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van Breugel ME, van Kruijsbergen I, Mittal C, Lieftink C, Brouwer I, van den Brand T, Kluin RJC, Hoekman L, Menezes RX, van Welsem T, Del Cortona A, Malik M, Beijersbergen RL, Lenstra TL, Verstrepen KJ, Pugh BF, van Leeuwen F. Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly. Mol Cell 2023; 83:4205-4221.e9. [PMID: 37995691 DOI: 10.1016/j.molcel.2023.10.037] [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: 04/18/2023] [Revised: 09/27/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Transcription of tRNA genes by RNA polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the local chromatin proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII-regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced, and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and tuning the physiological response to changing metabolic demands.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Chitvan Mittal
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ineke Brouwer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Teun van den Brand
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Renée X Menezes
- Biostatistics Centre and Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Andrea Del Cortona
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
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Khan P, Singha P, Nag Chaudhuri R. RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes. Mol Cell Biol 2023; 43:596-610. [PMID: 37937370 PMCID: PMC10761024 DOI: 10.1080/10985549.2023.2270912] [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: 05/25/2023] [Accepted: 10/05/2023] [Indexed: 11/09/2023] Open
Abstract
Nucleosome dynamics in the coding region of a transcriptionally active locus is critical for understanding how RNA polymerase II progresses through the gene body. Histone acetylation and deacetylation critically influence nucleosome accessibility during DNA metabolic processes like transcription. Effect of such histone modifications is context and residue dependent. Rather than effect of individual histone residues, the network of modifications of several histone residues in combination generates a chromatin landscape that is conducive for transcription. Here we show that in Saccharomyces cerevisiae, crosstalk between deacetylation of the H4 N-terminal tail residue H4K16 and acetylation of the H3 core domain residue H3K56, promotes RNA polymerase II progression through the gene body. Results indicate that deacetylation of H4K16 precedes and in turn induces H3K56 acetylation. Effectively, recruitment of Rtt109, the HAT responsible for H3K56 acetylation is essentially dependent on H4K16 deacetylation. In Hos2 deletion strains, where H4K16 deacetylation is abolished, both H3K56 acetylation and RNA polymerase II recruitment gets significantly impaired. Notably, H4K16 deacetylation and H3K56 acetylation are found to be essentially dependent on active transcription. In summary, H4K16 deacetylation promotes H3K56 acetylation and the two modifications together work towards successful functioning of RNA polymerase II during active transcription.
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Affiliation(s)
- Preeti Khan
- Department of Biotechnology, St Xavier’s College, Kolkata, India
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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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Opalek M, Tutaj H, Pirog A, Smug BJ, Rutkowska J, Wloch-Salamon D. A Systematic Review on Quiescent State Research Approaches in S. cerevisiae. Cells 2023; 12:1608. [PMID: 37371078 DOI: 10.3390/cells12121608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/02/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast Saccharomyces cerevisiae. We group research articles into those that consider all cells comprising the stationary-phase (SP) population as quiescent and those that recognize heterogeneity within the SP by distinguishing phenotypically distinct subpopulations. Furthermore, we investigate the chronological age of the quiescent populations under study and the methods used to induce the quiescent state, such as gradual starvation or abrupt environmental change. We also assess whether the strains used in research are prototrophic or auxotrophic. By combining the above features, we identify 48 possible experimental setups that can be used to study quiescence, which can be misleading when drawing general conclusions. We therefore summarize our review by proposing guidelines and recommendations pertaining to the information included in research articles. We believe that more rigorous reporting on the features of quiescent populations will facilitate knowledge transfer within and between disciplines, thereby stimulating valuable scientific discussion.
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Affiliation(s)
- Monika Opalek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Hanna Tutaj
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Adrian Pirog
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Bogna J Smug
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Rutkowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
| | - Dominika Wloch-Salamon
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, 30-387 Krakow, Poland
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Martin BJE, Howe LJ. Reply to: Pitfalls in using phenanthroline to study the causal relationship between promoter nucleosome acetylation and transcription. Nat Commun 2022; 13:3725. [PMID: 35768425 PMCID: PMC9243053 DOI: 10.1038/s41467-022-30351-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, BCMP, LHRRB Building, Room 201a, 240 Longwood Ave., Boston, MA, 02115, USA
| | - LeAnn J Howe
- Department of Biochemistry and Molecular Biology, Life Sciences Centre, University of British Columbia, 2350 Health Sciences Mall, Vancouver, B.C., V6T 1Z3, Canada.
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Nussinov R, Tsai CJ, Jang H. How can same-gene mutations promote both cancer and developmental disorders? SCIENCE ADVANCES 2022; 8:eabm2059. [PMID: 35030014 PMCID: PMC8759737 DOI: 10.1126/sciadv.abm2059] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/22/2021] [Indexed: 05/05/2023]
Abstract
The question of how same-gene mutations can drive both cancer and neurodevelopmental disorders has been puzzling. It has also been puzzling why those with neurodevelopmental disorders have a high risk of cancer. Ras, MEK, PI3K, PTEN, and SHP2 are among the oncogenic proteins that can harbor mutations that encode diseases other than cancer. Understanding why some of their mutations can promote cancer, whereas others promote neurodevelopmental diseases, and why even the same mutations may promote both phenotypes, has important clinical ramifications. Here, we review the literature and address these tantalizing questions. We propose that cell type–specific expression of the mutant protein, and of other proteins in the respective pathway, timing of activation (during embryonic development or sporadic emergence), and the absolute number of molecules that the mutations activate, alone or in combination, are pivotal in determining the pathological phenotypes—cancer and (or) developmental disorders.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
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van Breugel ME, van Leeuwen F. Epi-Decoder: Decoding the Local Proteome of a Genomic Locus by Massive Parallel Chromatin Immunoprecipitation Combined with DNA-Barcode Sequencing. Methods Mol Biol 2022; 2458:123-150. [PMID: 35103966 DOI: 10.1007/978-1-0716-2140-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The genome in a eukaryotic cell is packaged into chromatin and regulated by chromatin-binding and chromatin-modifying factors. Many of these factors and their complexes have been identified before, but how each genomic locus interacts with its surrounding proteins in the nucleus over time and in changing conditions remains poorly described. Measuring protein-DNA interactions at a specific locus in the genome is challenging and current techniques such as capture of a locus followed by mass spectrometry require high levels of enrichment. Epi-Decoder, a method developed in budding yeast, enables systematic decoding of the proteome of a single genomic locus of interest without the need for locus enrichment. Instead, Epi-Decoder uses massive parallel chromatin immunoprecipitation of tagged proteins combined with barcoding a genomic locus and counting of coimmunoprecipitated barcodes by DNA sequencing (TAG-ChIP-Barcode-Seq). In this scenario, DNA barcode counts serve as a quantitative readout for protein binding of each tagged protein to the barcoded locus. Epi-Decoder can be applied to determine the protein-DNA interactions at a wide range of genomic loci, such as coding genes, noncoding genes, and intergenic regions. Furthermore, Epi-Decoder provides the option to study protein-DNA interactions upon changing cellular and/or genetic conditions. In this protocol, we describe in detail how to construct Epi-Decoder libraries and how to perform an Epi-Decoder analysis.
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Affiliation(s)
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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Cucinotta CE, Dell RH, Braceros KCA, Tsukiyama T. RSC primes the quiescent genome for hypertranscription upon cell-cycle re-entry. eLife 2021; 10:e67033. [PMID: 34042048 PMCID: PMC8186906 DOI: 10.7554/elife.67033] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Quiescence is a reversible G0 state essential for differentiation, regeneration, stem-cell renewal, and immune cell activation. Necessary for long-term survival, quiescent chromatin is compact, hypoacetylated, and transcriptionally inactive. How transcription activates upon cell-cycle re-entry is undefined. Here we report robust, widespread transcription within the first minutes of quiescence exit. During quiescence, the chromatin-remodeling enzyme RSC was already bound to the genes induced upon quiescence exit. RSC depletion caused severe quiescence exit defects: a global decrease in RNA polymerase II (Pol II) loading, Pol II accumulation at transcription start sites, initiation from ectopic upstream loci, and aberrant antisense transcription. These phenomena were due to a combination of highly robust Pol II transcription and severe chromatin defects in the promoter regions and gene bodies. Together, these results uncovered multiple mechanisms by which RSC facilitates initiation and maintenance of large-scale, rapid gene expression despite a globally repressive chromatin state.
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Affiliation(s)
| | - Rachel H Dell
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Keean CA Braceros
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Toshio Tsukiyama
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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