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Tripathy S, Nagari A, Chiu SP, Nandu T, Camacho CV, Mahendroo M, Kraus WL. Relaxin Modulates the Genomic Actions and Biological Effects of Estrogen in the Myometrium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589654. [PMID: 38659934 PMCID: PMC11042280 DOI: 10.1101/2024.04.15.589654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Estradiol (E2) and relaxin (Rln) are steroid and polypeptide hormones, respectively, with important roles in the female reproductive tract, including myometrium. Some actions of Rln, which are mediated by its membrane receptor RXFP1, require or are augmented by E2 signaling through its cognate nuclear steroid receptor, estrogen receptor alpha (ERα). In contrast, other actions of Rln act in opposition to the effects of E2. Here we explored the molecular and genomic mechanisms that underlie the functional interplay between E2 and Rln in the myometrium. We used both ovariectomized female mice and immortalized human myometrial cells expressing wild-type or mutant ERα (hTERT-HM-ERα cells). Our results indicate that Rln modulates the genomic actions and biological effects of estrogen in the myometrium and myometrial cells by reducing phosphorylation of ERα on serine 118 (S118), as well as by reducing the E2-dependent binding of ERα across the genome. These effects were associated with changes in the hormone-regulated transcriptome, including a decrease in the E2-dependent expression of some genes and enhanced expression of others. The inhibitory effects of Rln cotreatment on the E2-dependent phosphorylation of ERα required the nuclear dual-specificity phosphatases DUSP1 and DUSP5. Moreover, the inhibitory effects of Rln were reflected in a concomitant inhibition of the E2-dependent contraction of myometrial cells. Collectively, our results identify a pathway that integrates Rln/RXFP1 and E2/ERα signaling, resulting in a convergence of membrane and nuclear signaling pathways to control genomic and biological outcomes.
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Affiliation(s)
- Sudeshna Tripathy
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Laboratory of Cervical Remodeling and Preterm Birth, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Anusha Nagari
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shu-Ping Chiu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tulip Nandu
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Computational Core Facility, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cristel V. Camacho
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mala Mahendroo
- Laboratory of Cervical Remodeling and Preterm Birth, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - W. Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Section of Laboratory Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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2
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Kim HB, Kraus WL. Intracellular Retention of Estradiol is Augmented by GRAM Domain Containing Protein ASTER-B in Breast Cancer Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594581. [PMID: 38826375 PMCID: PMC11142117 DOI: 10.1101/2024.05.16.594581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Estrogens are naturally occurring steroid hormones that also act as the primary mitogens for estrogen receptor-positive (ER+) breast cancers. While elevated blood levels of estrogens have been associated with poor prognosis, the relationship between circulating hormone levels in the blood are related to intracellular hormone concentrations. Here, we observed that MCF-7 cells acutely treated with 17β-estradiol (E2) retain a substantial amount of the hormone even upon removal of the hormone from the culture medium. Moreover, global patterns of E2-dependent gene expression are sustained for hours after acute E2 treatment and hormone removal. While circulating E2 is sequestered by sex hormone binding globulin (SHBG), the mechanisms of intracellular E2 retention are poorly understood. We found that a mislocalized GRAM-domain containing protein ASTER-B in the nucleus, which is observed in a subset of patients, is associated with higher cellular E2 retention. Accumulation and retention of hormone are related to the steroidal properties of E2. Finally, we observed that nuclear ASTER-B-mediated E2 retention is required for sustained hormone-induced ERα chromatin occupancy at enhancers and gene expression, as well as subsequent cell growth responses. Our results add intracellular hormone retention as a mechanism controlling E2-dependent gene expression and downstream biological outcomes. S ignificance This study advances our understanding of how estradiol can be accumulated and retained intracellularly to drive a pro-proliferative gene expression program in ER+ breast cancer cells. Mechanistically, intracellular E2 retention is mediated in part by mislocalized, nuclear ASTER-B, which is aberrantly localized to the nuclei of cancer cells in some breast cancer patients.
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3
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Romo BA, Karakyriakou B, Cressey L, Brauer BL, Yang H, Warren A, Johnson AL, Kettenbach AN, Miller TW. TRIM33 Is a Co-Regulator of Estrogen Receptor Alpha. Cancers (Basel) 2024; 16:845. [PMID: 38473207 PMCID: PMC10930732 DOI: 10.3390/cancers16050845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024] Open
Abstract
Estrogen receptor alpha (ER)-positive breast cancer is responsible for over 60% of breast cancer cases in the U.S. Among patients diagnosed with early-stage ER+ disease, 1/3 will experience recurrence despite treatment with adjuvant endocrine therapy. ER is a nuclear hormone receptor responsible for estrogen-driven tumor growth. ER transcriptional activity is modulated by interactions with coregulators. Dysregulation of the levels of these coregulators is involved in the development of endocrine resistance. To identify ER interactors that modulate transcriptional activity in breast cancer, we utilized biotin ligase proximity profiling of ER interactomes. Mass spectrometry analysis revealed tripartite motif containing 33 (TRIM33) as an estrogen-dependent interactor of ER. shRNA knockdown showed that TRIM33 promoted ER transcriptional activity and estrogen-induced cell growth. Despite its known role as an E3 ubiquitin ligase, TRIM33 increased the stability of endogenous ER in breast cancer cells. TRIM33 offers a novel target for inhibiting estrogen-induced cancer cell growth, particularly in cases of endocrine resistance driven by ER (ESR1) gene amplification or overexpression.
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Affiliation(s)
- Bianca A. Romo
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Barbara Karakyriakou
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Lauren Cressey
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Brooke L. Brauer
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Huijuan Yang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Alexa Warren
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Anneka L. Johnson
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Arminja N. Kettenbach
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
| | - Todd W. Miller
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03755, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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4
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Ashton AW, Dhanjal HK, Rossner B, Mahmood H, Patel VI, Nadim M, Lota M, Shahid F, Li Z, Joyce D, Pajkos M, Dosztányi Z, Jiao X, Pestell RG. Acetylation of nuclear receptors in health and disease: an update. FEBS J 2024; 291:217-236. [PMID: 36471658 DOI: 10.1111/febs.16695] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/17/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a common reversible post-translational modification of proteins that plays a key role in regulating gene expression. Nuclear receptors (NRs) include ligand-inducible transcription factors and orphan receptors for which the ligand is undetermined, which together regulate the expression of genes involved in development, metabolism, homeostasis, reproduction and human diseases including cancer. Since the original finding that the ERα, AR and HNF4 are acetylated, we now understand that the vast majority of NRs are acetylated and that this modification has profound effects on NR function. Acetylation sites are often conserved and involve both ordered and disordered regions of NRs. The acetylated residues function as part of an intramolecular signalling platform intersecting phosphorylation, methylation and other modifications. Acetylation of NR has been shown to impact recruitment into chromatin, co-repressor and coactivator complex formation, sensitivity and specificity of regulation by ligand and ligand antagonists, DNA binding, subcellular distribution and transcriptional activity. A growing body of evidence in mice indicates a vital role for NR acetylation in metabolism. Additionally, mutations of the NR acetylation site occur in human disease. This review focuses on the role of NR acetylation in coordinating signalling in normal physiology and disease.
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Affiliation(s)
- Anthony W Ashton
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Lankenau Institute for Medical Research, Wynnewood, PA, USA
| | | | - Benjamin Rossner
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Huma Mahmood
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Vivek I Patel
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Mohammad Nadim
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Manpreet Lota
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Farhan Shahid
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
| | - Zhiping Li
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, USA
| | - David Joyce
- Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Matyas Pajkos
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Xuanmao Jiao
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, USA
| | - Richard G Pestell
- Xavier University School of Medicine at Aruba, Oranjestad, Aruba
- Pennsylvania Cancer and Regenerative Medicine Research Center, Baruch S. Blumberg Institute, Wynnewood, PA, USA
- The Wistar Cancer Center, Philadelphia, PA, USA
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5
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Hansda AK, Biswas B, Goswami R. 17-β Estradiol (E2) distinctly regulates the expression of IL-4 and IL-13 in Th2 cells via modulating the interplay between GATA3 and PU.1. Cytokine 2024; 173:156440. [PMID: 37984154 DOI: 10.1016/j.cyto.2023.156440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]
Abstract
17-β Estradiol (E2) has long standing known functions in regulating human physiology as well as immune system. E2 is known to elicit a protective role against experimental autoimmune encephalomyelitis (EAE) and has been used as a drug for treatment against multiple sclerosis. Moreover, E2 regulates the adaptive immune system by directly affecting the T helper cell subsets differentiation and antibody secretion mediated by B cells. Reports have shown that E2 promotes Th1 and Treg cell differentiation; whereas it attenuated the Th17 and Tfh cell differentiation. Albeit multiple and contrasting studies, the mechanisms of behind E2 action on Th2 cells remained understudied. Hence, we sought to dissect the impact of E2 in Th2 cell differentiation. In this study, we elucidated the molecular mechanisms behind E2-mediated regulation of the differentiation of Th2 cells. We observed that E2 significantly attenuated the IL-4-secreting Th2 population in an ERα-dependent manner. We validated these findings using ICI 182, 780, an antagonist to ERα, not ERβ and ectopically overexpressing ERα in Th2 cells. We further determined that ERα alters the recruitment of GATA3 and PU.1 to Il4 gene by directly interacting with them. This altered recruitment was observed to be stronger at Il4 than Il13 locus. Interestingly, we detected a distinct recruitment of GATA3 and PU.1 at Il13 gene; however, there was no E2-mediated broad alteration in the recruitment of histone-modifiers at Il13 locus. These findings suggest that E2 regulates Il4 in a distinctly separate mechanism as opposed to Il13 locus in Th2 cells.
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Affiliation(s)
| | - Biswajit Biswas
- School of Bioscience, Indian Institute of Technology Kharagpur, India
| | - Ritobrata Goswami
- School of Bioscience, Indian Institute of Technology Kharagpur, India.
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6
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Li AM, He B, Karagiannis D, Li Y, Jiang H, Srinivasan P, Ramirez Y, Zhou MN, Curtis C, Gruber JJ, Lu C, Rankin EB, Ye J. Serine starvation silences estrogen receptor signaling through histone hypoacetylation. Proc Natl Acad Sci U S A 2023; 120:e2302489120. [PMID: 37695911 PMCID: PMC10515173 DOI: 10.1073/pnas.2302489120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/07/2023] [Indexed: 09/13/2023] Open
Abstract
Loss of estrogen receptor (ER) pathway activity promotes breast cancer progression, yet how this occurs remains poorly understood. Here, we show that serine starvation, a metabolic stress often found in breast cancer, represses estrogen receptor alpha (ERα) signaling by reprogramming glucose metabolism and epigenetics. Using isotope tracing and time-resolved metabolomic analyses, we demonstrate that serine is required to maintain glucose flux through glycolysis and the TCA cycle to support acetyl-CoA generation for histone acetylation. Consequently, limiting serine depletes histone H3 lysine 27 acetylation (H3K27ac), particularly at the promoter region of ER pathway genes including the gene encoding ERα, ESR1. Mechanistically, serine starvation impairs acetyl-CoA-dependent gene expression by inhibiting the entry of glycolytic carbon into the TCA cycle and down-regulating the mitochondrial citrate exporter SLC25A1, a critical enzyme in the production of nucleocytosolic acetyl-CoA from glucose. Consistent with this model, total H3K27ac and ERα expression are suppressed by SLC25A1 inhibition and restored by acetate, an alternate source of acetyl-CoA, in serine-free conditions. We thus uncover an unexpected role for serine in sustaining ER signaling through the regulation of acetyl-CoA metabolism.
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Affiliation(s)
- Albert M Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
| | - Bo He
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Yang Li
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Haowen Jiang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Preethi Srinivasan
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Yaniel Ramirez
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Meng-Ning Zhou
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
| | - Christina Curtis
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Joshua J Gruber
- Department of Internal Medicine, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75235
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032
| | - Erinn B Rankin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305
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7
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GRHL2 Enhances Phosphorylated Estrogen Receptor (ER) Chromatin Binding and Regulates ER-Mediated Transcriptional Activation and Repression. Mol Cell Biol 2022; 42:e0019122. [PMID: 36036613 PMCID: PMC9584124 DOI: 10.1128/mcb.00191-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation of estrogen receptor α (ER) at serine 118 (pS118-ER) is induced by estrogen and is the most abundant posttranslational mark associated with a transcriptionally active receptor. Cistromic analysis of pS118-ER from our group revealed enrichment of the GRHL2 motif near pS118-ER binding sites. In this study, we used cistromic and transcriptomic analyses to interrogate the relationship between GRHL2 and pS118-ER. We found that GRHL2 is bound to chromatin at pS118-ER/GRHL2 co-occupancy sites prior to ligand treatment, and GRHL2 binding is required for maximal pS118-ER recruitment. pS118-ER/GRHL2 co-occupancy sites were enriched at active enhancers marked by H3K27ac and H3K4me1, along with FOXA1 and p300, compared to sites where each factor binds independently. Transcriptomic analysis yielded four subsets of ER/GRHL2-coregulated genes revealing that GRHL2 can both enhance and antagonize E2-mediated ER transcriptional activity. Gene ontology analysis indicated that coregulated genes are involved in cell migration. Accordingly, knockdown of GRHL2, combined with estrogen treatment, resulted in increased cell migration but no change in proliferation. These results support a model in which GRHL2 binds to selected enhancers and facilitates pS118-ER recruitment to chromatin, which then results in differential activation and repression of genes that control estrogen-regulated ER-positive breast cancer cell migration.
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8
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Hou TY, Kraus WL. Analysis of estrogen-regulated enhancer RNAs identifies a functional motif required for enhancer assembly and gene expression. Cell Rep 2022; 39:110944. [PMID: 35705040 PMCID: PMC9246336 DOI: 10.1016/j.celrep.2022.110944] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/12/2022] [Accepted: 05/20/2022] [Indexed: 11/03/2022] Open
Abstract
To better understand the functions of non-coding enhancer RNAs (eRNAs), we annotated the estrogen-regulated eRNA transcriptome in estrogen receptor α (ERα)-positive breast cancer cells using PRO-cap and RNA sequencing. We then cloned a subset of the eRNAs identified, fused them to single guide RNAs, and targeted them to their ERα enhancers of origin using CRISPR/dCas9. Some of the eRNAs tested modulated the expression of cognate, but not heterologous, target genes after estrogen treatment by increasing ERα recruitment and stimulating p300-catalyzed H3K27 acetylation at the enhancer. We identified a ∼40 nucleotide functional eRNA regulatory motif (FERM) present in many eRNAs that was necessary and sufficient to modulate gene expression, but not the specificity of activation, after estrogen treatment. The FERM interacted with BCAS2, an RNA-binding protein amplified in breast cancers. The ectopic expression of a targeted eRNA controlling the expression of an oncogene resulted in increased cell proliferation, demonstrating the regulatory potential of eRNAs in breast cancer.
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Affiliation(s)
- Tim Y Hou
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - W Lee Kraus
- Laboratory of Signaling and Gene Regulation, Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Division of Basic Research, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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9
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Epigenetic Factors as Etiological Agents, Diagnostic Markers, and Therapeutic Targets for Luminal Breast Cancer. Biomedicines 2022; 10:biomedicines10040748. [PMID: 35453496 PMCID: PMC9031900 DOI: 10.3390/biomedicines10040748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 11/16/2022] Open
Abstract
Luminal breast cancer, an etiologically heterogeneous disease, is characterized by high steroid hormone receptor activity and aberrant gene expression profiles. Endocrine therapy and chemotherapy are promising therapeutic approaches to mitigate breast cancer proliferation and recurrence. However, the treatment of therapy-resistant breast cancer is a major challenge. Recent studies on breast cancer etiology have revealed the critical roles of epigenetic factors in luminal breast cancer tumorigenesis and drug resistance. Tumorigenic epigenetic factor-induced aberrant chromatin dynamics dysregulate the onset of gene expression and consequently promote tumorigenesis and metastasis. Epigenetic dysregulation, a type of somatic mutation, is a high-risk factor for breast cancer progression and therapy resistance. Therefore, epigenetic modulators alone or in combination with other therapies are potential therapeutic agents for breast cancer. Several clinical trials have analyzed the therapeutic efficacy of potential epi-drugs for breast cancer and reported beneficial clinical outcomes, including inhibition of tumor cell adhesion and invasiveness and mitigation of endocrine therapy resistance. This review focuses on recent findings on the mechanisms of epigenetic factors in the progression of luminal breast cancer. Additionally, recent findings on the potential of epigenetic factors as diagnostic biomarkers and therapeutic targets for breast cancer are discussed.
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10
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Leonen CJA, Shimada M, Weller CE, Nakadai T, Hsu PL, Tyson EL, Mishra A, Shelton PM, Sadilek M, Hawkins RD, Zheng N, Roeder RG, Chatterjee C. Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts. eLife 2021; 10:67952. [PMID: 34747692 PMCID: PMC8626089 DOI: 10.7554/elife.67952] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 11/06/2021] [Indexed: 01/22/2023] Open
Abstract
The post-translational modification of histones by the small ubiquitin-like modifier (SUMO) protein has been associated with gene regulation, centromeric localization, and double-strand break repair in eukaryotes. Although sumoylation of histone H4 was specifically associated with gene repression, this could not be proven due to the challenge of site-specifically sumoylating H4 in cells. Biochemical crosstalk between SUMO and other histone modifications, such as H4 acetylation and H3 methylation, that are associated with active genes also remains unclear. We addressed these challenges in mechanistic studies using an H4 chemically modified at Lys12 by SUMO-3 (H4K12su) and incorporated into mononucleosomes and chromatinized plasmids for functional studies. Mononucleosome-based assays revealed that H4K12su inhibits transcription-activating H4 tail acetylation by the histone acetyltransferase p300, as well as transcription-associated H3K4 methylation by the extended catalytic module of the Set1/COMPASS (complex of proteins associated with Set1) histone methyltransferase complex. Activator- and p300-dependent in vitro transcription assays with chromatinized plasmids revealed that H4K12su inhibits both H4 tail acetylation and RNA polymerase II-mediated transcription. Finally, cell-based assays with a SUMO-H4 fusion that mimics H4 tail sumoylation confirmed the negative crosstalk between histone sumoylation and acetylation/methylation. Thus, our studies establish the key role for histone sumoylation in gene silencing and its negative biochemical crosstalk with active transcription-associated marks in human cells.
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Affiliation(s)
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
| | - Caroline E Weller
- Department of Chemistry, University of Washington, Seattle, United States
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States.,Project for Cancer Epigenomics, Cancer Institute of JFCR, Tokyo, Japan
| | - Peter L Hsu
- Department of Pharmacology, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Elizabeth L Tyson
- Department of Chemistry, University of Washington, Seattle, United States
| | - Arpit Mishra
- Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, United States
| | - Patrick Mm Shelton
- Department of Chemistry, University of Washington, Seattle, United States
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, United States
| | - R David Hawkins
- Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, United States
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, United States
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11
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Yoneda M, Yasui K, Nakagawa T, Hattori N, Ito T. Nucleosome assembly protein 1 (NAP-1) is a regulator of histone H1 acetylation. J Biochem 2021; 170:763-773. [PMID: 34551067 DOI: 10.1093/jb/mvab098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
Acetylation of histone H1 is generally considered to activate transcription, whereas deacetylation of H1 represses transcription. However, the precise mechanism of the acetylation is unknown. Here, using chromatography, we identified nucleosome assembly protein 1 (NAP-1) as having inhibitory activity against histone H1 acetylation by acetyltransferase p300. We found that native NAP-1 interacts with H1 in a Drosophila crude extract. We also found that it inhibits the deacetylation of histone H1 by histone deacetylase 1 (HDAC1). The core histones in nucleosomes were acetylated in a GAL4-VP16 transcriptional activator-dependent manner in vitro. This acetylation was strongly repressed by hypoacetylated H1 but to a lesser extent by hyperacetylated H1. Consistent with these findings, a micrococcal nuclease assay indicated that hypoacetylated H1, which represses activator-dependent acetylation, was incorporated into chromatin, whereas hyperacetylated H1 was not. To determine the contribution of NAP-1 to transcriptional regulation in vivo, we compared NAP-1 knockdown (KD) with coactivator CREB-binding protein (CBP) KD using RNA sequencing in Drosophila Schneider 2 cells. Most genes were downregulated rather than upregulated by NAP-1 KD, and those downregulated genes were also downregulated by CBP KD. Our results suggest that NAP-1 plays a role in transcriptional regulation by fine-tuning the acetylation of histone H1.
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Affiliation(s)
- Mitsuhiro Yoneda
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan
| | - Kiyoshi Yasui
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.,Department of Oncology, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Takeya Nakagawa
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan
| | - Naoko Hattori
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan
| | - Takashi Ito
- Department of Biochemistry, Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan.,Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8523, Japan
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12
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Waddell AR, Huang H, Liao D. CBP/p300: Critical Co-Activators for Nuclear Steroid Hormone Receptors and Emerging Therapeutic Targets in Prostate and Breast Cancers. Cancers (Basel) 2021; 13:2872. [PMID: 34201346 PMCID: PMC8229436 DOI: 10.3390/cancers13122872] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/10/2023] Open
Abstract
The CREB-binding protein (CBP) and p300 are two paralogous lysine acetyltransferases (KATs) that were discovered in the 1980s-1990s. Since their discovery, CBP/p300 have emerged as important regulatory proteins due to their ability to acetylate histone and non-histone proteins to modulate transcription. Work in the last 20 years has firmly established CBP/p300 as critical regulators for nuclear hormone signaling pathways, which drive tumor growth in several cancer types. Indeed, CBP/p300 are critical co-activators for the androgen receptor (AR) and estrogen receptor (ER) signaling in prostate and breast cancer, respectively. The AR and ER are stimulated by sex hormones and function as transcription factors to regulate genes involved in cell cycle progression, metabolism, and other cellular functions that contribute to oncogenesis. Recent structural studies of the AR/p300 and ER/p300 complexes have provided critical insights into the mechanism by which p300 interacts with and activates AR- and ER-mediated transcription. Breast and prostate cancer rank the first and forth respectively in cancer diagnoses worldwide and effective treatments are urgently needed. Recent efforts have identified specific and potent CBP/p300 inhibitors that target the acetyltransferase activity and the acetytllysine-binding bromodomain (BD) of CBP/p300. These compounds inhibit AR signaling and tumor growth in prostate cancer. CBP/p300 inhibitors may also be applicable for treating breast and other hormone-dependent cancers. Here we provide an in-depth account of the critical roles of CBP/p300 in regulating the AR and ER signaling pathways and discuss the potential of CBP/p300 inhibitors for treating prostate and breast cancer.
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Affiliation(s)
- Aaron R. Waddell
- UF Health Cancer Center, Department of Anatomy and Cell Biology, University Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA;
| | - Haojie Huang
- Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA;
| | - Daiqing Liao
- UF Health Cancer Center, Department of Anatomy and Cell Biology, University Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA;
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13
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Waddell A, Mahmud I, Ding H, Huo Z, Liao D. Pharmacological Inhibition of CBP/p300 Blocks Estrogen Receptor Alpha (ERα) Function through Suppressing Enhancer H3K27 Acetylation in Luminal Breast Cancer. Cancers (Basel) 2021; 13:2799. [PMID: 34199844 PMCID: PMC8200112 DOI: 10.3390/cancers13112799] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/23/2021] [Accepted: 05/29/2021] [Indexed: 01/10/2023] Open
Abstract
Estrogen receptor alpha (ER) is the oncogenic driver for ER+ breast cancer (BC). ER antagonists are the standard-of-care treatment for ER+ BC; however, primary and acquired resistance to these agents is common. CBP and p300 are critical ER co-activators and their acetyltransferase (KAT) domain and acetyl-lysine binding bromodomain (BD) represent tractable drug targets, but whether CBP/p300 inhibitors can effectively suppress ER signaling remains unclear. We report that the CBP/p300 KAT inhibitor A-485 and the BD inhibitor GNE-049 downregulate ER, attenuate estrogen-induced c-Myc and Cyclin D1 expression, and inhibit growth of ER+ BC cells through inducing senescence. Microarray and RNA-seq analysis demonstrates that A-485 or EP300 (encoding p300) knockdown globally inhibits expression of estrogen-regulated genes, confirming that ER inhibition is an on-target effect of A-485. Using ChIP-seq, we report that A-485 suppresses H3K27 acetylation in the enhancers of ER target genes (including MYC and CCND1) and this correlates with their decreased expression, providing a mechanism underlying how CBP/p300 inhibition downregulates ER gene network. Together, our results provide a preclinical proof-of-concept that CBP/p300 represent promising therapeutic targets in ER+ BC for inhibiting ER signaling.
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Affiliation(s)
- Aaron Waddell
- Department of Anatomy and Cell Biology, University Florida College of Medicine, UF Health Cancer Center, 2033 Mowry Road, Gainesville, FL 32610, USA; (A.W.); (I.M.)
| | - Iqbal Mahmud
- Department of Anatomy and Cell Biology, University Florida College of Medicine, UF Health Cancer Center, 2033 Mowry Road, Gainesville, FL 32610, USA; (A.W.); (I.M.)
| | - Haocheng Ding
- Departments of Biostatistics, University Florida College of Medicine, 2004 Mowry Road, Gainesville, FL 32610, USA; (H.D.); (Z.H.)
| | - Zhiguang Huo
- Departments of Biostatistics, University Florida College of Medicine, 2004 Mowry Road, Gainesville, FL 32610, USA; (H.D.); (Z.H.)
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, University Florida College of Medicine, UF Health Cancer Center, 2033 Mowry Road, Gainesville, FL 32610, USA; (A.W.); (I.M.)
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14
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Farcas AM, Nagarajan S, Cosulich S, Carroll JS. Genome-Wide Estrogen Receptor Activity in Breast Cancer. Endocrinology 2021; 162:bqaa224. [PMID: 33284960 PMCID: PMC7787425 DOI: 10.1210/endocr/bqaa224] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Indexed: 12/13/2022]
Abstract
The largest subtype of breast cancer is characterized by the expression and activity of the estrogen receptor alpha (ERalpha/ER). Although several effective therapies have significantly improved survival, the adaptability of cancer cells means that patients frequently stop responding or develop resistance to endocrine treatment. ER does not function in isolation and multiple associating factors have been reported to play a role in regulating the estrogen-driven transcriptional program. This review focuses on the dynamic interplay between some of these factors which co-occupy ER-bound regulatory elements, their contribution to estrogen signaling, and their possible therapeutic applications. Furthermore, the review illustrates how some ER association partners can influence and reprogram the genomic distribution of the estrogen receptor. As this dynamic ER activity enables cancer cell adaptability and impacts the clinical outcome, defining how this plasticity is determined is fundamental to our understanding of the mechanisms of disease progression.
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Affiliation(s)
- Anca M Farcas
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Sankari Nagarajan
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | | | - Jason S Carroll
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
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15
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Xu J, Wang W, Xu L, Chen JY, Chong J, Oh J, Leschziner AE, Fu XD, Wang D. Cockayne syndrome B protein acts as an ATP-dependent processivity factor that helps RNA polymerase II overcome nucleosome barriers. Proc Natl Acad Sci U S A 2020; 117:25486-25493. [PMID: 32989164 PMCID: PMC7568279 DOI: 10.1073/pnas.2013379117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
While loss-of-function mutations in Cockayne syndrome group B protein (CSB) cause neurological diseases, this unique member of the SWI2/SNF2 family of chromatin remodelers has been broadly implicated in transcription elongation and transcription-coupled DNA damage repair, yet its mechanism remains largely elusive. Here, we use a reconstituted in vitro transcription system with purified polymerase II (Pol II) and Rad26, a yeast ortholog of CSB, to study the role of CSB in transcription elongation through nucleosome barriers. We show that CSB forms a stable complex with Pol II and acts as an ATP-dependent processivity factor that helps Pol II across a nucleosome barrier. This noncanonical mechanism is distinct from the canonical modes of chromatin remodelers that directly engage and remodel nucleosomes or transcription elongation factors that facilitate Pol II nucleosome bypass without hydrolyzing ATP. We propose a model where CSB facilitates gene expression by helping Pol II bypass chromatin obstacles while maintaining their structures.
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Affiliation(s)
- Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Wei Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Liang Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Jia-Yu Chen
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093
| | - Xiang-Dong Fu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
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16
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Abstract
Transcription in several organisms from certain bacteria to humans has been observed to be stochastic in nature: toggling between active and inactive states. Periods of active nascent RNA synthesis known as bursts represent individual gene activation events in which multiple polymerases are initiated. Therefore, bursting is the single locus illustration of both gene activation and repression. Although transcriptional bursting was originally observed decades ago, only recently have technological advances enabled the field to begin elucidating gene regulation at the single-locus level. In this review, we focus on how biochemical, genomic, and single-cell data describe the regulatory steps of transcriptional bursts.
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Affiliation(s)
- Joseph Rodriguez
- National Institute of Environmental Health Sciences, Durham, North Carolina 27709, USA
| | - Daniel R. Larson
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
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17
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Zhang Z, Yu W, Tang D, Zhou Y, Bi M, Wang H, Zheng Y, Chen M, Li L, Xu X, Zhang W, Tao H, Jin VX, Liu Z, Chen L. Epigenomics-based identification of oestrogen-regulated long noncoding RNAs in ER+ breast cancer. RNA Biol 2020; 17:1590-1602. [PMID: 32506995 DOI: 10.1080/15476286.2020.1777769] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Breast cancer is one of the most prevalent cancers in women worldwide. Through the regulation of many coding and non-coding target genes, oestrogen (E2 or 17β-oestradiol) and its nuclear receptor ERα play important roles in breast cancer development and progression. Despite the astounding advances in our understanding of oestrogen-regulated coding genes over the past decades, our knowledge on oestrogen-regulated non-coding targets has just begun to expand. Here we leverage epigenomic approaches to systematically analyse oestrogen-regulated long non-coding RNAs (lncRNAs). Similar to the coding targets of ERα, the transcription of oestrogen-regulated lncRNAs correlates with the activation status of ERα enhancers, measured by eRNA production, chromatin accessibility, and the occupancy of the enhancer regulatory components including P300, MED1, and ARID1B. Our 3D chromatin architecture analyses suggest that lncRNAs and their neighbouring E2-resonsive coding genes, exemplified by LINC00160 and RUNX1, might be regulated as a 3D structural unit resulted from enhancer-promoter interactions. Finally, we evaluated the expression levels of LINC00160 and RUNX1 in various types of breast cancer and found that their expression positively correlated with the survival rate in ER+ breast cancer patients, implying that the oestrogen-regulated LINC00160 and its neighbouring RUNX1 might represent potential biomarkers for ER+ breast cancers.
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Affiliation(s)
- Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Wei Yu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA.,Department of Orthopedics, The Second Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou, Zhejiang, China
| | - Dan Tang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA.,Department of General Practice, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi, China
| | - Yufan Zhou
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Mingjun Bi
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Hu Wang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Yan Zheng
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Mingqiu Chen
- Department of Radiation Oncology, Fujian Cancer Hospital & Fujian Medical University , Fuzhou, China
| | - Li Li
- Department of Oncology, The Second People's Hospital of Jiaozuo , Jiaozuo City, Henan, China
| | - Xinping Xu
- Jiangxi Institute of Respiratory Disease, the Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi, China
| | - Wei Zhang
- Jiangxi Institute of Respiratory Disease, the Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi, China
| | - Huimin Tao
- Department of Orthopedics, The Second Affiliated Hospital, School of Medicine, Zhejiang University , Hangzhou, Zhejiang, China
| | - Victor X Jin
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
| | - Lizhen Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA.,Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio , San Antonio, TX, USA
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18
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Hankey W, Chen Z, Wang Q. Shaping Chromatin States in Prostate Cancer by Pioneer Transcription Factors. Cancer Res 2020; 80:2427-2436. [PMID: 32094298 PMCID: PMC7299826 DOI: 10.1158/0008-5472.can-19-3447] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/14/2020] [Accepted: 02/19/2020] [Indexed: 01/28/2023]
Abstract
The androgen receptor (AR) is a critical therapeutic target in prostate cancer that responds to antagonists in primary disease, but inevitably becomes reactivated, signaling onset of the lethal castration-resistant prostate cancer (CRPC) stage. Epigenomic investigation of the chromatin environment and interacting partners required for AR transcriptional activity has uncovered three pioneer factors that open up chromatin and facilitate AR-driven transcriptional programs. FOXA1, HOXB13, and GATA2 are required for normal AR transcription in prostate epithelial development and for oncogenic AR transcription during prostate carcinogenesis. AR signaling is dependent upon these three pioneer factors both before and after the clinical transition from treatable androgen-dependent disease to untreatable CRPC. Agents targeting their respective DNA binding or downstream chromatin-remodeling events have shown promise in preclinical studies of CRPC. AR-independent functions of FOXA1, HOXB13, and GATA2 are emerging as well. While all three pioneer factors exert effects that promote carcinogenesis, some of their functions may inhibit certain stages of prostate cancer progression. In all, these pioneer factors represent some of the most promising potential therapeutic targets to emerge thus far from the study of the prostate cancer epigenome.
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Affiliation(s)
- William Hankey
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Zhong Chen
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina.
| | - Qianben Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina.
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19
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Cramer P. Eukaryotic Transcription Turns 50. Cell 2020; 179:808-812. [PMID: 31675494 DOI: 10.1016/j.cell.2019.09.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 12/15/2022]
Abstract
This year we celebrate the 50th anniversary of the discovery of the three eukaryotic RNA polymerases. Ever since this seminal event in 1969, researchers have investigated the intricate mechanisms of gene transcription with great dedication. The transcription field continues to influence developmental, stem cell, and cancer biology.
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Affiliation(s)
- Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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20
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Organization and regulation of gene transcription. Nature 2019; 573:45-54. [PMID: 31462772 DOI: 10.1038/s41586-019-1517-4] [Citation(s) in RCA: 361] [Impact Index Per Article: 72.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/30/2019] [Indexed: 12/18/2022]
Abstract
The regulated transcription of genes determines cell identity and function. Recent structural studies have elucidated mechanisms that govern the regulation of transcription by RNA polymerases during the initiation and elongation phases. Microscopy studies have revealed that transcription involves the condensation of factors in the cell nucleus. A model is emerging for the transcription of protein-coding genes in which distinct transient condensates form at gene promoters and in gene bodies to concentrate the factors required for transcription initiation and elongation, respectively. The transcribing enzyme RNA polymerase II may shuttle between these condensates in a phosphorylation-dependent manner. Molecular principles are being defined that rationalize transcriptional organization and regulation, and that will guide future investigations.
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21
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The transformation of the DNA template in RNA polymerase II transcription: a historical perspective. Nat Struct Mol Biol 2019; 26:766-770. [PMID: 31439939 DOI: 10.1038/s41594-019-0278-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/10/2019] [Indexed: 11/08/2022]
Abstract
The discovery of RNA polymerases I, II, and III opened up a new era in gene expression. Here I provide a personal retrospective account of the transformation of the DNA template, as it evolved from naked DNA to chromatin, in the biochemical analysis of transcription by RNA polymerase II. These studies have revealed new insights into the mechanisms by which transcription factors function with chromatin to regulate gene expression.
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22
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Roeder RG. 50+ years of eukaryotic transcription: an expanding universe of factors and mechanisms. Nat Struct Mol Biol 2019; 26:783-791. [PMID: 31439941 DOI: 10.1038/s41594-019-0287-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/26/2019] [Indexed: 12/12/2022]
Abstract
The landmark 1969 discovery of nuclear RNA polymerases I, II and III in diverse eukaryotes represented a major turning point in the field that, with subsequent elucidation of the distinct structures and functions of these enzymes, catalyzed an avalanche of further studies. In this Review, written from a personal and historical perspective, I highlight foundational biochemical studies that led to the discovery of an expanding universe of the components of the transcriptional and regulatory machineries, and a parallel complexity in gene-specific mechanisms that continue to be explored to the present day.
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Affiliation(s)
- Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, New York, USA.
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23
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Jones D, Wilson L, Thomas H, Gaughan L, Wade MA. The Histone Demethylase Enzymes KDM3A and KDM4B Co-Operatively Regulate Chromatin Transactions of the Estrogen Receptor in Breast Cancer. Cancers (Basel) 2019; 11:cancers11081122. [PMID: 31390833 PMCID: PMC6721541 DOI: 10.3390/cancers11081122] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/29/2019] [Accepted: 08/03/2019] [Indexed: 02/07/2023] Open
Abstract
Many estrogen receptor (ER)-positive breast cancers develop resistance to endocrine therapy but retain canonical receptor signalling in the presence of selective ER antagonists. Numerous co-regulatory proteins, including enzymes that modulate the chromatin environment, control the transcriptional activity of the ER. Targeting ER co-regulators has therefore been proposed as a novel therapeutic approach. By assessing DNA-binding dynamics in ER-positive breast cancer cells, we have identified that the histone H3 lysine 9 demethylase enzymes, KDM3A and KDM4B, co-operate to regulate ER activity via an auto-regulatory loop that facilitates the recruitment of each co-activating enzyme to chromatin. We also provide evidence that suggests that KDM3A primes chromatin for deposition of the ER pioneer factor FOXA1 and recruitment of the ER-transcriptional complex, all prior to ER recruitment, therefore establishing an important mechanism of chromatin regulation involving histone demethylases and pioneer factors, which controls ER functionality. Importantly, we show via global gene-expression analysis that a KDM3A/KDM4B/FOXA1 co-regulated gene signature is enriched for pro-proliferative and ER-target gene sets, suggesting that abrogation of this network could be an efficacious therapeutic strategy. Finally, we show that depletion of both KDM3A and KDM4B has a greater inhibitory effect on ER activity and cell growth than knockdown of each individual enzyme, suggesting that targeting both enzymes represents a potentially efficacious therapeutic option for ER-driven breast cancer.
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Affiliation(s)
- Dominic Jones
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Laura Wilson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Huw Thomas
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Luke Gaughan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Mark A Wade
- Biomedical Sciences, Faculty of Health Sciences, University of Hull, Hull HU6 7RX, UK.
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24
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Zhu C, Li L, Zhang Z, Bi M, Wang H, Su W, Hernandez K, Liu P, Chen J, Chen M, Huang THM, Chen L, Liu Z. A Non-canonical Role of YAP/TEAD Is Required for Activation of Estrogen-Regulated Enhancers in Breast Cancer. Mol Cell 2019; 75:791-806.e8. [PMID: 31303470 DOI: 10.1016/j.molcel.2019.06.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/06/2019] [Accepted: 06/05/2019] [Indexed: 12/26/2022]
Abstract
YAP/TEAD are nuclear effectors of the Hippo pathway, regulating organ size and tumorigenesis largely through promoter-associated function. However, their function as enhancer regulators remains poorly understood. Through an in vivo proximity-dependent labeling (BioID) technique, we identified YAP1 and TEAD4 protein as co-regulators of ERα on enhancers. The binding of YAP1/TEAD4 to ERα-bound enhancers is augmented upon E2 stimulation and is required for the induction of E2/ERα target genes and E2-induced oncogenic cell growth. Furthermore, their enhancer binding is a prerequisite for enhancer activation marked by eRNA transcription and for the recruitment of the enhancer activation machinery component MED1. The binding of TEAD4 on active ERE-containing enhancers is independent of its DNA-binding behavior, and instead, occurs through protein-tethering trans-binding. Our data reveal a non-canonical function of YAP1 and TEAD4 as ERα cofactors in regulating cancer growth, highlighting the potential of YAP/TEAD as possible actionable drug targets for ERα+ breast cancer.
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Affiliation(s)
- Chi Zhu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Li Li
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Department of Oncology, The Second People's Hospital of Jiaozuo, Jiaozuo City, Henan 454001, China
| | - Zhao Zhang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Mingjun Bi
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Hu Wang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Wenyue Su
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Karen Hernandez
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Pingping Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Junqiang Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Mingqiu Chen
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou, Fujian 350014, China
| | - Tim Hui-Ming Huang
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Lizhen Chen
- Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Zhijie Liu
- Department of Molecular Medicine, Mays Cancer Center, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
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Challenges in the Structural-Functional Characterization of Multidomain, Partially Disordered Proteins CBP and p300: Preparing Native Proteins and Developing Nanobody Tools. Methods Enzymol 2018; 611:607-675. [PMID: 30471702 DOI: 10.1016/bs.mie.2018.09.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structural and functional characterization of large multidomain signaling proteins containing long disordered linker regions represents special methodological and conceptual challenges. These proteins show extreme structural heterogeneity and have complex posttranslational modification patterns, due to which traditional structural biology techniques provide results that are often difficult to interpret. As demonstrated through the example of two such multidomain proteins, CREB-binding protein (CBP) and its paralogue, p300, even the expression and purification of such proteins are compromised by their extreme proteolytic sensitivity and structural heterogeneity. In this chapter, we describe the effective expression of CBP and p300 in a eukaryotic host, Sf9 insect cells, followed by their tandem affinity purification based on two terminal tags to ensure their structural integrity. The major focus of this chapter is on the development of novel accessory tools, single-domain camelid antibodies (nanobodies), for structural-functional characterization. Specific nanobodies against full-length CBP and p300 can specifically target their different regions and can be used for their marking, labeling, and structural stabilization in a broad range of in vitro and in vivo studies. Here, we describe four high-affinity nanobodies binding to the KIX and the HAT domains, either mimicking known interacting partners or revealing new functionally relevant conformations. As immunization of llamas results in nanobody libraries with a great sequence variation, deep sequencing and interaction analysis with different regions of the proteins provide a novel approach toward developing a panel of specific nanobodies.
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Hilton HN, Clarke CL, Graham JD. Estrogen and progesterone signalling in the normal breast and its implications for cancer development. Mol Cell Endocrinol 2018; 466:2-14. [PMID: 28851667 DOI: 10.1016/j.mce.2017.08.011] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 08/11/2017] [Accepted: 08/18/2017] [Indexed: 12/31/2022]
Abstract
The ovarian hormones estrogen and progesterone are master regulators of the development and function of a broad spectrum of human tissues, including the breast, reproductive and cardiovascular systems, brain and bone. Acting through the nuclear estrogen (ER) and progesterone receptors (PR), both play complex and essential coordinated roles in the extensive development of the lobular alveolar epithelial structures of the normal breast during puberty, the normal menstrual cycle and pregnancy. The past decade has seen major advances in understanding the mechanisms of action of estrogen and progesterone in the normal breast and in the delineation of the complex hierarchy of cell types regulated by ovarian hormones in this tissue. There is evidence for a role for both ER and PR in driving breast cancer, and both are favourable prognostic markers with respect to outcome. In this review, we summarize current knowledge of the mechanisms of action of ER and PR in the normal breast, and implications for the development and management of breast cancer.
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Affiliation(s)
- Heidi N Hilton
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney Medical School - Westmead, The University of Sydney, Westmead, NSW 2145, Australia
| | - Christine L Clarke
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney Medical School - Westmead, The University of Sydney, Westmead, NSW 2145, Australia
| | - J Dinny Graham
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney Medical School - Westmead, The University of Sydney, Westmead, NSW 2145, Australia.
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27
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Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev 2018; 32:682-694. [PMID: 29759984 PMCID: PMC6004073 DOI: 10.1101/gad.313973.118] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/11/2018] [Indexed: 12/22/2022]
Abstract
Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome-destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and colocalizes with a subset of H3K36me3-enriched regions. Notably, the recruitment of NDF to gene bodies is accompanied by an increase in the transcript levels of many of the NDF-enriched genes. In addition, the global loss of NDF results in a decrease in the RNA levels of many genes. In humans, NDF is present at high levels in all tested tissue types, is essential in stem cells, and is frequently overexpressed in breast cancer. These findings indicate that NDF is a nucleosome-destabilizing factor that is recruited to gene bodies during transcriptional activation and facilitates Pol II transcription through nucleosomes.
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Affiliation(s)
- Jia Fei
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Haruhiko Ishii
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Franz Meitinger
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Center for Epigenomics, Institute of Genome Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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Cottone E, Orso F, Biglia N, Sismondi P, De Bortoli M. Role of Coactivators and Corepressors in Steroid and Nuclear Receptor Signaling: Potential Markers of Tumor Growth and Drug Sensitivity. Int J Biol Markers 2018; 16:151-66. [PMID: 11605727 DOI: 10.1177/172460080101600301] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Nuclear receptors regulate target gene expression in response to steroid and thyroid hormones, retinoids, vitamin D and other ligands. These ligand-dependent transcription factors function by contacting various nuclear cooperating proteins, called coactivators and corepressors, which mediate local chromatin remodeling as well as communication with the basal transcriptional apparatus. Nuclear receptors and their coregulatory proteins play a role in cancer and other diseases, one leading example being the estrogen receptor pathway in breast cancer. Coregulators are often present in limiting amounts in cell nuclei and modifications of their level of expression and/or structure lead to alterations in nuclear receptor functioning, which may be as pronounced as a complete inversion of signaling, i.e. from stimulating to repressing certain genes in response to an identical stimulus. In addition, hemizygous knock-out of certain coactivator genes has been demonstrated to produce cancer-prone phenotypes in mice. Thus, assessment of coactivator and corepressor expression and structure in tumors may turn out to be essential to determine the role of nuclear receptors in cancer and to predict prognosis and response to therapy.
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Affiliation(s)
- E Cottone
- Department of Animal and Human Biology, University of Turin, Italy
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Hegarty KG, Drummond FJ, Daly M, Shanahan F, Molloy MG. GREB1 genetic variants are associated with bone mineral density in Caucasians. J Bone Miner Metab 2018; 36:189-199. [PMID: 28293781 DOI: 10.1007/s00774-017-0823-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/11/2017] [Indexed: 01/23/2023]
Abstract
Gaining an understanding of factors contributing to bone quality is key to the development of effective preventative treatments for osteoporosis and reduction in osteoporotic fractures. Oestrogen is a strong regulator of bone remodelling which maintains skeletal structural integrity. The growth regulation by oestrogen in breast cancer 1 (GREB1) gene, with an as yet undefined function, is an early response gene in the oestrogen-regulated pathway. Suggestive evidence of linkage with bone mineral density (BMD) variation has been reported with D2S168, located telomeric of GREB1. The aim of this study was to determine if genetic variation within GREB1 was associated with BMD variation at two sites with high fracture rates-the lumbar spine (LS) and the femoral neck (FN). Informative GREB1 single-nucleotide polymorphisms (SNPs) (n = 12) were selected for genotyping and tested for association in a family-based dataset (n = 508 individuals from 229 families). Significantly associated SNPs were tested further in a postmenopausal dataset from the same geographic region (n = 477 individuals). One intronic SNP, rs5020877, was significantly associated with LS and FN BMD in the family-based dataset (P ≤ 0.005). The association was not observed in the postmenopausal dataset (P > 0.017); however, rs10929757 was significantly associated with FN BMD (P = 0.006). Markers, rs5020877 and rs10929757, were constituent SNPs in one GREB1 linkage disequilibrium block, although not historically correlated (r 2 = 0.07). Our findings suggest that GREB1 is a novel gene target for osteoporosis genetics and needs to be investigated further.
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Affiliation(s)
- Kevin G Hegarty
- Department of Medicine, University College Cork, Cork, Ireland.
| | - Frances J Drummond
- Department of Epidemiology and Public Health, University College Cork, Cork, Ireland
| | - Mary Daly
- Department of Medicine, University College Cork, Cork, Ireland
| | - Fergus Shanahan
- Department of Medicine, University College Cork, Cork, Ireland
| | - Michael G Molloy
- Department of Rheumatology and Medicine, University College Cork, Cork, Ireland
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Cook S, Hung V, Duncan KA. Crosstalk between Estrogen Withdrawal and NFκB Signaling following Penetrating Brain Injury. Neuroimmunomodulation 2018; 25:193-200. [PMID: 30423555 DOI: 10.1159/000493506] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/04/2018] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Characterized by neuroinflammation, traumatic brain injury (TBI) induces neuropathological changes and cognitive deficits. Estrogens are neuroprotective by increasing cell survival and this increase is mediated by a decrease in neuroinflammation. To further explore the relationship between estrogens, brain injury, and neuroinflammation, we examined the expression of the IKK/NFκB complex. The IKK/NFκB complex is a pleiotropic regulator of many cellular signaling pathways linked to inflammation, as well as three major cytokines (IL-1β, IL-6, and TNF-α). We hypothesized that NFκB expression would be upregulated following injury and that this increase would be exacerbated when circulating estrogens were decreased with fadrozole (aromatase inhibitor). METHODS Using adult zebra finches, we first determined the expression of major components of the NFκB complex (NFκB, IκB-α, and IκB-β) following injury using qPCR. Next, male and female finches were collected at 2 time points (2 or 24 h after injury) and brain tissue was analyzed to determine whether NFκB expression was differentially expressed in males and females at either time point. Finally, we examined how the expression of NFκB changed when estrogen levels were decreased immediately after injury. RESULTS Our study documented an increase in the expression of the major components of the NFκB complex (NFκB, IκB-α, and IκB-β) following injury. Decreasing estrogen levels resulted in a surprising decrease in the NFκB complex studied here. DISCUSSION These data further expand the model of how estrogens and other steroid hormones interact with the inflammatory pathways following injury and may prove beneficial when developing therapies for treatment of TBI.
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Affiliation(s)
- Samarah Cook
- Program in Neuroscience and Behavior, Vassar College, Poughkeepsie, New York, USA
| | - Vanessa Hung
- Program in Neuroscience and Behavior, Vassar College, Poughkeepsie, New York, USA
| | - Kelli A Duncan
- Program in Neuroscience and Behavior, Vassar College, Poughkeepsie, New York, USA,
- Department of Biology, Vassar College, Poughkeepsie, New York, USA,
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31
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Madabhushi R, Kim TK. Emerging themes in neuronal activity-dependent gene expression. Mol Cell Neurosci 2017; 87:27-34. [PMID: 29254824 DOI: 10.1016/j.mcn.2017.11.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/23/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022] Open
Abstract
In this review, we attempt to discuss emerging themes in the regulation of neuronal activity-regulated genes, focusing primarily on an important subset of immediate-early genes. We first discuss earlier studies that have illuminated the role of cis-acting elements within the promoters of immediate-early genes, the corresponding transcription factors that bind these elements, and the roles of major activity-regulated signaling pathways. However, our emphasis is on new studies that have revealed an important role for epigenetic and topological mechanisms, including enhancer-promoter interactions, enhancer RNAs (eRNAs), and activity-induced DNA breaks, that have emerged as important factors that govern the temporal dynamics of activity-induced gene transcription.
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Affiliation(s)
- Ram Madabhushi
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Tae-Kyung Kim
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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32
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Li SJ, Kao YH, Chung CC, Chen WY, Cheng WL, Chen YJ. Activated p300 acetyltransferase activity modulates aortic valvular calcification with osteogenic transdifferentiation and downregulation of Klotho. Int J Cardiol 2017; 232:271-279. [PMID: 28111052 DOI: 10.1016/j.ijcard.2017.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 12/30/2016] [Accepted: 01/03/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND The calcific aortic valve (AV) disease is a common disease with the unclear mechanism, and optimal pharmacological treatment remains unavailable. Epigenetic modulation by histone acetyltransferase (HAT) plays a critical role in osteogenic transdifferentiation and atherosclerosis. The purposes of this study were to investigate whether HAT contributes to the pathophysiology of AV calcification and assess the therapeutic potential of HAT inhibition. METHODS Porcine valvular interstitial cells (VICs) were treated with osteogenic medium (10ng/mL of tumor necrosis factor-α and 4mmol/L of high phosphate) for 7days. We analyzed the RNA and protein expression of myofibroblastic (α-SMA, vimentin, collagen 1A1, collagen 3, Egr-1, MMP2, MMP9) and osteoblastic markers (osteocalcin and alkaline phosphatase) in VICs, and studied the effects of a p300 inhibitor (C646, 10μmol/L) on calcification (Alizarin Red S staining), osteogenesis, HAT activity, the mitogen-activated protein kinase (MAPK) and Akt pathway, and Klotho expression on VICs. RESULTS Osteogenic medium treated VICs had higher expressions of osteocalcin, alkaline phosphatase and acetylated lysine-9 of histone H3 (ac-H3K9) than control cells. C646 attenuated osteogenesis of VICs with simultaneous inhibition of the HAT activity of p300. There was neither significant increase of p300 protein nor p300 transcript during the osteogenesis process. Additionally, osteogenic medium treated VICs decreased the expression of Klotho, which is attenuated by C646. CONCLUSIONS Activated HAT activity of p300 modulates AV calcification through osteogenic transdifferentiation of VICs with Klotho modulation. P300 inhibition is a potential therapeutic target for AV calcification.
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Affiliation(s)
- Shao-Jung Li
- Grarduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Cardiovascular Surgery, Department of Surgery, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yu-Hsun Kao
- Grarduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Medical Education and Research, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
| | - Cheng-Chih Chung
- Grarduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Cardiovascular Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wei-Yu Chen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Wan-Li Cheng
- Grarduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Jen Chen
- Grarduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Cardiovascular Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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33
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Yaşar P, Ayaz G, User SD, Güpür G, Muyan M. Molecular mechanism of estrogen-estrogen receptor signaling. Reprod Med Biol 2016; 16:4-20. [PMID: 29259445 PMCID: PMC5715874 DOI: 10.1002/rmb2.12006] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/16/2016] [Indexed: 02/06/2023] Open
Abstract
17β‐Estradiol (E2), as the main circulating estrogen hormone, regulates many tissue and organ functions in physiology. The effects of E2 on cells are mediated by the transcription factors and estrogen receptor (ER)α and ERβ that are encoded by distinct genes. Localized at the peri‐membrane, mitochondria, and the nucleus of cells that are dependent on estrogen target tissues, the ERs share similar, as well as distinct, regulatory potentials. Different intracellular localizations of the ERs result in dynamically integrated and finely tuned E2 signaling cascades that orchestrate cellular growth, differentiation, and death. The deregulation of E2–ER signaling plays a critical role in the initiation and progression of target tissue malignancies. A better understanding of the complex regulatory mechanisms that underlie ER actions in response to E2 therefore holds a critical trajectory for the development of novel prognostic and therapeutic approaches with substantial impacts on the systemic management of target tissue diseases.
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Affiliation(s)
- Pelin Yaşar
- Department of Biological Sciences Middle East Technical University Ankara Turkey
| | - Gamze Ayaz
- Department of Biological Sciences Middle East Technical University Ankara Turkey
| | - Sırma Damla User
- Department of Biological Sciences Middle East Technical University Ankara Turkey
| | - Gizem Güpür
- Department of Biological Sciences Middle East Technical University Ankara Turkey.,Present address: Cell and Molecular Biology Program Duke University Durham North Carolina USA
| | - Mesut Muyan
- Department of Biological Sciences Middle East Technical University Ankara Turkey
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Lee DH, Asare BK, Rajnarayanan RV. Discovery at the interface: Toward novel anti-proliferative agents targeting human estrogen receptor/S100 interactions. Cell Cycle 2016; 15:2806-18. [PMID: 27580430 DOI: 10.1080/15384101.2016.1220460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Estrogen Receptor Alpha (ER) is expressed in about 70% of breast cancer and mediates various cellular signaling events including cell cycle. The antiestrogen tamoxifen is currently administered to patients in order to induce regression of the tumor growth of estrogen receptor positive (ER+) breast cancer. However, upon continued administration, patients develop resistance to tamoxifen. In addition, calcium binding proteins (EF-hand proteins) such as, Calmodulin and S100, are significantly overexpressed in breast cancer cells, can activate transcription of target genes by directly binding to ER in lieu of estrogen. Calmodulin antagonists (w7 and melatonin) have been shown to significantly inhibit ER mediated activities including cell proliferation and transcriptional activity. Furthermore, S100P is shown to mediate tamoxifen resistance and cell migration capacity in MCF-7 breast cancer cells. Molecules targeting specific ER-EF hand protein interfaces could potentially provide an alternative therapeutic strategy to combat these scenarios. Using theoretical 3D models of ER-S100 protein we identified ER conformation-sensing regions of the interacting EF hand proteins and evaluated their ability to bind to ER in silico and to inhibit breast cancer cell proliferation and viability in vitro. The recognition motif of the binding interface was sensitive to small changes in partner orientation as evidenced by significant anti cell proliferative activity of the short peptide derived from S100P residues 74-78, when compared with a longer peptide with altered orientation of the recognition motif derived from S100P 74-81. Structural clues and pharmacophores from peptide-ER interactions can be used to design novel anti-cancer agents.
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Affiliation(s)
- David H Lee
- a Department of Pharmacology and Toxicology , Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY , Buffalo , NY , USA
| | - Bethany K Asare
- a Department of Pharmacology and Toxicology , Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY , Buffalo , NY , USA
| | - Rajendram V Rajnarayanan
- a Department of Pharmacology and Toxicology , Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, SUNY , Buffalo , NY , USA
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35
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Carroll JS. Mechanisms of oestrogen receptor (ER) gene regulation in breast cancer. Eur J Endocrinol 2016; 175:R41-9. [PMID: 26884552 PMCID: PMC5065078 DOI: 10.1530/eje-16-0124] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 02/10/2016] [Accepted: 02/15/2016] [Indexed: 12/24/2022]
Abstract
Most breast cancers are driven by a transcription factor called oestrogen receptor (ER). Understanding the mechanisms of ER activity in breast cancer has been a major research interest and recent genomic advances have revealed extraordinary insights into how ER mediates gene transcription and what occurs during endocrine resistance. This review discusses our current understanding on ER activity, with an emphasis on several evolving, but important areas of ER biology.
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Affiliation(s)
- J S Carroll
- Cancer Research UKCambridge Institute, University of Cambridge, Cambridge, UK
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36
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Fei J, Torigoe SE, Brown CR, Khuong MT, Kassavetis GA, Boeger H, Kadonaga JT. The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev 2016; 29:2563-75. [PMID: 26680301 PMCID: PMC4699385 DOI: 10.1101/gad.272633.115] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fei et al. show that the prenucleosome is a stable alternate conformational isomer of the nucleosome. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. Chromatin comprises nucleosomes as well as nonnucleosomal histone–DNA particles. Prenucleosomes are rapidly formed histone–DNA particles that can be converted into canonical nucleosomes by a motor protein such as ACF. Here we show that the prenucleosome is a stable conformational isomer of the nucleosome. It consists of a histone octamer associated with ∼80 base pair (bp) of DNA, which is located at a position that corresponds to the central 80 bp of a nucleosome core particle. Monomeric prenucleosomes with free flanking DNA do not spontaneously fold into nucleosomes but can be converted into canonical nucleosomes by an ATP-driven motor protein such as ACF or Chd1. In addition, histone H3K56, which is located at the DNA entry and exit points of a canonical nucleosome, is specifically acetylated by p300 in prenucleosomes relative to nucleosomes. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. These findings suggest that the prenucleosome, the only known stable conformational isomer of the nucleosome, is related to nonnucleosomal histone–DNA species in the cell.
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Affiliation(s)
- Jia Fei
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Sharon E Torigoe
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Christopher R Brown
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Mai T Khuong
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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SMARCAD1 is an ATP-dependent stimulator of nucleosomal H2A acetylation via CBP, resulting in transcriptional regulation. Sci Rep 2016; 6:20179. [PMID: 26888216 PMCID: PMC4757861 DOI: 10.1038/srep20179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 12/23/2015] [Indexed: 12/21/2022] Open
Abstract
Histone acetylation plays a pivotal role in transcriptional regulation, and ATP-dependent nucleosome remodeling activity is required for optimal transcription from chromatin. While these two activities have been well characterized, how they are coordinated remains to be determined. We discovered ATP-dependent histone H2A acetylation activity in Drosophila nuclear extracts. This activity was column purified and demonstrated to be composed of the enzymatic activities of CREB-binding protein (CBP) and SMARCAD1, which belongs to the Etl1 subfamily of the Snf2 family of helicase-related proteins. SMARCAD1 enhanced acetylation by CBP of H2A K5 and K8 in nucleosomes in an ATP-dependent fashion. Expression array analysis of S2 cells having ectopically expressed SMARCAD1 revealed up-regulated genes. Using native genome templates of these up-regulated genes, we found that SMARCAD1 activates their transcription in vitro. Knockdown analysis of SMARCAD1 and CBP indicated overlapping gene control, and ChIP-seq analysis of these commonly controlled genes showed that CBP is recruited to the promoter prior to SMARCAD1. Moreover, Drosophila genetic experiments demonstrated interaction between SMARCAD1/Etl1 and CBP/nej during development. The interplay between the remodeling activity of SMARCAD1 and histone acetylation by CBP sheds light on the function of chromatin and the genome-integrity network.
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Han Y, Tanios F, Reeps C, Zhang J, Schwamborn K, Eckstein HH, Zernecke A, Pelisek J. Histone acetylation and histone acetyltransferases show significant alterations in human abdominal aortic aneurysm. Clin Epigenetics 2016; 8:3. [PMID: 26767057 PMCID: PMC4711037 DOI: 10.1186/s13148-016-0169-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/04/2016] [Indexed: 12/26/2022] Open
Abstract
Background Epigenetic modifications may play a relevant role in the pathogenesis of human abdominal aortic aneurysm (AAA). The aim of the study was therefore to investigate histone acetylation and expression of corresponding lysine [K] histone acetyltransferases (KATs) in AAA. Results A comparative study of AAA tissue samples (n = 37, open surgical intervention) and healthy aortae (n = 12, trauma surgery) was performed using quantitative PCR, immunohistochemistry (IHC), and Western blot. Expression of the KAT families GNAT (KAT2A, KAT2B), p300/CBP (KAT3A, KAT3B), and MYST (KAT5, KAT6A, KAT6B, KAT7, KAT8) was significantly higher in AAA than in controls (P ≤ 0.019). Highest expression was observed for KAT2B, KAT3A, KAT3B, and KAT6B (P ≤ 0.007). Expression of KAT2B significantly correlated with KAT3A, KAT3B, and KAT6B (r = 0.705, 0.564, and 0.528, respectively, P < 0.001), and KAT6B with KAT3A, KAT3B, and KAT6A (r = 0.407, 0.500, and 0.531, respectively, P < 0.05). Localization of highly expressed KAT2B, KAT3B, and KAT6B was further characterized by immunostaining. Significant correlations were observed between KAT2B with endothelial cells (ECs) (r = 0.486, P < 0.01), KAT3B with T cells and macrophages, (r = 0.421 and r = 0.351, respectively, P < 0.05), KAT6A with intramural ECs (r = 0.541, P < 0.001) and with a contractile phenotype of smooth muscle cells (SMCs) (r = 0.425, P < 0.01), and KAT6B with T cells (r = 0.553, P < 0.001). Furthermore, KAT2B was associated with AAA diameter (r = 0.382, P < 0.05), and KAT3B, KAT6A, and KAT6B correlated negatively with blood urea nitrogen (r = −0.403, −0.408, −0.478, P < 0.05). In addtion, acetylation of the histone substrates H3K9, H3K18 and H3K14 was increased in AAA compared to control aortae. Conclusions Our results demonstrate that aberrant epigenetic modifications such as changes in the expression of KATs and acetylation of corresponding histones are present in AAA. These findings may provide new insight in the pathomechanism of AAA. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0169-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yanshuo Han
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technische Universität München, Ismaninger Str. 22, 81675 Munich, Germany.,Department of Vascular and Surgery, The First Hospital of China Medical University, Shenyang, China.,Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fadwa Tanios
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technische Universität München, Ismaninger Str. 22, 81675 Munich, Germany
| | - Christian Reeps
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technische Universität München, Ismaninger Str. 22, 81675 Munich, Germany.,Department for Visceral, Thoracic and Vascular Surgery at the University Hospital, Technical University Dresden, Dresden, Germany
| | - Jian Zhang
- Department of Vascular and Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Kristina Schwamborn
- Institute of Pathology, Klinikum rechts der Isar der Technische Universität München, Munich, Germany
| | - Hans-Henning Eckstein
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technische Universität München, Ismaninger Str. 22, 81675 Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Alma Zernecke
- Institute of Experimental Biomedicine, University Hospital, University of Würzburg, Würzburg, Germany.,Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technische Universität München, Ismaninger Str. 22, 81675 Munich, Germany
| | - Jaroslav Pelisek
- Department of Vascular and Endovascular Surgery, Klinikum rechts der Isar der Technische Universität München, Ismaninger Str. 22, 81675 Munich, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
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39
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Dieci G, Fermi B, Bosio MC. Investigating transcription reinitiation through in vitro approaches. Transcription 2015; 5:e27704. [PMID: 25764113 DOI: 10.4161/trns.27704] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By influencing the number of RNA molecules repeatedly synthesized from the same gene, the control of transcription reinitiation has the potential to shape the transcriptome. Transcription reinitiation mechanisms have been mainly addressed in vitro, through approaches based on both crude and reconstituted systems. These studies support the notion that transcription reinitiation and its regulation rely on dedicated networks of molecular interactions within transcription machineries. At the same time, comparison with in vivo transcription rates suggests that additional mechanisms, factors and conditions must exist in the nucleus, whose biochemical elucidation is a fascinating challenge for future in vitro transcription studies.
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Affiliation(s)
- Giorgio Dieci
- a Dipartimento di Bioscienze; Università degli Studi di Parma; Parma, Italy
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40
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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41
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Schwartz-Roberts JL, Cook KL, Chen C, Shajahan-Haq AN, Axelrod M, Wärri A, Riggins RB, Jin L, Haddad BR, Kallakury BV, Baumann WT, Clarke R. Interferon regulatory factor-1 signaling regulates the switch between autophagy and apoptosis to determine breast cancer cell fate. Cancer Res 2015; 75:1046-55. [PMID: 25576084 PMCID: PMC4359953 DOI: 10.1158/0008-5472.can-14-1851] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Interferon regulatory factor-1 (IRF1) is a tumor suppressor that regulates cell fate in several cell types. Here, we report an inverse correlation in expression of nuclear IRF1 and the autophagy regulator ATG7 in human breast cancer cells that directly affects their cell fate. In mice harboring mutant Atg7, nuclear IRF1 was increased in mammary tumors, spleen, and kidney. Mechanistic investigations identified ATG7 and the cell death modulator beclin-1 (BECN1) as negative regulators of IRF1. Silencing ATG7 or BECN1 caused estrogen receptor-α to exit the nucleus at the time when IRF1 nuclear localization occurred. Conversely, silencing IRF1 promoted autophagy by increasing BECN1 and blunting IGF1 receptor and mTOR survival signaling. Loss of IRF1 promoted resistance to antiestrogens, whereas combined silencing of ATG7 and IRF1 restored sensitivity to these agents. Using a mathematical model to prompt signaling hypotheses, we developed evidence that ATG7 silencing could resensitize IRF1-attenuated cells to apoptosis through mechanisms that involve other estrogen-regulated genes. Overall, our work shows how inhibiting the autophagy proteins ATG7 and BECN1 can regulate IRF1-dependent and -independent signaling pathways in ways that engender a new therapeutic strategy to attack breast cancer.
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Affiliation(s)
- Jessica L Schwartz-Roberts
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Katherine L Cook
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Chun Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia. Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Ayesha N Shajahan-Haq
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Margaret Axelrod
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Anni Wärri
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Rebecca B Riggins
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Lu Jin
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Bassem R Haddad
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC
| | - Bhaskar V Kallakury
- Department of Pathology, Georgetown University Medical Center, Washington, DC
| | - William T Baumann
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia. Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia
| | - Robert Clarke
- Department of Physiology and Biophysics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC. Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC.
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42
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Yi P, Wang Z, Feng Q, Pintilie GD, Foulds CE, Lanz RB, Ludtke SJ, Schmid MF, Chiu W, O'Malley BW. Structure of a biologically active estrogen receptor-coactivator complex on DNA. Mol Cell 2015; 57:1047-1058. [PMID: 25728767 DOI: 10.1016/j.molcel.2015.01.025] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/05/2015] [Accepted: 01/20/2015] [Indexed: 12/17/2022]
Abstract
Estrogen receptor (ER/ESR1) is a transcription factor critical for development, reproduction, metabolism, and cancer. ER function hinges on its ability to recruit primary and secondary coactivators, yet structural information on the full-length receptor-coactivator complex to complement preexisting and sometimes controversial biochemical information is lacking. Here, we use cryoelectron microscopy (cryo-EM) to determine the quaternary structure of an active complex of DNA-bound ERα, steroid receptor coactivator 3 (SRC-3/NCOA3), and a secondary coactivator (p300/EP300). Our structural model suggests the following assembly mechanism for the complex: each of the two ligand-bound ERα monomers independently recruits one SRC-3 protein via the transactivation domain of ERα; the two SRC-3s in turn bind to different regions of one p300 protein through multiple contacts. We also present structural evidence for the location of activation function 1 (AF-1) in a full-length nuclear receptor, which supports a role for AF-1 in SRC-3 recruitment.
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Affiliation(s)
- Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Clayton Foundation for Research, Houston, TX 77056, USA
| | - Zhao Wang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qin Feng
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Grigore D Pintilie
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rainer B Lanz
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven J Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F Schmid
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wah Chiu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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43
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Guertin MJ, Zhang X, Coonrod SA, Hager GL. Transient estrogen receptor binding and p300 redistribution support a squelching mechanism for estradiol-repressed genes. Mol Endocrinol 2014; 28:1522-33. [PMID: 25051172 DOI: 10.1210/me.2014-1130] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Proper gene regulation is essential for proper organismal development and appropriate responses to external stimuli. Specialized factors, termed master regulators, are often responsible for orchestrating the molecular events that result from signaling cascades. Master regulators coordinate the activation and repression of specific gene classes. Estrogen receptor α (ER) precipitates the signaling cascade that results from endogenous or exogenous estrogen hormones. ER is a classic transcriptional activator and the mechanisms by which ER coordinates gene activation are well characterized. However, it remains unclear how ER coordinates the immediate repression of genes. We integrated genomic transcription, chromosome looping, transcription factor binding, and chromatin structure data to analyze the molecular cascade that results from estradiol (E2)-induced signaling in human MCF-7 breast cancer cells and addressed the context-specific nature of gene regulation. We defined a class of genes that are immediately repressed upon estrogen stimulation, and we compared and contrasted the molecular characteristics of these repressed genes vs activated and unregulated genes. The most striking and unique feature of the repressed gene class is transient binding of ER at early time points after estrogen stimulation. We also found that p300, a coactivator and acetyltransferase, quantitatively redistributes from non-ER enhancers to ER enhancers after E2 treatment. These data support an extension of the classic physiological squelching model, whereby ER hijacks coactivators from repressed genes and redistributes the coactivators to ER enhancers that activate transcription.
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Affiliation(s)
- Michael J Guertin
- Laboratory of Receptor Biology and Gene Expression (M.J.G., G.L.H.), National Cancer Institute, Bethesda, Maryland 20892; State Key Laboratory of Reproductive Medicine (X.Z.), Nanjing Medical University, Nanjing 210029, China; and Baker Institute for Animal Health (X.Z., S.A.C.), College of Veterinary Medicine, Cornell University, Ithaca, New York 14853
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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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45
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Di Cerbo V, Mohn F, Ryan DP, Montellier E, Kacem S, Tropberger P, Kallis E, Holzner M, Hoerner L, Feldmann A, Richter FM, Bannister AJ, Mittler G, Michaelis J, Khochbin S, Feil R, Schuebeler D, Owen-Hughes T, Daujat S, Schneider R. Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. eLife 2014; 3:e01632. [PMID: 24668167 PMCID: PMC3965291 DOI: 10.7554/elife.01632] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Post-translational modifications of proteins have emerged as a major mechanism for regulating gene expression. However, our understanding of how histone modifications directly affect chromatin function remains limited. In this study, we investigate acetylation of histone H3 at lysine 64 (H3K64ac), a previously uncharacterized acetylation on the lateral surface of the histone octamer. We show that H3K64ac regulates nucleosome stability and facilitates nucleosome eviction and hence gene expression in vivo. In line with this, we demonstrate that H3K64ac is enriched in vivo at the transcriptional start sites of active genes and it defines transcriptionally active chromatin. Moreover, we find that the p300 co-activator acetylates H3K64, and consistent with a transcriptional activation function, H3K64ac opposes its repressive counterpart H3K64me3. Our findings reveal an important role for a histone modification within the nucleosome core as a regulator of chromatin function and they demonstrate that lateral surface modifications can define functionally opposing chromatin states. DOI:http://dx.doi.org/10.7554/eLife.01632.001 DNA is a very long molecule, so it needs to be packaged carefully to fit into the nucleus of a cell. To achieve this, the DNA is wrapped around proteins called histones to form a structure termed a nucleosome, which is the building block of a more compacted substance called chromatin. However, to express the genes in the DNA it is necessary to open up parts of the chromatin to give various enzymes access to the DNA. Cells often chemically modify histones by adding acetyl or methyl groups, and these modifications are known to influence what proteins can bind to the nucleosomes, which ultimately influences what genes are expressed in the cell at a given time. It has been suspected for some time that histone modifications can also influence gene expression more directly, but there has been little evidence for this idea. Now Di Cerbo et al. have studied what happens when acetyl or methyl groups are added to a specific site within a histone called H3K64, which is close to where the DNA wraps around this histone. These experiments showed that this site tends to be acetylated when a nearby gene is active, and to be unmodified or methylated when this gene is not active. It appears that the addition of the acetyl group makes this region of the chromatin less stable: this, in turn, makes it easier for the chromatin to be unpacked, thus giving access to the enzymes that transcribe the DNA and allowing transcription to take place. The work of Di Cerbo et al. shows that methylation and acetylation at the same site within a histone can define two opposing states of chromatin and DNA: an active state and a repressive state. DOI:http://dx.doi.org/10.7554/eLife.01632.002
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Affiliation(s)
- Vincenzo Di Cerbo
- Department of Functional Genomics, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR, Strasbourg, France
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46
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Magnani L, Lupien M. Chromatin and epigenetic determinants of estrogen receptor alpha (ESR1) signaling. Mol Cell Endocrinol 2014; 382:633-641. [PMID: 23684889 DOI: 10.1016/j.mce.2013.04.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/16/2013] [Accepted: 04/29/2013] [Indexed: 12/30/2022]
Abstract
The oestrogen receptor alpha (ESR1) is a transcription factor that potentiates the response to diverse stimuli, including oestrogen and growth factors, in various tissue types. Its recruitment to the DNA is directly regulated by the chromatin landscape, inclusive of chromatin compaction and epigenetic modifications. In this review we discuss our current understanding of the interplay between ESR1 signaling and the chromatin landscape. We present how the chromatin landscape primes the lineage-specific response and contributes to stimuli-specific signaling. Finally, we discuss recent efforts to decipher the relationship between genetic and epigenetic as it relates to ESR1 signaling in breast cancer.
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Affiliation(s)
- Luca Magnani
- Ontario Cancer Institute, Princess Margaret Cancer Centre-University Health Network, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Mathieu Lupien
- Ontario Cancer Institute, Princess Margaret Cancer Centre-University Health Network, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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47
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ERα, SKP2 and E2F-1 form a feed forward loop driving late ERα targets and G1 cell cycle progression. Oncogene 2013; 33:2341-53. [PMID: 23770852 DOI: 10.1038/onc.2013.197] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 03/28/2013] [Accepted: 04/12/2013] [Indexed: 02/07/2023]
Abstract
Estrogen triggers transactivation coupled estrogen receptor α (ERα) proteolysis, but mechanisms thereof remain obscure. Present data link estrogen:ERα-driven transcription with cell cycle progression. Although liganded ERα induces many genes within 1-4 h, gene activation after 6 h is thought to be indirect. Here, we identify SKP2 as a late-acting coactivator that drives ERα targets to promote G1-to-S progression. Data support a model in which estrogen-activated cyclin E-CDK2 binds and phosphorylates ERαS341, to prime ERα-SCF(SKP2) binding via SKP2-L248QTLL252 in late G1. SKP2 activates ERα ubiquitylation and proteolysis. Putative late ERα targets were identified by expression profiling. SKP2 knockdown attenuated E2F-1 and BLM induction. SKP2 overexpression, but not coactivator motif mutant SKP2-L248QTAA252, enhanced estrogen-induced E2F-1 and BLM expression. SKP2 knockdown impaired estrogen-stimulated ERα, SKP2, SRC3 and RNA polymerase II recruitment to E2F-1 and BLM promoters. This work not only identifies these late-activated genes as bona fide ERα targets but describes a novel mechanism for their periodic activation. SKP2 serves as dual ERα E3 ligase/coactivator for late-activated target genes, revealing a novel mechanism whereby ERα/SCF(SKP2) transactivation of E2F-1 feeds forward to drive G1-to-S.
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48
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Modak R, Basha J, Bharathy N, Maity K, Mizar P, Bhat AV, Vasudevan M, Rao VK, Kok WK, Natesh N, Taneja R, Kundu TK. Probing p300/CBP associated factor (PCAF)-dependent pathways with a small molecule inhibitor. ACS Chem Biol 2013; 8:1311-23. [PMID: 23570531 DOI: 10.1021/cb4000597] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PCAF (KAT2B) belongs to the GNAT family of lysine acetyltransferases (KAT) and specifically acetylates the histone H3K9 residue and several nonhistone proteins. PCAF is also a transcriptional coactivator. Due to the lack of a PCAF KAT-specific small molecule inhibitor, the exclusive role of the acetyltransferase activity of PCAF is not well understood. Here, we report that a natural compound of the hydroxybenzoquinone class, embelin, specifically inhibits H3Lys9 acetylation in mice and inhibits recombinant PCAF-mediated acetylation with near complete specificity in vitro. Furthermore, using embelin, we have identified the gene networks that are regulated by PCAF during muscle differentiation, further highlighting the broader regulatory functions of PCAF in muscle differentiation in addition to the regulation via MyoD acetylation.
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Affiliation(s)
- Rahul Modak
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Jeelan Basha
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Narendra Bharathy
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Koustav Maity
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India 560012
| | - Pushpak Mizar
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Akshay V. Bhat
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
| | - Madavan Vasudevan
- Bionivid Technology [P] Ltd, 401 - 4 AB Cross, 1st Main, Kasturi Nagar,
East of NGEF, Bangalore, India 560043
| | - Vinay Kumar Rao
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Wai Kay Kok
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Nagashayana Natesh
- Central Government Health Scheme
Dispensary Number 3, Basavanagudi, Bangalore, India
| | - Reshma Taneja
- Department
of Physiology, Yong
Loo Lin School of Medicine, Block MD9, 2 Medical Drive, National University of Singapore, Singapore 117597
| | - Tapas K. Kundu
- Transcription
and Disease Laboratory,
Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore,
India 560064
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49
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Ghosh AK, Bhattacharyya S, Lafyatis R, Farina G, Yu J, Thimmapaya B, Wei J, Varga J. p300 is elevated in systemic sclerosis and its expression is positively regulated by TGF-β: epigenetic feed-forward amplification of fibrosis. J Invest Dermatol 2013; 133:1302-10. [PMID: 23303459 PMCID: PMC3626729 DOI: 10.1038/jid.2012.479] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fibrosis, the hallmark of systemic sclerosis (SSc), is characterized by persistent fibroblast activation triggered by transforming growth factor-β (TGF-β). As the acetyltransferase p300 has a key role in fibrosis and its availability governs the intensity of fibrotic responses, we investigated p300 expression in SSc and the molecular basis of its regulation. We found that expression of p300 was markedly elevated in SSc skin biopsies and was induced by TGF-β in explanted normal skin fibroblasts. Stimulation of p300 by TGF-β was independent of Smads and involved the early-immediate transcription factor Egr-1 (early growth response 1), a key regulator of profibrotic TGF-β signaling. Indeed, Egr-1 was both sufficient and necessary for p300 regulation in vitro and in vivo. Increased p300 accumulation in TGF-β-treated fibroblasts was associated with histone hyperacetylation, whereas p300 depletion, or selective pharmacological blockade of its acetyltransferase activity, attenuated TGF-β-induced responses. Moreover, TGF-β enhanced both p300 recruitment and in vivo histone H4 acetylation at the COL1A2 (collagen, type I, α2) locus. These findings implicate p300-mediated histone acetylation as a fundamental epigenetic mechanism in fibrogenesis and place Egr-1 upstream in TGF-β-driven stimulation of p300 gene expression. The results establish a firm link between fibrosis with aberrant p300 expression and epigenetic activity that, to our knowledge, is previously unreported. Targeted disruption of p300-mediated histone acetylation might therefore represent a viable antifibrotic strategy.
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Affiliation(s)
- Asish K Ghosh
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Swati Bhattacharyya
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | | | | | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology, SJTU-SM, Shanghai, China
| | - Bayar Thimmapaya
- Department of Microbiology and Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - Jun Wei
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
| | - John Varga
- Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL
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Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer. Cell 2013; 152:859-72. [PMID: 23415232 DOI: 10.1016/j.cell.2013.01.032] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 11/25/2012] [Accepted: 01/22/2013] [Indexed: 12/11/2022]
Abstract
Histone modifications are key regulators of chromatin function. However, little is known to what extent histone modifications can directly impact on chromatin. Here, we address how a modification within the globular domain of histones regulates chromatin function. We demonstrate that H3K122ac can be sufficient to stimulate transcription and that mutation of H3K122 impairs transcriptional activation, which we attribute to a direct effect of H3K122ac on histone-DNA binding. In line with this, we find that H3K122ac defines genome-wide genetic elements and chromatin features associated with active transcription. Furthermore, H3K122ac is catalyzed by the coactivators p300/CBP and can be induced by nuclear hormone receptor signaling. Collectively, this suggests that transcriptional regulators elicit their effects not only via signaling to histone tails but also via direct structural perturbation of nucleosomes by directing acetylation to their lateral surface.
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