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Bell CC, Balic JJ, Talarmain L, Gillespie A, Scolamiero L, Lam EYN, Ang CS, Faulkner GJ, Gilan O, Dawson MA. Comparative cofactor screens show the influence of transactivation domains and core promoters on the mechanisms of transcription. Nat Genet 2024; 56:1181-1192. [PMID: 38769457 DOI: 10.1038/s41588-024-01749-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/09/2024] [Indexed: 05/22/2024]
Abstract
Eukaryotic transcription factors (TFs) activate gene expression by recruiting cofactors to promoters. However, the relationships between TFs, promoters and their associated cofactors remain poorly understood. Here we combine GAL4-transactivation assays with comparative CRISPR-Cas9 screens to identify the cofactors used by nine different TFs and core promoters in human cells. Using this dataset, we associate TFs with cofactors, classify cofactors as ubiquitous or specific and discover transcriptional co-dependencies. Through a reductionistic, comparative approach, we demonstrate that TFs do not display discrete mechanisms of activation. Instead, each TF depends on a unique combination of cofactors, which influences distinct steps in transcription. By contrast, the influence of core promoters appears relatively discrete. Different promoter classes are constrained by either initiation or pause-release, which influences their dynamic range and compatibility with cofactors. Overall, our comparative cofactor screens characterize the interplay between TFs, cofactors and core promoters, identifying general principles by which they influence transcription.
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Affiliation(s)
- Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Queensland, Australia.
| | - Jesse J Balic
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Laure Talarmain
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Andrea Gillespie
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Laura Scolamiero
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
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2
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Cautereels C, Smets J, Bircham P, De Ruysscher D, Zimmermann A, De Rijk P, Steensels J, Gorkovskiy A, Masschelein J, Verstrepen KJ. Combinatorial optimization of gene expression through recombinase-mediated promoter and terminator shuffling in yeast. Nat Commun 2024; 15:1112. [PMID: 38326309 PMCID: PMC10850122 DOI: 10.1038/s41467-024-44997-7] [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: 08/10/2023] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
Microbes are increasingly employed as cell factories to produce biomolecules. This often involves the expression of complex heterologous biosynthesis pathways in host strains. Achieving maximal product yields and avoiding build-up of (toxic) intermediates requires balanced expression of every pathway gene. However, despite progress in metabolic modeling, the optimization of gene expression still heavily relies on trial-and-error. Here, we report an approach for in vivo, multiplexed Gene Expression Modification by LoxPsym-Cre Recombination (GEMbLeR). GEMbLeR exploits orthogonal LoxPsym sites to independently shuffle promoter and terminator modules at distinct genomic loci. This approach facilitates creation of large strain libraries, in which expression of every pathway gene ranges over 120-fold and each strain harbors a unique expression profile. When applied to the biosynthetic pathway of astaxanthin, an industrially relevant antioxidant, a single round of GEMbLeR improved pathway flux and doubled production titers. Together, this shows that GEMbLeR allows rapid and efficient gene expression optimization in heterologous biosynthetic pathways, offering possibilities for enhancing the performance of microbial cell factories.
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Affiliation(s)
- Charlotte Cautereels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Jolien Smets
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter Bircham
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Dries De Ruysscher
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Anna Zimmermann
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, 2610, Belgium
- Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Jan Steensels
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Anton Gorkovskiy
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium
| | - Joleen Masschelein
- Molecular Biotechnology of Plants and Micro-organisms, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, box 2438, Leuven, 3001, Belgium
- Laboratory for Biomolecular Discovery & Engineering, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium
| | - Kevin J Verstrepen
- VIB Laboratory for Systems Biology, VIB-KU Leuven Center for Microbiology, Leuven, 3001, Belgium.
- Laboratory of Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2S, KU Leuven, Gaston Geenslaan 1, Leuven, 3001, Belgium.
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3
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Malik S, Roeder RG. Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators. Nat Rev Genet 2023; 24:767-782. [PMID: 37532915 PMCID: PMC11088444 DOI: 10.1038/s41576-023-00630-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 08/04/2023]
Abstract
The RNA polymerase II (Pol II) pre-initiation complex (PIC) is a critical node in eukaryotic transcription regulation, and its formation is the major rate-limiting step in transcriptional activation. Diverse cellular signals borne by transcriptional activators converge on this large, multiprotein assembly and are transduced via intermediary factors termed coactivators. Cryogenic electron microscopy, multi-omics and single-molecule approaches have recently offered unprecedented insights into both the structure and cellular functions of the PIC and two key PIC-associated coactivators, Mediator and TFIID. Here, we review advances in our understanding of how Mediator and TFIID interact with activators and affect PIC formation and function. We also discuss how their functions are influenced by their chromatin environment and selected cofactors. We consider how, through its multifarious interactions and functionalities, a Mediator-containing and TFIID-containing PIC can yield an integrated signal processing system with the flexibility to determine the unique temporal and spatial expression pattern of a given gene.
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Affiliation(s)
- Sohail Malik
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA.
| | - Robert G Roeder
- Laboratory of Biochemistry & Molecular Biology, The Rockefeller University, New York, NY, USA
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4
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Lupo O, Kumar DK, Livne R, Chappleboim M, Levy I, Barkai N. The architecture of binding cooperativity between densely bound transcription factors. Cell Syst 2023; 14:732-745.e5. [PMID: 37527656 DOI: 10.1016/j.cels.2023.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/23/2023] [Accepted: 06/27/2023] [Indexed: 08/03/2023]
Abstract
The binding of transcription factors (TFs) along genomes is restricted to a subset of sites containing their preferred motifs. TF-binding specificity is often attributed to the co-binding of interacting TFs; however, apart from specific examples, this model remains untested. Here, we define dependencies among budding yeast TFs that localize to overlapping promoters by profiling the genome-wide consequences of co-depleting multiple TFs. We describe unidirectional interactions, revealing Msn2 as a central factor allowing TF binding at its target promoters. By contrast, no case of mutual cooperation was observed. Particularly, Msn2 retained binding at its preferred promoters upon co-depletion of fourteen similarly bound TFs. Overall, the consequences of TF co-depletions were moderate, limited to a subset of promoters, and failed to explain the role of regions outside the DNA-binding domain in directing TF-binding preferences. Our results call for re-evaluating the role of cooperative interactions in directing TF-binding preferences.
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Affiliation(s)
- Offir Lupo
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Divya Krishna Kumar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Livne
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Michal Chappleboim
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Idan Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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5
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Mahendrawada L, Warfield L, Donczew R, Hahn S. Surprising connections between DNA binding and function for the near-complete set of yeast transcription factors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550593. [PMID: 37546716 PMCID: PMC10402042 DOI: 10.1101/2023.07.25.550593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
DNA sequence-specific transcription factors (TFs) modulate transcription and chromatin architecture, acting from regulatory sites in enhancers and promoters of eukaryotic genes. How TFs locate their DNA targets and how multiple TFs cooperate to regulate individual genes is still unclear. Most yeast TFs are thought to regulate transcription via binding to upstream activating sequences, situated within a few hundred base pairs upstream of the regulated gene. While this model has been validated for individual TFs and specific genes, it has not been tested in a systematic way with the large set of yeast TFs. Here, we have integrated information on the binding and expression targets for the near-complete set of yeast TFs. While we found many instances of functional TF binding sites in upstream regulatory regions, we found many more instances that do not fit this model. In many cases, rapid TF depletion affects gene expression where there is no detectable binding of that TF to the upstream region of the affected gene. In addition, for most TFs, only a small fraction of bound TFs regulates the nearby gene, showing that TF binding does not automatically correspond to regulation of the linked gene. Finally, we found that only a small percentage of TFs are exclusively strong activators or repressors with most TFs having dual function. Overall, our comprehensive mapping of TF binding and regulatory targets have both confirmed known TF relationships and revealed surprising properties of TF function.
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6
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Kaplan CD. Mediator and Pol II go to eleven (CTD repeats). Proc Natl Acad Sci U S A 2023; 120:e2304596120. [PMID: 37094154 PMCID: PMC10160946 DOI: 10.1073/pnas.2304596120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Affiliation(s)
- Craig D. Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA15260
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7
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Schofield JA, Hahn S. Broad compatibility between yeast UAS elements and core promoters and identification of promoter elements that determine cofactor specificity. Cell Rep 2023; 42:112387. [PMID: 37058407 PMCID: PMC10567116 DOI: 10.1016/j.celrep.2023.112387] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/30/2023] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
Three classes of yeast protein-coding genes are distinguished by their dependence on the transcription cofactors TFIID, SAGA, and Mediator (MED) Tail, but whether this dependence is determined by the core promoter, upstream activating sequences (UASs), or other gene features is unclear. Also unclear is whether UASs can broadly activate transcription from the different promoter classes. Here, we measure transcription and cofactor specificity for thousands of UAS-core promoter combinations and find that most UASs broadly activate promoters regardless of regulatory class, while few display strong promoter specificity. However, matching UASs and promoters from the same gene class is generally important for optimal expression. We find that sensitivity to rapid depletion of MED Tail or SAGA is dependent on the identity of both UAS and core promoter, while dependence on TFIID localizes to only the promoter. Finally, our results suggest the role of TATA and TATA-like promoter sequences in MED Tail function.
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Affiliation(s)
- Jeremy A Schofield
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98105, USA
| | - Steven Hahn
- Basic Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Avenue N, Seattle, WA 98105, USA.
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8
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Donovan MG, Galbraith MD, Espinosa JM. Multi-omics investigation reveals functional specialization of transcriptional cyclin dependent kinases in cancer biology. Sci Rep 2022; 12:22505. [PMID: 36577800 PMCID: PMC9797569 DOI: 10.1038/s41598-022-26860-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
Transcriptional addiction is recognized as a valid therapeutic target in cancer, whereby the dependency of cancer cells on oncogenic transcriptional regulators may be pharmacologically exploited. However, a comprehensive understanding of the key factors within the transcriptional machinery that might afford a useful therapeutic window remains elusive. Herein, we present a cross-omics investigation into the functional specialization of the transcriptional cyclin dependent kinases (tCDKs) through analysis of high-content genetic dependency, gene expression, patient survival, and drug response datasets. This analysis revealed specialization among tCDKs in terms of contributions to cancer cell fitness, clinical prognosis, and interaction with oncogenic signaling pathways. CDK7 and CDK9 stand out as the most relevant targets, albeit through distinct mechanisms of oncogenicity and context-dependent contributions to cancer survival and drug sensitivity. Genetic ablation of CDK9, but not CDK7, mimics the effect on cell viability the loss of key components of the transcriptional machinery. Pathway analysis of genetic co-dependency and drug sensitivity data show CDK7 and CDK9 have distinct relationships with major oncogenic signatures, including MYC and E2F targets, oxidative phosphorylation, and the unfolded protein response. Altogether, these results inform the improved design of therapeutic strategies targeting tCDKs in cancer.
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Affiliation(s)
- Micah G Donovan
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew D Galbraith
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joaquin M Espinosa
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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