1
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Masumoto H, Muto H, Yano K, Kurosaki Y, Niki H. The Ty1 retrotransposon harbors a DNA region that performs dual functions as both a gene silencing and chromatin insulator. Sci Rep 2024; 14:16641. [PMID: 39025990 PMCID: PMC11258251 DOI: 10.1038/s41598-024-67242-z] [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: 12/18/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
In various eukaryotic kingdoms, long terminal repeat (LTR) retrotransposons repress transcription by infiltrating heterochromatin generated within their elements. In contrast, the budding yeast LTR retrotransposon Ty1 does not itself undergo transcriptional repression, although it is capable of repressing the transcription of the inserted genes within it. In this study, we identified a DNA region within Ty1 that exerts its silencing effect via sequence orientation. We identified a DNA region within the Ty1 group-specific antigen (GAG) gene that causes gene silencing, termed GAG silencing (GAGsi), in which the silent chromatin in the GAGsi region is created by euchromatin-specific histone modifications. A characteristic inverted repeat (IR) sequence is present at the 5' end of this region, forming a chromatin boundary between promoter-specific chromatin upstream of the IR sequence and silent chromatin downstream of the IR sequence. In addition, Esc2 and Rad57, which are involved in DNA repair, were required for GAGsi silencing. Finally, the chromatin boundary was required for the transcription of Ty1 itself. Thus, the GAGsi sequence contributes to the creation of a chromatin environment that promotes Ty1 transcription.
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Affiliation(s)
- Hiroshi Masumoto
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
| | - Hideki Muto
- Biomedical Research Support Center (BRSC), Nagasaki University School of Medicine, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Koichi Yano
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1,111 Yata, Mishima, Shizuoka, 411-8540, Japan
- Department of Life Science, College of Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Yohei Kurosaki
- National Research Center for the Control and Prevention of Infectious Diseases, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
| | - Hironori Niki
- Microbial Physiology Laboratory, Department of Gene Function and Phenomics, National Institute of Genetics, 1,111 Yata, Mishima, Shizuoka, 411-8540, Japan
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2
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Nguyen MC, Rostamian H, Raman A, Wei P, Becht DC, Erbse AH, Klein BJ, Gilbert TM, Zhang G, Blanco MA, Strahl BD, Taverna SD, Kutateladze TG. Molecular insight into interactions between the Taf14, Yng1 and Sas3 subunits of the NuA3 complex. Nat Commun 2024; 15:5335. [PMID: 38914563 PMCID: PMC11196586 DOI: 10.1038/s41467-024-49730-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
The NuA3 complex is a major regulator of gene transcription and the cell cycle in yeast. Five core subunits are required for complex assembly and function, but it remains unclear how these subunits interact to form the complex. Here, we report that the Taf14 subunit of the NuA3 complex binds to two other subunits of the complex, Yng1 and Sas3, and describe the molecular mechanism by which the extra-terminal domain of Taf14 recognizes the conserved motif present in Yng1 and Sas3. Structural, biochemical, and mutational analyses show that two motifs are sandwiched between the two extra-terminal domains of Taf14. The head-to-toe dimeric complex enhances the DNA binding activity of Taf14, and the formation of the hetero-dimer involving the motifs of Yng1 and Sas3 is driven by sequence complementarity. In vivo assays in yeast demonstrate that the interactions of Taf14 with both Sas3 and Yng1 are required for proper function of the NuA3 complex in gene transcription and DNA repair. Our findings suggest a potential basis for the assembly of three core subunits of the NuA3 complex, Taf14, Yng1 and Sas3.
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Affiliation(s)
- Minh Chau Nguyen
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Hosein Rostamian
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Pengcheng Wei
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, 530004, China
| | - Dustin C Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Annette H Erbse
- Department of Biochemistry, University of Colorado, Boulder, CO, 80303, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Tonya M Gilbert
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gongyi Zhang
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206, USA
| | - M Andres Blanco
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, PA, 19104, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72202, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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3
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Mittal C, Lang O, Lai WKM, Pugh BF. An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters. Genes Dev 2022; 36:985-1001. [PMID: 36302553 PMCID: PMC9732905 DOI: 10.1101/gad.350026.122] [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: 09/08/2022] [Accepted: 10/11/2022] [Indexed: 02/05/2023]
Abstract
Genome-wide, little is understood about how proteins organize at inducible promoters before and after induction and to what extent inducible and constitutive architectures depend on cofactors. We report that sequence-specific transcription factors and their tethered cofactors (e.g., SAGA [Spt-Ada-Gcn5-acetyltransferase], Mediator, TUP, NuA4, SWI/SNF, and RPD3-L) are generally bound to promoters prior to induction ("poised"), rather than recruited upon induction, whereas induction recruits the preinitiation complex (PIC) to DNA. Through depletion and/or deletion experiments, we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 acetylates +1 nucleosomes there. When inducible promoters are poised, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. When induced, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID (transcription factor II-D) to stably associate, rather than creating a completely TFIID-independent PIC, as generally thought. These findings suggest that inducible systems, where present, are integrated with constitutive systems.
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Affiliation(s)
- Chitvan Mittal
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Olivia Lang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - William K M Lai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16801, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
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4
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Barissi S, Sala A, Wieczór M, Battistini F, Orozco M. DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors. Nucleic Acids Res 2022; 50:9105-9114. [PMID: 36018808 PMCID: PMC9458447 DOI: 10.1093/nar/gkac708] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022] Open
Abstract
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can be extended to epigenetic variants, mismatches, mutations, or any non-coding nucleobases. When complemented with chromatin structure information, our in vitro trained method provides also good estimates of in vivo binding sites in yeast.
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Affiliation(s)
| | | | - Miłosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona). The Barcelona Institute of Science and Technology. Baldiri Reixac 10–12, 08028 Barcelona, Spain,Department of Physical Chemistry. Gdansk University of Technology, 80-233 Gdańsk, Poland
| | | | - Modesto Orozco
- Correspondence may also be addressed to Modesto Orozco. Tel: +34 934 037 156;
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5
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Shao D, Kellogg GD, Nematbakhsh A, Kuntala PK, Mahony S, Pugh BF, Lai WKM. PEGR: a flexible management platform for reproducible epigenomic and genomic research. Genome Biol 2022; 23:99. [PMID: 35440038 PMCID: PMC9016988 DOI: 10.1186/s13059-022-02671-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/07/2022] [Indexed: 11/27/2022] Open
Abstract
Reproducibility is a significant challenge in (epi)genomic research due to the complexity of experiments composed of traditional biochemistry and informatics. Recent advances have exacerbated this as high-throughput sequencing data is generated at an unprecedented pace. Here, we report the development of a Platform for Epi-Genomic Research (PEGR), a web-based project management platform that tracks and quality controls experiments from conception to publication-ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at the bench, while fully supporting reproducibility and reliability for bioinformaticians through integration with the Galaxy platform.
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Affiliation(s)
- Danying Shao
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Gretta D Kellogg
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14850, USA
| | - Ali Nematbakhsh
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14850, USA
| | - Prashant K Kuntala
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Shaun Mahony
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - William K M Lai
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA. .,Department of Computational Biology, Cornell University, Ithaca, NY, 14850, USA.
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6
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Uzun Ü, Brown T, Fischl H, Angel A, Mellor J. Spt4 facilitates the movement of RNA polymerase II through the +2 nucleosomal barrier. Cell Rep 2021; 36:109755. [PMID: 34592154 PMCID: PMC8492961 DOI: 10.1016/j.celrep.2021.109755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/18/2021] [Accepted: 09/02/2021] [Indexed: 02/06/2023] Open
Abstract
Spt4 is a transcription elongation factor with homologs in organisms with nucleosomes. Structural and in vitro studies implicate Spt4 in transcription through nucleosomes, and yet the in vivo function of Spt4 is unclear. Here, we assess the precise position of Spt4 during transcription and the consequences of the loss of Spt4 on RNA polymerase II (RNAPII) dynamics and nucleosome positioning in Saccharomyces cerevisiae. In the absence of Spt4, the spacing between gene-body nucleosomes increases and RNAPII accumulates upstream of the nucleosomal dyad, most dramatically at nucleosome +2. Spt4 associates with elongating RNAPII early in transcription, and its association dynamically changes depending on nucleosome positions. Together, our data show that Spt4 regulates early elongation dynamics, participates in co-transcriptional nucleosome positioning, and promotes RNAPII movement through the gene-body nucleosomes, especially the +2 nucleosome.
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Affiliation(s)
- Ülkü Uzun
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Thomas Brown
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Harry Fischl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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7
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Donczew R, Hahn S. BET family members Bdf1/2 modulate global transcription initiation and elongation in Saccharomyces cerevisiae. eLife 2021; 10:e69619. [PMID: 34137374 PMCID: PMC8266393 DOI: 10.7554/elife.69619] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/16/2021] [Indexed: 01/10/2023] Open
Abstract
Human bromodomain and extra-terminal domain (BET) family members are promising targets for therapy of cancer and immunoinflammatory diseases, but their mechanisms of action and functional redundancies are poorly understood. Bdf1/2, yeast homologues of the human BET factors, were previously proposed to target transcription factor TFIID to acetylated histone H4, analogous to bromodomains that are present within the largest subunit of metazoan TFIID. We investigated the genome-wide roles of Bdf1/2 and found that their important contributions to transcription extend beyond TFIID function as transcription of many genes is more sensitive to Bdf1/2 than to TFIID depletion. Bdf1/2 co-occupy the majority of yeast promoters and affect preinitiation complex formation through recruitment of TFIID, Mediator, and basal transcription factors to chromatin. Surprisingly, we discovered that hypersensitivity of genes to Bdf1/2 depletion results from combined defects in transcription initiation and early elongation, a striking functional similarity to human BET proteins, most notably Brd4. Our results establish Bdf1/2 as critical for yeast transcription and provide important mechanistic insights into the function of BET proteins in all eukaryotes.
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Affiliation(s)
- Rafal Donczew
- Fred Hutchinson Cancer Research Center, Division of Basic SciencesSeattleUnited States
| | - Steven Hahn
- Fred Hutchinson Cancer Research Center, Division of Basic SciencesSeattleUnited States
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8
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Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, Kuzu G, Bocklund K, Farrell NP, Blanda TR, Mairose JD, Basting AV, Mistretta KS, Rocco DJ, Perkinson ES, Kellogg GD, Mahony S, Pugh BF. A high-resolution protein architecture of the budding yeast genome. Nature 2021; 592:309-314. [PMID: 33692541 PMCID: PMC8035251 DOI: 10.1038/s41586-021-03314-8] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is not well defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP-exo/seq)1,2 to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex. Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI-SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs engaged with their cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.
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Affiliation(s)
- Matthew J Rossi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Prashant K Kuntala
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - William K M Lai
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Naomi Yamada
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Nitika Badjatia
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Chitvan Mittal
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Guray Kuzu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Kylie Bocklund
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Nina P Farrell
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Thomas R Blanda
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Joshua D Mairose
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Ann V Basting
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Katelyn S Mistretta
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - David J Rocco
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Emily S Perkinson
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Gretta D Kellogg
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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9
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What do Transcription Factors Interact With? J Mol Biol 2021; 433:166883. [PMID: 33621520 DOI: 10.1016/j.jmb.2021.166883] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/11/2022]
Abstract
Although we have made significant progress, we still possess a limited understanding of how genomic and epigenomic information directs gene expression programs through sequence-specific transcription factors (TFs). Extensive research has settled on three general classes of TF targets in metazoans: promoter accessibility via chromatin regulation (e.g., SAGA), assembly of the general transcription factors on promoter DNA (e.g., TFIID), and recruitment of RNA polymerase (Pol) II (e.g., Mediator) to establish a transcription pre-initiation complex (PIC). Here we discuss TFs and their targets. We also place this in the context of our current work with Saccharomyces (yeast), where we find that promoters typically lack an architecture that supports TF function. Moreover, yeast promoters that support TF binding also display interactions with cofactors like SAGA and Mediator, but not TFIID. It is unknown to what extent all genes in metazoans require TFs and their cofactors.
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