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Shelansky R, Abrahamsson S, Brown CR, Doody M, Lenstra TL, Larson DR, Boeger H. Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription. Nat Commun 2024; 15:6226. [PMID: 39043639 PMCID: PMC11266658 DOI: 10.1038/s41467-024-50419-5] [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: 08/22/2023] [Accepted: 07/04/2024] [Indexed: 07/25/2024] Open
Abstract
Fluctuations in the initiation rate of transcription, the first step in gene expression, ensue from the stochastic behavior of the molecular process that controls transcription. In steady state, the regulatory process is often assumed to operate reversibly, i.e., in equilibrium. However, reversibility imposes fundamental limits to information processing. For instance, the assumption of equilibrium is difficult to square with the precision with which the regulatory process executes its task in eukaryotes. Here we provide evidence - from microscopic analyses of the transcription dynamics at a single gene copy of yeast - that the regulatory process for transcription is cyclic and irreversible (out of equilibrium). The necessary coupling to reservoirs of free energy occurs via sequence-specific transcriptional activators and the recruitment, in part, of ATP-dependent chromatin remodelers. Our findings may help explain how eukaryotic cells reconcile the dual but opposing requirements for fast regulatory kinetics and high regulatory specificity.
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Affiliation(s)
- Robert Shelansky
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Sara Abrahamsson
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, CA, USA
| | - Christopher R Brown
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
- Korro Bio, Cambridge, MA, USA
| | - Michael Doody
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam, The Netherlands
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hinrich Boeger
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
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Asthana A, Ramanan P, Hirschi A, Guiley KZ, Wijeratne TU, Shelansky R, Doody MJ, Narasimhan H, Boeger H, Tripathi S, Müller GA, Rubin SM. The MuvB complex binds and stabilizes nucleosomes downstream of the transcription start site of cell-cycle dependent genes. Nat Commun 2022; 13:526. [PMID: 35082292 PMCID: PMC8792015 DOI: 10.1038/s41467-022-28094-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/10/2022] [Indexed: 11/25/2022] Open
Abstract
The chromatin architecture in promoters is thought to regulate gene expression, but it remains uncertain how most transcription factors (TFs) impact nucleosome position. The MuvB TF complex regulates cell-cycle dependent gene-expression and is critical for differentiation and proliferation during development and cancer. MuvB can both positively and negatively regulate expression, but the structure of MuvB and its biochemical function are poorly understood. Here we determine the overall architecture of MuvB assembly and the crystal structure of a subcomplex critical for MuvB function in gene repression. We find that the MuvB subunits LIN9 and LIN37 function as scaffolding proteins that arrange the other subunits LIN52, LIN54 and RBAP48 for TF, DNA, and histone binding, respectively. Biochemical and structural data demonstrate that MuvB binds nucleosomes through an interface that is distinct from LIN54-DNA consensus site recognition and that MuvB increases nucleosome occupancy in a reconstituted promoter. We find in arrested cells that MuvB primarily associates with a tightly positioned +1 nucleosome near the transcription start site (TSS) of MuvB-regulated genes. These results support a model that MuvB binds and stabilizes nucleosomes just downstream of the TSS on its target promoters to repress gene expression. The MuvB protein complex regulates genes that are differentially expressed through the cell cycle, yet its precise molecular function has remained unclear. Here the authors reveal MuvB associates with the nucleosome adjacent to the transcription start site of cell-cycle genes and that the tight positioning of this nucleosome correlates with MuvB-dependent gene repression.
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Affiliation(s)
- Anushweta Asthana
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Parameshwaran Ramanan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Alexander Hirschi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Keelan Z Guiley
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Tilini U Wijeratne
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Robert Shelansky
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Michael J Doody
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Haritha Narasimhan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
| | - Gerd A Müller
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA.
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3
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Merkl PE, Schächner C, Pilsl M, Schwank K, Hergert K, Längst G, Milkereit P, Griesenbeck J, Tschochner H. Analysis of Yeast RNAP I Transcription of Nucleosomal Templates In Vitro. Methods Mol Biol 2022; 2533:39-59. [PMID: 35796981 PMCID: PMC9761914 DOI: 10.1007/978-1-0716-2501-9_3] [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: 06/15/2023]
Abstract
Nuclear eukaryotic RNA polymerases (RNAPs) transcribe a chromatin template in vivo. Since the basic unit of chromatin, the nucleosome, renders the DNA largely inaccessible, RNAPs have to overcome the nucleosomal barrier for efficient RNA synthesis. Gaining mechanistical insights in the transcription of chromatin templates will be essential to understand the complex process of eukaryotic gene expression. In this article we describe the use of defined in vitro transcription systems for comparative analysis of highly purified RNAPs I-III from S. cerevisiae (hereafter called yeast) transcribing in vitro reconstituted nucleosomal templates. We also provide a protocol to study promoter-dependent RNAP I transcription of purified native 35S ribosomal RNA (rRNA) gene chromatin.
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Affiliation(s)
- Philipp E Merkl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
- TUM ForTe, Technische Universität München, Munich, Germany
| | - Christopher Schächner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Michael Pilsl
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Katrin Schwank
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Kristin Hergert
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Gernot Längst
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
| | - Philipp Milkereit
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Joachim Griesenbeck
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany.
| | - Herbert Tschochner
- Universität Regensburg, Regensburg Center for Biochemistry (RCB), Lehrstuhl Biochemie III, Regensburg, Germany
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Kubik S, Bruzzone MJ, Shore D. Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler. Bioessays 2017; 39. [PMID: 28345796 DOI: 10.1002/bies.201600237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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Fei J, Torigoe SE, Brown CR, Khuong MT, Kassavetis GA, Boeger H, Kadonaga JT. The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev 2016; 29:2563-75. [PMID: 26680301 PMCID: PMC4699385 DOI: 10.1101/gad.272633.115] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fei et al. show that the prenucleosome is a stable alternate conformational isomer of the nucleosome. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. Chromatin comprises nucleosomes as well as nonnucleosomal histone–DNA particles. Prenucleosomes are rapidly formed histone–DNA particles that can be converted into canonical nucleosomes by a motor protein such as ACF. Here we show that the prenucleosome is a stable conformational isomer of the nucleosome. It consists of a histone octamer associated with ∼80 base pair (bp) of DNA, which is located at a position that corresponds to the central 80 bp of a nucleosome core particle. Monomeric prenucleosomes with free flanking DNA do not spontaneously fold into nucleosomes but can be converted into canonical nucleosomes by an ATP-driven motor protein such as ACF or Chd1. In addition, histone H3K56, which is located at the DNA entry and exit points of a canonical nucleosome, is specifically acetylated by p300 in prenucleosomes relative to nucleosomes. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. These findings suggest that the prenucleosome, the only known stable conformational isomer of the nucleosome, is related to nonnucleosomal histone–DNA species in the cell.
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Affiliation(s)
- Jia Fei
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Sharon E Torigoe
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Christopher R Brown
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Mai T Khuong
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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