563 DOI: 10.1080/07391102.2010.10507326] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BRCA1, the protein product of the Breast Cancer Susceptibility Gene (BRCA1) has been implicated in multiple pathways that preserve genome stability, including cell cycle control, DNA repair, transcription, and chromatin remodeling. BRCA1, in complex with another RING-domain protein BARD1, possesses ubiquitin-ligase activity. Only a few targets for this activity have been identified in vivo. Nucleosomal histones may also be targets in vivo since they can be modified by the BRCA1/BARD1 complex in vitro. Here we demonstrate that the BRCA1/BARD1 complex can ubiquitylate both free H2A and H2B histones and histones in the context of nucleosomal particles. These results raise the possibility that BRCA1/BARD1 can directly affect nucleosomal structure, dynamics, and function through its ability to modify nucleosomal histones.
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Affiliation(s)
- Amit Thakar
- Dept of Molecular Biology University of Wyoming, Laramie, WY 82071, USA
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68
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Understanding the functions of BRCA1 in the DNA-damage response. Biochem Soc Trans 2009; 37:597-604. [PMID: 19442256 DOI: 10.1042/bst0370597] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Inheritance of a mutation in BRCA1 (breast cancer 1 early-onset) results in predisposition to early-onset breast and ovarian cancer. Tumours in these individuals arise after somatic mutation or loss of the wild-type allele. Loss of BRCA1 function leads to a profound increase in genomic instability involving the accumulation of mutations, DNA breaks and gross chromosomal rearrangements. Accordingly, BRCA1 has been implicated as an important factor involved in both the repair of DNA lesions and in the regulation of cell-cycle checkpoints in response to DNA damage. However, the molecular mechanism through which BRCA1 functions to preserve genome stability remains unclear. In the present article, we examine the different ways in which BRCA1 might influence the repair of DNA damage and the preservation of genome integrity, taking into account what is currently known about its interactions with other proteins, its biochemical activity and its nuclear localization.
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69
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Yung TM, Narita T, Komori T, Yamaguchi Y, Handa H. Cellular dynamics of the negative transcription elongation factor NELF. Exp Cell Res 2009; 315:1693-705. [DOI: 10.1016/j.yexcr.2009.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 02/12/2009] [Accepted: 02/12/2009] [Indexed: 10/21/2022]
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70
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Sirchia SM, Tabano S, Monti L, Recalcati MP, Gariboldi M, Grati FR, Porta G, Finelli P, Radice P, Miozzo M. Misbehaviour of XIST RNA in breast cancer cells. PLoS One 2009; 4:e5559. [PMID: 19440381 PMCID: PMC2679222 DOI: 10.1371/journal.pone.0005559] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 04/14/2009] [Indexed: 11/18/2022] Open
Abstract
A role of X chromosome inactivation process in the development of breast cancer have been suggested. In particular, the relationship between the breast cancer predisposing gene BRCA1 and XIST, the main mediator of X chromosome inactivation, has been intensely investigated, but still remains controversial. We investigated this topic by assessing XIST behaviour in different groups of breast carcinomas and in a panel of breast cancer cell lines both BRCA1 mutant and wild type. In addition, we evaluated the occurrence of broader defects of heterochromatin in relation to BRCA1 status in breast cancer cells. We provide evidence that in breast cancer cells BRCA1 is involved in XIST regulation on the active X chromosome, but not in its localization as previously suggested, and that XIST can be unusually expressed by an active X and can decorate it. This indicates that the detection of XIST cloud in cancer cell is not synonymous of the presence of an inactive X chromosome. Moreover, we show that global heterochromatin defects observed in breast tumor cells are independent of BRCA1 status. Our observations sheds light on a possible previously uncharacterized mechanism of breast carcinogenesis mediated by XIST misbehaviour, particularly in BRCA1-related cancers. Moreover, the significant higher levels of XIST-RNA detected in BRCA1-associated respect to sporadic basal-like cancers, opens the possibility to use XIST expression as a marker to discriminate between the two groups of tumors.
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Affiliation(s)
- Silvia M Sirchia
- Department of Medicine, Surgery and Dentistry, Medical Genetics Unit, Università degli Studi di Milano, Milano, Italy.
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71
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Winter SL, Wong P, Alexandrow MG. In vivo chromatin decondensation assays: molecular genetic analysis of chromatin unfolding characteristics of selected proteins. Methods Mol Biol 2009; 523:27-40. [PMID: 19381923 DOI: 10.1007/978-1-59745-190-1_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Of critical importance to many of the events underlying transcriptional control of gene expression are modifications to core and linker histones that regulate the accessibility of trans-acting factors to the DNA substrate within the context of chromatin. Likewise, control over the initiation of DNA replication, as well as the ability of the replication machinery to proceed during elongation through the multiple levels of chromatin condensation that are likely to be encountered, is almost certain to involve the creation of chromatin accessibility. In the latter case in particular, chromatin access will likely need to be a transient event so as to prevent total genomic unraveling of the chromatin that would be deleterious to cells. While there are many molecular and biochemical approaches in use to study histone changes and their relationship to transcription and chromatin accessibility, few techniques exist that allow a molecular dissection of the events underlying DNA replication control as it pertains to chromatin changes and accessibility. In this review, we outline a novel experimental strategy for addressing the ability of specific proteins to induce large-scale chromatin unfolding (decondensation) in vivo upon site-specific targeting to an engineered locus. We have used this system successfully to directly address the ability of DNA replication proteins to create chromatin accessibility and have incorporated modifications to the basic approach that allow for a molecular genetic analysis of the players involved in causing chromatin decondensation by a protein of interest. Here, we briefly describe the nature of the experimental system, its history, and a basic protocol for using the system. Alternative approaches involving co-transfections, concurrent drug treatments, and analysis of co-localizing histone modifications are also addressed, which are useful for extending basic findings to physiological mechanisms.
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Affiliation(s)
- Sherry L Winter
- Molecular Oncology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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72
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Mouse cofactor of BRCA1 (Cobra1) is required for early embryogenesis. PLoS One 2009; 4:e5034. [PMID: 19340312 PMCID: PMC2661135 DOI: 10.1371/journal.pone.0005034] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Accepted: 02/26/2009] [Indexed: 11/19/2022] Open
Abstract
Background Negative elongation factor (NELF) is a four-subunit protein complex conserved from Drosophila to humans. In vitro biochemical and tissue culture-based studies have demonstrated an important role of NELF in controlling RNA polymerase II (Pol II) pausing in transcription. However, the physiological significance of NELF function is not clear due to the lack of any genetic systems for studying NELF. Principal Findings Here we show that disruption of the mouse B subunit of NELF (NELF-B), also known as cofactor of BRCA1 (Cobra1), causes inner cell mass (ICM) deficiency and embryonic lethality at the time of implantation. Consistent with the phenotype of the Cobra1 knockout (KO) embryos, knockdown of Cobra1 in mouse embryonic stem cells (ESCs) reduces the efficiency of colony formation and increases spontaneous differentiation. Cobra1-depleted ESCs maintain normal levels of Oct4, Nanog, and Sox2, master regulators of pluripotency in ESCs. However, knockdown of Cobra1 leads to precocious expression of developmental regulators including lymphoid enhancer-binding factor 1 (Lef1). Chromatin immunoprecipitation (ChIP) indicates that Cobra1 binds to the Lef1 promoter and modulates the abundance of promoter-bound RNA polymerase. Conclusions Cobra1 is essential for early embryogenesis. Our findings also indicate that Cobra1 helps maintain the undifferentiated state of mESCs by preventing unscheduled expression of developmental genes.
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73
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Wang Y, Ji P, Liu J, Broaddus RR, Xue F, Zhang W. Centrosome-associated regulators of the G(2)/M checkpoint as targets for cancer therapy. Mol Cancer 2009; 8:8. [PMID: 19216791 PMCID: PMC2657106 DOI: 10.1186/1476-4598-8-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 02/13/2009] [Indexed: 01/04/2023] Open
Abstract
In eukaryotic cells, control mechanisms have developed that restrain cell-cycle transitions in response to stress. These regulatory pathways are termed cell-cycle checkpoints. The G(2)/M checkpoint prevents cells from entering mitosis when DNA is damaged in order to afford these cells an opportunity to repair the damaged DNA before propagating genetic defects to the daughter cells. If the damage is irreparable, checkpoint signaling might activate pathways that lead to apoptosis. Since alteration of cell-cycle control is a hallmark of tumorigenesis, cell-cycle regulators represent potential targets for therapy. The centrosome has recently come into focus as a critical cellular organelle that integrates G(2)/M checkpoint control and repairs signals in response to DNA damage. A growing number of G(2)/M checkpoint regulators have been found in the centrosome, suggesting that centrosome has an important role in G(2)/M checkpoint function. In this review, we discuss centrosome-associated regulators of the G(2)/M checkpoint, the dysregulation of this checkpoint in cancer, and potential candidate targets for cancer therapy.
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Affiliation(s)
- Yingmei Wang
- Tianjin General Hospital, Tianjin Medical University, Tianjin, PR China.
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74
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Reguart N, Cardona AF, Carrasco E, Gomez P, Taron M, Rosell R. BRCA1: A New Genomic Marker for Non–Small-Cell Lung Cancer. Clin Lung Cancer 2008; 9:331-9. [PMID: 19073515 DOI: 10.3816/clc.2008.n.048] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Noemí Reguart
- Medical Oncology Service, Catalan Institute of Oncology, ICO, Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
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75
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Gilchrist DA, Nechaev S, Lee C, Ghosh SKB, Collins JB, Li L, Gilmour DS, Adelman K. NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly. Genes Dev 2008; 22:1921-33. [PMID: 18628398 DOI: 10.1101/gad.1643208] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Negative Elongation Factor (NELF) is a transcription regulatory complex that induces stalling of RNA polymerase II (Pol II) during early transcription elongation and represses expression of several genes studied to date, including Drosophila Hsp70, mammalian proto-oncogene junB, and HIV RNA. To determine the full spectrum of NELF target genes in Drosophila, we performed a microarray analysis of S2 cells depleted of NELF and discovered that NELF RNAi affects many rapidly inducible genes involved in cellular responses to stimuli. Surprisingly, only one-third of NELF target genes were, like Hsp70, up-regulated by NELF-depletion, whereas the majority of target genes showed decreased expression levels upon NELF RNAi. Our data reveal that the presence of stalled Pol II at this latter group of genes enhances gene expression by maintaining a permissive chromatin architecture around the promoter-proximal region, and that loss of Pol II stalling at these promoters is accompanied by a significant increase in nucleosome occupancy and a decrease in histone H3 Lys 4 trimethylation. These findings identify a novel, positive role for stalled Pol II in regulating gene expression and suggest that there is a dynamic interplay between stalled Pol II and chromatin structure.
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Affiliation(s)
- Daniel A Gilchrist
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
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76
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Sun J, Watkins G, Blair AL, Moskaluk C, Ghosh S, Jiang WG, Li R. Deregulation of cofactor of BRCA1 expression in breast cancer cells. J Cell Biochem 2008; 103:1798-807. [PMID: 17910036 PMCID: PMC8822876 DOI: 10.1002/jcb.21568] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cofactor of BRCA1 (COBRA1) is an integral component of the human negative elongation factor (NELF), a four-subunit protein complex that inhibits transcription elongation. Previous in vivo work indicates that COBRA1 and the rest of the NELF complex repress estrogen-dependent transcription and the growth of breast cancer cells. In light of the COBRA1 function in breast cancer-related gene expression, we sought to examine regulation of COBRA1 expression in both established breast cancer cell lines and breast carcinoma tissues. We found that COBRA1 expression was inversely correlated with breast cancer progression, as tumor samples of patients who had distant metastasis and local recurrence expressed very low levels of COBRA1 mRNA when compared to those who were disease free for over 10 years (P = 0.0065 and 0.0081, respectively). Using both breast and prostate cancer cell lines, we also explored the possible mechanisms by which COBRA1 expression is regulated. Our results indicate that the protein abundance of COBRA1 and the other NELF subunits are mutually influenced in a tightly coordinated fashion. Small interfering RNA (siRNA) that targeted at one NELF subunit dampened the protein levels of all four subunits. Conversely, ectopic expression of COBRA1 in the knockdown cells partially rescues the co-depletion of the NELF subunits. In addition, our study suggests that a post-transcriptional, proteasome-independent mechanism is involved in the interdependent regulation of the NELF abundance. Furthermore, a lack of COBRA1 expression in breast carcinoma may serve as a useful indicator for poor prognosis.
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Affiliation(s)
- Jianlong Sun
- Department of Molecular Medicine, Institute of Biotechnology, 15355 Lambda Drive, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245
| | - Gareth Watkins
- Metastasis and Angiogenesis Research Group, University Department of Surgery, School of Medicine Cardiff University, Cardiff, UK
| | - Ashley L. Blair
- Department of Biochemistry and Molecular Genetics, School of Medicine, P.O. Box 800733, University of Virginia, Charlottesville, Virginia 22908-0733
| | - Christopher Moskaluk
- Department of Pathology, School of Medicine, P.O. Box 800733, University of Virginia, Charlottesville, Virginia 22908-0733
| | - Sagar Ghosh
- Department of Molecular Medicine, Institute of Biotechnology, 15355 Lambda Drive, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245
| | - Wen G. Jiang
- Metastasis and Angiogenesis Research Group, University Department of Surgery, School of Medicine Cardiff University, Cardiff, UK
| | - Rong Li
- Department of Molecular Medicine, Institute of Biotechnology, 15355 Lambda Drive, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245
- Correspondence to: Rong Li, Department of Molecular Medicine, Institute of Biotechnology, 15355 Lambda Drive, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245.
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77
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Evidence for a structural relationship between BRCT domains and the helicase domains of the replication initiators encoded by the Polyomaviridae and Papillomaviridae families of DNA tumor viruses. J Virol 2008; 82:8849-62. [PMID: 18579587 DOI: 10.1128/jvi.00553-08] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Studies of DNA tumor viruses have provided important insights into fundamental cellular processes and oncogenic transformation. They have revealed, for example, that upon expression of virally encoded proteins, cellular pathways involved in DNA repair and cell cycle control are disrupted. Herein, evidence is presented that BRCT-related regions are present in the helicase domains of the viral initiators encoded by the Polyomaviridae and Papillomaviridae viral families. Of interest, BRCT domains in cellular proteins recruit factors involved in diverse pathways, including DNA repair and the regulation of cell cycle progression. Therefore, the viral BRCT-related regions may compete with host BRCT domains for particular cellular ligands, a process that would help to explain the pleiotropic effects associated with infections with many DNA tumor viruses.
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78
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Bennett CB, Westmoreland TJ, Verrier CS, Blanchette CAB, Sabin TL, Phatnani HP, Mishina YV, Huper G, Selim AL, Madison ER, Bailey DD, Falae AI, Galli A, Olson JA, Greenleaf AL, Marks JR. Yeast screens identify the RNA polymerase II CTD and SPT5 as relevant targets of BRCA1 interaction. PLoS One 2008; 3:e1448. [PMID: 18197258 PMCID: PMC2174531 DOI: 10.1371/journal.pone.0001448] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 12/13/2007] [Indexed: 11/30/2022] Open
Abstract
BRCA1 has been implicated in numerous DNA repair pathways that maintain genome integrity, however the function responsible for its tumor suppressor activity in breast cancer remains obscure. To identify the most highly conserved of the many BRCA1 functions, we screened the evolutionarily distant eukaryote Saccharomyces cerevisiae for mutants that suppressed the G1 checkpoint arrest and lethality induced following heterologous BRCA1 expression. A genome-wide screen in the diploid deletion collection combined with a screen of ionizing radiation sensitive gene deletions identified mutants that permit growth in the presence of BRCA1. These genes delineate a metabolic mRNA pathway that temporally links transcription elongation (SPT4, SPT5, CTK1, DEF1) to nucleopore-mediated mRNA export (ASM4, MLP1, MLP2, NUP2, NUP53, NUP120, NUP133, NUP170, NUP188, POM34) and cytoplasmic mRNA decay at P-bodies (CCR4, DHH1). Strikingly, BRCA1 interacted with the phosphorylated RNA polymerase II (RNAPII) carboxy terminal domain (P-CTD), phosphorylated in the pattern specified by the CTDK-I kinase, to induce DEF1-dependent cleavage and accumulation of a RNAPII fragment containing the P-CTD. Significantly, breast cancer associated BRCT domain defects in BRCA1 that suppressed P-CTD cleavage and lethality in yeast also suppressed the physical interaction of BRCA1 with human SPT5 in breast epithelial cells, thus confirming SPT5 as a relevant target of BRCA1 interaction. Furthermore, enhanced P-CTD cleavage was observed in both yeast and human breast cells following UV-irradiation indicating a conserved eukaryotic damage response. Moreover, P-CTD cleavage in breast epithelial cells was BRCA1-dependent since damage-induced P-CTD cleavage was only observed in the mutant BRCA1 cell line HCC1937 following ectopic expression of wild type BRCA1. Finally, BRCA1, SPT5 and hyperphosphorylated RPB1 form a complex that was rapidly degraded following MMS treatment in wild type but not BRCA1 mutant breast cells. These results extend the mechanistic links between BRCA1 and transcriptional consequences in response to DNA damage and suggest an important role for RNAPII P-CTD cleavage in BRCA1-mediated cancer suppression.
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Affiliation(s)
- Craig B Bennett
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America.
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79
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Aiyar SE, Cho H, Lee J, Li R. Concerted transcriptional regulation by BRCA1 and COBRA1 in breast cancer cells. Int J Biol Sci 2007; 3:486-92. [PMID: 18071589 PMCID: PMC2096739 DOI: 10.7150/ijbs.3.486] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 11/22/2007] [Indexed: 12/17/2022] Open
Abstract
Cofactor of BRCA1 (COBRA1) was first identified as a protein that binds to the breast cancer susceptibility gene product BRCA1. COBRA1 modulates estrogen-dependent and independent transcription and suppresses the growth of breast cancer cells. Its expression is significantly reduced in metastatic and recurrent breast cancer, pointing to a tumor suppressor function in breast cancer development. In light of these initial implications of COBRA1 in human breast cancer, the current investigation sought to obtain more direct functional evidence that links COBRA1 with BRCA1 in transcriptional regulation in breast cancer cells. Small hairpin RNA (shRNA)-mediated gene knockdown and gene expression microarray were used to study the impact of COBRA1 and BRCA1 on global transcription in the same breast cancer cell background. The gene expression profiling study in tissue culture cells uncovers a significant overlap of COBRA1- and BRCA1-regulated genes, many of which have been previously implicated in breast cancer progression. The data shown herein support the notion that COBRA1 and BRCA1 may engage in common gene regulatory pathways to suppress breast cancer progression.
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Affiliation(s)
- Sarah E Aiyar
- 1. Department of Biochemistry, Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
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80
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Sun J, Blair AL, Aiyar SE, Li R. Cofactor of BRCA1 modulates androgen-dependent transcription and alternative splicing. J Steroid Biochem Mol Biol 2007; 107:131-9. [PMID: 17659869 PMCID: PMC2701476 DOI: 10.1016/j.jsbmb.2007.05.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
Transcriptional activity of nuclear receptors (NRs) is influenced by a large number of coregulators that exert their actions predominantly at the transcription initiation step. Unlike most well-characterized NR coregulators, cofactor of BRCA1 (COBRA1), a subunit of the negative elongation factor (NELF), binds to estrogen receptor alpha (ERalpha) and modulates estrogen-dependent transcription by impeding the movement of RNA polymerase II (RNAPII) during the transcription elongation stage. Here we show that, in addition to ERalpha, COBRA1 also displays various degrees of affinity for several other NRs. In particular, COBRA1 binds strongly to androgen receptor (AR) via its ligand-binding domain (LBD). Small hairpin RNA (shRNA)-mediated reduction of endogenous COBRA1 enhances androgen-mediated transcription. The effect of COBRA1 knockdown can be rescued by a silent mutant COBRA1 that is refractory to the shRNA action. Using a reporter assay for alternative splicing, we also provide evidence for a role of COBRA1 in influencing the exon skipping/inclusion of nascent transcripts produced from an androgen-dependent promoter. These findings suggest that COBRA1 may coordinate multiple steps in ligand-dependent gene expression, which in turn ensures both the quantity and quality of hormone-stimulated gene products.
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Affiliation(s)
- Jianlong Sun
- Department of Molecular Medicine, Institute of Biotechnology, 15355 Lambda Drive, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245
| | - Ashley L. Blair
- Department of Biochemistry and Molecular Genetics, School of Medicine, P.O. Box 800733, University of Virginia, Charlottesville, VA 22908-0733
| | - Sarah E. Aiyar
- Department of Biochemistry and Molecular Genetics, School of Medicine, P.O. Box 800733, University of Virginia, Charlottesville, VA 22908-0733
| | - Rong Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, P.O. Box 800733, University of Virginia, Charlottesville, VA 22908-0733
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81
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Pageau GJ, Hall LL, Ganesan S, Livingston DM, Lawrence JB. The disappearing Barr body in breast and ovarian cancers. Nat Rev Cancer 2007; 7:628-33. [PMID: 17611545 DOI: 10.1038/nrc2172] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interest has recently reawakened in whether loss of the heterochromatic X chromosome (Barr body) is prevalent in certain breast and ovarian cancers, and new insights into the mechanisms involved have emerged. Mitotic segregation errors commonly explain the loss of the inactive X chromosome (Xi), but compromise of Xi heterochromatin in some cancers may signal broader deficits of nuclear heterochromatin. The debated link between BRCA1 and Xi might reflect a general relationship between BRCA1 and heterochromatin, which could connect BRCA1 to both epigenetic and genetic instability. We suggest that heterochromatic instability is a common but largely unexplored mechanism, leading to widespread genomic misregulation and the evolution of some cancers.
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Affiliation(s)
- Gayle J Pageau
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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82
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Narita T, Yung TMC, Yamamoto J, Tsuboi Y, Tanabe H, Tanaka K, Yamaguchi Y, Handa H. NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs. Mol Cell 2007; 26:349-65. [PMID: 17499042 DOI: 10.1016/j.molcel.2007.04.011] [Citation(s) in RCA: 176] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2006] [Revised: 03/12/2007] [Accepted: 04/10/2007] [Indexed: 11/22/2022]
Abstract
Negative elongation factor (NELF) is a four subunit transcription elongation factor that has been implicated in numerous diseases ranging from neurological disorders to cancer. Here we show that NELF interacts with the nuclear cap binding complex (CBC), a multifunctional factor that plays important roles in several mRNA processing steps, and the two factors together participate in the 3' end processing of replication-dependent histone mRNAs, most likely through association with the histone stem-loop binding protein (SLBP). Strikingly, absence of NELF and CBC causes aberrant production of polyadenylated histone mRNAs. Moreover, NELF is physically associated with histone gene loci and forms distinct intranuclear foci that we call NELF bodies, which often overlap with Cajal bodies and cleavage bodies. Our results point to a surprising role of NELF in the 3' end processing of histone mRNAs and also suggest that NELF is a new factor that coordinates different mRNA processing steps during transcription.
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Affiliation(s)
- Takashi Narita
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa 226-8501, Japan
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83
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Auboeuf D, Batsché E, Dutertre M, Muchardt C, O'Malley BW. Coregulators: transducing signal from transcription to alternative splicing. Trends Endocrinol Metab 2007; 18:122-9. [PMID: 17320409 DOI: 10.1016/j.tem.2007.02.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 01/10/2007] [Accepted: 02/08/2007] [Indexed: 01/07/2023]
Abstract
Cells respond to many external stimuli by modulating gene expression. A key step in this regulation is the control of transcription, which determines the concentrations of pre-mRNA that are produced. A second level of control involves maturation of pre-mRNAs; many are alternatively spliced, which changes the exon content of transcripts and therefore the 'message' of the genes. Recent data indicate that the two control levels are linked. Here, we describe how transcriptional regulators and coregulators influence alternative splicing, with a focus on genes that are controlled by steroid hormones. Recent technical advances that help to elucidate the impact of stimuli on the exon content of regulated gene transcripts are also discussed.
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Affiliation(s)
- Didier Auboeuf
- INSERM, U685/AVENIR, Centre G. Hayem, Hôpital Saint Louis, 1 Avenue Claude Vellefaux, 75010 Paris, France.
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84
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Klokk TI, Kurys P, Elbi C, Nagaich AK, Hendarwanto A, Slagsvold T, Chang CY, Hager GL, Saatcioglu F. Ligand-specific dynamics of the androgen receptor at its response element in living cells. Mol Cell Biol 2007; 27:1823-43. [PMID: 17189428 PMCID: PMC1820481 DOI: 10.1128/mcb.01297-06] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/24/2006] [Accepted: 12/08/2006] [Indexed: 12/29/2022] Open
Abstract
Androgens have key roles in normal physiology and in male sexual differentiation as well as in pathological conditions such as prostate cancer. Androgens act through the androgen receptor (AR), which is a ligand-modulated transcription factor. Antiandrogens block AR function and are widely used in disease states, but little is known about their mechanism of action in vivo. Here, we describe a rapid differential interaction of AR with target genomic sites in living cells in the presence of agonists which coincides with the recruitment of BRM ATPase complex and chromatin remodeling, resulting in transcriptional activation. In contrast, the interaction of antagonist-bound or mutant AR with its target was found to be kinetically different: it was dramatically faster, occurred without chromatin remodeling, and resulted in the lack of transcriptional inhibition. Fluorescent resonance energy transfer analysis of wild-type AR and a transcriptionally compromised mutant at the hormone response element showed that intramolecular interactions between the N and C termini of AR play a key functional role in vivo compared to intermolecular interactions between two neighboring ARs. These data provide a kinetic and mechanistic basis for regulation of gene expression by androgens and antiandrogens in living cells.
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MESH Headings
- Adenocarcinoma/pathology
- Androgen Antagonists/pharmacology
- Androgens/pharmacology
- Anilides/pharmacology
- Animals
- Cell Line, Tumor
- Chromatin Assembly and Disassembly
- Cyproterone Acetate/pharmacology
- Dihydrotestosterone/pharmacology
- Female
- Fluorescence Recovery After Photobleaching
- Flutamide/analogs & derivatives
- Flutamide/pharmacology
- Genes, Reporter
- Green Fluorescent Proteins/metabolism
- In Situ Hybridization, Fluorescence
- Ligands
- Luciferases/metabolism
- Mammary Neoplasms, Animal/pathology
- Mammary Tumor Virus, Mouse/genetics
- Metribolone/pharmacology
- Mice
- Microscopy, Video
- Mifepristone/pharmacology
- Models, Biological
- Nitriles/pharmacology
- Plasmids
- Promoter Regions, Genetic
- Receptors, Androgen/drug effects
- Receptors, Androgen/metabolism
- Response Elements/physiology
- Testosterone/pharmacology
- Tosyl Compounds/pharmacology
- Transcription, Genetic
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Affiliation(s)
- Tove I Klokk
- Department of Molecular Biosciences, University of Oslo, Postboks 1041 Blindern, 0316 Oslo, Norway
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85
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Abstract
The nuclear envelope (NE) is composed of inner and outer nuclear membranes (INM and ONM, respectively), nuclear pore complexes and an underlying mesh like supportive structure--the lamina. It has long been known that heterochromatin clusters at the nuclear periphery adjacent to the nuclear lamina, hinting that proteins of the lamina may participate in regulation of gene expression. Recent studies on the molecular mechanisms involved show that proteins of the nuclear envelope participate in regulation of transcription on several levels, from direct binding to transcription factors to induction of epigenetic histone modifications. Three INM proteins; lamin B receptor, lamina-associated polypeptide 2beta and emerin, were shown to bind chromatin modifiers and/or transcriptional repressors inducing, at least in one case, histone deacetylation. Emerin and another INM protein, MAN1, have been linked to down-regulation of specific signaling pathways, the retino blastoma 1/E2F MyoD and transforming growth factor beta/bone morphogenic protein, respectively. Therefore, cumulative data suggests that proteins of the nuclear lamina regulate transcription by recruiting chromatin modifiers and transcription factors to the nuclear periphery. In this minireview we describe the recent literature concerning mechanisms of gene repression by proteins of the NE and suggest the hypothesis that the epigenetic "histone code", dictating transcriptional repression, is "written" in part, at the NE by its proteins. Finally, as aberrant gene expression is one of the mechanisms speculated to underlie the newly discovered group of genetic diseases termed nuclear envelopathies/laminopathies, elucidating the repressive role of NE proteins is a major challenge to both researchers and clinicians.
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Affiliation(s)
- Sigal Shaklai
- Sheba Cancer Research Center and the Institute of Hematology, The Chaim Sheba Medical Center, Tel Hashomer and the Sackler School of Medicine, Tel Aviv University, Israel
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86
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Karchin R, Monteiro ANA, Tavtigian SV, Carvalho MA, Sali A. Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol 2006; 3:e26. [PMID: 17305420 PMCID: PMC1797820 DOI: 10.1371/journal.pcbi.0030026] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 12/27/2006] [Indexed: 11/19/2022] Open
Abstract
Many individuals tested for inherited cancer susceptibility at the BRCA1 gene locus are discovered to have variants of unknown clinical significance (UCVs). Most UCVs cause a single amino acid residue (missense) change in the BRCA1 protein. They can be biochemically assayed, but such evaluations are time-consuming and labor-intensive. Computational methods that classify and suggest explanations for UCV impact on protein function can complement functional tests. Here we describe a supervised learning approach to classification of BRCA1 UCVs. Using a novel combination of 16 predictive features, the algorithms were applied to retrospectively classify the impact of 36 BRCA1 C-terminal (BRCT) domain UCVs biochemically assayed to measure transactivation function and to blindly classify 54 documented UCVs. Majority vote of three supervised learning algorithms is in agreement with the assay for more than 94% of the UCVs. Two UCVs found deleterious by both the assay and the classifiers reveal a previously uncharacterized putative binding site. Clinicians may soon be able to use computational classifiers such as those described here to better inform patients. These classifiers can be adapted to other cancer susceptibility genes and systematically applied to prioritize the growing number of potential causative loci and variants found by large-scale disease association studies.
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Affiliation(s)
- Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute of Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail: (RK); (AS)
| | - Alvaro N. A Monteiro
- Risk Assessment, Detection, and Intervention Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | | | - Marcelo A Carvalho
- Risk Assessment, Detection, and Intervention Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, United States of America
| | - Andrej Sali
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail: (RK); (AS)
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87
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Wright R, Dornan E, Donaldson M, Morgan I. TopBP1 contains a transcriptional activation domain suppressed by two adjacent BRCT domains. Biochem J 2006; 400:573-82. [PMID: 16984230 PMCID: PMC1698607 DOI: 10.1042/bj20060831] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TopBP1 has eight BRCT [BRCA1 (breast-cancer susceptibility gene 1) C-terminus] domains and is involved in initiating DNA replication, and DNA damage checkpoint signalling and repair. Several BRCT-domain-containing proteins involved in mediating DNA repair have transcriptional regulatory domains, and as demonstrated for BRCA1 these regulatory domains are important in mediating the functions of these proteins. These transcriptional regulatory processes involve modification of chromatin, and recent evidence has clearly demonstrated that the ability to modify chromatin plays an important role in regulating DNA damage signalling and repair. Here we report the identification of a TopBP1 transcriptional activation domain that is rich in hydrophobic residues, interspersed with acidic amino acids, characteristics that are typical of transcriptional activation domains identified previously. Two adjacent repressor domains encoded by BRCT2 and BRCT5 silence this activator and experiments suggest that these repressors actively recruit repressor complexes. Both the activator and BRCT2 repressor domains function in yeast. The present study identifies several chromatin modification domains encoded by TopBP1, and the implications of these findings are discussed in the context of the DNA damage response and the understanding of TopBP1 function.
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Affiliation(s)
- Roni H. G. Wright
- Institute of Comparative Medicine, Division of Pathological Sciences, University of Glasgow Faculty of Veterinary Medicine, Garscube Estate, Switchback Road, Glasgow G61 1QH, Scotland U.K
| | - Edward S. Dornan
- Institute of Comparative Medicine, Division of Pathological Sciences, University of Glasgow Faculty of Veterinary Medicine, Garscube Estate, Switchback Road, Glasgow G61 1QH, Scotland U.K
| | - Mary M. Donaldson
- Institute of Comparative Medicine, Division of Pathological Sciences, University of Glasgow Faculty of Veterinary Medicine, Garscube Estate, Switchback Road, Glasgow G61 1QH, Scotland U.K
| | - Iain M. Morgan
- Institute of Comparative Medicine, Division of Pathological Sciences, University of Glasgow Faculty of Veterinary Medicine, Garscube Estate, Switchback Road, Glasgow G61 1QH, Scotland U.K
- To whom correspondence should be addressed (email )
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88
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Sun Y, Ding L, Zhang H, Han J, Yang X, Yan J, Zhu Y, Li J, Song H, Ye Q. Potentiation of Smad-mediated transcriptional activation by the RNA-binding protein RBPMS. Nucleic Acids Res 2006; 34:6314-26. [PMID: 17099224 PMCID: PMC1669761 DOI: 10.1093/nar/gkl914] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 10/15/2006] [Accepted: 10/16/2006] [Indexed: 11/25/2022] Open
Abstract
Smad2, Smad3 and Smad4 proteins are considered to be key mediators of transforming growth factor-beta (TGF-beta) signaling. However, the identities of the Smad partners mediating TGF-beta signaling are not fully understood. Here, we show that RNA-binding protein with multiple splicing (RBPMS), a member of the RNA-binding protein family, physically interacts with Smad2, Smad3 and Smad4 both in vitro and in vivo. The presence of TGF-beta increases the binding of RBPMS with these Smad proteins. Consistent with the binding results, overexpression of RBPMS enhances Smad-dependent transcriptional activity in a TGF-beta-dependent manner, whereas knockdown of RBPMS decreases this activity. RBPMS interacts with TGF-beta receptor type I (TbetaR-I), increases phosphorylation of C-terminal SSXS regions in Smad2 and Smad3, and promotes the nuclear accumulation of the Smad proteins. Moreover, RBPMS fails to enhance the transcriptional activity of Smad2 and Smad3 that lack the C-terminal phosphorylation sites. Our data provide the first evidence for an RNA-binding protein playing a role in regulation of Smad-mediated transcriptional activity and suggest that RBPMS stimulates Smad-mediated transactivation possibly through enhanced phosphorylation of Smad2 and Smad3 at the C-terminus and promotion of the nuclear accumulation of the Smad proteins.
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Affiliation(s)
- Yan Sun
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Lihua Ding
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Hao Zhang
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Juqiang Han
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Xiao Yang
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Jinghua Yan
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Yunfeng Zhu
- The 307 Hospital, Beijing 100071People's Republic of China
| | - Jiezhi Li
- Beijing Institute of Biotechnology, Beijing 100850People's Republic of China
- The 307 Hospital, Beijing 100071People's Republic of China
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Haifeng Song
- Beijing Institute of Radiation Medicine, Beijing 100850People's Republic of China
| | - Qinong Ye
- To whom correspondence should be addressed. Tel: +8610 6818 0809; Fax: +8610 6824 8045;
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89
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Mullan PB, Quinn JE, Harkin DP. The role of BRCA1 in transcriptional regulation and cell cycle control. Oncogene 2006; 25:5854-63. [PMID: 16998500 DOI: 10.1038/sj.onc.1209872] [Citation(s) in RCA: 223] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The exact functions of BRCA1 have not been fully described but it now seems apparent that it has roles in DNA damage repair, transcriptional regulation, cell cycle control and most recently in ubiquitylation. These functions of BRCA1 are most likely interdependent but this review will focus on the role of BRCA1 in relation to transcriptional regulation and in particular how this impacts upon cell cycle control. We will (i) describe the structure of BRCA1 and how it may contribute to its transcription function; (ii) describe the interaction of BRCA1 with the core transcriptional machinery (RNA polII); (iii) describe how BRCA1 may regulate transcription at an epigenetic level through chromatin modification; (iv) discuss the role of BRCA1 in modulating transcription through its association with sequence-specific transcription factors. Finally, we will discuss the possible effects of BRCA1 transcriptional regulation on downstream targets with known roles in cell cycle control.
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Affiliation(s)
- P B Mullan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Lisburn Road Belfast, Northern Ireland, UK
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90
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Aiyar SE, Blair AL, Hopkinson DA, Bekiranov S, Li R. Regulation of clustered gene expression by cofactor of BRCA1 (COBRA1) in breast cancer cells. Oncogene 2006; 26:2543-53. [PMID: 17043641 DOI: 10.1038/sj.onc.1210047] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eucaryotic genes that are coordinately expressed tend to be clustered. Furthermore, gene clusters across chromosomal regions are often upregulated in various tumors. However, relatively little is known about how gene clusters are coordinately expressed in physiological or pathological conditions. Cofactor of BRCA1 (COBRA1), a subunit of the human negative elongation factor, has been shown to repress estrogen-stimulated transcription of trefoil factor 1 (TFF1 or pS2) by stalling RNA polymerase II. Here, we carried out a genome-wide study to identify additional physiological target genes of COBRA1 in breast cancer cells. The study identified a total of 134 genes that were either activated or repressed upon small hairpin RNA-mediated reduction of COBRA1. Interestingly, many COBRA1-regulated genes reside as clusters on the chromosomes and have been previously implicated in cancer development. Detailed examination of two such clusters on chromosome 21 (21q22) and chromosome X (Xp11) reveals that COBRA1 is physically associated with a subset of its regulated genes in each cluster. In addition, COBRA1 was shown to regulate both estrogen-dependent and -independent transcription of the gene cluster at 21q22, which encompasses the previously identified COBRA1-regulated TFF1 (pS2) locus. Thus, COBRA1 plays a critical role in the regulation of clustered gene expression at preferred chromosomal domains in breast cancer cells.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Chromatin Immunoprecipitation
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, X/genetics
- Gene Expression Regulation, Neoplastic
- Genome, Human
- Humans
- Immunoblotting
- Multigene Family
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Oligonucleotide Array Sequence Analysis
- RNA Polymerase II/genetics
- RNA Polymerase II/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/pharmacology
- Receptors, Estrogen
- Reverse Transcriptase Polymerase Chain Reaction
- Transcription Factors
- Transcription, Genetic
- Trefoil Factor-1
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- S E Aiyar
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA, USA
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91
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Feng X, Bonni S, Riabowol K. HSP70 induction by ING proteins sensitizes cells to tumor necrosis factor alpha receptor-mediated apoptosis. Mol Cell Biol 2006; 26:9244-55. [PMID: 17030616 PMCID: PMC1698524 DOI: 10.1128/mcb.01538-06] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
ING proteins affect apoptosis, growth, and DNA repair by transducing stress signals such as DNA damage, binding histones, and subsequently regulating chromatin structure and p53 activity. p53 target genes, including the p21 cyclin-dependent kinase inhibitor and Bax, an inducer of apoptosis, are regulated by ING proteins. To identify additional targets downstream of p33ING1 and p32ING2, cDNA microarrays were performed on phenotypically normal human primary fibroblasts. The 0.36% of genes affected by ING proteins in primary fibroblasts were distinct from targets seen in established cells and included the HSP70 heat shock gene, whose promoter was specifically induced >10-fold. ING1-induced expression of HSP70 shifted cells from survival to a death pathway in response to tumor necrosis factor alpha (TNF-alpha), and p33ING1b protein showed synergy with TNF-alpha in inducing apoptosis, which correlated with reduced NF-kappaB-dependent transcription. These findings are consistent with previous reports that HSP70 promotes TNF-alpha-mediated apoptosis by binding I-kappaBeta kinase gamma and impairing NF-kappaB survival signaling. Induction of HSP70 required the amino terminus of ING1b but not the plant homeodomain region that was recently identified as a histone binding domain. Regulation of HSP70 gene expression by the ING tumor suppressors provides a novel link between the INGs and the stress-regulated NF-kappaB survival pathway important in hypoxia and angiogenesis.
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Affiliation(s)
- Xiaolan Feng
- Southern Alberta Cancer Research Institute, Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada T2N 4N1
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92
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Aida M, Chen Y, Nakajima K, Yamaguchi Y, Wada T, Handa H. Transcriptional pausing caused by NELF plays a dual role in regulating immediate-early expression of the junB gene. Mol Cell Biol 2006; 26:6094-104. [PMID: 16880520 PMCID: PMC1592793 DOI: 10.1128/mcb.02366-05] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole sensitivity-inducing factor (DSIF) and negative elongation factor (NELF) negatively regulate transcription elongation by RNA polymerase II (RNAPII) in vitro. However, the physiological roles of this negative regulation are not well understood. Here, by using a number of approaches to identify protein-DNA interactions in vivo, we show that DSIF- and NELF-mediated transcriptional pausing has a dual function in regulating immediate-early expression of the human junB gene. Before induction by interleukin-6, RNAPII, DSIF, and NELF accumulate in the promoter-proximal region of junB, mainly at around position +50 from the transcription initiation site. After induction, the association of these proteins with the promoter-proximal region continues whereas RNAPII and DSIF are also found in the downstream regions. Depletion of a subunit of NELF by RNA interference enhances the junB mRNA level both before and after induction, indicating that DSIF- and NELF-mediated pausing contributes to the negative regulation of junB expression, not only by inducing RNAPII pausing before induction but also by attenuating transcription after induction. These regulatory mechanisms appear to be conserved in other immediate-early genes as well.
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Affiliation(s)
- Masatoshi Aida
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8503, Japan
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93
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Ziv Y, Bielopolski D, Galanty Y, Lukas C, Taya Y, Schultz DC, Lukas J, Bekker-Jensen S, Bartek J, Shiloh Y. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat Cell Biol 2006; 8:870-6. [PMID: 16862143 DOI: 10.1038/ncb1446] [Citation(s) in RCA: 555] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2006] [Accepted: 07/04/2006] [Indexed: 12/13/2022]
Abstract
The cellular DNA-damage response is a signaling network that is vigorously activated by cytotoxic DNA lesions, such as double-strand breaks (DSBs). The DSB response is mobilized by the nuclear protein kinase ATM, which modulates this process by phosphorylating key players in these pathways. A long-standing question in this field is whether DSB formation affects chromatin condensation. Here, we show that DSB formation is followed by ATM-dependent chromatin relaxation. ATM's effector in this pathway is the protein KRAB-associated protein (KAP-1, also known as TIF1beta, KRIP-1 or TRIM28), previously known as a corepressor of gene transcription. In response to DSB induction, KAP-1 is phosphorylated in an ATM-dependent manner on Ser 824. KAP-1 is phosphorylated exclusively at the damage sites, from which phosphorylated KAP-1 spreads rapidly throughout the chromatin. Ablation of the phosphorylation site of KAP-1 leads to loss of DSB-induced chromatin decondensation and renders the cells hypersensitive to DSB-inducing agents. Knocking down KAP-1, or mimicking a constitutive phosphorylation of this protein, leads to constitutive chromatin relaxation. These results suggest that chromatin relaxation is a fundamental pathway in the DNA-damage response and identify its primary mediators.
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Affiliation(s)
- Yael Ziv
- The David and Inez Myers Laboratory for Genetic Research, Department of Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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94
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Han J, Ding L, Yuan B, Yang X, Wang X, Li J, Lu Q, Huang C, Ye Q. Hepatitis B virus X protein and the estrogen receptor variant lacking exon 5 inhibit estrogen receptor signaling in hepatoma cells. Nucleic Acids Res 2006; 34:3095-106. [PMID: 16757575 PMCID: PMC1475750 DOI: 10.1093/nar/gkl389] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Hepatitis B virus (HBV) X protein (HBx) is considered to play a role in the development of hepatocellular carcinoma (HCC) during HBV infection. HCC was shown to be more prevalent in men than in women. Estrogen, which exerts its biological function through estrogen receptor (ER), can inhibit HBV replication. ERDelta5, an ERalpha variant lacking exon 5, was found to be preferentially expressed in patients with HCC compared with patients with normal livers. Here, we report the biological role of ERDelta5 and a novel link between HBx and ERalpha signaling in hepatoma cells. ERDelta5 interacts with ERalpha in vitro and in vivo and functions as a dominant negative receptor. Both ERalpha and ERDelta5 associate with HBx. HBx decreases ERalpha-dependent transcriptional activity, and HBx and ERDelta5 have additive effect on suppression of ERalpha transactivation. The HBx deletion mutant that lacks the ERalpha-binding site abolishes the HBx repression of ERalpha. HBx, ERalpha and histone deacetylase 1 (HDAC1) form a ternary complex. Trichostatin A, a specific inhibitor of HDAC enzyme, can restore the transcriptional activity of ERalpha inhibited by HBx. Our data suggest that HBx and ERDelta5 may play a negative role in ERalpha signaling and that ERalpha agonists may be developed for HCC therapy.
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Affiliation(s)
| | | | | | | | | | | | - Qiujun Lu
- Beijing Institute of Radiation MedicineBeijing 100850, People's Republic of China
| | | | - Qinong Ye
- To whom correspondence should be addressed. Tel: +8610 6818 0809; Fax: +8610 6824 8045;
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95
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Kang HJ, Kim HJ, Kim SK, Barouki R, Cho CH, Khanna KK, Rosen EM, Bae I. BRCA1 Modulates Xenobiotic Stress-inducible Gene Expression by Interacting with ARNT in Human Breast Cancer Cells. J Biol Chem 2006; 281:14654-62. [PMID: 16567799 DOI: 10.1074/jbc.m601613200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Previously, we have reported that BRCA1 regulates the expression of various classes of genes, including genes involved in xenobiotic stress responses (Bae, I., Fan, S., Meng, Q., Rih, J. K., Kim, H. J., Kang, H. J., Xu, J., Goldberg, I. D., Jaiswal, A. K., and Rosen, E. M. (2004) Cancer Res. 64, 7893-7909). In the present study, we have investigated the effects of BRCA1 on xenobiotic stress-inducible gene expression. In response to aryl hydrocarbon receptor (AhR) ligands, cytoplasmic AhR becomes activated and then translocates to the nucleus where it forms a complex with the aryl hydrocarbon receptor nuclear translocator (ARNT). Subsequently, the AhR.ARNT complex binds to the enhancer or promoter of genes containing a xenobiotic stress-responsive element and regulates the expression of multiple target genes including cytochrome P450 subfamily polypeptide 1 (CYP1A1). In this study, we have found that endogenous and overexpressed exogenous wild-type BRCA1 affect xenobiotic stress-induced CYP1A1 gene expression. Using a standard chromatin immunoprecipitation assay, we have demonstrated that BRCA1 is recruited to the promoter regions of CYP1A1 and CYP1B1 along with ARNT and/or AhR following xenobiotic exposure. Our findings suggest that BRCA1 may be physiologically important for mounting a normal response to xenobiotic insults and that it may function as a coactivator for ARNT activity. Using immunoprecipitation, Western blotting, and glutathione S-transferase capture assays, a xenobiotic-independent interaction between BRCA1 and ARNT has been identified, although it is not yet known whether this is a direct or indirect interaction. We have also found that the inducibility of CYP1A1 and CYP1B1 transcripts following xenobiotic stress was significantly attenuated in BRCA1 knockdown cells. This reduced inducibility is associated with an altered stability of ARNT and was almost completely reversed in cells transfected with an ARNT expression vector. Finally, we have found that xenobiotic (TCDD) treatments of breast cancer cells containing reduced levels of BRCA1 cause the transcription factor ARNT to become unstable.
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Affiliation(s)
- Hyo Jin Kang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, 3970 Reservoir Road NW, Washington, DC 20057, USA
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96
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McChesney PA, Aiyar SE, Lee OJ, Zaika A, Moskaluk C, Li R, El-Rifai W. Cofactor of BRCA1: A Novel Transcription Factor Regulator in Upper Gastrointestinal Adenocarcinomas. Cancer Res 2006; 66:1346-53. [PMID: 16452188 DOI: 10.1158/0008-5472.can-05-3593] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cofactor of BRCA1 (COBRA1) is a newly characterized member of the negative elongation factor (NELF) complex. In this work, we show that COBRA1 is overexpressed in the majority of primary upper gastrointestinal adenocarcinomas (UGC), and its overexpression correlates with down-regulation of TFF1. We have detected overexpression of COBRA1 mRNA using quantitative real-time reverse transcription-PCR in 28 (79%) primary UGCs. Immunohistochemical analysis of UGC tissue arrays that contained 70 tumor samples showed moderate-strong staining for COBRA1 in 60 (84%) tumors. Interestingly, the tumor samples showed absent-weak staining for TFF1 in 45 (65%) of the tumors. Simultaneous loss of TFF1 expression and overexpression of COBRA1 was observed in 42 of 70 (60%) tumors. Using small interfering RNA technology with gastric cancer cells, we have shown that COBRA1 inhibition leads to increased TFF1 promoter activity and gene expression. Promoter analysis of TFF1 indicated that regulation of TFF1 by COBRA1 is estrogen independent in contrast to breast cancer. Moreover, COBRA1 regulation of TFF1 in gastric cancer cells was independent of NELF-E. Using several truncated mutants and site mutants of the TFF1 promoter, we have shown that COBRA1 can negatively regulate the activator protein-1 (AP-1) complex at the TFF1 promoter and thus down-regulate TFF1 expression in gastric cancer cell lines. Electrophoretic mobility shift assay showed that COBRA1 attenuates AP-1 binding to DNA. Our results suggest COBRA1 as a novel oncogene in UGCs that regulate AP-1 binding and the expression of TFF1 in upper gastric epithelia.
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Affiliation(s)
- Patricia A McChesney
- Department of Internal Medicine, University of Virginia, Charlottesville, VA, USA
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97
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Oishi H, Kitagawa H, Wada O, Takezawa S, Tora L, Kouzu-Fujita M, Takada I, Yano T, Yanagisawa J, Kato S. An hGCN5/TRRAP Histone Acetyltransferase Complex Co-activates BRCA1 Transactivation Function through Histone Modification. J Biol Chem 2006; 281:20-6. [PMID: 16260778 DOI: 10.1074/jbc.m510157200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It is well established that genetic mutations that impair BRCA1 function predispose women to early onset of breast and ovarian cancer. However, the co-regulatory factors that support normal BRCA1 functions remain to be identified. Using a biochemical approach to search for such co-regulatory factors, we identified hGCN5, TRRAP, and hMSH2/6 as BRCA1-interacting proteins. Genetic mutations in the C-terminal transactivation domain of BRCA1, as found in breast cancer patients (Chapman, M. S., and Verma, I. M. (1996) Nature 382, 678-679), caused the loss of physical interaction between BRCA1 and TRRAP and significantly reduced the co-activation of BRCA1 transactivation function by hGCN5/TRRAP. The reported transcriptional squelching between BRCA1 and estrogen receptor alpha (Fan, S., Wang, J., Yuan, R., Ma, Y., Meng, Q., Erdos, M. R., Pestell, R. G., Yuan, F., Auborn, K. J., Goldberg, I. D., and Rosen, E. M. (1999) Science 284, 1354-1356) was rescued by the overexpression of TRRAP or hGCN5. Histone acetyltransferase hGCN5 activity appeared to be indispensable for coregulator complex function in both BRCA1-mediated gene regulation and DNA repair. Biochemical purification of the hGCN5/TRRAP-containing complex suggested that hGCN5/TRRAP formed a complex with hMSH2/hMSH6, presumably as a novel subclass of hGCN5/TRRAP-containing known TFTC (TBP-free TAF-containing)-type histone acetyltransferase complex (hTFTC, hPCAF, and hSTAGA) (Yanagisawa, J., Kitagawa, H., Yanagida, M., Wada, O., Ogawa, S., Nakagomi, M., Oishi, H., Yamamoto, Y., Nagasawa, H., McMahon, S. B., Cole, M. D., Tora, L., Takahashi, N., and Kato, S. (2002) Mol. Cell 9, 553-562). Unlike other subclasses, the isolated complex harbored a previously unknown combination of components including hMSH2 and hMSH6, major components of the BRCA1 genome surveillance repair complex (BASC). Thus, our results suggested that the multiple BRCA1 functions require a novel hGCN5/TRRAP histone acetyltransferase complex subclass.
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Affiliation(s)
- Hajime Oishi
- Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan
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98
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Rajab NF, McKenna DJ, Diamond J, Williamson K, Hamilton PW, McKelvey-Martin VJ. Prediction of radiosensitivity in human bladder cell lines using nuclear chromatin phenotype. Cytometry A 2006; 69:1077-85. [PMID: 16924636 DOI: 10.1002/cyto.a.20329] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Nuclear texture analysis measures phenotypic changes in chromatin distribution within a cell nucleus, while the alkaline Comet assay is a sensitive method for measuring the extent of DNA breakage in individual cells. The authors aim to use both methods to provide information about the sensitivity of cells to ionizing radiation. METHODS The alkaline Comet assay was performed on six human bladder carcinoma cell lines and one human urothelial cell line exposed to gamma-radiation doses from 0 to 10 Gy. Nuclear chromatin texture analysis of 40 features was then performed in the same cell lines exposed to 0, 2, and 6 Gy to explore if nuclear phenotype was related to radiation sensitivity. RESULTS Comet assay results demonstrated that the cell lines exhibited different levels of radiosensitivity and could be divided into a radiosensitive and a radioresistant group at >6 Gy. Using stepwise discriminant analysis, a subset of important nuclear texture features that best discriminated between sensitive and resistant cell lines were identified A classification function, defined using these features, correctly classified 81.75% of all cells into their radiosensitive or radioresistant groups based on their pretreatment chromatin phenotype. Posttreatment chromatin changes also varied between cell lines, with sensitive cell lines showing a relaxed chromatin conformation following radiation, whereas resistant cell lines exhibited chromatin condensation. CONCLUSIONS The authors conclude that the alkaline Comet assay and nuclear texture methodologies may prove to be valuable aids in predicting the response of tumor cells to radiotherapy.
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Affiliation(s)
- Nor F Rajab
- Cancer and Ageing Research Group, School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, United Kingdom
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99
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Dapic V, Carvalho MA, Monteiro ANA. Breast cancer susceptibility and the DNA damage response. Cancer Control 2005; 12:127-36. [PMID: 15855896 DOI: 10.1177/107327480501200210] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Vesna Dapic
- Strang Cancer Prevention Center, New York, USA
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100
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Chadwick BP, Lane TF. BRCA1 associates with the inactive X chromosome in late S-phase, coupled with transient H2AX phosphorylation. Chromosoma 2005; 114:432-9. [PMID: 16240122 DOI: 10.1007/s00412-005-0029-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 09/05/2005] [Accepted: 09/12/2005] [Indexed: 10/25/2022]
Abstract
The BRCA1 tumor suppressor gene encodes an E3-ubiquitin ligase that has been implicated in several distinct biochemical processes. As the cell cycle progresses, BRCA1 proteins interact transiently with nuclear foci containing DNA replication and DNA double-strand repair machinery. A hallmark of these foci is the presence of S139 phosphorylated histone H2AX. BRCA1 was recently shown to associate with facultative heterochromatin at the inactive X chromosome (Xi), where it may play a role in maintaining gene silencing. As the kinetics of this interaction has not been described, we sought to establish whether association of BRCA1 with the Xi also correlated with replication. Here we demonstrate that the interaction of BRCA1 and the Xi is transient, occurring during late S-phase. This interaction is concomitant with the presence of distinct foci of S139 phospho-H2AX and specifically corresponds with late replication of the Xi. BRCA1 and phospho-H2AX appear on the Xi immediately adjacent to CAF-1, a known marker of replication fork activity. Taken together, these data implicate BRCA1 and the H2AX kinase in replication of facultative heterochromatin on the Xi, most likely in a fashion similar to that performed at sites of DNA replication and double-strand break repair observed on somatic chromosomes.
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Affiliation(s)
- Brian P Chadwick
- Department of Cell Biology, Duke University Medical Center & Institute for Genome Science and Policy, Durham, NC 27710, USA.
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