51
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Terme JM, Millán-Ariño L, Mayor R, Luque N, Izquierdo-Bouldstridge A, Bustillos A, Sampaio C, Canes J, Font I, Sima N, Sancho M, Torrente L, Forcales S, Roque A, Suau P, Jordan A. Dynamics and dispensability of variant-specific histone H1 Lys-26/Ser-27 and Thr-165 post-translational modifications. FEBS Lett 2014; 588:2353-62. [PMID: 24873882 DOI: 10.1016/j.febslet.2014.05.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 12/31/2022]
Abstract
In mammals, the linker histone H1, involved in DNA packaging into chromatin, is represented by a family of variants. H1 tails undergo post-translational modifications (PTMs) that can be detected by mass spectrometry. We developed antibodies to analyze several of these as yet unexplored PTMs including the combination of H1.4 K26 acetylation or trimethylation and S27 phosphorylation. H1.2-T165 phosphorylation was detected at S and G2/M phases of the cell cycle and was dispensable for chromatin binding and cell proliferation; while the H1.4-K26 residue was essential for proper cell cycle progression. We conclude that histone H1 PTMs are dynamic over the cell cycle and that the recognition of modified lysines may be affected by phosphorylation of adjacent residues.
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Affiliation(s)
- Jean-Michel Terme
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Millán-Ariño
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Regina Mayor
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Neus Luque
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | | | - Alberto Bustillos
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Sampaio
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Jordi Canes
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Isaura Font
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Núria Sima
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain
| | - Mónica Sancho
- Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Laura Torrente
- Institut de Medecina Predictiva i Personalitzada del Cancer, Badalona, Catalonia, Spain
| | - Sonia Forcales
- Institut de Medecina Predictiva i Personalitzada del Cancer, Badalona, Catalonia, Spain
| | - Alicia Roque
- Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pere Suau
- Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Albert Jordan
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Parc Científic de Barcelona, Barcelona, Catalonia, Spain.
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52
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Abstract
The nuclear receptor (NR) family comprises 48 transcription factors (TFs) with essential and diverse roles in development, metabolism and disease. Differently from other TFs, NRs engage with well-defined DNA-regulatory elements, mostly after ligand-induced structural changes. However, NR binding is not stochastic, and only a fraction of the cognate regulatory elements within the genome actively engage with NRs. In this review, we summarize recent advances in the understanding of the interactions between NRs and DNA. We discuss how chromatin accessibility and epigenetic modifications contribute to the recruitment and transactivation of NRs. Lastly, we present novel evidence of the interplay between non-coding RNA and NRs in the mediation of the assembly of the transcriptional machinery.
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Affiliation(s)
- Raffaella Maria Gadaleta
- Division of Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, W12 0NN, UK
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53
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Genome-wide activity of unliganded estrogen receptor-α in breast cancer cells. Proc Natl Acad Sci U S A 2014; 111:4892-7. [PMID: 24639548 DOI: 10.1073/pnas.1315445111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Estrogen receptor-α (ERα) has central role in hormone-dependent breast cancer and its ligand-induced functions have been extensively characterized. However, evidence exists that ERα has functions that are independent of ligands. In the present work, we investigated the binding of ERα to chromatin in the absence of ligands and its functions on gene regulation. We demonstrated that in MCF7 breast cancer cells unliganded ERα binds to more than 4,000 chromatin sites. Unexpectedly, although almost entirely comprised in the larger group of estrogen-induced binding sites, we found that unliganded-ERα binding is specifically linked to genes with developmental functions, compared with estrogen-induced binding. Moreover, we found that siRNA-mediated down-regulation of ERα in absence of estrogen is accompanied by changes in the expression levels of hundreds of coding and noncoding RNAs. Down-regulated mRNAs showed enrichment in genes related to epithelial cell growth and development. Stable ERα down-regulation using shRNA, which caused cell growth arrest, was accompanied by increased H3K27me3 at ERα binding sites. Finally, we found that FOXA1 and AP2γ binding to several sites is decreased upon ERα silencing, suggesting that unliganded ERα participates, together with other factors, in the maintenance of the luminal-specific cistrome in breast cancer cells.
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54
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Varga-Weisz PD. Chromatin remodeling: a collaborative effort. Nat Struct Mol Biol 2014; 21:14-6. [PMID: 24389547 DOI: 10.1038/nsmb.2748] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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55
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Millán-Ariño L, Islam ABMMK, Izquierdo-Bouldstridge A, Mayor R, Terme JM, Luque N, Sancho M, López-Bigas N, Jordan A. Mapping of six somatic linker histone H1 variants in human breast cancer cells uncovers specific features of H1.2. Nucleic Acids Res 2014; 42:4474-93. [PMID: 24476918 PMCID: PMC3985652 DOI: 10.1093/nar/gku079] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Seven linker histone H1 variants are present in human somatic cells with distinct prevalence across cell types. Despite being key structural components of chromatin, it is not known whether the different variants have specific roles in the regulation of nuclear processes or are differentially distributed throughout the genome. Using variant-specific antibodies to H1 and hemagglutinin (HA)-tagged recombinant H1 variants expressed in breast cancer cells, we have investigated the distribution of six H1 variants in promoters and genome-wide. H1 is depleted at promoters depending on its transcriptional status and differs between variants. Notably, H1.2 is less abundant than other variants at the transcription start sites of inactive genes, and promoters enriched in H1.2 are different from those enriched in other variants and tend to be repressed. Additionally, H1.2 is enriched at chromosomal domains characterized by low guanine–cytosine (GC) content and is associated with lamina-associated domains. Meanwhile, other variants are associated with higher GC content, CpG islands and gene-rich domains. For instance, H1.0 and H1X are enriched at gene-rich chromosomes, whereas H1.2 is depleted. In short, histone H1 is not uniformly distributed along the genome and there are differences between variants, H1.2 being the one showing the most specific pattern and strongest correlation with low gene expression.
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Affiliation(s)
- Lluís Millán-Ariño
- Department of Molecular Genomics, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, E-08028 Spain, Research Programme on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, E-08003 Spain, Department of Genetic Engineering, Biotechnology, University of Dhaka, Dhaka-1000, Bangladesh, Centro de Investigación Príncipe Felipe, Valencia, E-46012 Spain and Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, E-08010 Spain
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56
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Herz HM, Garruss A, Shilatifard A. SET for life: biochemical activities and biological functions of SET domain-containing proteins. Trends Biochem Sci 2013; 38:621-39. [PMID: 24148750 DOI: 10.1016/j.tibs.2013.09.004] [Citation(s) in RCA: 219] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/06/2013] [Accepted: 09/12/2013] [Indexed: 01/23/2023]
Affiliation(s)
- Hans-Martin Herz
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
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57
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Raghuram N, Strickfaden H, McDonald D, Williams K, Fang H, Mizzen C, Hayes JJ, Th'ng J, Hendzel MJ. Pin1 promotes histone H1 dephosphorylation and stabilizes its binding to chromatin. ACTA ACUST UNITED AC 2013; 203:57-71. [PMID: 24100296 PMCID: PMC3798258 DOI: 10.1083/jcb.201305159] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The prolyl isomerase Pin1 stimulates the dephosphorylation of histone H1, stabilizing its binding to chromatin at transcriptionally active chromatin. Histone H1 plays a crucial role in stabilizing higher order chromatin structure. Transcriptional activation, DNA replication, and chromosome condensation all require changes in chromatin structure and are correlated with the phosphorylation of histone H1. In this study, we describe a novel interaction between Pin1, a phosphorylation-specific prolyl isomerase, and phosphorylated histone H1. A sub-stoichiometric amount of Pin1 stimulated the dephosphorylation of H1 in vitro and modulated the structure of the C-terminal domain of H1 in a phosphorylation-dependent manner. Depletion of Pin1 destabilized H1 binding to chromatin only when Pin1 binding sites on H1 were present. Pin1 recruitment and localized histone H1 phosphorylation were associated with transcriptional activation independent of RNA polymerase II. We thus identify a novel form of histone H1 regulation through phosphorylation-dependent proline isomerization, which has consequences on overall H1 phosphorylation levels and the stability of H1 binding to chromatin.
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Affiliation(s)
- Nikhil Raghuram
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R7, Canada
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58
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Rangasamy S, D’Mello SR, Narayanan V. Epigenetics, autism spectrum, and neurodevelopmental disorders. Neurotherapeutics 2013; 10:742-56. [PMID: 24104594 PMCID: PMC3805864 DOI: 10.1007/s13311-013-0227-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Epigenetic marks are modifications of DNA and histones. They are considered to be permanent within a single cell during development, and are heritable across cell division. Programming of neurons through epigenetic mechanisms is believed to be critical in neural development. Disruption or alteration in this process causes an array of neurodevelopmental disorders, including autism spectrum disorders (ASDs). Recent studies have provided evidence for an altered epigenetic landscape in ASDs and demonstrated the central role of epigenetic mechanisms in their pathogenesis. Many of the genes linked to the ASDs encode proteins that are involved in transcriptional regulation and chromatin remodeling. In this review we highlight selected neurodevelopmental disorders in which epigenetic dysregulation plays an important role. These include Rett syndrome, fragile X syndrome, Prader-Willi syndrome, Angelman syndrome, and Kabuki syndrome. For each of these disorders, we discuss how advances in our understanding of epigenetic mechanisms may lead to novel therapeutic approaches.
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Affiliation(s)
- Sampathkumar Rangasamy
- />Developmental Neurogenetics Laboratory, Barrow Neurological Institute, Phoenix, AZ 85013 USA
| | | | - Vinodh Narayanan
- />Developmental Neurogenetics Laboratory, Barrow Neurological Institute, Phoenix, AZ 85013 USA
- />Developmental Neurogenetic Laboratory, Barrow Neurological Institute, Phoenix, AZ 85013 USA
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59
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Frantzi M, Zoidakis J, Papadopoulos T, Zürbig P, Katafigiotis I, Stravodimos K, Lazaris A, Giannopoulou I, Ploumidis A, Mischak H, Mullen W, Vlahou A. IMAC fractionation in combination with LC-MS reveals H2B and NIF-1 peptides as potential bladder cancer biomarkers. J Proteome Res 2013; 12:3969-79. [PMID: 23924207 DOI: 10.1021/pr400255h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Improvement in bladder cancer (BC) management requires more effective diagnosis and prognosis of disease recurrence and progression. Urinary biomarkers attract special interest because of the noninvasive means of urine collection. Proteomic analysis of urine entails the adoption of a fractionation methodology to reduce sample complexity. In this study, we applied immobilized metal affinity chromatography in combination with high-resolution LC-MS/MS for the discovery of native urinary peptides potentially associated with BC aggressiveness. This approach was employed toward urine samples from patients with invasive BC, noninvasive BC, and benign urogenital diseases. A total of 1845 peptides were identified, corresponding to a total of 638 precursor proteins. Specific enrichment for proteins involved in nucleosome assembly and for zinc-finger transcription factors was observed. The differential expression of two candidate biomarkers, histone H2B and NIF-1 (zinc finger 335) in BC, was verified in independent sets of urine samples by ELISA and by immunohistochemical analysis of BC tissue. The results collectively support changes in the expression of both of these proteins with tumor progression, suggesting their potential role as markers for discriminating BC stages. In addition, the data indicate a possible involvement of NIF-1 in BC progression, likely as a suppressor and through interactions with Sox9 and HoxA1.
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Affiliation(s)
- Maria Frantzi
- Biomedical Research Foundation Academy of Athens, Athens, Greece
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60
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Scaffold attachment factor B1 regulates the androgen receptor in concert with the growth inhibitory kinase MST1 and the methyltransferase EZH2. Oncogene 2013; 33:3235-45. [PMID: 23893242 DOI: 10.1038/onc.2013.294] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/12/2013] [Accepted: 05/07/2013] [Indexed: 12/16/2022]
Abstract
The androgen receptor (AR) is a transcription factor that employs many diverse interactions with coregulatory proteins in normal physiology and in prostate cancer (PCa). The AR mediates cellular responses in association with chromatin complexes and kinase cascades. Here we report that the nuclear matrix protein, scaffold attachment factor B1 (SAFB1), regulates AR activity and AR levels in a manner that suggests its involvement in PCa. SAFB1 mRNA expression was lower in PCa in comparison with normal prostate tissue in a majority of publicly available RNA expression data sets. SAFB1 protein levels were also reduced with disease progression in a cohort of human PCa that included metastatic tumors. SAFB1 bound to AR and was phosphorylated by the MST1 (Hippo homolog) serine-threonine kinase, previously shown to be an AR repressor, and MST1 localization to AR-dependent promoters was inhibited by SAFB1 depletion. Knockdown of SAFB1 in androgen-dependent LNCaP PCa cells increased AR and prostate-specific antigen (PSA) levels, stimulated growth of cultured cells and subcutaneous xenografts and promoted a more aggressive phenotype, consistent with a repressive AR regulatory function. SAFB1 formed a complex with the histone methyltransferase EZH2 at AR-interacting chromatin sites in association with other polycomb repressive complex 2 (PRC2) proteins. We conclude that SAFB1 acts as a novel AR co-regulator at gene loci where signals from the MST1/Hippo and EZH2 pathways converge.
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61
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Vicent GP, Nacht AS, Zaurin R, Font-Mateu J, Soronellas D, Le Dily F, Reyes D, Beato M. Unliganded progesterone receptor-mediated targeting of an RNA-containing repressive complex silences a subset of hormone-inducible genes. Genes Dev 2013; 27:1179-97. [PMID: 23699411 DOI: 10.1101/gad.215293.113] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A close chromatin conformation precludes gene expression in eukaryotic cells. Genes activated by external cues have to overcome this repressive state by locally changing chromatin structure to a more open state. Although much is known about hormonal gene activation, how basal repression of regulated genes is targeted to the correct sites throughout the genome is not well understood. Here we report that in breast cancer cells, the unliganded progesterone receptor (PR) binds genomic sites and targets a repressive complex containing HP1γ (heterochromatin protein 1γ), LSD1 (lysine-specific demethylase 1), HDAC1/2, CoREST (corepressor for REST [RE1 {neuronal repressor element 1} silencing transcription factor]), KDM5B, and the RNA SRA (steroid receptor RNA activator) to 20% of hormone-inducible genes, keeping these genes silenced prior to hormone treatment. The complex is anchored via binding of HP1γ to H3K9me3 (histone H3 tails trimethylated on Lys 9). SRA interacts with PR, HP1γ, and LSD1, and its depletion compromises the loading of the repressive complex to target chromatin-promoting aberrant gene derepression. Upon hormonal treatment, the HP1γ-LSD1 complex is displaced from these constitutively poorly expressed genes as a result of rapid phosphorylation of histone H3 at Ser 10 mediated by MSK1, which is recruited to the target sites by the activated PR. Displacement of the repressive complex enables the loading of coactivators needed for chromatin remodeling and activation of this set of genes, including genes involved in apoptosis and cell proliferation. These results highlight the importance of the unliganded PR in hormonal regulation of breast cancer cells.
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62
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Beato M, Vicent GP. A new role for an old player: steroid receptor RNA Activator (SRA) represses hormone inducible genes. Transcription 2013; 4:167-71. [PMID: 23863201 DOI: 10.4161/trns.25777] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In breast cancer cells the Steroid Receptor ¬RNA Activator (SRA) acts as scaffold of a complex containing HP1γ, LSD1, HDAC1/2 and CoREST, which contributes to repression of key hormone-inducible genes that must be kept silent in the absence of hormone.
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63
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Ballaré C, Zaurin R, Vicent GP, Beato M. More help than hindrance: nucleosomes aid transcriptional regulation. Nucleus 2013; 4:189-94. [PMID: 23756349 DOI: 10.4161/nucl.25108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A major challenge of modern human biology is to understand how a differentiated somatic cell integrates the response to external signals in the complex context of basic metabolic and tissue-specific gene expression programs. This requires exploring two interconnected basic processes: the signaling network and the global function of the key transcription factors on which signaling acts to modulate gene expression. An apparently simple model to study these questions has been steroid hormones action, since their intracellular receptors both initiate signaling and are the key transcription factors orchestrating the cellular response. We have used progesterone action in breast cancer cells to elucidate the intricacies of progesterone receptor (PR) signaling crosstalk with protein kinases, histone modifying enzymes and ATP-dependent chromatin remodeling complexes. ( 1) Recently we have described the cistrome of PR in these cells at different times after addition of hormone and its relationship to chromatin structure. ( 2) The role of chromatin in transcription factor binding to the genome is still debated, but the dominant view is that factors bind preferentially to nucleosome-depleted regions, usually identified as DNaseI-hypersensitive sites (DHS). In contrast with this vision, we have shown that PR requires nucleosomes for optimal binding and function. In breast cancer cells treated with progestins we identified 25,000 PR binding sites (PRbs), the majority encompassing several copies of the hexanucleotide TGTYCY, highly abundant in the genome. We found that strong functional PRbs accumulate around progesterone-induced genes mainly in enhancers, are enriched in DHS but exhibit high nucleosome occupancy. Progestin stimulation results in remodeling of these nucleosomes with displacement of histones H1 and H2A/H2B dimers. Our results strongly suggest that nucleosomes play crucial role in PR binding and hormonal gene regulation.
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Affiliation(s)
- Cecilia Ballaré
- Gene Regulation Stem Cells and Cancer Program, Centre for Genomic Regulation CRG, Barcelona, Spain
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64
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Popova EY, Grigoryev SA, Fan Y, Skoultchi AI, Zhang SS, Barnstable CJ. Developmentally regulated linker histone H1c promotes heterochromatin condensation and mediates structural integrity of rod photoreceptors in mouse retina. J Biol Chem 2013; 288:17895-907. [PMID: 23645681 DOI: 10.1074/jbc.m113.452144] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Mature rod photoreceptor cells contain very small nuclei with tightly condensed heterochromatin. We observed that during mouse rod maturation, the nucleosomal repeat length increases from 190 bp at postnatal day 1 to 206 bp in the adult retina. At the same time, the total level of linker histone H1 increased reaching the ratio of 1.3 molecules of total H1 per nucleosome, mostly via a dramatic increase in H1c. Genetic elimination of the histone H1c gene is functionally compensated by other histone variants. However, retinas in H1c/H1e/H1(0) triple knock-outs have photoreceptors with bigger nuclei, decreased heterochromatin area, and notable morphological changes suggesting that the process of chromatin condensation and rod cell structural integrity are partly impaired. In triple knock-outs, nuclear chromatin exposed several epigenetic histone modification marks masked in the wild type chromatin. Dramatic changes in exposure of a repressive chromatin mark, H3K9me2, indicate that during development linker histone plays a role in establishing the facultative heterochromatin territory and architecture in the nucleus. During retina development, the H1c gene and its promoter acquired epigenetic patterns typical of rod-specific genes. Our data suggest that histone H1c gene expression is developmentally up-regulated to promote facultative heterochromatin in mature rod photoreceptors.
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Affiliation(s)
- Evgenya Y Popova
- Department of Neural and Behavioral Sciences, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, USA
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65
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Bertucci PY, Nacht AS, Alló M, Rocha-Viegas L, Ballaré C, Soronellas D, Castellano G, Zaurin R, Kornblihtt AR, Beato M, Vicent GP, Pecci A. Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation. Nucleic Acids Res 2013; 41:6072-86. [PMID: 23640331 PMCID: PMC3695497 DOI: 10.1093/nar/gkt327] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Steroid receptors were classically described for regulating transcription by binding to target gene promoters. However, genome-wide studies reveal that steroid receptors-binding sites are mainly located at intragenic regions. To determine the role of these sites, we examined the effect of progestins on the transcription of the bcl-x gene, where only intragenic progesterone receptor-binding sites (PRbs) were identified. We found that in response to hormone treatment, the PR is recruited to these sites along with two histone acetyltransferases CREB-binding protein (CBP) and GCN5, leading to an increase in histone H3 and H4 acetylation and to the binding of the SWI/SNF complex. Concomitant, a more relaxed chromatin was detected along bcl-x gene mainly in the regions surrounding the intragenic PRbs. PR also mediated the recruitment of the positive elongation factor pTEFb, favoring RNA polymerase II (Pol II) elongation activity. Together these events promoted the re-distribution of the active Pol II toward the 3′-end of the gene and a decrease in the ratio between proximal and distal transcription. These results suggest a novel mechanism by which PR regulates gene expression by facilitating the proper passage of the polymerase along hormone-dependent genes.
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66
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Makrythanasis P, van Bon BW, Steehouwer M, Rodríguez-Santiago B, Simpson M, Dias P, Anderlid BM, Arts P, Bhat M, Augello B, Biamino E, Bongers EMHF, del Campo M, Cordeiro I, Cueto-González AM, Cuscó I, Deshpande C, Frysira E, Izatt L, Flores R, Galán E, Gener B, Gilissen C, Granneman SM, Hoyer J, Yntema HG, Kets CM, Koolen DA, Marcelis CL, Medeira A, Micale L, Mohammed S, de Munnik SA, Nordgren A, Psoni S, Reardon W, Revencu N, Roscioli T, Ruiterkamp-Versteeg M, Santos HG, Schoumans J, Schuurs-Hoeijmakers JHM, Silengo MC, Toledo L, Vendrell T, van der Burgt I, van Lier B, Zweier C, Reymond A, Trembath RC, Perez-Jurado L, Dupont J, de Vries BBA, Brunner HG, Veltman JA, Merla G, Antonarakis SE, Hoischen A. MLL2mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study. Clin Genet 2013; 84:539-45. [DOI: 10.1111/cge.12081] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 12/17/2012] [Accepted: 12/17/2012] [Indexed: 01/25/2023]
Affiliation(s)
- P Makrythanasis
- Departement of Genetic Medicine and Development; University of Geneva; Geneva Switzerland
| | - BW van Bon
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - M Steehouwer
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - B Rodríguez-Santiago
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
- Unitat de Genètica; Universitat Pompeu Fabra
- Hospital del Mas Medical Research Institute (IMIM)
- Quantitative Genomic Medicine Laboratories, Ltd (qGenomics); Barcelona Spain
| | - M Simpson
- Hospital de Santa Maria; Serviço de Genética Médica; Lisbon Portugal
| | - P Dias
- Hospital de Santa Maria; Serviço de Genética Médica; Lisbon Portugal
| | - BM Anderlid
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine; Karolinska Institutet
- Department of Clinical Genetics; Karolinska University Hospital; Stockholm Sweden
| | - P Arts
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - M Bhat
- Centre for Human Genetics; Bangalore India
| | - B Augello
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo
| | - E Biamino
- Dipartimento di Scienze Pediatriche; Università di Torino; Torino Italy
| | - EMHF Bongers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - M del Campo
- Unitat de Genètica; Universitat Pompeu Fabra
- Hospital del Mas Medical Research Institute (IMIM)
- Quantitative Genomic Medicine Laboratories, Ltd (qGenomics); Barcelona Spain
- CIBER de enfermedades raras (CIBERER)
- Programa de Medicina Molecular y Genética; Hospital Vall d'Hebron
| | - I Cordeiro
- Hospital de Santa Maria; Serviço de Genética Médica; Lisbon Portugal
| | - AM Cueto-González
- Programa de Medicina Molecular y Genética; Hospital Vall d'Hebron
- Pediatric Service, Hospital Universitari Mútua de Terrassa; Terrassa (Barcelona) Spain
| | - I Cuscó
- Unitat de Genètica; Universitat Pompeu Fabra
- Hospital del Mas Medical Research Institute (IMIM)
- Quantitative Genomic Medicine Laboratories, Ltd (qGenomics); Barcelona Spain
- CIBER de enfermedades raras (CIBERER)
| | - C Deshpande
- Clinical Genetics, Guy's Hospital; Guy's and St. Thomas' National Health Service (NHS) Foundation Trust; London UK
| | - E Frysira
- Laboratory of Medical Genetics, Medical School; University of Athens; Athens Greece
| | - L Izatt
- Servicio de Genética, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo; Bizkaia, Spain
| | - R Flores
- Unitat de Genètica; Universitat Pompeu Fabra
- Hospital del Mas Medical Research Institute (IMIM)
- Quantitative Genomic Medicine Laboratories, Ltd (qGenomics); Barcelona Spain
- CIBER de enfermedades raras (CIBERER)
| | - E Galán
- Servicio de Genética, BioCruces Health Research Institute, Hospital Universitario Cruces, Barakaldo; Bizkaia, Spain
| | - B Gener
- Clinical Genetics Unit; Hospital de Cruces; Barakaldo Bizkaia Spain
| | - C Gilissen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - SM Granneman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - J Hoyer
- Institute of Human Genetics; Friedrich-Alexander-University Erlangen-Nuremberg; Erlangen Germany
| | - HG Yntema
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - CM Kets
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - DA Koolen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - CL Marcelis
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - A Medeira
- Hospital de Santa Maria; Serviço de Genética Médica; Lisbon Portugal
| | - L Micale
- Department of Clinical Genetics; Karolinska University Hospital; Stockholm Sweden
| | - S Mohammed
- Clinical Genetics, Guy's Hospital; Guy's and St. Thomas' National Health Service (NHS) Foundation Trust; London UK
| | - SA de Munnik
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - A Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine; Karolinska Institutet
- Department of Clinical Genetics; Karolinska University Hospital; Stockholm Sweden
| | - S Psoni
- Laboratory of Medical Genetics, Medical School; University of Athens; Athens Greece
| | - W Reardon
- National Centre for Medical Genetics; Our Lady's Hospital for Sick Children; Dublin 12 Ireland
| | - N Revencu
- Centre for Human Genetics, Cliniques Universitaires Saint-Luc; Université Catholique de Louvain; Brussels Belgium
| | - T Roscioli
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
- School of Women's and Children's Health, Sydney Children's Hospital; University of New South Wales; Sydney Australia
| | - M Ruiterkamp-Versteeg
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - HG Santos
- Hospital de Santa Maria; Serviço de Genética Médica; Lisbon Portugal
| | - J Schoumans
- Department of Medical Genetics, Cancer Cytogenetic Unit; University Hospital of Lausanne; Lausanne Switzerland
- Department of Molecular Medicine and Surgery; Karolinska Institutet; Stockholm Sweden
| | - JHM Schuurs-Hoeijmakers
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - MC Silengo
- Dipartimento di Scienze Pediatriche; Università di Torino; Torino Italy
| | - L Toledo
- Hospital Materno Infantil; Unidad de Neurologia Infantil; Las Palmas de Gran Canaria Spain
| | - T Vendrell
- Programa de Medicina Molecular y Genética; Hospital Vall d'Hebron
| | - I van der Burgt
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - B van Lier
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - C Zweier
- Institute of Human Genetics; Friedrich-Alexander-University Erlangen-Nuremberg; Erlangen Germany
| | - A Reymond
- The Center for Integrative Genomics; University of Lausanne; Lausanne
| | - RC Trembath
- Division of Genetics and Molecular Medicine, Guy's Hospital; King's College London School of Medicine; London UK
| | - L Perez-Jurado
- Unitat de Genètica; Universitat Pompeu Fabra
- Hospital del Mas Medical Research Institute (IMIM)
- Quantitative Genomic Medicine Laboratories, Ltd (qGenomics); Barcelona Spain
- CIBER de enfermedades raras (CIBERER)
| | - J Dupont
- Hospital de Santa Maria; Serviço de Genética Médica; Lisbon Portugal
| | - BBA de Vries
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - HG Brunner
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - JA Veltman
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
| | - G Merla
- Medical Genetics Unit; IRCCS Casa Sollievo della Sofferenza; San Giovanni Rotondo
| | - SE Antonarakis
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
- Service of Genetic Medicine; University Hospitals of Geneva; Geneva Switzerland
| | - A Hoischen
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders; Radboud University Nijmegen Medical Centre; Nijmegen The Netherlands
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67
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Activation of mitogen- and stress-activated kinase 1 is required for proliferation of breast cancer cells in response to estrogens or progestins. Oncogene 2013; 33:1570-80. [PMID: 23604116 DOI: 10.1038/onc.2013.95] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/08/2013] [Accepted: 01/18/2013] [Indexed: 12/13/2022]
Abstract
Growth of breast cancers is often dependent on ovarian steroid hormones making the tumors responsive to antagonists of hormone receptors. However, eventually the tumors become hormone independent, raising the need to identify downstream targets for the inhibition of tumor growth. One possibility is to focus on the signaling mechanisms used by ovarian steroid hormones to induce breast cancer cell proliferation. Here we report that the mitogen- and stress-activated kinase 1 (MSK1) could be a potential druggable target. Using the breast cancer cell line T47D, we show that estrogens (E2) and progestins activate MSK1, which forms a complex with the corresponding hormone receptor. Inhibition of MSK1 activity with H89 or its depletion by MSK1 short hairpin RNAs (shRNAs) specifically abrogates cell proliferation in response to E2 or progestins without affecting serum-induced cell proliferation. MSK1 activity is required for the transition from the G1- to the S-phase of the cell cycle and inhibition of MSK1 compromises both estradiol- and progestin-dependent induction of cell cycle genes. ChIP-seq experiments identified binding of MSK1 to progesterone receptor-binding sites associated with hormone-responsive genes. MSK1 recruitment to epigenetically defined enhancer regions supports the need of MSK1 as a chromatin remodeler in hormone-dependent regulation of gene transcription. In agreement with this interpretation, expression of a histone H3 mutated at S10 eliminates the hormonal effect on cell proliferation and on induction of relevant target genes. Finally, we show that E2- or progestin-dependent growth of T47D cells xenografted in immunodefficient mice is inhibited by depletion of MSK1, indicating that our findings are not restricted to cultured cells, and that MSK1 plays an important role for hormone-dependent breast cancer growth in a more physiological context.
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68
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Coffey K, Rogerson L, Ryan-Munden C, Alkharaif D, Stockley J, Heer R, Sahadevan K, O’Neill D, Jones D, Darby S, Staller P, Mantilla A, Gaughan L, Robson CN. The lysine demethylase, KDM4B, is a key molecule in androgen receptor signalling and turnover. Nucleic Acids Res 2013; 41:4433-46. [PMID: 23435229 PMCID: PMC3632104 DOI: 10.1093/nar/gkt106] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 01/29/2013] [Accepted: 01/30/2013] [Indexed: 01/23/2023] Open
Abstract
The androgen receptor (AR) is a key molecule involved in prostate cancer (PC) development and progression. Post-translational modification of the AR by co-regulator proteins can modulate its transcriptional activity. To identify which demethylases might be involved in AR regulation, an siRNA screen was performed to reveal that the demethylase, KDM4B, may be an important co-regulator protein. KDM4B enzymatic activity is required to enhance AR transcriptional activity; however, independently of this activity, KDM4B can enhance AR protein stability via inhibition of AR ubiquitination. Importantly, knockdown of KDM4B in multiple cell lines results in almost complete depletion of AR protein levels. For the first time, we have identified KDM4B to be an androgen-regulated demethylase enzyme, which can influence AR transcriptional activity not only via demethylation activity but also via modulation of ubiquitination. Together, these findings demonstrate the close functional relationship between AR and KDM4B, which work together to amplify the androgen response. Furthermore, KDM4B expression in clinical PC specimens positively correlates with increasing cancer grade (P < 0.001). Consequently, KDM4B is a viable therapeutic target in PC.
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Affiliation(s)
- Kelly Coffey
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Lynsey Rogerson
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Claudia Ryan-Munden
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Dhuha Alkharaif
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Jacqueline Stockley
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Rakesh Heer
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kanagasabai Sahadevan
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Daniel O’Neill
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Dominic Jones
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Steven Darby
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Peter Staller
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Alejandra Mantilla
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Luke Gaughan
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Craig N. Robson
- Solid Tumour Target Discovery Laboratory, Newcastle Cancer Centre, Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK and Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
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69
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Abstract
Members of histone H1 family bind to nucleosomal and linker DNA to assist in stabilization of higher-order chromatin structures. Moreover, histone H1 is involved in regulation of a variety of cellular processes by interactions with cytosolic and nuclear proteins. Histone H1, composed of a series of subtypes encoded by distinct genes, is usually differentially expressed in specialized cells and frequently non-randomly distributed in different chromatin regions. Moreover, a role of specific histone H1 subtype might be also modulated by post-translational modifications and/or presence of polymorphic isoforms. While the significance of covalently modified histone H1 subtypes has been partially recognized, much less is known about the importance of histone H1 polymorphic variants identified in various plant and animal species, and human cells as well. Recent progress in elucidating amino acid composition-dependent functioning and interactions of the histone H1 with a variety of molecular partners indicates a potential role of histone H1 polymorphic variation in adopting specific protein conformations essential for chromatin function. The histone H1 allelic variants might affect chromatin in order to modulate gene expression underlying some physiological traits and, therefore could modify the course of diverse histone H1-dependent biological processes. This review focuses on the histone H1 allelic variability, and biochemical and genetic aspects of linker histone allelic isoforms to emphasize their likely biological relevance.
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70
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Ballaré C, Castellano G, Gaveglia L, Althammer S, González-Vallinas J, Eyras E, Le Dily F, Zaurin R, Soronellas D, Vicent G, Beato M. Nucleosome-Driven Transcription Factor Binding and Gene Regulation. Mol Cell 2013. [DOI: 10.1016/j.molcel.2012.10.019] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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71
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Herz HM, Mohan M, Garruss AS, Liang K, Takahashi YH, Mickey K, Voets O, Verrijzer CP, Shilatifard A. Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4. Genes Dev 2012; 26:2604-20. [PMID: 23166019 DOI: 10.1101/gad.201327.112] [Citation(s) in RCA: 285] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Monomethylation of histone H3 on Lys 4 (H3K4me1) and acetylation of histone H3 on Lys 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and on enhancers. Although in yeast all H3K4 methylation patterns, including H3K4me1, are implemented by Set1/COMPASS (complex of proteins associated with Set1), there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax, and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of the mammalian Mll3/4 COMPASS-like complexes, can function as a major H3K4 monomethyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac levels in various tissues. Assays with the cut wing margin enhancer implied a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrated that Trr is required to maintain the H3K4me1 and H3K27ac chromatin signature that resembles the histone modification patterns described for enhancers. Furthermore, studies in the mammalian system suggested a role for the Trr homolog Mll3 in similar processes. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 monomethyltransferases Trr/Mll3/Mll4 and the H3K27 demethylase UTX cooperate to regulate the transition from inactive/poised to active enhancers.
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Affiliation(s)
- Hans-Martin Herz
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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72
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Wright RHG, Castellano G, Bonet J, Le Dily F, Font-Mateu J, Ballaré C, Nacht AS, Soronellas D, Oliva B, Beato M. CDK2-dependent activation of PARP-1 is required for hormonal gene regulation in breast cancer cells. Genes Dev 2012; 26:1972-83. [PMID: 22948662 DOI: 10.1101/gad.193193.112] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Eukaryotic gene regulation implies that transcription factors gain access to genomic information via poorly understood processes involving activation and targeting of kinases, histone-modifying enzymes, and chromatin remodelers to chromatin. Here we report that progestin gene regulation in breast cancer cells requires a rapid and transient increase in poly-(ADP)-ribose (PAR), accompanied by a dramatic decrease of cellular NAD that could have broad implications in cell physiology. This rapid increase in nuclear PARylation is mediated by activation of PAR polymerase PARP-1 as a result of phosphorylation by cyclin-dependent kinase CDK2. Hormone-dependent phosphorylation of PARP-1 by CDK2, within the catalytic domain, enhances its enzymatic capabilities. Activated PARP-1 contributes to the displacement of histone H1 and is essential for regulation of the majority of hormone-responsive genes and for the effect of progestins on cell cycle progression. Both global chromatin immunoprecipitation (ChIP) coupled with deep sequencing (ChIP-seq) and gene expression analysis show a strong overlap between PARP-1 and CDK2. Thus, progestin gene regulation involves a novel signaling pathway that connects CDK2-dependent activation of PARP-1 with histone H1 displacement. Given the multiplicity of PARP targets, this new pathway could be used for the pharmacological management of breast cancer.
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73
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Wright RHG, Beato M. PARty promoters: hormone-dependent gene regulation requires CDK2 activation of PARP1. Cell Cycle 2012; 11:4291-3. [PMID: 23095674 PMCID: PMC3552903 DOI: 10.4161/cc.22531] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Epigenetic control and cancer: the potential of histone demethylases as therapeutic targets. Pharmaceuticals (Basel) 2012; 5:963-90. [PMID: 24280700 PMCID: PMC3816642 DOI: 10.3390/ph5090963] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/21/2012] [Accepted: 08/17/2012] [Indexed: 01/01/2023] Open
Abstract
The development of cancer involves an immense number of factors at the molecular level. These factors are associated principally with alterations in the epigenetic mechanisms that regulate gene expression profiles. Studying the effects of chromatin structure alterations, which are caused by the addition/removal of functional groups to specific histone residues, are of great interest as a promising way to identify markers for cancer diagnosis, classify the disease and determine its prognosis, and these markers could be potential targets for the treatment of this disease in its different forms. This manuscript presents the current point of view regarding members of the recently described family of proteins that exhibit histone demethylase activity; histone demethylases are genetic regulators that play a fundamental role in both the activation and repression of genes and whose expression has been observed to increase in many types of cancer. Some fundamental aspects of their association with the development of cancer and their relevance as potential targets for the development of new therapeutic strategies at the epigenetic level are discussed in the following manuscript.
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75
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Chauhan C, Zraly CB, Parilla M, Diaz MO, Dingwall AK. Histone recognition and nuclear receptor co-activator functions of Drosophila cara mitad, a homolog of the N-terminal portion of mammalian MLL2 and MLL3. Development 2012; 139:1997-2008. [PMID: 22569554 DOI: 10.1242/dev.076687] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
MLL2 and MLL3 histone lysine methyltransferases are conserved components of COMPASS-like co-activator complexes. In vertebrates, the paralogous MLL2 and MLL3 contain multiple domains required for epigenetic reading and writing of the histone code involved in hormone-stimulated gene programming, including receptor-binding motifs, SET methyltransferase, HMG and PHD domains. The genes encoding MLL2 and MLL3 arose from a common ancestor. Phylogenetic analyses reveal that the ancestral gene underwent a fission event in some Brachycera dipterans, including Drosophila species, creating two independent genes corresponding to the N- and C-terminal portions. In Drosophila, the C-terminal SET domain is encoded by trithorax-related (trr), which is required for hormone-dependent gene activation. We identified the cara mitad (cmi) gene, which encodes the previously undiscovered N-terminal region consisting of PHD and HMG domains and receptor-binding motifs. The cmi gene is essential and its functions are dosage sensitive. CMI associates with TRR, as well as the EcR-USP receptor, and is required for hormone-dependent transcription. Unexpectedly, although the CMI and MLL2 PHDf3 domains could bind histone H3, neither showed preference for trimethylated lysine 4. Genetic tests reveal that cmi is required for proper global trimethylation of H3K4 and that hormone-stimulated transcription requires chromatin binding by CMI, methylation of H3K4 by TRR and demethylation of H3K27 by the demethylase UTX. The evolutionary split of MLL2 into two distinct genes in Drosophila provides important insight into distinct epigenetic functions of conserved readers and writers of the histone code.
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Affiliation(s)
- Chhavi Chauhan
- Oncology Institute, Stritch School of Medicine, Loyola University of Chicago, Maywood, IL 60153, USA
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76
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Bryant JM, Govin J, Zhang L, Donahue G, Pugh BF, Berger SL. The linker histone plays a dual role during gametogenesis in Saccharomyces cerevisiae. Mol Cell Biol 2012; 32:2771-83. [PMID: 22586276 PMCID: PMC3416202 DOI: 10.1128/mcb.00282-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 05/07/2012] [Indexed: 11/20/2022] Open
Abstract
The differentiation of gametes involves dramatic changes to chromatin, affecting transcription, meiosis, and cell morphology. Sporulation in Saccharomyces cerevisiae shares many chromatin features with spermatogenesis, including a 10-fold compaction of the nucleus. To identify new proteins involved in spore nuclear organization, we purified chromatin from mature spores and discovered a significant enrichment of the linker histone (Hho1). The function of Hho1 has proven to be elusive during vegetative growth, but here we demonstrate its requirement for efficient sporulation and full compaction of the spore genome. Hho1 chromatin immunoprecipitation followed by sequencing (ChIP-seq) revealed increased genome-wide binding in mature spores and provides novel in vivo evidence of the linker histone binding to nucleosomal linker DNA. We also link Hho1 function to the transcription factor Ume6, the master repressor of early meiotic genes. Hho1 and Ume6 are depleted during meiosis, and analysis of published ChIP-chip data obtained during vegetative growth reveals a high binding correlation of both proteins at promoters of early meiotic genes. Moreover, Ume6 promotes binding of Hho1 to meiotic gene promoters. Thus, Hho1 may play a dual role during sporulation: Hho1 and Ume6 depletion facilitates the onset of meiosis via activation of Ume6-repressed early meiotic genes, whereas Hho1 enrichment in mature spores contributes to spore genome compaction.
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Affiliation(s)
- Jessica M. Bryant
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Biomedical Graduate Studies, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jérôme Govin
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Liye Zhang
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
- The Integrative Biosciences Graduate Program in Cell and Developmental Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Greg Donahue
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - B. Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shelley L. Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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77
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Beato M, Vicent GP. Impact of chromatin structure and dynamics on PR signaling. The initial steps in hormonal gene regulation. Mol Cell Endocrinol 2012; 357:37-42. [PMID: 21945605 DOI: 10.1016/j.mce.2011.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 08/03/2011] [Accepted: 09/02/2011] [Indexed: 11/16/2022]
Abstract
Gene regulation requires access of transcription factors to DNA sequences of target genes, which is limited by the compaction of DNA in chromatin. Based on our studies on the Progesterone receptor (PR)-dependent hormonal induction of mouse mammary tumor virus (MMTV) promoter we found that remodeling of the various levels of chromatin organization is a complex and necessary prerequisite for regulation. Two consecutive cycles are essential for transcriptional activation, both involving the collaboration between activated protein kinases, histone modifying enzymes and ATP-dependent chromatin remodelers. The first cycle ends with the displacement of histone H1 and decompaction of higher order chromatin structure. The second cycle leads to the displacement of dimers of histones H2A and H2B resulting in opening of nucleosomes. In both cases the hormone receptor recruits an ATP-dependent chromatin remodeler, whose binding to chromatin is stabilized by distinct histone modifications. The final result is to facilitate full occupancy of the cis regulatory sites and access for the basal transcription machinery. Thus, activation of PR-target genes involves a very rapid coordination of enzymatic activities via crosstalk with various kinase-signaling pathways.
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Affiliation(s)
- Miguel Beato
- Centre de Regulació Genòmica and Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain.
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78
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Knutson TP, Daniel AR, Fan D, Silverstein KAT, Covington KR, Fuqua SAW, Lange CA. Phosphorylated and sumoylation-deficient progesterone receptors drive proliferative gene signatures during breast cancer progression. Breast Cancer Res 2012; 14:R95. [PMID: 22697792 PMCID: PMC3446358 DOI: 10.1186/bcr3211] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Revised: 05/21/2012] [Accepted: 06/14/2012] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION Progesterone receptors (PR) are emerging as important breast cancer drivers. Phosphorylation events common to breast cancer cells impact PR transcriptional activity, in part by direct phosphorylation. PR-B but not PR-A isoforms are phosphorylated on Ser294 by mitogen activated protein kinase (MAPK) and cyclin dependent kinase 2 (CDK2). Phospho-Ser294 PRs are resistant to ligand-dependent Lys388 SUMOylation (that is, a repressive modification). Antagonism of PR small ubiquitin-like modifier (SUMO)ylation by mitogenic protein kinases suggests a mechanism for derepression (that is, transcriptional activation) of target genes. As a broad range of PR protein expression is observed clinically, a PR gene signature would provide a valuable marker of PR contribution to early breast cancer progression. METHODS Global gene expression patterns were measured in T47D and MCF-7 breast cancer cells expressing either wild-type (SUMOylation-capable) or K388R (SUMOylation-deficient) PRs and subjected to pathway analysis. Gene sets were validated by RT-qPCR. Recruitment of coregulators and histone methylation levels were determined by chromatin immunoprecipitation. Changes in cell proliferation and survival were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays and western blotting. Finally, human breast tumor cohort datasets were probed to identify PR-associated gene signatures; metagene analysis was employed to define survival rates in patients whose tumors express a PR gene signature. RESULTS 'SUMO-sensitive' PR target genes primarily include genes required for proliferative and pro-survival signaling. DeSUMOylated K388R receptors are preferentially recruited to enhancer regions of derepressed genes (that is, MSX2, RGS2, MAP1A, and PDK4) with the steroid receptor coactivator, CREB-(cAMP-response element-binding protein)-binding protein (CBP), and mixed lineage leukemia 2 (MLL2), a histone methyltransferase mediator of nucleosome remodeling. PR SUMOylation blocks these events, suggesting that SUMO modification of PR prevents interactions with mediators of early chromatin remodeling at 'closed' enhancer regions. SUMO-deficient (phospho-Ser294) PR gene signatures are significantly associated with human epidermal growth factor 2 (ERBB2)-positive luminal breast tumors and predictive of early metastasis and shortened survival. Treatment with antiprogestin or MEK inhibitor abrogated expression of SUMO-sensitive PR target-genes and inhibited proliferation in BT-474 (estrogen receptor (ER)+/PR+/ERBB2+) breast cancer cells. CONCLUSIONS We conclude that reversible PR SUMOylation/deSUMOylation profoundly alters target gene selection in breast cancer cells. Phosphorylation-induced PR deSUMOylation favors a permissive chromatin environment via recruitment of CBP and MLL2. Patients whose ER+/PR+ tumors are driven by hyperactive (that is, derepressed) phospho-PRs may benefit from endocrine (antiestrogen) therapies that contain an antiprogestin.
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Affiliation(s)
- Todd P Knutson
- Departments of Medicine (Division of Hematology, Oncology, and Transplantation) and Pharmacology, Masonic Cancer Center, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455 USA
| | - Andrea R Daniel
- Departments of Medicine (Division of Hematology, Oncology, and Transplantation) and Pharmacology, Masonic Cancer Center, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455 USA
| | - Danhua Fan
- Biostatistics and Bioinformatics Core, Masonic Cancer Center, 425 Delaware St SE, University of Minnesota, Minneapolis, MN 55455 USA
| | - Kevin AT Silverstein
- Biostatistics and Bioinformatics Core, Masonic Cancer Center, 425 Delaware St SE, University of Minnesota, Minneapolis, MN 55455 USA
| | - Kyle R Covington
- Department of Medicine, Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Suzanne AW Fuqua
- Department of Medicine, Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Carol A Lange
- Departments of Medicine (Division of Hematology, Oncology, and Transplantation) and Pharmacology, Masonic Cancer Center, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455 USA
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79
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Immediate-early gene activation by the MAPK pathways: what do and don't we know? Biochem Soc Trans 2012; 40:58-66. [PMID: 22260666 DOI: 10.1042/bst20110636] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The study of IE (immediate-early) gene activation mechanisms has provided numerous paradigms for how transcription is controlled in response to extracellular signalling. Many of the findings have been derived from investigating one of the IE genes, FOS, and the models extrapolated to regulatory mechanisms for other IE genes. However, whereas the overall principles of activation appear similar, recent evidence suggests that the underlying mechanistic details may differ depending on cell type, cellular stimulus and IE gene under investigation. In the present paper, we review recent advances in our understanding of IE gene transcription, chiefly focusing on FOS and its activation by ERK (extracellular-signal-regulated kinase) MAPK (mitogen-activated protein kinase) pathway signalling. We highlight important fundamental regulatory principles, but also illustrate the gaps in our current knowledge and the potential danger in making assumptions based on extrapolation from disparate studies.
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80
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Anderson AM, Carter KW, Anderson D, Wise MJ. Coexpression of nuclear receptors and histone methylation modifying genes in the testis: implications for endocrine disruptor modes of action. PLoS One 2012; 7:e34158. [PMID: 22496781 PMCID: PMC3319570 DOI: 10.1371/journal.pone.0034158] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 02/23/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Endocrine disruptor chemicals elicit adverse health effects by perturbing nuclear receptor signalling systems. It has been speculated that these compounds may also perturb epigenetic mechanisms and thus contribute to the early origin of adult onset disease. We hypothesised that histone methylation may be a component of the epigenome that is susceptible to perturbation. We used coexpression analysis of publicly available data to investigate the combinatorial actions of nuclear receptors and genes involved in histone methylation in normal testis and when faced with endocrine disruptor compounds. METHODOLOGY/PRINCIPAL FINDINGS The expression patterns of a set of genes were profiled across testis tissue in human, rat and mouse, plus control and exposed samples from four toxicity experiments in the rat. Our results indicate that histone methylation events are a more general component of nuclear receptor mediated transcriptional regulation in the testis than previously appreciated. Coexpression patterns support the role of a gatekeeper mechanism involving the histone methylation modifiers Kdm1, Prdm2, and Ehmt1 and indicate that this mechanism is a common determinant of transcriptional integrity for genes critical to diverse physiological endpoints relevant to endocrine disruption. Coexpression patterns following exposure to vinclozolin and dibutyl phthalate suggest that coactivity of the demethylase Kdm1 in particular warrants further investigation in relation to endocrine disruptor mode of action. CONCLUSIONS/SIGNIFICANCE This study provides proof of concept that a bioinformatics approach that profiles genes related to a specific hypothesis across multiple biological settings can provide powerful insight into coregulatory activity that would be difficult to discern at an individual experiment level or by traditional differential expression analysis methods.
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Affiliation(s)
- Alison M Anderson
- Computer Science and Software Engineering, University of Western Australia, Perth, Australia.
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81
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Stratmann A, Haendler B. Histone demethylation and steroid receptor function in cancer. Mol Cell Endocrinol 2012; 348:12-20. [PMID: 21958694 DOI: 10.1016/j.mce.2011.09.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 09/05/2011] [Accepted: 09/13/2011] [Indexed: 10/17/2022]
Abstract
Steroid receptors recruit various cofactors to form multi-protein complexes which locally alter chromatin structure and control DNA accessibility in order to regulate gene transcription. Some of these factors are enzymes that add or remove histone marks in the vicinity of regulatory regions of target genes. Numerous histone modifications added by specific writer enzymes and removed by eraser enzymes have been identified. Histone methylation is a modification with a complex outcome, as it can lead to gene activation or repression, depending on the modified residue and the context. Methylation marks are added by different enzyme families displaying exquisite substrate specificity. Lysine methylation is reversible and two different demethylase families have been identified in humans, the Jumonji C and the lysine-specific demethylase families. A regulatory role of histone demethylases in fine-tuning the function of steroid receptors, especially the androgen receptor and estrogen receptor, has emerged in recent years. This is mostly inferred from in vitro studies, but more recently first in vivo data have further supported this concept. This and the deregulated expression observed for several histone demethylases suggest a role in tumours such as prostate and breast cancer.
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Affiliation(s)
- Antje Stratmann
- Therapeutic Research Group Oncology/Gynecological Therapies and Global Biomarker, Bayer Pharma AG, Bayer HealthCare, D-13342 Berlin, Germany
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Belikov S, Holmqvist PH, Åstrand C, Wrange Ö. FoxA1 and glucocorticoid receptor crosstalk via histone H4K16 acetylation at a hormone regulated enhancer. Exp Cell Res 2012; 318:61-74. [DOI: 10.1016/j.yexcr.2011.09.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/02/2011] [Accepted: 09/29/2011] [Indexed: 12/17/2022]
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83
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Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. ACTA ACUST UNITED AC 2011; 27:3333-40. [PMID: 21994224 PMCID: PMC3232367 DOI: 10.1093/bioinformatics/btr570] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Availability: Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy Contact:eduardo.eyras@upf.edu Supplementary Information:Supplementary data are available at Bioinformatics online.
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