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Phongbunchoo Y, Braikia FZ, Pessoa-Rodrigues C, Ramamoorthy S, Ramachandran H, Grosschedl A, Ma F, Cauchy P, Akhtar A, Sen R, Mittler G, Grosschedl R. YY1-mediated enhancer-promoter communication in the immunoglobulin μ locus is regulated by MSL/MOF recruitment. Cell Rep 2024; 43:114456. [PMID: 38990722 DOI: 10.1016/j.celrep.2024.114456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 05/02/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
The rearrangement and expression of the immunoglobulin μ heavy chain (Igh) gene require communication of the intragenic Eμ and 3' regulatory region (RR) enhancers with the variable (VH) gene promoter. Eμ binding of the transcription factor YY1 has been implicated in enhancer-promoter communication, but the YY1 protein network remains obscure. By analyzing the comprehensive proteome of the 1-kb Eμ wild-type enhancer and that of Eμ lacking the YY1 binding site, we identified the male-specific lethal (MSL)/MOF complex as a component of the YY1 protein network. We found that MSL2 recruitment depends on YY1 and that gene knockout of Msl2 in primary pre-B cells reduces μ gene expression and chromatin looping of Eμ to the 3' RR enhancer and VH promoter. Moreover, Mof heterozygosity in mice impaired μ expression and early B cell differentiation. Together, these data suggest that the MSL/MOF complex regulates Igh gene expression by augmenting YY1-mediated enhancer-promoter communication.
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Affiliation(s)
- Yutthaphong Phongbunchoo
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fatima-Zohra Braikia
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cecilia Pessoa-Rodrigues
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Haribaskar Ramachandran
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Anna Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Fei Ma
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Pierre Cauchy
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Ranjan Sen
- Laboratory of Molecular Biology & Immunology, National Institute on Aging, NIH, Baltimore, MD, USA.
| | - Gerhard Mittler
- Proteomics Facility, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Rudolf Grosschedl
- Laboratory of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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2
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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3
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Noberini R, Bonaldi T. Proteomics contributions to epigenetic drug discovery. Proteomics 2023; 23:e2200435. [PMID: 37727062 DOI: 10.1002/pmic.202200435] [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: 06/09/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
The combined activity of epigenetic features, which include histone post-translational modifications, DNA methylation, and nucleosome positioning, regulates gene expression independently from changes in the DNA sequence, defining how the shared genetic information of an organism is used to generate different cell phenotypes. Alterations in epigenetic processes have been linked with a multitude of diseases, including cancer, fueling interest in the discovery of drugs targeting the proteins responsible for writing, erasing, or reading histone and DNA modifications. Mass spectrometry (MS)-based proteomics has emerged as a versatile tool that can assist drug discovery pipelines from target validation, through target deconvolution, to monitoring drug efficacy in vivo. Here, we provide an overview of the contributions of MS-based proteomics to epigenetic drug discovery, describing the main approaches that can be used to support different drug discovery pipelines and highlighting how they contributed to the development and characterization of epigenetic drugs.
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Affiliation(s)
- Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
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4
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MacKenzie TMG, Cisneros R, Maynard RD, Snyder MP. Reverse-ChIP Techniques for Identifying Locus-Specific Proteomes: A Key Tool in Unlocking the Cancer Regulome. Cells 2023; 12:1860. [PMID: 37508524 PMCID: PMC10377898 DOI: 10.3390/cells12141860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/30/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
A phenotypic hallmark of cancer is aberrant transcriptional regulation. Transcriptional regulation is controlled by a complicated array of molecular factors, including the presence of transcription factors, the deposition of histone post-translational modifications, and long-range DNA interactions. Determining the molecular identity and function of these various factors is necessary to understand specific aspects of cancer biology and reveal potential therapeutic targets. Regulation of the genome by specific factors is typically studied using chromatin immunoprecipitation followed by sequencing (ChIP-Seq) that identifies genome-wide binding interactions through the use of factor-specific antibodies. A long-standing goal in many laboratories has been the development of a 'reverse-ChIP' approach to identify unknown binding partners at loci of interest. A variety of strategies have been employed to enable the selective biochemical purification of sequence-defined chromatin regions, including single-copy loci, and the subsequent analytical detection of associated proteins. This review covers mass spectrometry techniques that enable quantitative proteomics before providing a survey of approaches toward the development of strategies for the purification of sequence-specific chromatin as a 'reverse-ChIP' technique. A fully realized reverse-ChIP technique holds great potential for identifying cancer-specific targets and the development of personalized therapeutic regimens.
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Affiliation(s)
| | - Rocío Cisneros
- Sarafan ChEM-H/IMA Postbaccalaureate Fellow in Target Discovery, Stanford University, Stanford, CA 94305, USA
| | - Rajan D Maynard
- Genetics Department, Stanford University, Stanford, CA 94305, USA
| | - Michael P Snyder
- Genetics Department, Stanford University, Stanford, CA 94305, USA
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5
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Liu Z, Wu Y, Mao X, Kwan KCJ, Cheng X, Li X, Jing Y, Li XD. Development of multifunctional synthetic nucleosomes to interrogate chromatin-mediated protein interactions. SCIENCE ADVANCES 2023; 9:eade5186. [PMID: 37134166 PMCID: PMC10156118 DOI: 10.1126/sciadv.ade5186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Various proteins bind to chromatin to regulate DNA and its associated processes such as replication, transcription, and damage repair. The identification and characterization of these chromatin-associating proteins remain a challenge, as their interactions with chromatin often occur within the context of the local nucleosome or chromatin structure, which makes conventional peptide-based strategies unsuitable. Here, we developed a simple and robust protein labeling chemistry to prepare synthetic multifunctional nucleosomes that carry a photoreactive group, a biorthogonal handle, and a disulfide moiety to examine chromatin-protein interactions in a nucleosomal context. Using the prepared protein- and nucleosome-based photoaffinity probes, we examined a number of protein-protein and protein-nucleosome interactions. In particular, we (i) mapped the binding sites for the HMGN2-nucleosome interaction, (ii) provided the evidence for transition between the active and poised states of DOT1L in recognizing H3K79 within the nucleosome, and (iii) identified OARD1 and LAP2α as nucleosome acidic patch-associating proteins. This study provides powerful and versatile chemical tools for interrogating chromatin-associating proteins.
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Affiliation(s)
- Zheng Liu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yiping Wu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xin Mao
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Xinxin Cheng
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Xin Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen 518055, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen 518055, China
| | - Xiang David Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
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6
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Nickel GA, Diehl KL. Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications. ACS Chem Biol 2023; 18:1014-1026. [PMID: 35238546 PMCID: PMC9440160 DOI: 10.1021/acschembio.1c00794] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In eukaryotes, DNA is packaged with histone proteins in a complex known as chromatin. Both the DNA and histone components of chromatin can be chemically modified in a wide variety of ways, resulting in a complex landscape often referred to as the "epigenetic code". These modifications are recognized by effector proteins that remodel chromatin and modulate transcription, translation, and repair of the underlying DNA. In this Review, we examine the development of methods for characterizing proteins that interact with these histone and DNA modifications. "Mark first" approaches utilize chemical, peptide, nucleosome, or oligonucleotide probes to discover interactors of a specific modification. "Reader first" approaches employ arrays of peptides, nucleosomes, or oligonucleotides to profile the binding preferences of interactors. These complementary strategies have greatly enhanced our understanding of how chromatin modifications effect changes in genomic regulation, bringing us ever closer to deciphering this complex language.
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Affiliation(s)
- Garrison A. Nickel
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - Katharine L. Diehl
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
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7
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Ruprecht B, Wei L, Zheng L, Bodea S, Mo X, Maschberger M, Stoehr G, Hahne H, Cornella-Taracido I, Chi A. Chemoproteomic profiling to identify activity changes and functional inhibitors of DNA-binding proteins. Cell Chem Biol 2022; 29:1639-1648.e4. [PMID: 36356585 DOI: 10.1016/j.chembiol.2022.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 07/04/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022]
Abstract
DNA-binding proteins are promising therapeutic targets but are notoriously difficult to drug. Here, we evaluate a chemoproteomic DNA interaction platform as a complementary strategy for parallelized compound profiling. To enable this approach, we determined the proteomic binding landscape of 92 immobilized DNA sequences. Perturbation-induced activity changes of captured transcription factors in disease-relevant settings demonstrated functional relevance of the enriched subproteome. Chemoproteomic profiling of >300 cysteine-directed compounds against a coverage optimized bead mixture, which specifically captures >150 DNA binders, revealed competition of several DNA-binding proteins, including the transcription factors ELF1 and ELF2. We also discovered the first compound that displaces the DNA-repair complex MSH2-MSH3 from DNA. Compound binding to cysteine 252 on MSH3 was confirmed using chemoproteomic reactive cysteine profiling. Overall, these results suggested that chemoproteomic DNA bead pull-downs enable the specific readout of transcription factor activity and can identify functional "hotspots" on DNA binders toward expanding the druggable proteome.
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Affiliation(s)
| | - Lan Wei
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Li Zheng
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Smaranda Bodea
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | - Xuan Mo
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA
| | | | | | - Hannes Hahne
- OmicScouts GmbH, 85354 Freising, Bavaria, Germany
| | | | - An Chi
- Chemical Biology, Merck & Co., Inc, Boston, MA 02115, USA.
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8
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Yang G, Zhang Y, Wei X, Cui L, Nie X. Genetic Diversity of Transcription Factor Genes in Triticum and Mining for Promising Haplotypes for Beneficial Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2022; 13:899292. [PMID: 35873966 PMCID: PMC9305608 DOI: 10.3389/fpls.2022.899292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/20/2022] [Indexed: 05/28/2023]
Abstract
Transcription factor (TF) is a class of the sequence-specific DNA-binding proteins that modulate the transcription of target genes, and thus regulate their expressions. Variations in TF are the crucial determinants for phenotypic traits. Although much progress has been made in the functions of TF genes in wheat, one of the most important staple crops globally, the diversity of TF genes in wheat and its progenitors are not well understood, especially the agronomically promising haplotypes have not yet been characterized. Here, we identified a total of 6,023 TF genes from hexaploid wheat through a genome-search method and classified them into 59 gene families based on the conserved domain. The characteristics and dN/dS values of these genes showed evidently selective effects. Based on re-sequencing data, we found a strong genetic bottleneck among these TF genes on A and D subgenomes while no found in B subgenome during wheat domestication. Combined with selective signals and known QTLs on the whole genome, 21 TF genes were preliminarily found to be associated with yield-related traits. The haplotype frequency of these TF genes was further investigated in bread wheat and its progenitors and 13 major haplotypes were the casual loci related to key traits. Finally, the tissue-specific TF genes were also identified using RNA-seq analysis. This study provided insights into the diversity and evolution of TF genes and the identified TF genes and excellent haplotypes associating with traits will contribute to wheat genetic improvement.
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Affiliation(s)
- Guang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Ying Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Xinyu Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Licao Cui
- College of Biological Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
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9
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The emerging role of mass spectrometry-based proteomics in drug discovery. Nat Rev Drug Discov 2022; 21:637-654. [PMID: 35351998 DOI: 10.1038/s41573-022-00409-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2022] [Indexed: 12/14/2022]
Abstract
Proteins are the main targets of most drugs; however, system-wide methods to monitor protein activity and function are still underused in drug discovery. Novel biochemical approaches, in combination with recent developments in mass spectrometry-based proteomics instrumentation and data analysis pipelines, have now enabled the dissection of disease phenotypes and their modulation by bioactive molecules at unprecedented resolution and dimensionality. In this Review, we describe proteomics and chemoproteomics approaches for target identification and validation, as well as for identification of safety hazards. We discuss innovative strategies in early-stage drug discovery in which proteomics approaches generate unique insights, such as targeted protein degradation and the use of reactive fragments, and provide guidance for experimental strategies crucial for success.
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10
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Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization. Int J Mol Sci 2022; 23:ijms23042179. [PMID: 35216300 PMCID: PMC8879271 DOI: 10.3390/ijms23042179] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/11/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
The different niches through which bacteria move during their life cycle require a fast response to the many environmental queues they encounter. The sensing of these stimuli and their correct response is driven primarily by transcriptional regulators. This kind of protein is involved in sensing a wide array of chemical species, a process that ultimately leads to the regulation of gene transcription. The allosteric-coupling mechanism of sensing and regulation is a central aspect of biological systems and has become an important field of research during the last decades. In this review, we summarize the state-of-the-art techniques applied to unravel these complex mechanisms. We introduce a roadmap that may serve for experimental design, depending on the answers we seek and the initial information we have about the system of study. We also provide information on databases containing available structural information on each family of transcriptional regulators. Finally, we discuss the recent results of research about the allosteric mechanisms of sensing and regulation involving many transcriptional regulators of interest, highlighting multipronged strategies and novel experimental techniques. The aim of the experiments discussed here was to provide a better understanding at a molecular level of how bacteria adapt to the different environmental threats they face.
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11
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Wang H, Qian L, Shang Z, Wang Z, Zhang Y, Cao C, Xiao H. Immobilized Titanium (IV) Ion Affinity Chromatography Contributes to Efficient Proteomics Analysis of Cellular Nucleic Acid-Binding Proteins. J Proteome Res 2021; 21:220-231. [PMID: 34780180 DOI: 10.1021/acs.jproteome.1c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellular nucleic acid-binding proteins (NABPs), namely, DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in many biological processes. However, extracting NABPs with high efficiency in living cells is challenging, which greatly limited their proteomics analysis and comprehensive characterization. Here, we discovered that titanium (IV) ion-immobilized metal affinity chromatography (Ti4+-IMAC) material could enrich DNA and RNA with high efficiency (96.82 ± 2.67 and 85.75 ± 2.99%, respectively). We therefore developed a Ti4+-IMAC method for the joint extraction of DBPs and RBPs. Through utilizing formaldehyde (FA) cross-linking, DBPs and RBPs were covalently linked to nucleic acids (NAs) and further denatured by organic solvents. After Ti4+-IMAC capture, 2000 proteins were identified in 293T cells, among which 417 DBPs and 999 RBPs were revealed, showing promising selectivity for NABPs. We further applied the Ti4+-IMAC capture method to lung cancer cell lines 95C and 95D, which have different tumor progression abilities. The DNA- and RNA-binding capabilities of many proteins have been dysregulated in 95D. Under our conditions, Ti4+-IMAC can be used as a selective and powerful tool for the comprehensive characterization of both DBPs and RBPs, which might be utilized to study their dynamic interactions with nucleic acids.
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Affiliation(s)
- Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liqiang Qian
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zhi Shang
- Institute of Clinical Immunology, Department of Liver Diseases, Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai 200021, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chengxi Cao
- Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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12
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Cozzolino F, Iacobucci I, Monaco V, Monti M. Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era. J Proteome Res 2021; 20:3018-3030. [PMID: 33961438 PMCID: PMC8280749 DOI: 10.1021/acs.jproteome.1c00074] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
The fields of application
of functional proteomics are not limited
to the study of protein–protein interactions; they also extend
to those involving protein complexes that bind DNA or RNA. These interactions
affect fundamental processes such as replication, transcription, and
repair in the case of DNA, as well as transport, translation, splicing,
and silencing in the case of RNA. Analytical or preparative experimental
approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins
by exploiting the advantage of the affinity shown by these proteins
toward a specific oligonucleotide sequence. The present review proposes
an overview of the approaches most commonly employed in proteomics
applications for the identification of nucleic acid-binding proteins,
such as affinity purification (AP) protocols, EMSA, chromatin purification
methods, and CRISPR-based chromatin affinity purification, which are
generally associated with mass spectrometry methodologies for the
unbiased protein identification.
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Affiliation(s)
- Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.,Interuniversity Consortium National Institute of Biostructures and Biosystems (INBB), Viale Medaglie d'Oro, 305-00136 Rome, Italy
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.,CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
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13
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Belver L, Albero R, Ferrando AA. Deregulation of enhancer structure, function, and dynamics in acute lymphoblastic leukemia. Trends Immunol 2021; 42:418-431. [PMID: 33858773 PMCID: PMC8091164 DOI: 10.1016/j.it.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/25/2022]
Abstract
Enhancers control dynamic changes in gene expression and orchestrate the tightly controlled transcriptional circuitries that direct and coordinate cell growth, proliferation, survival, lineage commitment, and differentiation during lymphoid development. Enhancer hijacking and neoenhancer formation at oncogene loci, as well as aberrant activation of oncogene-associated enhancers, can induce constitutive activation of self-perpetuating oncogenic transcriptional circuitries, and contribute to the malignant transformation of immature lymphoid progenitors in acute lymphoblastic leukemia (ALL). In this review, we present recent discoveries of the role of enhancer dynamics in mouse and human lymphoid development, and discuss how genetic and epigenetic alterations of enhancer function can promote leukemogenesis, and potential strategies for targeting the enhancer machinery in the treatment of ALL.
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Affiliation(s)
- Laura Belver
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, 08916, Spain
| | - Robert Albero
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA
| | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, 10032, USA; Department of Systems Biology, Columbia University, New York, NY, 10032, USA; Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA; Department of Pathology, Columbia University Medical Center, New York, NY, 10032, USA.
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14
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Tsang O, Wong JWH. Proteogenomic interrogation of cancer cell lines: an overview of the field. Expert Rev Proteomics 2021; 18:221-232. [PMID: 33877947 DOI: 10.1080/14789450.2021.1914594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Introduction: Cancer cell lines (CCLs) have been a major resource for cancer research. Over the past couple of decades, they have been instrumental in omic profiling method development and as model systems to generate new knowledge in cell and cancer biology. More recently, with the increasing amount of genomic, transcriptomic and proteomic data being generated in hundreds of CCLs, there is growing potential for integrative proteogenomic data analyses to be performed.Areas covered: In this review, we first describe the most commonly used proteome profiling methods in CCLs. We then discuss how these proteomics data can be integrated with genomics data for proteogenomics analyses. Finally, we highlight some of the recent biological discoveries that have arisen from proteogenomics analyses of CCLs.Expert opinion: Protegeonomics analyses of CCLs have so far enabled the discovery of novel proteins and proteoforms. It has also improved our understanding of biological processes including post-transcriptional regulation of protein abundance and the presentation of antigens by major histocompatibility complex alleles. With proteomics data to be generated in hundreds to thousands of CCLs in coming years, there will be further potential for large-scale proteogenomics analyses and data integration with the phenotypically well-characterized CCLs.
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Affiliation(s)
- Olson Tsang
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
| | - Jason W H Wong
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR.,School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR
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15
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Akerman I, Maestro MA, De Franco E, Grau V, Flanagan S, García-Hurtado J, Mittler G, Ravassard P, Piemonti L, Ellard S, Hattersley AT, Ferrer J. Neonatal diabetes mutations disrupt a chromatin pioneering function that activates the human insulin gene. Cell Rep 2021; 35:108981. [PMID: 33852861 PMCID: PMC8052186 DOI: 10.1016/j.celrep.2021.108981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 01/04/2021] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Despite the central role of chromosomal context in gene transcription, human noncoding DNA variants are generally studied outside of their genomic location. This limits our understanding of disease-causing regulatory variants. INS promoter mutations cause recessive neonatal diabetes. We show that all INS promoter point mutations in 60 patients disrupt a CC dinucleotide, whereas none affect other elements important for episomal promoter function. To model CC mutations, we humanized an ∼3.1-kb region of the mouse Ins2 gene. This recapitulated developmental chromatin states and cell-specific transcription. A CC mutant allele, however, abrogated active chromatin formation during pancreas development. A search for transcription factors acting through this element revealed that another neonatal diabetes gene product, GLIS3, has a pioneer-like ability to derepress INS chromatin, which is hampered by the CC mutation. Our in vivo analysis, therefore, connects two human genetic defects in an essential mechanism for developmental activation of the INS gene.
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Affiliation(s)
- Ildem Akerman
- Institute of Metabolism and Systems Research (IMSR), Medical School, University of Birmingham, Birmingham, UK; Centre for Endocrinology, Diabetes and Metabolism (CEDAM), University of Birmingham, Birmingham, UK.
| | - Miguel Angel Maestro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Elisa De Franco
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Vanessa Grau
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Sarah Flanagan
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Javier García-Hurtado
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
| | - Gerhard Mittler
- Max-Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Philippe Ravassard
- INSERM, CNRS, Paris Brain Institute - Hôpital Pitié-Salpêtrière, Paris, France
| | - Lorenzo Piemonti
- Diabetes Research Institute, IRCCS Ospedale San Raffaele and Università Vita-Salute San Raffaele, Milan, Italy
| | - Sian Ellard
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK; Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Andrew T Hattersley
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain; Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
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16
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Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R. Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. eLife 2020; 9:e55308. [PMID: 32955440 PMCID: PMC7567609 DOI: 10.7554/elife.55308] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 09/18/2020] [Indexed: 01/28/2023] Open
Abstract
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium Escherichia coli, for ≈65% of promoters we remain ignorant of their regulation. Until we crack this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method, Reg-Seq, that links massively parallel reporter assays with mass spectrometry to produce a base pair resolution dissection of more than a E. coli promoters in 12 growth conditions. We demonstrate that the method recapitulates known regulatory information. Then, we examine regulatory architectures for more than 80 promoters which previously had no known regulatory information. In many cases, we also identify which transcription factors mediate their regulation. This method clears a path for highly multiplexed investigations of the regulatory genome of model organisms, with the potential of moving to an array of microbes of ecological and medical relevance.
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Affiliation(s)
- William T Ireland
- Department of Physics, California Institute of TechnologyPasadenaUnited States
| | - Suzannah M Beeler
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Emanuel Flores-Bautista
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Nicholas S McCarty
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Tom Röschinger
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Nathan M Belliveau
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of TechnologyPasadenaUnited States
| | - Annie Moradian
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman Institute, California Institute of TechnologyPasadenaUnited States
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborUnited States
| | - Rob Phillips
- Department of Physics, California Institute of TechnologyPasadenaUnited States
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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17
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Huang Y, Xiang Y, Xie Z, Cai Y, Yang Q, Huang H, Chen Z, Xiao Z, He Q. Mass spectrometry-based proteomic capture of proteins bound to the MACC1 promoter in colon cancer. Clin Exp Metastasis 2020; 37:477-487. [PMID: 32613480 DOI: 10.1007/s10585-020-10045-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022]
Abstract
MACC1 (metastasis associated in colon cancer 1) is a key driver that induces metastasis in colon cancer. However, the mechanisms by which MACC1 expression is transcriptionally regulated and the factors enriched at the MACC1 promoter remain largely unknown. The binding of proteins to specific DNA sites in the genome is a major determinant of genomic maintenance and the regulation of specific genes. The study herein utilized two methods to study the binding proteins of the MACC1 promoter region in colon cancer. Specifically, we adopted CRISPR-based chromatin affinity purification with mass spectrometry (CRISPR-ChAP-MS) and a biotin-streptavidin pulldown assay coupled with MS to identify the specific proteome bound to the MACC1 promoter in two colon cell lines with different metastatic potential. A total of 24 proteins were identified by CRISPR-ChAP-MS as binding to the MACC1 promoter, among which c-JUN was validated by ChIP-PCR. A total of 739 binding protein candidates were identified by biotin-streptavidin pulldown assays coupled with MS, of which HNF4G and PAX6 were validated and compared for their binding to the same promoter sites in the two cell lines. Our studies suggest distinctive proteomic factors associated with the MACC1 promoter in colon cells with different metastatic potential. The dynamic regulatory factors accumulated at the promoter of MACC1 may provide novel insights into the regulatory mechanisms of MACC1 transcription.
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Affiliation(s)
- Yahui Huang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.,Department of Pathology, Xuchang Central Hospital, Henan University of Science and Technology, Xuchang, Henan, People's Republic of China
| | - Yi Xiang
- School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhongpeng Xie
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.,Department of Pathology, Hainan General Hospital, Haikou, Hainan, People's Republic of China
| | - Yuxiang Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Qiongzhi Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Huichao Huang
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhuchu Chen
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Zhefeng Xiao
- NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China.
| | - Qiongqiong He
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China. .,School of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.
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18
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Mass Spectrometry to Study Chromatin Compaction. BIOLOGY 2020; 9:biology9060140. [PMID: 32604817 PMCID: PMC7345930 DOI: 10.3390/biology9060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.
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19
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Cardinale CJ, March ME, Lin X, Liu Y, Spruce LA, Bradfield JP, Wei Z, Seeholzer SH, Grant SFA, Hakonarson H. Regulation of Janus Kinase 2 by an Inflammatory Bowel Disease Causal Non-coding Single Nucleotide Polymorphism. J Crohns Colitis 2020; 14:646-653. [PMID: 32271392 DOI: 10.1093/ecco-jcc/jjz213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Among the >240 genetic loci described to date which confer susceptibility to inflammatory bowel disease, a small subset have been fine-mapped to an individual, non-coding single nucleotide polymorphism [SNP]. To illustrate a model mechanism by which a presumed-causal non-coding SNP can function, we analysed rs1887428, located in the promoter region of the Janus kinase 2 [JAK2] gene. METHODS We utilized comparative affinity purification-mass spectrometry, DNA-protein binding assays, CRISPR/Cas9 genome editing, transcriptome sequencing and methylome quantitative trait locus methods to characterize the role of this SNP. RESULTS We determined that the risk allele of rs1887428 is bound by the transcription factor [TF] RBPJ, while the protective allele is bound by the homeobox TF CUX1. While rs188748 only has a very modest influence on JAK2 expression, this effect was amplified downstream through the expression of pathway member STAT5B and epigenetic modification of the JAK2 locus. CONCLUSION Despite the absence of a consensus TF-binding motif or expression quantitative trait locus, we have used improved methods to characterize a putatively causal SNP to yield insight into inflammatory bowel disease mechanisms. PODCAST This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast.
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Affiliation(s)
| | - Michael E March
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiang Lin
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lynn A Spruce
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, USA
| | - Steven H Seeholzer
- Proteomics Core Facility, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Struan F A Grant
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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20
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Delacher M, Barra MM, Herzig Y, Eichelbaum K, Rafiee MR, Richards DM, Träger U, Hofer AC, Kazakov A, Braband KL, Gonzalez M, Wöhrl L, Schambeck K, Imbusch CD, Abramson J, Krijgsveld J, Feuerer M. Quantitative Proteomics Identifies TCF1 as a Negative Regulator of Foxp3 Expression in Conventional T Cells. iScience 2020; 23:101127. [PMID: 32422593 PMCID: PMC7229326 DOI: 10.1016/j.isci.2020.101127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/02/2020] [Accepted: 04/29/2020] [Indexed: 12/14/2022] Open
Abstract
Regulatory T cells are important regulators of the immune system and have versatile functions for the homeostasis and repair of tissues. They express the forkhead box transcription factor Foxp3 as a lineage-defining protein. Negative regulators of Foxp3 expression are not well understood. Here, we generated double-stranded DNA probes complementary to the Foxp3 promoter sequence and performed a pull-down with nuclear protein in vitro, followed by elution of bound proteins and quantitative mass spectrometry. Of the Foxp3-promoter-binding transcription factors identified with this approach, one was T cell factor 1 (TCF1). Using viral over-expression, we identified TCF1 as a repressor of Foxp3 expression. In TCF1-deficient animals, increased levels of Foxp3intermediateCD25negative T cells were identified. CRISPR-Cas9 knockout studies in primary human and mouse conventional CD4 T (Tconv) cells revealed that TCF1 protects Tconv cells from inadvertent Foxp3 expression. Our data implicate a role of TCF1 in suppressing Foxp3 expression in activated T cells.
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Affiliation(s)
- Michael Delacher
- Chair for Immunology, Regensburg University, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany; Regensburg Center for Interventional Immunology (RCI), Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany; Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Melanie M Barra
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Yonatan Herzig
- Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 76100 Rehovot, Israel
| | - Katrin Eichelbaum
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Mahmoud-Reza Rafiee
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - David M Richards
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ulrike Träger
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ann-Cathrin Hofer
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Alexander Kazakov
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Kathrin L Braband
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Marina Gonzalez
- Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Lukas Wöhrl
- Regensburg Center for Interventional Immunology (RCI), Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Kathrin Schambeck
- Regensburg Center for Interventional Immunology (RCI), Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Charles D Imbusch
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany; Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Jakub Abramson
- Department of Immunology, Weizmann Institute of Science, 234 Herzl Street, 76100 Rehovot, Israel
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany; Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, 69120 Heidelberg, Germany
| | - Markus Feuerer
- Chair for Immunology, Regensburg University, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany; Regensburg Center for Interventional Immunology (RCI), Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany; Immune Tolerance Group, Tumor Immunology Program, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
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21
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Purification and enrichment of specific chromatin loci. Nat Methods 2020; 17:380-389. [PMID: 32152500 DOI: 10.1038/s41592-020-0765-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/29/2020] [Indexed: 12/20/2022]
Abstract
Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then describe the published strategies and discuss their advantages and limitations. We conclude by discussing why significant technology developments are required to unambiguously describe the composition of small single loci.
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22
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ChromID identifies the protein interactome at chromatin marks. Nat Biotechnol 2020; 38:728-736. [PMID: 32123383 PMCID: PMC7289633 DOI: 10.1038/s41587-020-0434-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 01/23/2020] [Indexed: 01/05/2023]
Abstract
Chromatin modifications regulate genome function by recruiting protein factors to the genome. However, the protein composition at distinct chromatin modifications remains to be fully characterized. Here, we use natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone tri-methylation at H3K4, H3K9 a H3K27 residues. We first demonstrate their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localisation, genomic distribution and histone modification–binding preference. By fusing eCRs to the biotin ligase BASU, we establish ChromID, a method for identifying the chromatin-dependent protein interactome based on proximity biotinylation, and apply it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncover the protein composition at bivalent promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.
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23
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Sequeira VM, Vermeulen M. Identifying Readers for (hydroxy)methylated DNA Using Quantitative Interaction Proteomics: Advances and Challenges Ahead. J Mol Biol 2020:S0022-2836(19)30714-4. [DOI: 10.1016/j.jmb.2019.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 01/23/2023]
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24
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Prall W, Sharma B, Gregory BD. Transcription Is Just the Beginning of Gene Expression Regulation: The Functional Significance of RNA-Binding Proteins to Post-transcriptional Processes in Plants. PLANT & CELL PHYSIOLOGY 2019; 60:1939-1952. [PMID: 31155676 DOI: 10.1093/pcp/pcz067] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Plants have developed sophisticated mechanisms to compensate and respond to ever-changing environmental conditions. Research focus in this area has recently shifted towards understanding the post-transcriptional mechanisms that contribute to RNA transcript maturation, abundance and function as key regulatory steps in allowing plants to properly react and adapt to these never-ending shifts in their environments. At the center of these regulatory mechanisms are RNA-binding proteins (RBPs), the functional mediators of all post-transcriptional processes. In plants, RBPs are becoming increasingly appreciated as the critical modulators of core cellular processes during development and in response to environmental stimuli. With the majority of research on RBPs and their functions historically in prokaryotic and mammalian systems, it has more recently been unveiled that plants have expanded families of conserved and novel RBPs compared with their eukaryotic counterparts. To better understand the scope of RBPs in plants, we present past and current literature detailing specific roles of RBPs during stress response, development and other fundamental transition periods. In this review, we highlight examples of complex regulation coordinated by RBPs with a focus on the diverse mechanisms of plant RBPs and the unique processes they regulate. Additionally, we discuss the importance for additional research into understanding global interactions of RBPs on a systems and network-scale, with genome mining and annotation providing valuable insight for potential uses in improving crop plants in order to maintain high-level production in this era of global climate change.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Bishwas Sharma
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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25
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Karl M, Sommer C, Gabriel CH, Hecklau K, Venzke M, Hennig AF, Radbruch A, Selbach M, Baumgrass R. Recruitment of Histone Methyltransferase Ehmt1 to Foxp3 TSDR Counteracts Differentiation of Induced Regulatory T Cells. J Mol Biol 2019; 431:3606-3625. [PMID: 31362003 DOI: 10.1016/j.jmb.2019.07.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/13/2019] [Accepted: 07/17/2019] [Indexed: 12/21/2022]
Abstract
Differentiation toward CD4+ regulatory T (Treg) cells is essentially dependent on an epigenetic program at Treg signature genes, which involves remodeling of the Treg-specific demethylated regions (TSDRs). In particular, the epigenetic status of the conserved non-coding sequence 2 of Foxp3 (Foxp3 TSDR) determines expression stability of the master transcription factor and thus Treg lineage identity. However, the molecular mechanisms controlling the epigenetic remodeling at TSDRs in Treg and conventional T cells are largely unknown. Using a combined approach of DNA pull-down and mass spectrometric analysis, we report a novel regulatory mechanism in which transcription factor Wiz recruits the histone methyltransferase Ehmt1 to Foxp3 TSDR. We show that both Wiz and Ehmt1 are crucial for shaping the region with the repressive histone modification H3K9me2 in conventional T cells. Consistently, knocking out either Ehmt1 or Wiz by CRISPR/Cas resulted in the loss of H3K9me2 and enhanced Foxp3 expression during iTreg differentiation. Moreover, the essential role of the Wiz-Ehmt1 interaction as observed at several TSDRs indicates a global function of Ehmt1 in the Treg differentiation program.
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Affiliation(s)
- Martin Karl
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian Sommer
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christian H Gabriel
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Katharina Hecklau
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Melanie Venzke
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Anna Floriane Hennig
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany
| | - Andreas Radbruch
- Cell Biology, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany; Charité-University Medicine, Charitéplatz 1, 10117 Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Ria Baumgrass
- Signal Transduction, German Rheumatism Research Center (DRFZ), A Leibniz Institute, Charitéplatz 1, 10117 Berlin, Germany.
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26
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Murarka P, Srivastava P. An improved method for the isolation and identification of unknown proteins that bind to known DNA sequences by affinity capture and mass spectrometry. PLoS One 2018; 13:e0202602. [PMID: 30138440 PMCID: PMC6107227 DOI: 10.1371/journal.pone.0202602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 08/05/2018] [Indexed: 12/13/2022] Open
Abstract
Transcription of a gene can be regulated at many different levels. One such fundamental level is interaction between protein and DNA. Protein(s) binds to distinct sites on the DNA, which activate, enhance or repress transcription. Despite being such an important process, very few tools exist to identify the proteins that interact with chromosome, most of which are in vitro in nature. Here, we propose an in vivo based method for identification of DNA binding protein(s) in bacteria where the DNA-protein complex formed in vivo is crosslinked by formaldehyde. This complex is further isolated and the bound proteins are identified. The method was used to isolate promoter DNA binding proteins, which bind and regulate the dsz operon in Gordonia sp. IITR 100 responsible for biodesulfurization of organosulfurs. The promoter binding proteins were identified by MALDI ToF MS/MS and the binding was confirmed by gel shift assay. Unlike other reported in vivo methods, this improved method does not require sequence of the whole genome or a chip and can be scaled up to improve yields.
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Affiliation(s)
- Pooja Murarka
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Preeti Srivastava
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
- * E-mail: ,
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27
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Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling. Nat Methods 2018; 15:437-439. [PMID: 29735997 PMCID: PMC6202184 DOI: 10.1038/s41592-018-0007-1] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/12/2018] [Indexed: 12/26/2022]
Abstract
Regulation of gene expression is primarily controlled by changes in the proteins that occupy their regulatory elements. Chromatin immunoprecipitation can confirm a protein’s occupancy at a genomic locus but requires specific, high-quality, IP-competent antibodies against nominated proteins, limiting its utility. Here, we combine, genome targeting, proximity labeling, and quantitative proteomics to develop genomic locus proteomics, a method able to identify proteins associated a specific genomic locus in native cellular contexts.
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28
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Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Proc Natl Acad Sci U S A 2018; 115:E4796-E4805. [PMID: 29728462 PMCID: PMC6003448 DOI: 10.1073/pnas.1722055115] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Organisms must constantly make regulatory decisions in response to a change in cellular state or environment. However, while the catalog of genomes expands rapidly, we remain ignorant about how the genes in these genomes are regulated. Here, we show how a massively parallel reporter assay, Sort-Seq, and information-theoretic modeling can be used to identify regulatory sequences. We then use chromatography and mass spectrometry to identify the regulatory proteins that bind these sequences. The approach results in quantitative base pair-resolution models of promoter mechanism and was shown in both well-characterized and unannotated promoters in Escherichia coli. Given the generality of the approach, it opens up the possibility of quantitatively dissecting the mechanisms of promoter function in a wide range of bacteria. Gene regulation is one of the most ubiquitous processes in biology. However, while the catalog of bacterial genomes continues to expand rapidly, we remain ignorant about how almost all of the genes in these genomes are regulated. At present, characterizing the molecular mechanisms by which individual regulatory sequences operate requires focused efforts using low-throughput methods. Here, we take a first step toward multipromoter dissection and show how a combination of massively parallel reporter assays, mass spectrometry, and information-theoretic modeling can be used to dissect multiple bacterial promoters in a systematic way. We show this approach on both well-studied and previously uncharacterized promoters in the enteric bacterium Escherichia coli. In all cases, we recover nucleotide-resolution models of promoter mechanism. For some promoters, including previously unannotated ones, the approach allowed us to further extract quantitative biophysical models describing input–output relationships. Given the generality of the approach presented here, it opens up the possibility of quantitatively dissecting the mechanisms of promoter function in E. coli and a wide range of other bacteria.
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29
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Taylor MS, Altukhov I, Molloy KR, Mita P, Jiang H, Adney EM, Wudzinska A, Badri S, Ischenko D, Eng G, Burns KH, Fenyö D, Chait BT, Alexeev D, Rout MP, Boeke JD, LaCava J. Dissection of affinity captured LINE-1 macromolecular complexes. eLife 2018; 7:30094. [PMID: 29309035 PMCID: PMC5821459 DOI: 10.7554/elife.30094] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 12/18/2017] [Indexed: 12/31/2022] Open
Abstract
Long Interspersed Nuclear Element-1 (LINE-1, L1) is a mobile genetic element active in human genomes. L1-encoded ORF1 and ORF2 proteins bind L1 RNAs, forming ribonucleoproteins (RNPs). These RNPs interact with diverse host proteins, some repressive and others required for the L1 lifecycle. Using differential affinity purifications, quantitative mass spectrometry, and next generation RNA sequencing, we have characterized the proteins and nucleic acids associated with distinctive, enzymatically active L1 macromolecular complexes. Among them, we describe a cytoplasmic intermediate that we hypothesize to be the canonical ORF1p/ORF2p/L1-RNA-containing RNP, and we describe a nuclear population containing ORF2p, but lacking ORF1p, which likely contains host factors participating in target-primed reverse transcription.
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Affiliation(s)
- Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Paolo Mita
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Emily M Adney
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Aleksandra Wudzinska
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Sana Badri
- Department of Pathology, NYU Langone Health, New York, United States
| | - Dmitry Ischenko
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - George Eng
- Department of Pathology, Massachusetts General Hospital, Boston, United States
| | - Kathleen H Burns
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, United States
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | | | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States
| | - John LaCava
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, United States.,Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
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30
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Liu Y, Zheng X, Yu Q, Wang H, Tan F, Zhu Q, Yuan L, Jiang H, Yu L, Zeng S. Epigenetic activation of the drug transporter OCT2 sensitizes renal cell carcinoma to oxaliplatin. Sci Transl Med 2017; 8:348ra97. [PMID: 27440728 DOI: 10.1126/scitranslmed.aaf3124] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 06/21/2016] [Indexed: 12/13/2022]
Abstract
Renal cell carcinoma (RCC) is known for its multidrug resistance. Using data obtained from the cancer transcriptome database Oncomine and the proteome database The Human Protein Atlas, we identified the repression of organic cation transporter OCT2 as a potential factor contributing to oxaliplatin resistance in RCC. By analyzing OCT2 expression in collected patient tissues and commercial tissue microarray specimens, we demonstrated OCT2 repression in RCC at both transcription and protein levels. Epigenetic analysis revealed that the repressed OCT2 promoter in RCC is characterized by hypermethylated CpG islands and the absence of H3K4 methylation. Further mechanistic studies showed that DNA hypermethylation blocked MYC activation of OCT2 by disrupting its interaction with the E-Box motif, which prevented MYC from recruiting MLL1 to catalyze H3K4me3 at the OCT2 promoter and resulted in repressed OCT2 transcription. Targeting this mechanism, we designed a sequential combination therapy and demonstrated that epigenetic activation of OCT2 by decitabine sensitizes RCC cells to oxaliplatin both in vitro and in xenografts. Our study highlights the potential of translating "omics" data into the development of targeted therapies.
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Affiliation(s)
- Yanqing Liu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoli Zheng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qinqin Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hua Wang
- Department of Urology, Cancer Hospital of Zhejiang Province, Hangzhou 310022, China
| | - Fuqing Tan
- Department of Urology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Qianying Zhu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lingmin Yuan
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huidi Jiang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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31
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Williams P, Li L, Dong X, Wang Y. Identification of SLIRP as a G Quadruplex-Binding Protein. J Am Chem Soc 2017; 139:12426-12429. [PMID: 28859475 DOI: 10.1021/jacs.7b07563] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The guanine quadruplex (G4) structure in DNA is a secondary structure motif that plays important roles in DNA replication, transcriptional regulation, and maintenance of genomic stability. Here, we employed a quantitative mass spectrometry-based approach to profile the interaction proteomes of three well-defined G4 structures derived from the human telomere and the promoters of cMYC and cKIT genes. We identified SLIRP as a novel G4-interacting protein. We also demonstrated that the protein could bind directly with G4 DNA with Kd values in the low nanomolar range and revealed that the robust binding of the protein toward G4 DNA requires its RRM domain. We further assessed, by using CRISPR-Cas9-introduced affinity tag and ChIP-Seq analysis, the genome-wide occupancy of SLIRP, and showed that the protein binds preferentially to G-rich DNA sequences that can fold into G4 structures. Together, our results uncovered a novel cellular protein that can interact directly with G4 DNA, which underscored the complex regulatory networks involved in G4 biology.
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Affiliation(s)
- Preston Williams
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Xiaoli Dong
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside , Riverside, California 92521-0403, United States
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32
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Lee H, Qian K, von Toerne C, Hoerburger L, Claussnitzer M, Hoffmann C, Glunk V, Wahl S, Breier M, Eck F, Jafari L, Molnos S, Grallert H, Dahlman I, Arner P, Brunner C, Hauner H, Hauck SM, Laumen H. Allele-specific quantitative proteomics unravels molecular mechanisms modulated by cis-regulatory PPARG locus variation. Nucleic Acids Res 2017; 45:3266-3279. [PMID: 28334807 PMCID: PMC5389726 DOI: 10.1093/nar/gkx105] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/07/2017] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies identified numerous disease risk loci. Delineating molecular mechanisms influenced by cis-regulatory variants is essential to understand gene regulation and ultimately disease pathophysiology. Combining bioinformatics and public domain chromatin information with quantitative proteomics supports prediction of cis-regulatory variants and enabled identification of allele-dependent binding of both, transcription factors and coregulators at the type 2 diabetes associated PPARG locus. We found rs7647481A nonrisk allele binding of Yin Yang 1 (YY1), confirmed by allele-specific chromatin immunoprecipitation in primary adipocytes. Quantitative proteomics also found the coregulator RING1 and YY1 binding protein (RYBP) whose mRNA levels correlate with improved insulin sensitivity in primary adipose cells carrying the rs7647481A nonrisk allele. Our findings support a concept with diverse cis-regulatory variants contributing to disease pathophysiology at one locus. Proteome-wide identification of both, transcription factors and coregulators, can profoundly improve understanding of mechanisms underlying genetic associations.
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Affiliation(s)
- Heekyoung Lee
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany
| | - Kun Qian
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Christine von Toerne
- German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Lena Hoerburger
- ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Paediatric Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany
| | - Melina Claussnitzer
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Hebrew SeniorLife Institute for Aging Research, Harvard Medical School, Boston, MA 02131, USA
| | - Christoph Hoffmann
- ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Molecular Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany
| | - Viktoria Glunk
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany
| | - Simone Wahl
- German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michaela Breier
- German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Franziska Eck
- Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Leili Jafari
- Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Sophie Molnos
- German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Harald Grallert
- Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ingrid Dahlman
- Department of Medicine, Huddinge, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Peter Arner
- Department of Medicine, Huddinge, Karolinska Institutet, SE-141 86 Stockholm, Sweden
| | - Cornelia Brunner
- Klinik für Hals-Nasen-Ohrenheilkunde, Universitätsklinik Ulm, 89075 Ulm, Germany
| | - Hans Hauner
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Klinikum rechts der Isar, Technische Universität München, 81675 Munich, Germany
| | - Stefanie M Hauck
- German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Helmut Laumen
- Else Kroener-Fresenius-Center for Nutritional Medicine, Chair of Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Clinical Cooperation Group Nutrigenomics and Type 2 Diabetes, Helmholtz Zentrum München and Technische Universität München, 85354 Freising-Weihenstephan, Germany.,German Center for Diabetes Research (DZD), Germany.,Research Unit Protein Science, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Else Kroener-Fresenius-Center for Nutritional Medicine, Paediatric Nutritional Medicine, Technische Universität München, 85354 Freising-Weihenstephan, Germany.,Institute of Experimental Genetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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33
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Bauer AJ, Martin KA. Coordinating Regulation of Gene Expression in Cardiovascular Disease: Interactions between Chromatin Modifiers and Transcription Factors. Front Cardiovasc Med 2017; 4:19. [PMID: 28428957 PMCID: PMC5382160 DOI: 10.3389/fcvm.2017.00019] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/20/2017] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular disease is a leading cause of death with increasing economic burden. The pathogenesis of cardiovascular diseases is complex, but can arise from genetic and/or environmental risk factors. This can lead to dysregulated gene expression in numerous cell types including cardiomyocytes, endothelial cells, vascular smooth muscle cells, and inflammatory cells. While initial studies addressed transcriptional control of gene expression, epigenetics has been increasingly appreciated to also play an important role in this process through alterations in chromatin structure and gene accessibility. Chromatin-modifying proteins including enzymes that modulate DNA methylation, histone methylation, and histone acetylation can influence gene expression in numerous ways. These chromatin modifiers and their marks can promote or prevent transcription factor recruitment to regulatory regions of genes through modifications to DNA, histones, or the transcription factors themselves. This review will focus on the emerging question of how epigenetic modifiers and transcription factors interact to coordinately regulate gene expression in cardiovascular disease. While most studies have addressed the roles of either epigenetic or transcriptional control, our understanding of the integration of these processes is only just beginning. Interrogating these interactions is challenging, and improved technical approaches will be needed to fully dissect the temporal and spatial relationships between transcription factors, chromatin modifiers, and gene expression in cardiovascular disease. We summarize the current state of the field and provide perspectives on limitations and future directions. Through studies of epigenetic and transcriptional interactions, we can advance our understanding of the basic mechanisms of cardiovascular disease pathogenesis to develop novel therapeutics.
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Affiliation(s)
- Ashley J Bauer
- Department of Medicine (Cardiovascular Medicine), Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Pharmacology, Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
| | - Kathleen A Martin
- Department of Medicine (Cardiovascular Medicine), Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA.,Department of Pharmacology, Cardiovascular Research Center, Yale University School of Medicine, New Haven, CT, USA
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34
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Unnikrishnan A, Guan YF, Huang Y, Beck D, Thoms JAI, Peirs S, Knezevic K, Ma S, de Walle IV, de Jong I, Ali Z, Zhong L, Raftery MJ, Taghon T, Larsson J, MacKenzie KL, Van Vlierberghe P, Wong JWH, Pimanda JE. A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network. Nucleic Acids Res 2016; 44:10644-10661. [PMID: 27604872 PMCID: PMC5159545 DOI: 10.1093/nar/gkw804] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 12/14/2022] Open
Abstract
Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34+ haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.
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MESH Headings
- Base Sequence
- Binding Sites
- Cell Line, Tumor
- Consensus Sequence
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Humans
- Ikaros Transcription Factor/physiology
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Prognosis
- Proportional Hazards Models
- Protein Binding
- Proteome
- Proteomics
- Proto-Oncogene Proteins c-ets/physiology
- Repressor Proteins/physiology
- Transcription, Genetic
- Transcriptional Regulator ERG/physiology
- ETS Translocation Variant 6 Protein
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Affiliation(s)
- Ashwin Unnikrishnan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yi F Guan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yizhou Huang
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Dominik Beck
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Center for Medical Genetics, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Julie A I Thoms
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Sofie Peirs
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Kathy Knezevic
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Shiyong Ma
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Inge V de Walle
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Ineke de Jong
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Zara Ali
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Tom Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Karen L MacKenzie
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Pieter Van Vlierberghe
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Jason W H Wong
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - John E Pimanda
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Department of Haematology, Prince of Wales Hospital, Sydney, 2031, Australia
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35
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Guven M, Barnouin K, Snijders AP, Karran P. Photosensitized UVA-Induced Cross-Linking between Human DNA Repair and Replication Proteins and DNA Revealed by Proteomic Analysis. J Proteome Res 2016; 15:4612-4623. [PMID: 27654267 PMCID: PMC5154610 DOI: 10.1021/acs.jproteome.6b00717] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Indexed: 11/29/2022]
Abstract
Long wavelength ultraviolet radiation (UVA, 320-400 nm) interacts with chromophores present in human cells to induce reactive oxygen species (ROS) that damage both DNA and proteins. ROS levels are amplified, and the damaging effects of UVA are exacerbated if the cells are irradiated in the presence of UVA photosensitizers such as 6-thioguanine (6-TG), a strong UVA chromophore that is extensively incorporated into the DNA of dividing cells, or the fluoroquinolone antibiotic ciprofloxacin. Both DNA-embedded 6-TG and ciprofloxacin combine synergistically with UVA to generate high levels of ROS. Importantly, the extensive protein damage induced by these photosensitizer+UVA combinations inhibits DNA repair. DNA is maintained in intimate contact with the proteins that effect its replication, transcription, and repair, and DNA-protein cross-links (DPCs) are a recognized reaction product of ROS. Cross-linking of DNA metabolizing proteins would compromise these processes by introducing physical blocks and by depleting active proteins. We describe a sensitive and statistically rigorous method to analyze DPCs in cultured human cells. Application of this proteomics-based analysis to cells treated with 6-TG+UVA and ciprofloxacin+UVA identified proteins involved in DNA repair, replication, and gene expression among those most vulnerable to cross-linking under oxidative conditions.
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Affiliation(s)
- Melisa Guven
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
| | - Karin Barnouin
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
| | - Ambrosius P. Snijders
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
| | - Peter Karran
- The
Francis Crick Institute, Clare Hall Laboratory, South Mimms, Herts EN6
3LD, U.K.
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36
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Beresova L, Vesela E, Chamrad I, Voller J, Yamada M, Furst T, Lenobel R, Chroma K, Gursky J, Krizova K, Mistrik M, Bartek J. Role of DNA Repair Factor Xeroderma Pigmentosum Protein Group C in Response to Replication Stress As Revealed by DNA Fragile Site Affinity Chromatography and Quantitative Proteomics. J Proteome Res 2016; 15:4505-4517. [PMID: 27794614 DOI: 10.1021/acs.jproteome.6b00622] [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: 02/04/2023]
Abstract
Replication stress (RS) fuels genomic instability and cancer development and may contribute to aging, raising the need to identify factors involved in cellular responses to such stress. Here, we present a strategy for identification of factors affecting the maintenance of common fragile sites (CFSs), which are genomic loci that are particularly sensitive to RS and suffer from increased breakage and rearrangements in tumors. A DNA probe designed to match the high flexibility island sequence typical for the commonly expressed CFS (FRA16D) was used as specific DNA affinity bait. Proteins significantly enriched at the FRA16D fragment under normal and replication stress conditions were identified using stable isotope labeling of amino acids in cell culture-based quantitative mass spectrometry. The identified proteins interacting with the FRA16D fragment included some known CFS stabilizers, thereby validating this screening approach. Among the hits from our screen so far not implicated in CFS maintenance, we chose Xeroderma pigmentosum protein group C (XPC) for further characterization. XPC is a key factor in the DNA repair pathway known as global genomic nucleotide excision repair (GG-NER), a mechanism whose several components were enriched at the FRA16D fragment in our screen. Functional experiments revealed defective checkpoint signaling and escape of DNA replication intermediates into mitosis and the next generation of XPC-depleted cells exposed to RS. Overall, our results provide insights into an unexpected biological role of XPC in response to replication stress and document the power of proteomics-based screening strategies to elucidate mechanisms of pathophysiological significance.
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Affiliation(s)
- Lucie Beresova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic.,Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacky University , Olomouc, Czech Republic
| | - Eva Vesela
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Ivo Chamrad
- Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacky University , Olomouc, Czech Republic
| | - Jiri Voller
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Masayuki Yamada
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Tomas Furst
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Rene Lenobel
- Department of Protein Biochemistry and Proteomics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacky University , Olomouc, Czech Republic
| | - Katarina Chroma
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Jan Gursky
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Katerina Krizova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic
| | - Jiri Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University , Olomouc, Czech Republic.,Danish Cancer Society Research Center , Copenhagen, Denmark.,Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Biochemistry and Biophysics, Karolinska Institute , Stockholm, Sweden
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37
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Yao X, Xing M, Ooi WF, Tan P, Teh BT. Epigenomic Consequences of Coding and Noncoding Driver Mutations. Trends Cancer 2016; 2:585-605. [PMID: 28741489 DOI: 10.1016/j.trecan.2016.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/30/2016] [Accepted: 09/02/2016] [Indexed: 12/27/2022]
Abstract
Chromatin alterations are integral to the pathogenic process of cancer, as demonstrated by recent discoveries of frequent mutations in chromatin-modifier genes and aberrant DNA methylation states in different cancer types. Progress is being made on elucidating how chromatin alterations, and how proteins catalyzing these alterations, mechanistically contribute to tissue-specific tumorigenesis. In parallel, technologies enabling the genome-wide profiling of histone modifications have revealed the existence of noncoding driver genetic alterations in cancer. In this review, we survey the current knowledge of coding and noncoding cancer drivers, and discuss their impact on the chromatin landscape. Translational implications of these findings for novel cancer therapies are also presented.
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Affiliation(s)
- Xiaosai Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Manjie Xing
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore.
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore; National Cancer Centre, 11 Hospital Drive, Singapore 169610, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; SingHealth/Duke-NUS Precision Medicine Institute, Singapore 168752, Singapore; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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38
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Trung NT, Kremmer E, Mittler G. Biochemical and cellular characterization of transcription factors binding to the hyperconserved core promoter-associated M4 motif. BMC Genomics 2016; 17:693. [PMID: 27576892 PMCID: PMC5006282 DOI: 10.1186/s12864-016-3033-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/22/2016] [Indexed: 01/06/2023] Open
Abstract
Background The motif ACTAYRNNNCCCR (Y being C or T, R being A or G, and N any nucleotide), called M4, was discovered as a putative cis-regulatory element, present 520 times in human promoter regions. Of these, 317 (61 %) are conserved within promoter sequences of four related organisms: human, mouse, rat, and dog. Recent genome-wide studies have described M4 as a transcription factor (TF) binding site for THAP11 that does often overlap with SBS (STAF Binding Site) a second core-promoter associated TF binding module, which associates with the TFs STAF/ZNF143 and RBP-J. Human M4-promoter genes show enhanced expression in cells of hematopoietic origin, especially in B lymphoblasts and peripheral blood B and T cells. Apart from RBP-J that is well known to recruit ICN1 (the intracellular transcriptional mediator of activated Notch1), the functional role of the hyperconserved M4 cis-element in the context of transcriptional regulation of M4-genes in lymphoid cells remains poorly defined. Results Here, we present a quantitative proteomic investigation of the M4 motif TF binding landscape in lymphoid cell lines that is further validated by ChIP experiments and functional assays. Our data strongly suggest that THAP11 and Ikaros interact directly, while NFKB1 (NF-kappa B p50) and HCF-1 are binding indirectly to M4-promoters in vitro and in living cells. Further analysis reveals that M4 is a bipartite composite cis-element, which is recognized by THAP11 via binding to the ACTAYR sequence module, thereby promoting ternary complex formation with HCF-1. Similarly, Ikaros binds to the CCCR module of the M4 motif and this interaction is crucial for recruiting NFKB1 to M4 harboring genes. Transient reporter assays in HEK293 and loss-of-function experiments in Molt4 T cells unequivocally demonstrate that binding of Ikaros and/or THAP11 to M4 bearing promoters is functionally important and therefore biologically relevant. Accordingly, this study validates our SILAC-based DNA protein interaction screening methodology as a valuable surrogate for a bona fide reverse ChIP technology. Conclusions The M4 motif (ACTAYRNNNCCCR) is a functional regulatory bipartite cis-element, which engages a THAP11/HCF-1 complex via binding to the ACTAYR module, while the CCCRRNRNRC subsequence part constitutes a binding platform for Ikaros and NFKB1. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3033-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ngo Tat Trung
- Department of Cellular and Molecular Immunology, Proteomics Core Facility, Max-Planck-Institute of Immunobiology and Epigenetics, D-79108, Freiburg, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany.,Present address: Tran Hung Dao University Hospital (Benh Vien TWQD 108), No 1, Tran Hung Dao Str, Hai Ba Trung Dist, Hanoi, Vietnam
| | - Elisabeth Kremmer
- Institute of Molecular Immunology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), D-81377, München, Germany.,Present address: Ludwig-Maximilians-University Munich, Biocenter, Humanbiologie und Bioimaging, D-82152, Martinsried, Germany
| | - Gerhard Mittler
- Department of Cellular and Molecular Immunology, Proteomics Core Facility, Max-Planck-Institute of Immunobiology and Epigenetics, D-79108, Freiburg, Germany. .,BIOSS, Center for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, D-79104, Freiburg, Germany.
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39
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Wierer M, Mann M. Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes. Hum Mol Genet 2016; 25:R106-R114. [PMID: 27402878 PMCID: PMC5036873 DOI: 10.1093/hmg/ddw208] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/24/2016] [Indexed: 01/30/2023] Open
Abstract
High-resolution mass spectrometry (MS)-based proteomics is a powerful method for the identification of soluble protein complexes and large-scale affinity purification screens can decode entire protein interaction networks. In contrast, protein complexes residing on chromatin have been much more challenging, because they are difficult to purify and often of very low abundance. However, this is changing due to recent methodological and technological advances in proteomics. Proteins interacting with chromatin marks can directly be identified by pulldowns with synthesized histone tails containing posttranslational modifications (PTMs). Similarly, pulldowns with DNA baits harbouring single nucleotide polymorphisms or DNA modifications reveal the impact of those DNA alterations on the recruitment of transcription factors. Accurate quantitation – either isotope-based or label free – unambiguously pinpoints proteins that are significantly enriched over control pulldowns. In addition, protocols that combine classical chromatin immunoprecipitation (ChIP) methods with mass spectrometry (ChIP-MS) target gene regulatory complexes in their in-vivo context. Similar to classical ChIP, cells are crosslinked with formaldehyde and chromatin sheared by sonication or nuclease digested. ChIP-MS baits can be proteins in tagged or endogenous form, histone PTMs, or lncRNAs. Locus-specific ChIP-MS methods would allow direct purification of a single genomic locus and the proteins associated with it. There, loci can be targeted either by artificial DNA-binding sites and corresponding binding proteins or via proteins with sequence specificity such as TAL or nuclease deficient Cas9 in combination with a specific guide RNA. We predict that advances in MS technology will soon make such approaches generally applicable tools in epigenetics.
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Affiliation(s)
- Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany
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40
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Zhao Z, Wang L, Di L. Compartmentation of metabolites in regulating epigenome of cancer. Mol Med 2016; 22:349-360. [PMID: 27258652 DOI: 10.2119/molmed.2016.00051] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 04/14/2016] [Indexed: 01/10/2023] Open
Abstract
Covalent modification of DNA and histones are important epigenetic events and the genome wide reshaping of epigenetic markers is common in cancer. The epigenetic markers are produced by enzymatic reactions and some of these reactions require the presence of metabolites as cofactors (termed Epigenetic Enzyme Required Metabolites, EERMs). Recent studies found that the abundance of these EERMs correlates with epigenetic enzyme activities. Also, the subcellular compartmentation, especially the nuclear localization of these EERMs may play a role in regulating the activities of epigenetic enzymes. Moreover, gene specific recruitment of enzymes which produce the EERMs in the proximity of the epigenetic modification events accompanying the gene expression regulation, were proposed. Therefore, it is of importance to summarize these findings of the EERMs in regulating the epigenetic modifications at both DNA and histone levels, and to understand how EERMs contribute to cancer development by addressing their global versus local distribution.
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Affiliation(s)
- Zhiqiang Zhao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Li Wang
- Faculty of Health Sciences, University of Macau, Macau SAR, China.,Metabolomics Core, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Lijun Di
- Faculty of Health Sciences, University of Macau, Macau SAR, China
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41
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Telorac J, Prykhozhij SV, Schöne S, Meierhofer D, Sauer S, Thomas-Chollier M, Meijsing SH. Identification and characterization of DNA sequences that prevent glucocorticoid receptor binding to nearby response elements. Nucleic Acids Res 2016; 44:6142-56. [PMID: 27016732 PMCID: PMC5291246 DOI: 10.1093/nar/gkw203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/16/2016] [Indexed: 01/13/2023] Open
Abstract
Out of the myriad of potential DNA binding sites of the glucocorticoid receptor (GR) found in the human genome, only a cell-type specific minority is actually bound, indicating that the presence of a recognition sequence alone is insufficient to specify where GR binds. Cooperative interactions with other transcription factors (TFs) are known to contribute to binding specificity. Here, we reasoned that sequence signals preventing GR recruitment to certain loci provide an alternative means to confer specificity. Motif analyses uncovered candidate Negative Regulatory Sequences (NRSs) that interfere with genomic GR binding. Subsequent functional analyses demonstrated that NRSs indeed prevent GR binding to nearby response elements. We show that NRS activity is conserved across species, found in most tissues and that they also interfere with the genomic binding of other TFs. Interestingly, the effects of NRSs appear not to be a simple consequence of changes in chromatin accessibility. Instead, we find that NRSs interact with proteins found at sub-nuclear structures called paraspeckles and that these proteins might mediate the repressive effects of NRSs. Together, our studies suggest that the joint influence of positive and negative sequence signals partition the genome into regions where GR can bind and those where it cannot.
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Affiliation(s)
- Jonas Telorac
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Sergey V Prykhozhij
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Stefanie Schöne
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - David Meierhofer
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
| | - Sascha Sauer
- CU Systems Medicine, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Morgane Thomas-Chollier
- Computational Systems Biology, Institut de Biologie de l'Ecole Normale, Supérieure (IBENS), CNRS, Inserm, Ecole Normale Supérieure, PSL Research University, F-75005 Paris, France
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
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42
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Noberini R, Sigismondo G, Bonaldi T. The contribution of mass spectrometry-based proteomics to understanding epigenetics. Epigenomics 2016; 8:429-45. [DOI: 10.2217/epi.15.108] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin is a macromolecular complex composed of DNA and histones that regulate gene expression and nuclear architecture. The concerted action of DNA methylation, histone post-translational modifications and chromatin-associated proteins control the epigenetic regulation of the genome, ultimately determining cell fate and the transcriptional outputs of differentiated cells. Deregulation of this complex machinery leads to disease states, and exploiting epigenetic drugs is becoming increasingly attractive for therapeutic intervention. Mass spectrometry (MS)-based proteomics emerged as a powerful tool complementary to genomic approaches for epigenetic research, allowing the unbiased and comprehensive analysis of histone post-translational modifications and the characterization of chromatin constituents and chromatin-associated proteins. Furthermore, MS holds great promise for epigenetic biomarker discovery and represents a useful tool for deconvolution of epigenetic drug targets. Here, we will provide an overview of the applications of MS-based proteomics in various areas of chromatin biology.
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Affiliation(s)
- Roberta Noberini
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia, via Adamello 16, Milano, Italy
| | - Gianluca Sigismondo
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, via Adamello 16, Milano, Italy
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43
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Chechenova MB, Maes S, Cripps RM. Expression of the Troponin C at 41C Gene in Adult Drosophila Tubular Muscles Depends upon Both Positive and Negative Regulatory Inputs. PLoS One 2015; 10:e0144615. [PMID: 26641463 PMCID: PMC4671713 DOI: 10.1371/journal.pone.0144615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/20/2015] [Indexed: 12/05/2022] Open
Abstract
Most animals express multiple isoforms of structural muscle proteins to produce tissues with different physiological properties. In Drosophila, the adult muscles include tubular-type muscles and the fibrillar indirect flight muscles. Regulatory processes specifying tubular muscle fate remain incompletely understood, therefore we chose to analyze the transcriptional regulation of TpnC41C, a Troponin C gene expressed in the tubular jump muscles, but not in the fibrillar flight muscles. We identified a 300-bp promoter fragment of TpnC41C sufficient for the fiber-specific reporter expression. Through an analysis of this regulatory element, we identified two sites necessary for the activation of the enhancer. Mutations in each of these sites resulted in 70% reduction of enhancer activity. One site was characterized as a binding site for Myocyte Enhancer Factor-2. In addition, we identified a repressive element that prevents activation of the enhancer in other muscle fiber types. Mutation of this site increased jump muscle-specific expression of the reporter, but more importantly reporter expression expanded into the indirect flight muscles. Our findings demonstrate that expression of the TpnC41C gene in jump muscles requires integration of multiple positive and negative transcriptional inputs. Identification of the transcriptional regulators binding the cis-elements that we identified will reveal the regulatory pathways controlling muscle fiber differentiation.
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Affiliation(s)
- Maria B Chechenova
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, United States of America
| | - Sara Maes
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, United States of America
| | - Richard M Cripps
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, United States of America
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High-Frequency Variation of Purine Biosynthesis Genes Is a Mechanism of Success in Campylobacter jejuni. mBio 2015; 6:e00612-15. [PMID: 26419875 PMCID: PMC4611032 DOI: 10.1128/mbio.00612-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED Phenotypic variation is prevalent in the zoonotic pathogen Campylobacter jejuni, the leading agent of enterocolitis in the developed world. Heterogeneity enhances the survival and adaptive malleability of bacterial populations because variable phenotypes may allow some cells to be protected against future stress. Exposure to hyperosmotic stress previously revealed prevalent differences in growth between C. jejuni strain 81-176 colonies due to resistant or sensitive phenotypes, and these isolated colonies continued to produce progeny with differential phenotypes. In this study, whole-genome sequencing of isolated colonies identified allelic variants of two purine biosynthesis genes, purF and apt, encoding phosphoribosyltransferases that utilize a shared substrate. Genetic analyses determined that purF was essential for fitness, while apt was critical. Traditional and high-depth amplicon-sequencing analyses confirmed extensive intrapopulation genetic variation of purF and apt that resulted in viable strains bearing alleles with in-frame insertion duplications, deletions, or missense polymorphisms. Different purF and apt alleles were associated with various stress survival capabilities under several niche-relevant conditions and contributed to differential intracellular survival in an epithelial cell infection model. Amplicon sequencing revealed that intracellular survival selected for stress-fit purF and apt alleles, as did exposure to oxygen and hyperosmotic stress. Putative protein recognition direct repeat sequences were identified in purF and apt, and a DNA-protein affinity screen captured a predicted exonuclease that promoted the global spontaneous mutation rate. This work illustrates the adaptive properties of high-frequency genetic variation in two housekeeping genes, which influences C. jejuni survival under stress and promotes its success as a pathogen. IMPORTANCE C. jejuni is an important cause of bacterial diarrheal illness. Bacterial populations have many strategies for stress survival, but phenotypic variation due to genetic diversity has a powerful advantage: no matter how swift the change in environment, a fraction of the population already expresses the survival trait. Nonclonality is thus increasingly viewed as a mechanism of population success. Our previous work identified prominent resistant/sensitive colonial variation in C. jejuni bacteria in response to hyperosmotic stress; in the work presented here, we attribute that to high-frequency genetic variation in two purine biosynthesis genes, purF and apt. We demonstrated selective pressure for nonlethal mutant alleles of both genes, showed that single-cell variants had the capacity to give rise to diverse purF and apt populations, and determined that stress exposure selected for desirable alleles. Thus, a novel C. jejuni adaptive strategy was identified, which was, unusually, reliant on prevalent genetic variation in two housekeeping genes.
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45
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Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
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Gillespie MA, Gold ES, Ramsey SA, Podolsky I, Aderem A, Ranish JA. An LXR-NCOA5 gene regulatory complex directs inflammatory crosstalk-dependent repression of macrophage cholesterol efflux. EMBO J 2015; 34:1244-58. [PMID: 25755249 DOI: 10.15252/embj.201489819] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 02/13/2015] [Indexed: 02/04/2023] Open
Abstract
LXR-cofactor complexes activate the gene expression program responsible for cholesterol efflux in macrophages. Inflammation antagonizes this program, resulting in foam cell formation and atherosclerosis; however, the molecular mechanisms underlying this antagonism remain to be fully elucidated. We use promoter enrichment-quantitative mass spectrometry (PE-QMS) to characterize the composition of gene regulatory complexes assembled at the promoter of the lipid transporter Abca1 following downregulation of its expression. We identify a subset of proteins that show LXR ligand- and binding-dependent association with the Abca1 promoter and demonstrate they differentially control Abca1 expression. We determine that NCOA5 is linked to inflammatory Toll-like receptor (TLR) signaling and establish that NCOA5 functions as an LXR corepressor to attenuate Abca1 expression. Importantly, TLR3-LXR signal crosstalk promotes recruitment of NCOA5 to the Abca1 promoter together with loss of RNA polymerase II and reduced cholesterol efflux. Together, these data significantly expand our knowledge of regulatory inputs impinging on the Abca1 promoter and indicate a central role for NCOA5 in mediating crosstalk between pro-inflammatory and anti-inflammatory pathways that results in repression of macrophage cholesterol efflux.
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Affiliation(s)
| | | | - Stephen A Ramsey
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
| | | | - Alan Aderem
- Seattle Biomedical Research Institute, Seattle, WA, USA
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47
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Hubner NC, Nguyen LN, Hornig NC, Stunnenberg HG. A quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood. J Proteome Res 2015; 14:1315-29. [PMID: 25546135 DOI: 10.1021/pr5009515] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interactions between transcription factors and genomic DNA, and in particular their impact on disease and cell fate, have been extensively studied on a global level using techniques based on next-generation sequencing. These approaches, however, do not allow an unbiased study of protein complexes that bind to certain DNA sequences. DNA pulldowns from crude lysates combined with quantitative mass spectrometry were recently introduced to close this gap. Established protocols, however, are restricted to cell lines because they are based on metabolic labeling or require large amounts of material. We introduce a high-throughput-compatible DNA pulldown that combines on-bead digestion with direct dimethyl labeling or label-free protein quantification. We demonstrate that our method can efficiently identify transcription factors binding to their consensus DNA motifs in extracts from primary foreskin fibroblasts and peripheral blood mononuclear cells (PBMCs) freshly isolated from human donors. Nuclear proteomes with absolute quantification of nearly 7000 proteins in K562 cells and PBMCs clearly link differential interactions to differences in protein abundance, hence stressing the importance of selecting relevant cell extracts for any interaction in question. As shown for rs6904029, a SNP highly associated with chronic lymphocytic leukemia, our approach can provide invaluable functional data, for example, through integration with GWAS.
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Affiliation(s)
- Nina C Hubner
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen , Nijmegen 6525 GA, The Netherlands
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Spruijt CG, Vermeulen M. DNA methylation: old dog, new tricks? Nat Struct Mol Biol 2015; 21:949-54. [PMID: 25372310 DOI: 10.1038/nsmb.2910] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/30/2014] [Indexed: 12/17/2022]
Abstract
DNA methylation is an epigenetic modification that is generally associated with repression of transcription initiation at CpG-island promoters. Here we argue that, on the basis of recent high-throughput genomic and proteomic screenings, DNA methylation can also have different outcomes, including activation of transcription. This is evidenced by the fact that transcription factors can interact with methylated DNA sequences. Furthermore, in certain cellular contexts, genes containing methylated promoters are highly transcribed. Interestingly, this uncoupling between methylated DNA and repression of transcription seems to be particularly evident in germ cells and pluripotent cells. Thus, contrary to previous assumptions, DNA methylation is not exclusively associated with repression of transcription initiation.
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Affiliation(s)
- Cornelia G Spruijt
- Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Michiel Vermeulen
- 1] Department of Molecular Cancer Research, University Medical Center Utrecht, Utrecht, the Netherlands. [2] Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, the Netherlands. [3] Cancer Genomics Netherlands, the Netherlands
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Ward AM, Gunaratne J, Garcia-Blanco MA. Identification of dengue RNA binding proteins using RNA chromatography and quantitative mass spectrometry. Methods Mol Biol 2014; 1138:253-70. [PMID: 24696342 DOI: 10.1007/978-1-4939-0348-1_16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A major challenge in dengue virus (DENV) research has been to understand the interaction of the viral RNA with host cell proteins during infection. Until recently, there were no comprehensive studies identifying host RNA binding proteins that interact with DENV RNA (Ward et al. RNA Biol 8 (6):1173-1186, 2011). Here, we describe a method for identifying proteins that associate with DENV RNA using RNA chromatography and quantitative mass spectrometry. The method utilizes a tobramycin RNA aptamer incorporated into an RNA containing the dengue 5' and 3' untranslated regions (UTRs) in order to reversibly bind RNA to a tobramycin matrix. The RNA-tobramycin matrix is incubated with SILAC-labeled cell lysates, and bound proteins are eluted using an excess of tobramycin. The eluate is analyzed using quantitative mass spectrometry, which allows direct and quantitative comparison of proteins bound to DENV UTRs and a control RNA-tobramycin matrix. This technique has the advantage of allowing one to distinguish between specific and nonspecific binding proteins based on the ratio of protein preferentially bound to the DENV UTRs versus the control RNA. This methodology can also be used for validation of quantitative mass spectrometry results using conventional Western blotting for specific proteins. Furthermore, though it was specifically developed to identify DENV RNA binding proteins, the RNA chromatography method described here can be applied to a broad range of viral and cellular RNAs for identification of interacting proteins.
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Affiliation(s)
- Alex M Ward
- Emerging Infectious Diseases Program, Duke-NUS Graduate Medical School, Singapore, Singapore
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Abstract
During interphase, chromatin hosts fundamental cellular processes, such as gene expression, DNA replication and DNA damage repair. To analyze chromatin on a proteomic scale, we have developed chromatin enrichment for proteomics (ChEP), which is a simple biochemical procedure that enriches interphase chromatin in all its complexity. It enables researchers to take a 'snapshot' of chromatin and to isolate and identify even transiently bound factors. In ChEP, cells are fixed with formaldehyde; subsequently, DNA together with all cross-linked proteins is isolated by centrifugation under denaturing conditions. This approach enables the analysis of global chromatin composition and its changes, which is in contrast with existing chromatin enrichment procedures, which either focus on specific chromatin loci (e.g., affinity purification) or are limited in specificity, such as the analysis of the chromatin pellet (i.e., analysis of all insoluble nuclear material). ChEP takes half a day to complete and requires no specialized laboratory skills or equipment. ChEP enables the characterization of chromatin response to drug treatment or physiological processes. Beyond proteomics, ChEP may preclear chromatin for chromatin immunoprecipitation (ChIP) analyses.
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Affiliation(s)
- Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Karen L H Wills
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Cristina Furlan
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- 1] Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK. [2] Department of Biotechnology, Institute of Bioanalytics, Technische Universität Berlin, Berlin, Germany
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