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Joosten SEP, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Yavuz K, Donaldson Collier M, Morova T, Altintaş UB, Kim Y, Canisius S, Moelans CB, van Diest PJ, Korkmaz G, Lack NA, Vermeulen M, Linn SC, Zwart W. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. Genome Res 2024; 34:539-555. [PMID: 38719469 PMCID: PMC11146591 DOI: 10.1101/gr.278680.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
Abstract
Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1+ breast cancers to explore inter-patient heterogeneity in ESR1 DNA binding to reveal a striking inter-tumor heterogeneity of ESR1 action. Of note, commonly shared ESR1 sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1 and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we can confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ESR1-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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Affiliation(s)
- Stacey E P Joosten
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Suzan Stelloo
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
| | - Elif Yapıcı
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Kerim Yavuz
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Maria Donaldson Collier
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tunç Morova
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Umut Berkay Altintaş
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Yongsoo Kim
- Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Gozde Korkmaz
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Nathan A Lack
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Michiel Vermeulen
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
- Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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Hosseinzadeh L, Kikhtyak Z, Laven-Law G, Pederson SM, Puiu CG, D'Santos CS, Lim E, Carroll JS, Tilley WD, Dwyer AR, Hickey TE. The androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer. Genome Biol 2024; 25:44. [PMID: 38317241 PMCID: PMC10840202 DOI: 10.1186/s13059-023-03161-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 12/27/2023] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast context are largely unknown. Herein, we employ an unbiased chromatin immunoprecipitation-based proteomic technique to identify endogenous AR interacting co-regulatory proteins in ER positive and negative models of breast cancer to gain new insight into mechanisms of AR signaling in this disease. RESULTS The DNA-binding factor GATA3 is identified and validated as a novel AR interacting protein in breast cancer cells irrespective of ER status. AR activation by the natural ligand 5α-dihydrotestosterone (DHT) increases nuclear AR-GATA3 interactions, resulting in AR-dependent enrichment of GATA3 chromatin binding at a sub-set of genomic loci. Silencing GATA3 reduces but does not prevent AR DNA binding and transactivation of genes associated with AR/GATA3 co-occupied loci, indicating a co-regulatory role for GATA3 in AR signaling. DHT-induced AR/GATA3 binding coincides with upregulation of luminal differentiation genes, including EHF and KDM4B, established master regulators of a breast epithelial cell lineage. These findings are validated in a patient-derived xenograft model of breast cancer. Interaction between AR and GATA3 is also associated with AR-mediated growth inhibition in ER positive and ER negative breast cancer. CONCLUSIONS AR and GATA3 interact to transcriptionally regulate luminal epithelial cell differentiation in breast cancer regardless of ER status. This interaction facilitates the tumor suppressor function of AR and mechanistically explains why AR expression is associated with less proliferative, more differentiated breast tumors and better overall survival in breast cancer.
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Affiliation(s)
- Leila Hosseinzadeh
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Zoya Kikhtyak
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Geraldine Laven-Law
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Stephen M Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Caroline G Puiu
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Clive S D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Elgene Lim
- Garvan Institute of Medical Research, University of New South Wales, Sydney, Australia
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Amy R Dwyer
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, Australia.
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Perez AA, Goronzy IN, Blanco MR, Guo JK, Guttman M. ChIP-DIP: A multiplexed method for mapping hundreds of proteins to DNA uncovers diverse regulatory elements controlling gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571730. [PMID: 38187704 PMCID: PMC10769186 DOI: 10.1101/2023.12.14.571730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Gene expression is controlled by the dynamic localization of thousands of distinct regulatory proteins to precise regions of DNA. Understanding this cell-type specific process has been a goal of molecular biology for decades yet remains challenging because most current DNA-protein mapping methods study one protein at a time. To overcome this, we developed ChIP-DIP (ChIP Done In Parallel), a split-pool based method that enables simultaneous, genome-wide mapping of hundreds of diverse regulatory proteins in a single experiment. We demonstrate that ChIP-DIP generates highly accurate maps for all classes of DNA-associated proteins, including histone modifications, chromatin regulators, transcription factors, and RNA Polymerases. Using these data, we explore quantitative combinations of protein localization on genomic DNA to define distinct classes of regulatory elements and their functional activity. Our data demonstrate that ChIP-DIP enables the generation of 'consortium level', context-specific protein localization maps within any molecular biology lab.
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Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Estrogen Receptor alpha (ERα) is the main driver and prime drug target in luminal breast. ERα chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ERα chromatin action, along with its biological implications. Here, we use a large set of ERα ChIP-seq data from 70 ERα+ breast cancers to explore inter-patient heterogeneity in ERα DNA binding, to reveal a striking inter-tumor heterogeneity of ERα action. Interestingly, commonly-shared ERα sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERα-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ERα and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ERα-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERα landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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5
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Bang I, Lee SM, Park S, Park JY, Nong LK, Gao Y, Palsson BO, Kim D. Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling. Brief Bioinform 2023; 24:7005164. [PMID: 36702751 DOI: 10.1093/bib/bbad024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/02/2023] [Accepted: 01/08/2023] [Indexed: 01/28/2023] Open
Abstract
Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair resolution. However, the peak calling step hinders ChIP-exo application since the published algorithms tend to generate false-positive and false-negative predictions. Here, we report the development of DEOCSU (DEep-learning Optimized ChIP-exo peak calling SUite), a novel machine learning-based ChIP-exo peak calling suite. DEOCSU entails the deep convolutional neural network model which was trained with curated ChIP-exo peak data to distinguish the visualized data of bona fide peaks from false ones. Performance validation of the trained deep-learning model indicated its high accuracy, high precision and high recall of over 95%. Applying the new suite to both in-house and publicly available ChIP-exo datasets obtained from bacteria, eukaryotes and archaea revealed an accurate prediction of peaks containing canonical motifs, highlighting the versatility and efficiency of DEOCSU. Furthermore, DEOCSU can be executed on a cloud computing platform or the local environment. With visualization software included in the suite, adjustable options such as the threshold of peak probability, and iterable updating of the pre-trained model, DEOCSU can be optimized for users' specific needs.
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Affiliation(s)
- Ina Bang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Seojoung Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Ye Gao
- Department of Bioengineering, University of California San Diego, La Jolla CA 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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Bang I, Khanh Nong L, Young Park J, Thi Le H, Mok Lee S, Kim D. ChEAP: ChIP-exo analysis pipeline and the investigation of Escherichia coli RpoN protein-DNA interactions. Comput Struct Biotechnol J 2022; 21:99-104. [PMID: 36544470 PMCID: PMC9735260 DOI: 10.1016/j.csbj.2022.11.053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Genome-scale studies of the bacterial regulatory network have been leveraged by declining sequencing cost and advances in ChIP (chromatin immunoprecipitation) methods. Of which, ChIP-exo has proven competent with its near-single base-pair resolution. While several algorithms and programs have been developed for different analytical steps in ChIP-exo data processing, there is a lack of effort in incorporating them into a convenient bioinformatics pipeline that is intuitive and publicly available. In this paper, we developed ChIP-exo Analysis Pipeline (ChEAP) that executes the one-step process, starting from trimming and aligning raw sequencing reads to visualization of ChIP-exo results. The pipeline was implemented on the interactive web-based Python development environment - Jupyter Notebook, which is compatible with the Google Colab cloud platform to facilitate the sharing of codes and collaboration among researchers. Additionally, users could exploit the free GPU and CPU resources allocated by Colab to carry out computing tasks regardless of the performance of their local machines. The utility of ChEAP was demonstrated with the ChIP-exo datasets of RpoN sigma factor in E. coli K-12 MG1655. To analyze two raw data files, ChEAP runtime was 2 min and 25 s. Subsequent analyses identified 113 RpoN binding sites showing a conserved RpoN binding pattern in the motif search. ChEAP application in ChIP-exo data analysis is extensive and flexible for the parallel processing of data from various organisms.
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Affiliation(s)
- Ina Bang
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Linh Khanh Nong
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hoa Thi Le
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sang- Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Schools of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea,Corresponding author at: School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea.
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Dobson T, Swaminathan J. Chromatin Immunoprecipitation Assays on Medulloblastoma Cell Line DAOY. Methods Mol Biol 2022; 2423:39-50. [PMID: 34978686 DOI: 10.1007/978-1-0716-1952-0_4] [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] [Indexed: 06/14/2023]
Abstract
Studies of DNA-protein interactions have revealed regulatory mechanisms of DNA replication, repair, remodeling, and transcription. Perturbation of any or all of these processes result in differential gene expression that can lead to tumor development. Chromatin immunoprecipitation assay (ChIP), currently the only method available to explore DNA-binding in vivo, has become a vastly utilized tool for cancer research. In this article we discuss an assay specified for a pediatric medulloblastoma (MB) cell line DAOY used to determine binding of transcription factors, to detect histone modifications, and to identify novel therapeutic targets.
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Affiliation(s)
- Tara Dobson
- Department of Pediatrics, UT MD Anderson Cancer Center, Houston, TX, USA
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8
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Blombach F, Smollett KL, Werner F. ChIP-Seq Occupancy Mapping of the Archaeal Transcription Machinery. Methods Mol Biol 2022; 2522:209-222. [PMID: 36125752 DOI: 10.1007/978-1-0716-2445-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genome-wide occupancy studies for RNA polymerases and their basal transcription factors deliver information about transcription dynamics and the recruitment of transcription elongation and termination factors in eukaryotes and prokaryotes. The primary method to determine genome-wide occupancies is chromatin immunoprecipitation combined with deep sequencing (ChIP-seq). Archaea possess a transcription machinery that is evolutionarily closer related to its eukaryotic counterpart but it operates in a prokaryotic cellular context. Studies on archaeal transcription brought insight into the evolution of transcription machineries and the universality of transcription mechanisms. Because of the limited resolution of ChIP-seq, the close spacing of promoters and transcription units found in archaeal genomes pose a challenge for ChIP-seq and the ensuing data analysis. The extreme growth temperature of many established archaeal model organisms necessitates further adaptations. This chapter describes a version of ChIP-seq adapted for the basal transcription machinery of thermophilic archaea and some modifications to the data analysis.
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Affiliation(s)
- Fabian Blombach
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.
| | - Kathy L Smollett
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Finn Werner
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK.
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Porras L, Ismail H, Mader S. Positive Regulation of Estrogen Receptor Alpha in Breast Tumorigenesis. Cells 2021; 10:cells10112966. [PMID: 34831189 PMCID: PMC8616513 DOI: 10.3390/cells10112966] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/23/2021] [Accepted: 10/24/2021] [Indexed: 12/31/2022] Open
Abstract
Estrogen receptor alpha (ERα, NR3A1) contributes through its expression in different tissues to a spectrum of physiological processes, including reproductive system development and physiology, bone mass maintenance, as well as cardiovascular and central nervous system functions. It is also one of the main drivers of tumorigenesis in breast and uterine cancer and can be targeted by several types of hormonal therapies. ERα is expressed in a subset of luminal cells corresponding to less than 10% of normal mammary epithelial cells and in over 70% of breast tumors (ER+ tumors), but the basis for its selective expression in normal or cancer tissues remains incompletely understood. The mapping of alternative promoters and regulatory elements has delineated the complex genomic structure of the ESR1 gene and shed light on the mechanistic basis for the tissue-specific regulation of ESR1 expression. However, much remains to be uncovered to better understand how ESR1 expression is regulated in breast cancer. This review recapitulates the current body of knowledge on the structure of the ESR1 gene and the complex mechanisms controlling its expression in breast tumors. In particular, we discuss the impact of genetic alterations, chromatin modifications, and enhanced expression of other luminal transcription regulators on ESR1 expression in tumor cells.
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10
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Blombach F, Fouqueau T, Matelska D, Smollett K, Werner F. Promoter-proximal elongation regulates transcription in archaea. Nat Commun 2021; 12:5524. [PMID: 34535658 PMCID: PMC8448881 DOI: 10.1038/s41467-021-25669-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 08/25/2021] [Indexed: 01/17/2023] Open
Abstract
Recruitment of RNA polymerase and initiation factors to the promoter is the only known target for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation are involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Saccharolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.
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Affiliation(s)
- Fabian Blombach
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
| | - Thomas Fouqueau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Dorota Matelska
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Katherine Smollett
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Finn Werner
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK.
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11
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Gallon J, Loomis E, Curry E, Martin N, Brody L, Garner I, Brown R, Flanagan JM. Chromatin accessibility changes at intergenic regions are associated with ovarian cancer drug resistance. Clin Epigenetics 2021; 13:122. [PMID: 34090482 PMCID: PMC8180030 DOI: 10.1186/s13148-021-01105-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Resistance to DNA damaging chemotherapies leads to cancer treatment failure and poor patient prognosis. We investigated how genomic distribution of accessible chromatin sites is altered during acquisition of cisplatin resistance using matched ovarian cell lines from high grade serous ovarian cancer (HGSOC) patients before and after becoming clinically resistant to platinum-based chemotherapy. Results Resistant lines show altered chromatin accessibility at intergenic regions, but less so at gene promoters. Clusters of cis-regulatory elements at these intergenic regions show chromatin changes that are associated with altered expression of linked genes, with enrichment for genes involved in the Fanconi anemia/BRCA DNA damage response pathway. Further, genome-wide distribution of platinum adducts associates with the chromatin changes observed and distinguish sensitive from resistant lines. In the resistant line, we observe fewer adducts around gene promoters and more adducts at intergenic regions.
Conclusions Chromatin changes at intergenic regulators of gene expression are associated with in vivo derived drug resistance and Pt-adduct distribution in patient-derived HGSOC drug resistance models. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01105-6.
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Affiliation(s)
- John Gallon
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Erick Loomis
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Edward Curry
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Nicholas Martin
- Trace Element Laboratory, Charing Cross Hospital, Imperial College NHS Trust, London, UK
| | - Leigh Brody
- Desktop Genetics, 28 Hanbury St, London, E1 6QR, UK
| | - Ian Garner
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Robert Brown
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK. .,Institute of Cancer Research, Sutton, London, SM2 5NG, UK.
| | - James M Flanagan
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK.
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12
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Li H, Guan Y. Fast decoding cell type-specific transcription factor binding landscape at single-nucleotide resolution. Genome Res 2021; 31:721-731. [PMID: 33741685 PMCID: PMC8015851 DOI: 10.1101/gr.269613.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/17/2021] [Indexed: 01/22/2023]
Abstract
Decoding the cell type-specific transcription factor (TF) binding landscape at single-nucleotide resolution is crucial for understanding the regulatory mechanisms underlying many fundamental biological processes and human diseases. However, limits on time and resources restrict the high-resolution experimental measurements of TF binding profiles of all possible TF-cell type combinations. Previous computational approaches either cannot distinguish the cell context-dependent TF binding profiles across diverse cell types or can only provide a relatively low-resolution prediction. Here we present a novel deep learning approach, Leopard, for predicting TF binding sites at single-nucleotide resolution, achieving the average area under receiver operating characteristic curve (AUROC) of 0.982 and the average area under precision recall curve (AUPRC) of 0.208. Our method substantially outperformed the state-of-the-art methods Anchor and FactorNet, improving the predictive AUPRC by 19% and 27%, respectively, when evaluated at 200-bp resolution. Meanwhile, by leveraging a many-to-many neural network architecture, Leopard features a hundredfold to thousandfold speedup compared with current many-to-one machine learning methods.
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Affiliation(s)
- Hongyang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
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13
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Genome-wide Identification of DNA-protein Interaction to Reconstruct Bacterial Transcription Regulatory Network. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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14
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Martin PC, Zabet NR. Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. Comput Struct Biotechnol J 2020; 18:3590-3605. [PMID: 33304457 PMCID: PMC7708957 DOI: 10.1016/j.csbj.2020.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 01/22/2023] Open
Abstract
Transcription Factors (TFs) bind to DNA and control activity of target genes. Here, we present ChIPanalyser, a user-friendly, versatile and powerful R/Bioconductor package predicting and modelling the binding of TFs to DNA. ChIPanalyser performs similarly to state-of-the-art tools, but is an explainable model and provides biological insights into binding mechanisms of TFs. We focused on investigating the binding mechanisms of three TFs that are known architectural proteins CTCF, BEAF-32 and su(Hw) in three Drosophila cell lines (BG3, Kc167 and S2). While CTCF preferentially binds only to a subset of high affinity sites located mainly in open chromatin, BEAF-32 binds to most of its high affinity binding sites available in open chromatin. In contrast, su(Hw) binds to both open chromatin and also partially closed chromatin. Most importantly, differences in TF binding profiles between cell lines for these TFs are mainly driven by differences in DNA accessibility and not by differences in TF concentrations between cell lines. Finally, we investigated binding of Hox TFs in Drosophila and found that Ubx binds only in open chromatin, while Abd-B and Dfd are capable to bind in both open and partially closed chromatin. Overall, our results show that TFs display different binding mechanisms and that our model is able to recapitulate their specific binding behaviour.
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Affiliation(s)
- Patrick C.N. Martin
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
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15
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Kong S, Li Q, Zhang G, Li Q, Huang Q, Huang L, Zhang H, Huang Y, Peng Y, Qin B, Zhang Y. Exonuclease combinations reduce noises in 3D genomics technologies. Nucleic Acids Res 2020; 48:e44. [PMID: 32128590 PMCID: PMC7192622 DOI: 10.1093/nar/gkaa106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/04/2020] [Accepted: 02/19/2020] [Indexed: 12/21/2022] Open
Abstract
Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source, which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased the valid-pairs ratio from ∼40% to ∼80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.
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Affiliation(s)
- Siyuan Kong
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qing Li
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Gaolin Zhang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qiujia Li
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qitong Huang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lei Huang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hui Zhang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yinghua Huang
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yanling Peng
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Baoming Qin
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yubo Zhang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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16
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Baker LA, Holliday H, Roden D, Krisp C, Wu SZ, Junankar S, Serandour AA, Mohammed H, Nair R, Sankaranarayanan G, Law AMK, McFarland A, Simpson PT, Lakhani S, Dodson E, Selinger C, Anderson L, Samimi G, Hacker NF, Lim E, Ormandy CJ, Naylor MJ, Simpson K, Nikolic I, O'Toole S, Kaplan W, Cowley MJ, Carroll JS, Molloy M, Swarbrick A. Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer. Breast Cancer Res 2020; 22:63. [PMID: 32527287 PMCID: PMC7291584 DOI: 10.1186/s13058-020-01306-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Basal-like breast cancer (BLBC) is a poorly characterised, heterogeneous disease. Patients are diagnosed with aggressive, high-grade tumours and often relapse with chemotherapy resistance. Detailed understanding of the molecular underpinnings of this disease is essential to the development of personalised therapeutic strategies. Inhibitor of differentiation 4 (ID4) is a helix-loop-helix transcriptional regulator required for mammary gland development. ID4 is overexpressed in a subset of BLBC patients, associating with a stem-like poor prognosis phenotype, and is necessary for the growth of cell line models of BLBC through unknown mechanisms. METHODS Here, we have defined unique molecular insights into the function of ID4 in BLBC and the related disease high-grade serous ovarian cancer (HGSOC), by combining RIME proteomic analysis, ChIP-seq mapping of genomic binding sites and RNA-seq. RESULTS These studies reveal novel interactions with DNA damage response proteins, in particular, mediator of DNA damage checkpoint protein 1 (MDC1). Through MDC1, ID4 interacts with other DNA repair proteins (γH2AX and BRCA1) at fragile chromatin sites. ID4 does not affect transcription at these sites, instead binding to chromatin following DNA damage. Analysis of clinical samples demonstrates that ID4 is amplified and overexpressed at a higher frequency in BRCA1-mutant BLBC compared with sporadic BLBC, providing genetic evidence for an interaction between ID4 and DNA damage repair deficiency. CONCLUSIONS These data link the interactions of ID4 with MDC1 to DNA damage repair in the aetiology of BLBC and HGSOC.
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Affiliation(s)
- Laura A Baker
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Holly Holliday
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Daniel Roden
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Christoph Krisp
- Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
- Mass Spectrometric Proteome Analysis, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Sunny Z Wu
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Simon Junankar
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Aurelien A Serandour
- Cancer Research UK, The University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Hisham Mohammed
- Cancer Research UK, The University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Radhika Nair
- Rajiv Gandhi Centre for Biotechnology, Thycaud Post, Poojappura, Thiruvananthapuram, Kerala, 695014, India
| | - Geetha Sankaranarayanan
- Cancer Research UK, The University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Andrew M K Law
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Andrea McFarland
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Peter T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Sunil Lakhani
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, The Royal Brisbane and Women's Hospital, Herston, , Brisbane, QLD, Australia
| | - Eoin Dodson
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Christina Selinger
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
| | - Lyndal Anderson
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Goli Samimi
- National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, MD, 20892, USA
| | - Neville F Hacker
- School of Women's and Children's Health, University of New South Wales, and Gynaecological Cancer Centre, Royal Hospital for Women, Sydney, NSW, Australia
| | - Elgene Lim
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Christopher J Ormandy
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Matthew J Naylor
- School of Medical Sciences and Bosch Institute, Sydney Medical School, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Kaylene Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3052, Australia
| | - Iva Nikolic
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Sandra O'Toole
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, 2050, Australia
- Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Warren Kaplan
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Mark J Cowley
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Jason S Carroll
- Cancer Research UK, The University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Mark Molloy
- Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Alexander Swarbrick
- The Kinghorn Cancer Centre and Cancer Research Division, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.
- St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, 2052, Australia.
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17
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Sharma V, Majumdar S. Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes. BMC Bioinformatics 2020; 21:65. [PMID: 32085702 PMCID: PMC7035708 DOI: 10.1186/s12859-020-3403-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/10/2020] [Indexed: 01/26/2023] Open
Abstract
Background ChIP (Chromatin immunoprecipitation)-exo has emerged as an important and versatile improvement over conventional ChIP-seq as it reduces the level of noise, maps the transcription factor (TF) binding location in a very precise manner, upto single base-pair resolution, and enables binding mode prediction. Availability of numerous peak-callers for analyzing ChIP-exo reads has motivated the need to assess their performance and report which tool executes reasonably well for the task. Results This study has focussed on comparing peak-callers that report direct binding events with those that report indirect binding events. The effect of strandedness of reads and duplication of data on the performance of peak-callers has been investigated. The number of peaks reported by each peak-caller is compared followed by a comparison of the annotated motifs present in the reported peaks. The significance of peaks is assessed based on the presence of a motif in top peaks. Indirect binding tools have been compared on the basis of their ability to identify annotated motifs and predict mode of protein-DNA interaction. Conclusion By studying the output of the peak-callers investigated in this study, it is concluded that the tools that use self-learning algorithms, i.e. the tools that estimate all the essential parameters from the aligned reads, perform better than the algorithms which require formation of peak-pairs. The latest tools that account for indirect binding of TFs appear to be an upgrade over the available tools, as they are able to reveal valuable information about the mode of binding in addition to direct binding. Furthermore, the quality of ChIP-exo reads have important consequences on the output of data analysis.
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Affiliation(s)
- Vasudha Sharma
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, 382355, India.
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18
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Rochette-Egly C. Retinoic Acid-Regulated Target Genes During Development: Integrative Genomics Analysis. Subcell Biochem 2020; 95:57-85. [PMID: 32297296 DOI: 10.1007/978-3-030-42282-0_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Retinoic acid (RA), a major natural active metabolite of vitamin A (VA) is well known to play critical roles in embryonic development. The effects of RA are mediated by nuclear receptors (RARs), which regulate the expression of gene batteries involved in cell growth and differentiation. Since the early 1990s several laboratories have focused on understanding how RA-regulated genes and RAR binding sites operate by studying the differentiation of embryonal carcinoma cells and embryonic stem cells. The development of hybridization-based microarray technology and high performance software analysis programs has allowed the characterization of thousands of RA-regulated genes. During the two last decades, publication of the genome sequence of various organisms has allowed advances in massive parallel sequencing and bioinformatics analysis of genome-wide data sets. These new generation sequencing (NGS) technologies have revolutionized the field by providing a global integrated picture of RA-regulated gene networks and the regulatory programs involved in cell fate decisions during embryonal carcinoma and embryonic stem cells differentiation. Now the challenge is to reconstruct the RA-regulated gene networks at the single cell level during the development of specialized embryonic tissues.
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Affiliation(s)
- Cecile Rochette-Egly
- Université de Strasbourg, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), INSERM, U964, CNRS, UMR7104, 1 rue Laurent Fries, BP 10142, 67404, Illkirch Cedex, France.
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19
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Yamada N, Lai WKM, Farrell N, Pugh BF, Mahony S. Characterizing protein-DNA binding event subtypes in ChIP-exo data. Bioinformatics 2019; 35:903-913. [PMID: 30165373 DOI: 10.1093/bioinformatics/bty703] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/14/2018] [Accepted: 08/23/2018] [Indexed: 01/21/2023] Open
Abstract
MOTIVATION Regulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein-protein interactions with other regulators. Each recruitment mechanism may be associated with distinct motifs and may also result in distinct characteristic patterns in high-resolution protein-DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein-DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5' → 3' exonuclease digestion. Since different regulatory complexes will result in different protein-DNA crosslinking signatures, analysis of ChIP-exo tag enrichment patterns should enable detection of multiple protein-DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type or rely on motifs to cluster binding events into subtypes. RESULTS To systematically detect multiple protein-DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype memberships of binding events using both ChIP-exo tag distribution patterns and DNA motifs. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix identifies possible recruitment mechanisms of FoxA1 and ERα, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes. AVAILABILITY AND IMPLEMENTATION ChExMix is available from https://github.com/seqcode/chexmix. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Naomi Yamada
- Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - William K M Lai
- Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Nina Farrell
- Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - B Franklin Pugh
- Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Shaun Mahony
- Department of Biochemistry & Molecular Biology and Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
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20
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Redmond AM, Omarjee S, Chernukhin I, Le Romancer M, Carroll JS. Analysis of HER2 genomic binding in breast cancer cells identifies a global role in direct gene regulation. PLoS One 2019; 14:e0225180. [PMID: 31747426 PMCID: PMC6867699 DOI: 10.1371/journal.pone.0225180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022] Open
Abstract
HER2 is a transmembrane receptor tyrosine kinase, which plays a key role in breast cancer due to a common genomic amplification. It is used as a marker to stratify patients in the clinic and is targeted by a number of drugs including Trastuzumab and Lapatinib. HER2 has previously been shown to translocate to the nucleus. In this study, we have explored the properties of nuclear HER2 by analysing the binding of this protein to the chromatin in two breast cancer cell lines. We find genome-wide re-programming of HER2 binding after treatment with the growth factor EGF and have identified a de novo motif at HER2 binding sites. Over 2,000 HER2 binding sites are found in both breast cancer cell lines after EGF treatment, and according to pathway analysis, these binding sites were enriched near genes involved in protein kinase activity and signal transduction. HER2 was shown to co-localise at a small subset of regions demarcated by H3K4me1, a hallmark of functional enhancer elements and HER2/H3K4me1 co-bound regions were enriched near EGF regulated genes providing evidence for their functional role as regulatory elements. A chromatin bound role for HER2 was verified by independent methods, including Proximity Ligation Assay (PLA), which confirmed a close association between HER2 and H3K4me1. Mass spectrometry analysis of the chromatin bound HER2 complex identified EGFR and STAT3 as interacting partners in the nucleus. These findings reveal a global role for HER2 as a chromatin-associated factor that binds to enhancer elements to elicit direct gene expression events in breast cancer cells.
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Affiliation(s)
- Aisling M. Redmond
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Soleilmane Omarjee
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Igor Chernukhin
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Muriel Le Romancer
- Université Lyon 1, Lyon, France
- Inserm U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Jason S. Carroll
- University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
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21
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Wang X, Srivastava Y, Jankowski A, Malik V, Wei Y, Del Rosario RC, Cojocaru V, Prabhakar S, Jauch R. DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1. Nucleic Acids Res 2019; 46:5470-5486. [PMID: 29669022 PMCID: PMC6009666 DOI: 10.1093/nar/gky259] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/12/2018] [Indexed: 12/16/2022] Open
Abstract
FOXA1 is a transcription factor capable to bind silenced chromatin to direct context-dependent cell fate conversion. Here, we demonstrate that a compact palindromic DNA element (termed 'DIV' for its diverging half-sites) induces the homodimerization of FOXA1 with strongly positive cooperativity. Alternative structural models are consistent with either an indirect DNA-mediated cooperativity or a direct protein-protein interaction. The cooperative homodimer formation is strictly constrained by precise half-site spacing. Re-analysis of chromatin immunoprecipitation sequencing data indicates that the DIV is effectively targeted by FOXA1 in the context of chromatin. Reporter assays show that FOXA1-dependent transcriptional activity declines when homodimeric binding is disrupted. In response to phosphatidylinositol-3 kinase inhibition DIV sites pre-bound by FOXA1 such as at the PVT1/MYC locus exhibit a strong increase in accessibility suggesting a role of the DIV configuration in the chromatin closed-open dynamics. Moreover, several disease-associated single nucleotide polymorphisms map to DIV elements and show allelic differences in FOXA1 homodimerization, reporter gene expression and are annotated as quantitative trait loci. This includes the rs541455835 variant at the MAPT locus encoding the Tau protein associated with Parkinson's disease. Collectively, the DIV guides chromatin engagement and regulation by FOXA1 and its perturbation could be linked to disease etiologies.
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Affiliation(s)
- Xuecong Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yogesh Srivastava
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Aleksander Jankowski
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warszawa, Poland.,Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanjie Wei
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ricardo Ch Del Rosario
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, 75 Ames St., Cambridge MA 02142, USA
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany.,Center for Multiscale Theory and Computation, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Shyam Prabhakar
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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22
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Cohen DM, Lim HW, Won KJ, Steger DJ. Shared nucleotide flanks confer transcriptional competency to bZip core motifs. Nucleic Acids Res 2019; 46:8371-8384. [PMID: 30085281 PMCID: PMC6144830 DOI: 10.1093/nar/gky681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 12/31/2022] Open
Abstract
Sequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at <1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites. Altered DNA specificity of CEBPs in cells occurs through heterodimerization with other bZip TFs, and approximately 40% of CEBP-binding sites in primary human cells harbor motifs characteristic of CEBP heterodimers. In addition, we uncover an important role for sequence bias at core-motif-flanking bases for CEBPs and demonstrate that flanking bases regulate motif function across mammalian bZip TFs. Favorable flanking bases confer efficient TF occupancy and transcriptional activity, and DNA shape may explain how the flanks alter TF binding. Importantly, motif optimization within the 10-mer is strongly correlated with cell-type-independent recruitment of CEBPβ, providing key insight into how sequence sub-optimization affects genomic occupancy of widely expressed CEBPs across cell types.
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Affiliation(s)
- Daniel M Cohen
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hee-Woong Lim
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kyoung-Jae Won
- The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - David J Steger
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.,The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
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Itkonen HM, Urbanucci A, Martin SES, Khan A, Mathelier A, Thiede B, Walker S, Mills IG. High OGT activity is essential for MYC-driven proliferation of prostate cancer cells. Am J Cancer Res 2019; 9:2183-2197. [PMID: 31149037 PMCID: PMC6531294 DOI: 10.7150/thno.30834] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/18/2019] [Indexed: 01/01/2023] Open
Abstract
O-GlcNAc transferase (OGT) is overexpressed in aggressive prostate cancer. OGT modifies intra-cellular proteins via single sugar conjugation (O-GlcNAcylation) to alter their activity. We recently discovered the first fast-acting OGT inhibitor OSMI-2. Here, we probe the stability and function of the chromatin O-GlcNAc and identify transcription factors that coordinate with OGT to promote proliferation of prostate cancer cells. Methods: Chromatin immunoprecipitation (ChIP) coupled to sequencing (seq), formaldehyde-assisted isolation of regulatory elements, RNA-seq and reverse-phase protein arrays (RPPA) were used to study the importance of OGT for chromatin structure and transcription. Mass spectrometry, western blot, RT-qPCR, cell cycle analysis and viability assays were used to establish the role of OGT for MYC-related processes. Prostate cancer patient data profiled for both mRNA and protein levels were used to validate findings. Results: We show for the first time that OGT inhibition leads to a rapid loss of O-GlcNAc chromatin mark. O-GlcNAc ChIP-seq regions overlap with super-enhancers (SE) and MYC binding sites. OGT inhibition leads to down-regulation of SE-dependent genes. We establish the first O-GlcNAc chromatin consensus motif, which we use as a bait for mass spectrometry. By combining the proteomic data from oligonucleotide enrichment with O-GlcNAc and MYC ChIP-mass spectrometry, we identify host cell factor 1 (HCF-1) as an interaction partner of MYC. Inhibition of OGT disrupts this interaction and compromises MYC's ability to confer androgen-independent proliferation to prostate cancer cells. We show that OGT is required for MYC-mediated stabilization of mitotic proteins, including Cyclin B1, and/or the increased translation of their coding transcripts. This implies that increased expression of mRNA is not always required to achieve increased protein expression and confer aggressive phenotype. Indeed, high expression of Cyclin B1 protein has strong predictive value in prostate cancer patients (p=0.000014) while mRNA does not. Conclusions: OGT promotes SE-dependent gene expression. OGT activity is required for the interaction between MYC and HCF-1 and expression of MYC-regulated mitotic proteins. These features render OGT essential for the androgen-independent, MYC-driven proliferation of prostate cancer cells. Androgen-independency is the major mechanism of prostate cancer progression, and our study identifies OGT as an essential mediator in this process.
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Venters BJ. Insights from resolving protein-DNA interactions at near base-pair resolution. Brief Funct Genomics 2019; 17:80-88. [PMID: 29211822 DOI: 10.1093/bfgp/elx043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the central goals in molecular biology is to understand how cell-type-specific expression patterns arise through selective recruitment of RNA polymerase II (Pol II) to a subset of gene promoters. Pol II needs to be recruited to a precise genomic position at the proper time to produce messenger RNA from a DNA template. Ostensibly, transcription is a relatively simple cellular process; yet, experimentally measuring and then understanding the combinatorial possibilities of transcriptional regulators remain a daunting task. Since its introduction in 1985, chromatin immunoprecipitation (ChIP) has remained a key tool for investigating protein-DNA contacts in vivo. Over 30 years of intensive research using ChIP have provided numerous insights into mechanisms of gene regulation. As functional genomic technologies improve, they present new opportunities to address key biological questions. ChIP-exo is a refined version of ChIP-seq that significantly reduces background signal, while providing near base-pair mapping resolution for protein-DNA interactions. This review discusses the evolution of the ChIP assay over the years; the methodological differences between ChIP-seq, ChIP-exo and ChIP-nexus; and highlight new insights into epigenetic and transcriptional mechanisms that were uniquely enabled with the near base-pair resolution of ChIP-exo.
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25
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Abstract
ChIP-seq and ChIP-exo identify where proteins bind along any genome in vivo. Although ChIP-seq is widely adopted in academic research, it has inherently high noise. In contrast, ChIP-exo has relatively low noise and achieves near-base pair resolution. Consequently, and unlike other genomic assays, ChIP-exo provides structural information on genome-wide binding proteins. Construction of ChIP-exo libraries is technically difficult. Here we describe greatly simplified ChIP-exo methods, each with use-specific advantages. This is achieved through assay optimization and use of Tn5 tagmentation and/or single-stranded DNA ligation. Greater library yields, lower processing time, and lower costs are achieved. In comparing assays, we reveal substantial limitations in other ChIP-based assays. Importantly, the new ChIP-exo assays allow high-resolution detection of some protein-DNA interactions in organs and in as few as 27,000 cells. It is suitable for high-throughput parallelization. The simplicity of ChIP-exo now makes it a highly appropriate substitute for ChIP-seq, and for broader adoption. While ChIP-exo is low noise and highly informative regarding genome-wide binding proteins, libraries are difficult to construct. Here the authors present a simplified ChIP-exo method for high-resolution detection of interactions.
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Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO. ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. PLoS One 2018; 13:e0197272. [PMID: 29771928 PMCID: PMC5957442 DOI: 10.1371/journal.pone.0197272] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70. The binding patterns of both Crp and σ70 are indicative of RNAP holoenzyme DNA footprinting profiles associated with stages during transcription initiation that occur post-recruitment. This is marked by a pronounced advancement of the template strand footprint profile to the +20 position relative to the transcription start site and a multimodal distribution on the nontemplate strand. This trend was also observed in the familial transcription factor, Fnr, but full protection of the motif was seen in the repressor ArcA. Given the time-scale of ChIP studies and that the rate-limiting step in transcription initiation is typically post recruitment, we propose a hypothesis where Crp is absent from the DNA motif but remains associated with RNAP holoenzyme post-recruitment during transcription initiation. The release of Crp from the DNA motif may be a result of energetic changes that occur as RNAP holoenzyme traverses the various stable intermediates towards elongation complex formation.
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Affiliation(s)
- Haythem Latif
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Stephen Federowicz
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Ali Ebrahim
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Janna Tarasova
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Richard Szubin
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Jose Utrilla
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
| | - Karsten Zengler
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Bernhard O. Palsson
- Bioengineering Department, University of California San Diego, La Jolla, California, United States of America
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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Jordán-Pla A, Visa N. Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments. Methods Mol Biol 2018; 1689:9-28. [PMID: 29027161 DOI: 10.1007/978-1-4939-7380-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation.In this chapter, we provide a general overview of the ChIP method and its most common variations, with a special focus on ChIP-seq. We try to address some of the most important aspects that need to be taken into account in order to design and perform experiments that generate the most reproducible, high-quality data. Some of the main topics covered include the use of properly characterized antibodies, alternatives to chromatin preparation, the need for proper controls, and some recommendations about ChIP-seq data analysis.
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Affiliation(s)
- Antonio Jordán-Pla
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden.
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden
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28
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Welch R, Chung D, Grass J, Landick R, Keles S. Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments. Nucleic Acids Res 2017; 45:e145. [PMID: 28911122 PMCID: PMC5587812 DOI: 10.1093/nar/gkx594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/12/2017] [Indexed: 01/03/2023] Open
Abstract
ChIP-exo/nexus experiments rely on innovative modifications of the commonly used ChIP-seq protocol for high resolution mapping of transcription factor binding sites. Although many aspects of the ChIP-exo data analysis are similar to those of ChIP-seq, these high throughput experiments pose a number of unique quality control and analysis challenges. We develop a novel statistical quality control pipeline and accompanying R/Bioconductor package, ChIPexoQual, to enable exploration and analysis of ChIP-exo and related experiments. ChIPexoQual evaluates a number of key issues including strand imbalance, library complexity, and signal enrichment of data. Assessment of these features are facilitated through diagnostic plots and summary statistics computed over regions of the genome with varying levels of coverage. We evaluated our QC pipeline with both large collections of public ChIP-exo/nexus data and multiple, new ChIP-exo datasets from Escherichia coli. ChIPexoQual analysis of these datasets resulted in guidelines for using these QC metrics across a wide range of sequencing depths and provided further insights for modelling ChIP-exo data.
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Affiliation(s)
- Rene Welch
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dongjun Chung
- Department of Public Health Sciences, Medical University of South Carolina, SC 29425, USA
| | - Jeffrey Grass
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keles
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA
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29
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Arnal JF, Lenfant F, Metivier R, Flouriot G, Henrion D, Adlanmerini M, Fontaine C, Gourdy P, Chambon P, Katzenellenbogen B, Katzenellenbogen J. Membrane and Nuclear Estrogen Receptor Alpha Actions: From Tissue Specificity to Medical Implications. Physiol Rev 2017; 97:1045-1087. [DOI: 10.1152/physrev.00024.2016] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
Estrogen receptor alpha (ERα) has been recognized now for several decades as playing a key role in reproduction and exerting functions in numerous nonreproductive tissues. In this review, we attempt to summarize the in vitro studies that are the basis of our current understanding of the mechanisms of action of ERα as a nuclear receptor and the key roles played by its two activation functions (AFs) in its transcriptional activities. We then depict the consequences of the selective inactivation of these AFs in mouse models, focusing on the prominent roles played by ERα in the reproductive tract and in the vascular system. Evidence has accumulated over the two last decades that ERα is also associated with the plasma membrane and activates non-nuclear signaling from this site. These rapid/nongenomic/membrane-initiated steroid signals (MISS) have been characterized in a variety of cell lines, and in particular in endothelial cells. The development of selective pharmacological tools that specifically activate MISS and the generation of mice expressing an ERα protein impeded for membrane localization have begun to unravel the physiological role of MISS in vivo. Finally, we discuss novel perspectives for the design of tissue-selective ER modulators based on the integration of the physiological and pathophysiological roles of MISS actions of estrogens.
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Affiliation(s)
- Jean-Francois Arnal
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Françoise Lenfant
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Raphaël Metivier
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Gilles Flouriot
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Daniel Henrion
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Marine Adlanmerini
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Coralie Fontaine
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Pierre Gourdy
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Pierre Chambon
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - Benita Katzenellenbogen
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
| | - John Katzenellenbogen
- I2MC, Institut National de la Santé et de la Recherche Médicale (INSERM) U 1048, Université de Toulouse 3 and CHU de Toulouse, Toulouse, France; Equipe SP@RTE UMR 6290 CNRS, Institut de Genétique et Développement de Rennes, Université de Rennes 1, Campus de Beaulieu, Rennes, France; Université de Rennes 1, Institut de Recherche en Santé, Environnement et Travail (Irest–INSERM UMR 1085), Equipe TREC, Rennes, France; Unité Mixte de Recherche 6214, Centre National de la Recherche Scientifique, Angers,
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He BZ, Zhou X, O'Shea EK. Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway. eLife 2017; 6:25157. [PMID: 28485712 PMCID: PMC5446240 DOI: 10.7554/elife.25157] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/29/2017] [Indexed: 01/23/2023] Open
Abstract
Although combinatorial regulation is a common feature in gene regulatory networks, how it evolves and affects network structure and function is not well understood. In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are required for gene induction and survival during phosphate starvation. In the related human commensal C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate starvation and is only partially required for inducing PHO genes. Phylogenetic survey suggests that reduced dependence on Pho2 evolved in C. glabrata and closely related species. In S. cerevisiae, less Pho2-dependent Pho4 orthologs induce more genes. In C. glabrata, its Pho4 binds to more locations and induces three times as many genes as Pho4 in S. cerevisiae does. Our work shows how evolution of combinatorial regulation allows for rapid expansion of a gene regulatory network’s targets, possibly extending its physiological functions. The diversity of life on Earth has intrigued generations of scientists and nature lovers alike. Research over recent decades has revealed that much of the diversity we can see did not require the invention of new genes. Instead, living forms diversified mostly by using old genes in new ways – for example, by changing when or where an existing gene became active. This kind of change is referred to as “regulatory evolution”. A class of proteins called transcription factors are hot spots in regulatory evolution. These proteins recognize specific sequences of DNA to control the activity of other genes, and so represent the “readers” of the genetic information. Small changes to how a transcription factor is regulated, or the genes it targets, can lead to dramatic changes in an organism. Before we can understand how life on Earth evolved to be so diverse, scientists must first answer how transcription factors evolve and what consequences this has on their target genes. So far, most studies of regulatory evolution have focused on networks of transcription factors and genes that control how an organism develops. He et al. have now studied a regulatory network that is behind a different process, namely how an organism responds to stress or starvation. These two types of regulatory networks are structured differently and work in different ways. These differences made He et al. wonder if the networks evolved differently too. The chemical phosphate is an essential nutrient for all living things, and He et al. compared how two different species of yeast responded to a lack of phosphate. The key difference was how much a major transcription factor known as Pho4 depended on a so-called co-activator protein named Pho2 to carry out its role. Baker’s yeast (Saccharomyces cerevisiae), which is commonly used in laboratory experiments, requires both Pho4 and Pho2 to activate about 20 genes when inorganic phosphate is not available in its environment. However, in a related yeast species called Candida glabrata, Pho4 has evolved to depend less on Pho2. He et al. went on to show that, as well as being less dependent on Pho2, Pho4 in C. glabrata activates more than three times as many genes as Pho4 in S. cerevisiae does in the absence of phosphate. These additional gene targets for Pho4 in C. glabrata are predicted to extend the network’s activities, and allow it to regulate new process including the yeast’s responses to other types of stress and the building of the yeast’s cell wall. Together these findings show a new way that regulatory networks can evolve, that is, by reducing its dependence on the co-activator, a transcription factor can expand the number of genes it targets. This has not been seen for regulatory networks related to development, suggesting that different networks can indeed evolve in different ways. Lastly, because disease-causing microbes are often stressed inside their hosts and C. glabrata sometimes infects humans, understanding how this yeast’s response to stress has evolved may lead to new ways to prevent and treat this infection.
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Affiliation(s)
- Bin Z He
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Xu Zhou
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Erin K O'Shea
- Faculty of Arts and Sciences Center for Systems Biology, Howard Hughes Medical Institute, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
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31
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Brönner C, Salvi L, Zocco M, Ugolini I, Halic M. Accumulation of RNA on chromatin disrupts heterochromatic silencing. Genome Res 2017; 27:1174-1183. [PMID: 28404620 PMCID: PMC5495069 DOI: 10.1101/gr.216986.116] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 04/11/2017] [Indexed: 12/13/2022]
Abstract
Long noncoding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics, and cell differentiation. They serve as a platform for RNA interference (RNAi)–mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe that heterochromatin is lost at transcribed regions in the absence of RNA degradation. We show that heterochromatic RNAs are retained on chromatin, form DNA:RNA hybrids, and need to be degraded by the Ccr4-Not complex or RNAi to maintain heterochromatic silencing. The Ccr4-Not complex is localized to chromatin independently of H3K9me and degrades chromatin-associated transcripts, which is required for transcriptional silencing. Overexpression of heterochromatic RNA, but not euchromatic RNA, leads to chromatin localization and loss of silencing of a distant ade6 reporter in wild-type cells. Our results demonstrate that chromatin-bound RNAs disrupt heterochromatin organization and need to be degraded in a process of heterochromatin formation.
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Affiliation(s)
- Cornelia Brönner
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Luca Salvi
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Manuel Zocco
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Ilaria Ugolini
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
| | - Mario Halic
- Department of Biochemistry, Gene Center, University of Munich (LMU), 81377 Munich, Germany
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Barfeld SJ, Urbanucci A, Itkonen HM, Fazli L, Hicks JL, Thiede B, Rennie PS, Yegnasubramanian S, DeMarzo AM, Mills IG. c-Myc Antagonises the Transcriptional Activity of the Androgen Receptor in Prostate Cancer Affecting Key Gene Networks. EBioMedicine 2017; 18:83-93. [PMID: 28412251 PMCID: PMC5405195 DOI: 10.1016/j.ebiom.2017.04.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022] Open
Abstract
Prostate cancer (PCa) is the most common non-cutaneous cancer in men. The androgen receptor (AR), a ligand-activated transcription factor, constitutes the main drug target for advanced cases of the disease. However, a variety of other transcription factors and signaling networks have been shown to be altered in patients and to influence AR activity. Amongst these, the oncogenic transcription factor c-Myc has been studied extensively in multiple malignancies and elevated protein levels of c-Myc are commonly observed in PCa. Its impact on AR activity, however, remains elusive. In this study, we assessed the impact of c-Myc overexpression on AR activity and transcriptional output in a PCa cell line model and validated the antagonistic effect of c-MYC on AR-targets in patient samples. We found that c-Myc overexpression partially reprogrammed AR chromatin occupancy and was associated with altered histone marks distribution, most notably H3K4me1 and H3K27me3. We found c-Myc and the AR co-occupy a substantial number of binding sites and these exhibited enhancer-like characteristics. Interestingly, c-Myc overexpression antagonised clinically relevant AR target genes. Therefore, as an example, we validated the antagonistic relationship between c-Myc and two AR target genes, KLK3 (alias PSA, prostate specific antigen), and Glycine N-Methyltransferase (GNMT), in patient samples. Our findings provide unbiased evidence that MYC overexpression deregulates the AR transcriptional program, which is thought to be a driving force in PCa. c-MYC and AR share one third of chromatin binding with enhancer-like features. c-MYC can repress the expression of a subset prostate cancer biomarkers, including PSA. c-MYC and AR antagonize the expression of, Glycine N-Methyltransferase (GNMT), responsible for sarcosine biosynthesis.
Prostate cancer is a heterogeneous disease. The most frequently used biomarker in clinical setting, a well described androgen receptor target gene, PSA, still performs poorly in stratifying patients at real risk of death due to the disease. Despite this, therapeutic approaches focus on suppressing androgen receptor signaling. However, this is only one of the recurrent alterations found in patients. This study focuses on c-MYC and the effects of its deregulation in advanced prostate cancer. We find that there is an inverse relationship between established biomarkers expression, including PSA. This inverse relationship could be used in clinics to select beneficial therapeutic approaches for a subset of prostate cancer cases.
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Affiliation(s)
- Stefan J Barfeld
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway.
| | - Alfonso Urbanucci
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
| | - Harri M Itkonen
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Ladan Fazli
- The Vancouver Prostate Centre, University of British Columbia, Canada
| | | | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Paul S Rennie
- The Vancouver Prostate Centre, University of British Columbia, Canada
| | | | - Angelo M DeMarzo
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ian G Mills
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; PCUK/Movember Centre of Excellence, CCRCB, Queen's University, Belfast, UK.
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Iwata A, Durai V, Tussiwand R, Briseño CG, Wu X, Grajales-Reyes GE, Egawa T, Murphy TL, Murphy KM. Quality of TCR signaling determined by differential affinities of enhancers for the composite BATF-IRF4 transcription factor complex. Nat Immunol 2017; 18:563-572. [PMID: 28346410 PMCID: PMC5401770 DOI: 10.1038/ni.3714] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 02/23/2017] [Indexed: 12/13/2022]
Abstract
Variable strengths of T cell receptor (TCR) signaling can produce divergent outcomes, but the mechanism remains obscure. The abundance of the transcription factor IRF4 increases with TCR signal strength, but how this would induce distinct types of responses is unclear. We compared TH2 gene expression with BATF/IRF4 enhancer occupancy at varying strengths of TCR stimulation. BATF/IRF4-dependent genes clustered into distinct TCR-sensitivities. Enhancers exhibited a spectrum of occupancy by BATF/IRF4 ternary complex that correlated with TCR-sensitivity of gene expression. DNA sequences immediately flanking the previously defined AICE motif controlled the affinity for BATF/IRF4 for direct binding to DNA. ChIP-exo analysis allowed identification of a novel high-affinity AICE2 motif at a human SNP of CTLA4 associated with resistance to autoimmunity. Thus, the affinity of different enhancers for the BATF-IRF4 complex may underlie divergent signaling outcomes in response to various strengths of TCR signaling.
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Affiliation(s)
- Arifumi Iwata
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Vivek Durai
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Roxane Tussiwand
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Carlos G Briseño
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Xiaodi Wu
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Gary E Grajales-Reyes
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Theresa L Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Kenneth M Murphy
- Department of Pathology and Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA.,Howard Hughes Medical Institute, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
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The Vitamin B 12-Dependent Photoreceptor AerR Relieves Photosystem Gene Repression by Extending the Interaction of CrtJ with Photosystem Promoters. mBio 2017; 8:mBio.00261-17. [PMID: 28325764 PMCID: PMC5362033 DOI: 10.1128/mbio.00261-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Purple nonsulfur bacteria adapt their physiology to a wide variety of environmental conditions often through the control of transcription. One of the main transcription factors involved in controlling expression of the Rhodobacter capsulatus photosystem is CrtJ, which functions as an aerobic repressor of photosystem genes. Recently, we reported that a vitamin B12 binding antirepressor of CrtJ called AerR is required for anaerobic expression of the photosystem. However, the mechanism whereby AerR regulates CrtJ activity is unclear. In this study, we used a combination of next-generation sequencing and biochemical methods to globally identify genes under control of CrtJ and the role of AerR in controlling this regulation. Our results indicate that CrtJ has a much larger regulon than previously known, with a surprising regulatory function under both aerobic and anaerobic photosynthetic growth conditions. A combination of in vivo chromatin immunoprecipitation-DNA sequencing (ChIP-seq) and ChIP-seq and exonuclease digestion (ChIP-exo) studies and in vitro biochemical studies demonstrate that AerR forms a 1:2 complex with CrtJ (AerR-CrtJ2) and that this complex binds to many promoters under photosynthetic conditions. The results of in vitro and in vivo DNA binding studies indicate that AerR-CrtJ2 anaerobically forms an extended interaction with the bacteriochlorophyll bchC promoter to relieve repression by CrtJ. This is contrasted by aerobic growth conditions where CrtJ alone functions as an aerobic repressor of bchC expression. These results indicate that the DNA binding activity of CrtJ is modified by interacting with AerR in a redox-regulated manner and that this interaction alters CrtJ’s function. Photoreceptors control a wide range of physiology often by regulating downstream gene expression in response to light absorption via a bound chromophore. Different photoreceptors are known to utilize a number of different compounds for light absorption, including the use of such compounds as flavins, linearized tetrapyrroles (bilins), and carotenoids. Recently, a novel class of photoreceptors that use vitamin B12 (cobalamin) as a blue-light-absorbing chromophore have been described. In this study, we analyzed the mechanism by which the vitamin B12 binding photoreceptor AerR controls the DNA binding activity of the photosystem regulator CrtJ. This study shows that a direct interaction between the vitamin B12 binding photoreceptor AerR with CrtJ modulates CrtJ binding to DNA and importantly, the regulatory outcome of gene expression, as shown here with photosystem promoters.
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SMiLE-seq identifies binding motifs of single and dimeric transcription factors. Nat Methods 2017; 14:316-322. [DOI: 10.1038/nmeth.4143] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 11/06/2016] [Indexed: 11/08/2022]
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Perreault AA, Venters BJ. The ChIP-exo Method: Identifying Protein-DNA Interactions with Near Base Pair Precision. J Vis Exp 2016. [PMID: 28060339 DOI: 10.3791/55016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise. The key distinction of the ChIP-exo methodology is the incorporation of lambda exonuclease digestion in the library preparation workflow to effectively footprint the left and right 5' DNA borders of the protein-DNA crosslink site. The ChIP-exo libraries are then subjected to high throughput sequencing. The resulting data can be leveraged to provide unique and ultra-high resolution insights into the functional organization of the genome. Here, we describe the ChIP-exo method that we have optimized and streamlined for mammalian systems and next-generation sequencing-by-synthesis platform.
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Affiliation(s)
- Andrea A Perreault
- Department of Molecular Physiology and Biophysics, Vanderbilt University
| | - Bryan J Venters
- Department of Molecular Physiology and Biophysics, Vanderbilt University;
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37
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Abstract
Glucocorticoid hormones (GC) regulate essential physiological functions including energy homeostasis, embryonic and postembryonic development, and the stress response. From the biomedical perspective, GC have garnered a tremendous amount of attention as highly potent anti-inflammatory and immunosuppressive medications indispensable in the clinic. GC signal through the GC receptor (GR), a ligand-dependent transcription factor whose structure, DNA binding, and the molecular partners that it employs to regulate transcription have been under intense investigation for decades. In particular, next-generation sequencing-based approaches have revolutionized the field by introducing a unified platform for a simultaneous genome-wide analysis of cellular activities at the level of RNA production, binding of transcription factors to DNA and RNA, and chromatin landscape and topology. Here we describe fundamental concepts of GC/GR function as established through traditional molecular and in vivo approaches and focus on the novel insights of GC biology that have emerged over the last 10 years from the rapidly expanding arsenal of system-wide genomic methodologies.
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Affiliation(s)
- Maria A Sacta
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
| | - Yurii Chinenov
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021;
| | - Inez Rogatsky
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
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Hansen P, Hecht J, Ibn-Salem J, Menkuec BS, Roskosch S, Truss M, Robinson PN. Q-nexus: a comprehensive and efficient analysis pipeline designed for ChIP-nexus. BMC Genomics 2016; 17:873. [PMID: 27814676 PMCID: PMC5097360 DOI: 10.1186/s12864-016-3164-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Background ChIP-nexus, an extension of the ChIP-exo protocol, can be used to map the borders of protein-bound DNA sequences at nucleotide resolution, requires less input DNA and enables selective PCR duplicate removal using random barcodes. However, the use of random barcodes requires additional preprocessing of the mapping data, which complicates the computational analysis. To date, only a very limited number of software packages are available for the analysis of ChIP-exo data, which have not yet been systematically tested and compared on ChIP-nexus data. Results Here, we present a comprehensive software package for ChIP-nexus data that exploits the random barcodes for selective removal of PCR duplicates and for quality control. Furthermore, we developed bespoke methods to estimate the width of the protected region resulting from protein-DNA binding and to infer binding positions from ChIP-nexus data. Finally, we applied our peak calling method as well as the two other methods MACE and MACS2 to the available ChIP-nexus data. Conclusions The Q-nexus software is efficient and easy to use. Novel statistics about duplication rates in consideration of random barcodes are calculated. Our method for the estimation of the width of the protected region yields unbiased signatures that are highly reproducible for biological replicates and at the same time very specific for the respective factors analyzed. As judged by the irreproducible discovery rate (IDR), our peak calling algorithm shows a substantially better reproducibility. An implementation of Q-nexus is available at http://charite.github.io/Q/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3164-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Peter Hansen
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany.,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jonas Ibn-Salem
- Faculty of Biology, Johannes Gutenberg University Mainz, Ackermannweg 4, Mainz, 55128, Germany.,Institute of Molecular Biology, Ackermannweg 4, Mainz, 55128, Germany
| | - Benjamin S Menkuec
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Sebastian Roskosch
- Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany
| | - Matthias Truss
- Labor für Pädiatrische Molekularbiologie, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany. .,Berlin Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, Berlin, 13353, Germany. .,Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 14, Berlin, 14195, Germany. .,Max Planck Institute for Molecular Genetics, Inhestr. 63-73, Berlin, 14195, Germany. .,Current address: The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, 06032, CT, USA.
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Bolduc N, Lehman AP, Farmer A. Preparation of Low-Input and Ligation-Free ChIP-seq Libraries Using Template-Switching Technology. ACTA ACUST UNITED AC 2016; 116:7.28.1-7.28.26. [PMID: 27723085 DOI: 10.1002/cpmb.24] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) has become the gold standard for mapping of transcription factors and histone modifications throughout the genome. However, for ChIP experiments involving few cells or targeting low-abundance transcription factors, the small amount of DNA recovered makes ligation of adapters very challenging. In this unit, we describe a ChIP-seq workflow that can be applied to small cell numbers, including a robust single-tube and ligation-free method for preparation of sequencing libraries from sub-nanogram amounts of ChIP DNA. An example ChIP protocol is first presented, resulting in selective enrichment of DNA-binding proteins and cross-linked DNA fragments immobilized on beads via an antibody bridge. This is followed by a protocol for fast and easy cross-linking reversal and DNA recovery. Finally, we describe a fast, ligation-free library preparation protocol, featuring DNA SMART technology, resulting in samples ready for Illumina sequencing. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Nathalie Bolduc
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.), Mountain View, California
| | - Alisa P Lehman
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.), Mountain View, California
| | - Andrew Farmer
- Takara Bio USA, Inc. (formerly Clontech Laboratories, Inc.), Mountain View, California
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40
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Hu DG, Selth LA, Tarulli GA, Meech R, Wijayakumara D, Chanawong A, Russell R, Caldas C, Robinson JLL, Carroll JS, Tilley WD, Mackenzie PI, Hickey TE. Androgen and Estrogen Receptors in Breast Cancer Coregulate Human UDP-Glucuronosyltransferases 2B15 and 2B17. Cancer Res 2016; 76:5881-5893. [PMID: 27496708 DOI: 10.1158/0008-5472.can-15-3372] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 07/14/2016] [Indexed: 11/16/2022]
Abstract
Glucuronidation is an enzymatic process that terminally inactivates steroid hormones, including estrogens and androgens, thereby influencing carcinogenesis in hormone-dependent cancers. While estrogens drive breast carcinogenesis via the estrogen receptor alpha (ERα), androgens play a critical role as prohormones for estrogen biosynthesis and ligands for the androgen receptor (AR). In this study, the expression and regulation of two androgen-inactivating enzymes, the UDP-glucuronosyltransferases UGT2B15 and UGT2B17, was assessed in breast cancer. In large clinical cohorts, high UGT2B15 and UGT2B17 levels positively influenced disease-specific survival in distinct molecular subgroups. Expression of these genes was highest in cases positive for ERα. In cell line models, ERα, AR, and the transcription factor FOXA1 cooperated to increase transcription via tandem binding events at their proximal promoters. ERα activity was dependent on FOXA1, facilitated by AR activation, and potently stimulated by estradiol as well as estrogenic metabolites of 5α-dihydrotestosterone. AR activity was mediated via binding to an estrogen receptor half-site 3' to the FOXA1 and ERα-binding sites. Although AR and FOXA1 bound the UGT promoters in AR-positive/ERα-negative breast cancer cell lines, androgen treatment did not influence basal transcription levels. Ex vivo culture of human breast tissue and ERα+ tumors provided evidence for upregulation of UGT2B15 and UGT2B17 by estrogen or androgen treatment. ERα binding was evident at the promoters of these genes in a small cohort of primary tumors and distant metastases. Collectively, these data provide insight into sex steroid receptor-mediated regulation of androgen-inactivating enzymes in ERα+ breast cancer, which may have subtype-specific consequences for disease progression and outcomes. Cancer Res; 76(19); 5881-93. ©2016 AACR.
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Affiliation(s)
- Dong G Hu
- Department of Clinical Pharmacology, Flinders University School of Medicine, Flinders Medical Centre, South Australia, Australia
| | - Luke A Selth
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, The University of Adelaide, South Australia, Australia. Freemasons Foundation Centre for Men's Health, School of Medicine, The University of Adelaide, South Australia, Australia
| | - Gerard A Tarulli
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, The University of Adelaide, South Australia, Australia
| | - Robyn Meech
- Department of Clinical Pharmacology, Flinders University School of Medicine, Flinders Medical Centre, South Australia, Australia
| | - Dhilushi Wijayakumara
- Department of Clinical Pharmacology, Flinders University School of Medicine, Flinders Medical Centre, South Australia, Australia
| | - Apichaya Chanawong
- Department of Clinical Pharmacology, Flinders University School of Medicine, Flinders Medical Centre, South Australia, Australia
| | - Roslin Russell
- Breast Cancer Genomics Group, Cancer Research UK, Cambridge Institute, Cambridge University, Cambridge, United Kingdom
| | - Carlos Caldas
- Breast Cancer Genomics Group, Cancer Research UK, Cambridge Institute, Cambridge University, Cambridge, United Kingdom
| | - Jessica L L Robinson
- Nuclear Transcription Factor Laboratory, Cancer Research UK, Cambridge Institute, Cambridge University, Cambridge, United Kingdom
| | - Jason S Carroll
- Nuclear Transcription Factor Laboratory, Cancer Research UK, Cambridge Institute, Cambridge University, Cambridge, United Kingdom
| | - Wayne D Tilley
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, The University of Adelaide, South Australia, Australia. Freemasons Foundation Centre for Men's Health, School of Medicine, The University of Adelaide, South Australia, Australia
| | - Peter I Mackenzie
- Department of Clinical Pharmacology, Flinders University School of Medicine, Flinders Medical Centre, South Australia, Australia
| | - Theresa E Hickey
- Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, The University of Adelaide, South Australia, Australia.
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41
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Terooatea TW, Pozner A, Buck-Koehntop BA. PAtCh-Cap: input strategy for improving analysis of ChIP-exo data sets and beyond. Nucleic Acids Res 2016; 44:e159. [PMID: 27550178 PMCID: PMC5137431 DOI: 10.1093/nar/gkw741] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/08/2016] [Accepted: 08/12/2016] [Indexed: 11/24/2022] Open
Abstract
Recently, a number of advances have been implemented into the core ChIP-seq (chromatin immunoprecipitation coupled with next-generation sequencing) methodology to streamline the process, reduce costs or improve data resolution. Several of these emerging ChIP-based methods perform additional chemical steps on bead-bound immunoprecipitated chromatin, posing a challenge for generating similarly treated input controls required for artifact removal during bioinformatics analyses. Here we present a versatile method for producing technique-specific input controls for ChIP-based methods that utilize additional bead-bound processing steps. This reported method, termed protein attached chromatin capture (PAtCh-Cap), relies on the non-specific capture of chromatin-bound proteins via their carboxylate groups, leaving the DNA accessible for subsequent chemical treatments in parallel with chromatin separately immunoprecipitated for the target protein. Application of this input strategy not only significantly enhanced artifact removal from ChIP-exo data, increasing confidence in peak identification and allowing for de novo motif searching, but also afforded discovery of a novel CTCF binding motif.
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Affiliation(s)
- Tommy W Terooatea
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Amir Pozner
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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Zhang Y, Zhang D, Li Q, Liang J, Sun L, Yi X, Chen Z, Yan R, Xie G, Li W, Liu S, Xu B, Li L, Yang J, He L, Shang Y. Nucleation of DNA repair factors by FOXA1 links DNA demethylation to transcriptional pioneering. Nat Genet 2016; 48:1003-13. [PMID: 27500525 DOI: 10.1038/ng.3635] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 07/01/2016] [Indexed: 12/14/2022]
Abstract
FOXA1 functions in epigenetic reprogramming and is described as a 'pioneer factor'. However, exactly how FOXA1 achieves these remarkable biological functions is not fully understood. Here we report that FOXA1 associates with DNA repair complexes and is required for genomic targeting of DNA polymerase β (POLB) in human cells. Genome-wide DNA methylomes demonstrate that the FOXA1 DNA repair complex is functionally linked to DNA demethylation in a lineage-specific fashion. Depletion of FOXA1 results in localized reestablishment of methylation in a large portion of FOXA1-bound regions, and the regions with the most consistent hypermethylation exhibit the greatest loss of POLB and are represented by active promoters and enhancers. Consistently, overexpression of FOXA1 commits its binding sites to active DNA demethylation in a POLB-dependent manner. Finally, FOXA1-associated DNA demethylation is tightly coupled with estrogen receptor genomic targeting and estrogen responsiveness. Together, these results link FOXA1-associated DNA demethylation to transcriptional pioneering by FOXA1.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Di Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Qian Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jing Liang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xia Yi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhe Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Ruorong Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Guojia Xie
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shumeng Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Bosen Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lei Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Lin He
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Hormones and Development (Ministry of Health), Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
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43
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Ang SY, Uebersohn A, Spencer CI, Huang Y, Lee JE, Ge K, Bruneau BG. KMT2D regulates specific programs in heart development via histone H3 lysine 4 di-methylation. Development 2016; 143:810-21. [PMID: 26932671 PMCID: PMC4813342 DOI: 10.1242/dev.132688] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
KMT2D, which encodes a histone H3K4 methyltransferase, has been implicated in human congenital heart disease in the context of Kabuki syndrome. However, its role in heart development is not understood. Here, we demonstrate a requirement for KMT2D in cardiac precursors and cardiomyocytes during cardiogenesis in mice. Gene expression analysis revealed downregulation of ion transport and cell cycle genes, leading to altered calcium handling and cell cycle defects. We further determined that myocardial Kmt2d deletion led to decreased H3K4me1 and H3K4me2 at enhancers and promoters. Finally, we identified KMT2D-bound regions in cardiomyocytes, of which a subset was associated with decreased gene expression and decreased H3K4me2 in mutant hearts. This subset included genes related to ion transport, hypoxia-reoxygenation and cell cycle regulation, suggesting that KMT2D is important for these processes. Our findings indicate that KMT2D is essential for regulating cardiac gene expression during heart development primarily via H3K4 di-methylation. Highlighted article: Cardiac-specific depletion of the H3K4 methyltransferase KMT2D causes dysregulation of genes associated with cell cycle regulation, ion homeostasis and hypoxia signaling.
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Affiliation(s)
- Siang-Yun Ang
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alec Uebersohn
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - C Ian Spencer
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Yu Huang
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Ji-Eun Lee
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
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44
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Ye Z, Chen Z, Sunkel B, Frietze S, Huang THM, Wang Q, Jin VX. Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1. Nucleic Acids Res 2016; 44:7540-54. [PMID: 27458208 PMCID: PMC5027512 DOI: 10.1093/nar/gkw659] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/12/2016] [Indexed: 11/24/2022] Open
Abstract
The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis-regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis-targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1 in LNCaP cells by our novel algorithm ePEST. We find that FOXA1 chromatin binding occurs via four distinct border modes (or footprint boundary patterns), with a preferential footprint boundary patterns relative to FOXA1 motif orientation. In addition, from this analysis three fundamental nucleotide positions (oG, oS and oH) emerged as major determinants for blocking exo-digestion and forming these four distinct border modes. By integrating histone MNase-seq data, we found an astonishingly consistent, ‘well-positioned’ configuration occurs between FOXA1 motifs and dyads of nucleosomes genome-wide. We further performed ChIP-seq of eight chromatin remodelers and found an increased occupancy of these remodelers on FOXA1 motifs for all four border modes (or footprint boundary patterns), indicating the full occupancy of FOXA1 complex on the three blocking sites (oG, oS and oH) likely produces an active regulatory status with well-positioned phasing for protein binding events. Together, our results suggest a positional-nucleosome-oriented accessing model for PFs seeking target motifs, in which FOXA1 can examine each underlying DNA nucleotide and is able to sense all potential motifs regardless of whether they face inward or outward from histone octamers along the DNA helix axis.
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Affiliation(s)
- Zhenqing Ye
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Zhong Chen
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University College of Medicine, OH 43210, USA Comprehensive Cancer Center, The Ohio State University College of Medicine, OH 43210, USA
| | - Benjamin Sunkel
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University College of Medicine, OH 43210, USA Comprehensive Cancer Center, The Ohio State University College of Medicine, OH 43210, USA
| | - Seth Frietze
- MLRS Department, University of Vermont, VT 05405, USA
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, TX 78229, USA
| | - Qianben Wang
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University College of Medicine, OH 43210, USA Comprehensive Cancer Center, The Ohio State University College of Medicine, OH 43210, USA
| | - Victor X Jin
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, TX 78229, USA
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45
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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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46
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Flach KD, Zwart W. The first decade of estrogen receptor cistromics in breast cancer. J Endocrinol 2016; 229:R43-56. [PMID: 26906743 DOI: 10.1530/joe-16-0003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 02/23/2016] [Indexed: 02/03/2023]
Abstract
The advent of genome-wide transcription factor profiling has revolutionized the field of breast cancer research. Estrogen receptor α (ERα), the major drug target in hormone receptor-positive breast cancer, has been known as a key transcriptional regulator in tumor progression for over 30 years. Even though this function of ERα is heavily exploited and widely accepted as an Achilles heel for hormonal breast cancer, only since the last decade we have been able to understand how this transcription factor is functioning on a genome-wide scale. Initial ChIP-on-chip (chromatin immunoprecipitation coupled with tiling array) analyses have taught us that ERα is an enhancer-associated factor binding to many thousands of sites throughout the human genome and revealed the identity of a number of directly interacting transcription factors that are essential for ERα action. More recently, with the development of massive parallel sequencing technologies and refinements thereof in sample processing, a genome-wide interrogation of ERα has become feasible and affordable with unprecedented data quality and richness. These studies have revealed numerous additional biological insights into ERα behavior in cell lines and especially in clinical specimens. Therefore, what have we actually learned during this first decade of cistromics in breast cancer and where may future developments in the field take us?
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Affiliation(s)
- Koen D Flach
- Division of Molecular PathologyThe Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Molecular PathologyThe Netherlands Cancer Institute, Amsterdam, The Netherlands
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47
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Sérandour AA, Avner S, Mahé EA, Madigou T, Guibert S, Weber M, Salbert G. Single-CpG resolution mapping of 5-hydroxymethylcytosine by chemical labeling and exonuclease digestion identifies evolutionarily unconserved CpGs as TET targets. Genome Biol 2016; 17:56. [PMID: 27025842 PMCID: PMC4810514 DOI: 10.1186/s13059-016-0919-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 03/09/2016] [Indexed: 12/26/2022] Open
Abstract
Conventional techniques for single-base resolution mapping of epigenetic modifications of DNA such as 5-hydroxymethylcytosine (5hmC) rely on the sequencing of bisulfite-modified DNA. Here we present an alternative approach called SCL-exo which combines selective chemical labeling (SCL) of 5hmC in genomic DNA with exonuclease (exo) digestion of the bead-trapped modified DNA molecules. Associated with a straightforward bioinformatic analysis, this new procedure provides an unbiased and fast method for mapping this epigenetic mark at high resolution. Implemented on mouse genomic DNA from in vitro-differentiated neural precursor cells, SCL-exo sheds light on an intrinsic lack of conservation of hydroxymethylated CpGs across vertebrates.
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Affiliation(s)
| | - Stéphane Avner
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France
| | - Elise A Mahé
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France
| | - Thierry Madigou
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France.,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France
| | - Sylvain Guibert
- CNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France
| | - Michaël Weber
- CNRS, Université de Strasbourg, UMR7242, Biotechnologie et signalisation cellulaire, 300 bd Sébastien Brant, Illkirch cedex, 67412, France
| | - Gilles Salbert
- CNRS UMR6290, Equipe SP@RTE, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes cedex, 35042, France. .,Université de Rennes 1, Campus de Beaulieu, Rennes Cedex, 35042, France.
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48
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Tang X, Liu H, Srivastava A, Pécot T, Chen Z, Wang Q, Huang K, Sáenz-Robles MT, Cantalupo P, Pipas J, Leone G. Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Sci Data 2016; 3:160008. [PMID: 26881867 PMCID: PMC4755127 DOI: 10.1038/sdata.2016.8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022] Open
Abstract
E2F3 and MYC are transcription factors that control cellular proliferation. To study their mechanism of action in the context of a regenerating tissue, we isolated both proliferating (crypts) and non-dividing (villi) cells from wild-type and Rb depleted small intestines of mice and performed ChIP-exo-seq (chromatin immunoprecipitation combined with lambda exonuclease digestion followed by high-throughput sequencing). The genome-wide chromatin occupancy of E2F3 and MYC was determined by mapping sequence reads to the genome and predicting preferred binding sites (peaks). Binding sites could be accurately identified within small regions of only 24 bp-28 bp long, highlighting the precision to which binding peaks can be identified by ChIP-exo-seq. Forty randomly selected E2F3- and MYC-specific binding sites were validated by ChIP-PCR. In addition, we also presented gene expression data sets from wild type, Rb-, E2f3- and Myc-depleted crypts and villi within this manuscript. These represent comprehensive and validated datasets that can be integrated to identify putative direct targets of E2F3 and MYC involved in the control of cellular proliferation in normal and Rb-deficient small intestines.
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Affiliation(s)
- Xing Tang
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.,Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Huayang Liu
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.,Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Arunima Srivastava
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.,Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Thierry Pécot
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.,Comprehensive Cancer Center, Columbus, Ohio 43210, USA
| | - Zhong Chen
- Department of Molecular and Cellular Biochemistry, Columbus, Ohio 43210, USA
| | - Qianben Wang
- Department of Molecular and Cellular Biochemistry, Columbus, Ohio 43210, USA
| | - Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | | | - Paul Cantalupo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - James Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
| | - Gustavo Leone
- Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.,Department of Molecular Genetics, College of Biological Sciences, Columbus, Ohio 43210, USA.,Comprehensive Cancer Center, Columbus, Ohio 43210, USA
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49
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Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MAH, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Müller CW, Bruneau BG. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell 2016; 164:999-1014. [PMID: 26875865 DOI: 10.1016/j.cell.2016.01.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 11/21/2015] [Accepted: 12/22/2015] [Indexed: 12/26/2022]
Abstract
Transcription factors (TFs) are thought to function with partners to achieve specificity and precise quantitative outputs. In the developing heart, heterotypic TF interactions, such as between the T-box TF TBX5 and the homeodomain TF NKX2-5, have been proposed as a mechanism for human congenital heart defects. We report extensive and complex interdependent genomic occupancy of TBX5, NKX2-5, and the zinc finger TF GATA4 coordinately controlling cardiac gene expression, differentiation, and morphogenesis. Interdependent binding serves not only to co-regulate gene expression but also to prevent TFs from distributing to ectopic loci and activate lineage-inappropriate genes. We define preferential motif arrangements for TBX5 and NKX2-5 cooperative binding sites, supported at the atomic level by their co-crystal structure bound to DNA, revealing a direct interaction between the two factors and induced DNA bending. Complex interdependent binding mechanisms reveal tightly regulated TF genomic distribution and define a combinatorial logic for heterotypic TF regulation of differentiation.
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Affiliation(s)
- Luis Luna-Zurita
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Christian U Stirnimann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sebastian Glatt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Bogac L Kaynak
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Sean Thomas
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Florence Baudin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany; UJF-EMBL-CNRS UMI 3265, Unit of Virus Host-Cell Interactions, 38042 Grenoble Cedex 9, France
| | | | - Daniel He
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA
| | - Eric M Small
- Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Maria Mileikovsky
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Obstetrics and Gynaecology and Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Alisha K Holloway
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Katherine S Pollard
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA; Roddenberry Center for Stem Cell Biology and Medicine at Gladstone, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA.
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50
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Barfeld SJ, Mills IG. Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing. Methods Mol Biol 2016; 1443:119-137. [PMID: 27246337 DOI: 10.1007/978-1-4939-3724-0_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of nonspecific background sequences in ChIPped samples. In this chapter, we provide a brief commentary on these methodological changes and describe a detailed ChIP-exo method able to generate narrower peaks and greater peak coverage from ChIPped material.
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Affiliation(s)
- Stefan J Barfeld
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership University of Oslo and Oslo University Hospital, Oslo, Norway.
- Molecular Oncology, Institute of Cancer Research and Oslo University Hospital, Oslo, Norway.
- Prostate Cancer Research Group, Centre for Cancer Research and Cell Biology (CCRCB), Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK.
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