1
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Tian X, Volkovinskiy A, Marchisio MA. RNAi-based Boolean gates in the yeast Saccharomyces cerevisiae. Front Bioeng Biotechnol 2024; 12:1392967. [PMID: 38895554 PMCID: PMC11184144 DOI: 10.3389/fbioe.2024.1392967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/06/2024] [Indexed: 06/21/2024] Open
Abstract
Boolean gates, the fundamental components of digital circuits, have been widely investigated in synthetic biology because they permit the fabrication of biosensors and facilitate biocomputing. This study was conducted to design and construct Boolean gates in the yeast Saccharomyces cerevisiae, the main component of which was the RNA interference pathway (RNAi) that is naturally absent from the budding yeast cells. We tested different expression cassettes for the siRNA precursor (a giant hairpin sequence, a DNA fragment-flanked by one or two introns-between convergent promoters or transcribed separately in the sense and antisense directions) and placed different components under the control of the circuit inputs (i.e., the siRNA precursor or proteins such as the Dicer and the Argonaute). We found that RNAi-based logic gates are highly sensitive to promoter leakage and, for this reason, challenging to implement in vivo. Convergent-promoter architecture turned out to be the most reliable solution, even though the overall best performance was achieved with the most difficult design based on the siRNA precursor as a giant hairpin.
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Affiliation(s)
- Ximing Tian
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Andrey Volkovinskiy
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
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2
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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3
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Robert F, Jeronimo C. Transcription-coupled nucleosome assembly. Trends Biochem Sci 2023; 48:978-992. [PMID: 37657993 DOI: 10.1016/j.tibs.2023.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.
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Affiliation(s)
- François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
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4
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Miller CLW, Warner JL, Winston F. Insights into Spt6: a histone chaperone that functions in transcription, DNA replication, and genome stability. Trends Genet 2023; 39:858-872. [PMID: 37481442 PMCID: PMC10592469 DOI: 10.1016/j.tig.2023.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/24/2023]
Abstract
Transcription elongation requires elaborate coordination between the transcriptional machinery and chromatin regulatory factors to successfully produce RNA while preserving the epigenetic landscape. Recent structural and genomic studies have highlighted that suppressor of Ty 6 (Spt6), a conserved histone chaperone and transcription elongation factor, sits at the crux of the transcription elongation process. Other recent studies have revealed that Spt6 also promotes DNA replication and genome integrity. Here, we review recent studies of Spt6 that have provided new insights into the mechanisms by which Spt6 controls transcription and have revealed the breadth of Spt6 functions in eukaryotic cells.
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Affiliation(s)
- Catherine L W Miller
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Genome Maintenance, Rockefeller University, New York, NY 10065, USA
| | - James L Warner
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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5
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Jonas F, Vidavski M, Benuck E, Barkai N, Yaakov G. Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding. Nucleic Acids Res 2023; 51:8496-8513. [PMID: 37493599 PMCID: PMC10484674 DOI: 10.1093/nar/gkad615] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/07/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
DNA packaging within chromatin depends on histone chaperones and remodelers that form and position nucleosomes. Cells express multiple such chromatin regulators with overlapping in-vitro activities. Defining specific in-vivo activities requires monitoring histone dynamics during regulator depletion, which has been technically challenging. We have recently generated histone-exchange sensors in Saccharomyces cerevisiae, which we now use to define the contributions of 15 regulators to histone dynamics genome-wide. While replication-independent exchange in unperturbed cells maps to promoters, regulator depletions primarily affected gene bodies. Depletion of Spt6, Spt16 or Chd1 sharply increased nucleosome replacement sequentially at the beginning, middle or end of highly expressed gene bodies. They further triggered re-localization of chaperones to affected gene body regions, which compensated for nucleosome loss during transcription complex passage, but concurred with extensive TF binding in gene bodies. We provide a unified quantitative screen highlighting regulator roles in retaining nucleosome binding during transcription and preserving genomic packaging.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Matan Vidavski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eli Benuck
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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6
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Miller CLW, Winston F. The conserved histone chaperone Spt6 is strongly required for DNA replication and genome stability. Cell Rep 2023; 42:112264. [PMID: 36924499 PMCID: PMC10106089 DOI: 10.1016/j.celrep.2023.112264] [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: 05/06/2022] [Revised: 12/31/2022] [Accepted: 02/27/2023] [Indexed: 03/17/2023] Open
Abstract
Histone chaperones are an important class of proteins that regulate chromatin accessibility for DNA-templated processes. Spt6 is a conserved histone chaperone and key regulator of transcription and chromatin structure. However, its functions outside of these roles have been little explored. In this work, we demonstrate a requirement for S. cerevisiae Spt6 in DNA replication and, more broadly, as a regulator of genome stability. Depletion or mutation of Spt6 impairs DNA replication in vivo. Additionally, spt6 mutants are sensitive to DNA replication stress-inducing agents. Interestingly, this sensitivity is independent of the association of Spt6 with RNA polymerase II (RNAPII), suggesting that spt6 mutants have a transcription-independent impairment of DNA replication. Specifically, genomic studies reveal that spt6 mutants have decreased loading of the MCM replicative helicase at replication origins, suggesting that Spt6 promotes origin licensing. Our results identify Spt6 as a regulator of genome stability, at least in part through a role in DNA replication.
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Affiliation(s)
- Catherine L W Miller
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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7
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Rao Y, Yang J, Wang J, Yang X, Zhang M, Zhan Y, Ma X, Cai D, Wang Z, Chen S. Minimization and optimization of α-amylase terminator for heterologous protein production in Bacillus licheniformis. BIORESOUR BIOPROCESS 2022; 9:108. [PMID: 38647575 PMCID: PMC10992175 DOI: 10.1186/s40643-022-00597-1] [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: 07/26/2022] [Accepted: 09/28/2022] [Indexed: 11/10/2022] Open
Abstract
Terminators serve as the regulatory role in gene transcription termination; however, few researches about terminator optimization have been conducted, which leads to the lack of available and universal terminator for gene expression regulation in Bacillus. To solve this problem and expand synthetic biology toolbox of Bacillus licheniformis, the terminator T1 of endogenous α-amylase gene (amyL) was characterized in this research, with a termination efficiency of 87.81%. Then, we explored and optimized the termination strength of terminator T1 from four aspects: the distance between stop codon and terminator, GC content at the bottom of stem structure, loop size, and U-tract length, and the best terminator T24 was attained by combination optimization strategy, which termination efficiency was increased to 97.97%, better than the commonly used terminator T7 (T7P) from Escherichia coli. Finally, terminator T24 was applied to protein expression, which, respectively, led to 33.00%, 25.93%, and 11.78% increases of green fluorescence intensity, red fluorescence intensity, and keratinase activity, indicating its universality in protein expression. Taken together, this research not only expands a plug-and-play synthetic biology toolbox in B. licheniformis but also provides a reference for the artificial design of versatile intrinsic terminator.
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Affiliation(s)
- Yi Rao
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Jingyao Yang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Jiaqi Wang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Xinyuan Yang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Mengxi Zhang
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Yangyang Zhan
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Xin Ma
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Dongbo Cai
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China
| | - Zhangqian Wang
- Hubei Engineering Research Center for Deep Processing of Green Se-Rich Agricultural Products, School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-Rich Agricultural Products Processing, Wuhan Polytechnic University, Wuhan, 430023, People's Republic of China.
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme EngineeringEnvironmental Microbial Technology Center of Hubei ProvinceCollege of Life Sciences, Hubei University, 368 Youyi Avenue, Wuchang District, Wuhan, 430062, Hubei, People's Republic of China.
- Fujian Provincial Key Laboratory of Eco-Industrial Green Technology, College of Ecological and Resource Engineering, Wuyi University, Nanping, 354300, Wuyishan, People's Republic of China.
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8
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Jeronimo C, Robert F. The histone chaperone FACT: a guardian of chromatin structure integrity. Transcription 2022; 13:16-38. [PMID: 35485711 PMCID: PMC9467567 DOI: 10.1080/21541264.2022.2069995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specificregulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancerstrategy.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada.,Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada.,Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
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9
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Gopalakrishnan R, Winston F. The histone chaperone Spt6 is required for normal recruitment of the capping enzyme Abd1 to transcribed regions. J Biol Chem 2021; 297:101205. [PMID: 34543624 PMCID: PMC8511950 DOI: 10.1016/j.jbc.2021.101205] [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: 05/13/2021] [Revised: 08/20/2021] [Accepted: 09/15/2021] [Indexed: 10/29/2022] Open
Abstract
The histone chaperone Spt6 is involved in promoting elongation of RNA polymerase II (RNAPII), maintaining chromatin structure, regulating cotranscriptional histone modifications, and controlling mRNA processing. These diverse functions of Spt6 are partly mediated through its interactions with RNAPII and other factors in the transcription elongation complex. In this study, we used mass spectrometry to characterize the differences in RNAPII-interacting factors between wildtype cells and those depleted for Spt6, leading to the identification of proteins that depend on Spt6 for their interaction with RNAPII. The altered association of some of these factors could be attributed to changes in steady-state protein levels. However, Abd1, the mRNA cap methyltransferase, had decreased association with RNAPII after Spt6 depletion despite unchanged Abd1 protein levels, showing a requirement for Spt6 in mediating the Abd1-RNAPII interaction. Genome-wide studies showed that Spt6 is required for maintaining the level of Abd1 over transcribed regions, as well as the level of Spt5, another protein known to recruit Abd1 to chromatin. Abd1 levels were particularly decreased at the 5' ends of genes after Spt6 depletion, suggesting a greater need for Spt6 in Abd1 recruitment over these regions. Together, our results show that Spt6 is important in regulating the composition of the transcription elongation complex and reveal a previously unknown function for Spt6 in the recruitment of Abd1.
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Affiliation(s)
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.
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10
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Li J, Singh U, Arendsee Z, Wurtele ES. Landscape of the Dark Transcriptome Revealed Through Re-mining Massive RNA-Seq Data. Front Genet 2021; 12:722981. [PMID: 34484307 PMCID: PMC8415361 DOI: 10.3389/fgene.2021.722981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022] Open
Abstract
The "dark transcriptome" can be considered the multitude of sequences that are transcribed but not annotated as genes. We evaluated expression of 6,692 annotated genes and 29,354 unannotated open reading frames (ORFs) in the Saccharomyces cerevisiae genome across diverse environmental, genetic and developmental conditions (3,457 RNA-Seq samples). Over 30% of the highly transcribed ORFs have translation evidence. Phylostratigraphic analysis infers most of these transcribed ORFs would encode species-specific proteins ("orphan-ORFs"); hundreds have mean expression comparable to annotated genes. These data reveal unannotated ORFs most likely to be protein-coding genes. We partitioned a co-expression matrix by Markov Chain Clustering; the resultant clusters contain 2,468 orphan-ORFs. We provide the aggregated RNA-Seq yeast data with extensive metadata as a project in MetaOmGraph (MOG), a tool designed for interactive analysis and visualization. This approach enables reuse of public RNA-Seq data for exploratory discovery, providing a rich context for experimentalists to make novel, experimentally testable hypotheses about candidate genes.
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Affiliation(s)
- Jing Li
- Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
| | - Urminder Singh
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
| | - Zebulun Arendsee
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
| | - Eve Syrkin Wurtele
- Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, United States
- Center for Metabolic Biology, Iowa State University, Ames, IA, United States
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States
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11
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Narain A, Bhandare P, Adhikari B, Backes S, Eilers M, Dölken L, Schlosser A, Erhard F, Baluapuri A, Wolf E. Targeted protein degradation reveals a direct role of SPT6 in RNAPII elongation and termination. Mol Cell 2021; 81:3110-3127.e14. [PMID: 34233157 PMCID: PMC8354102 DOI: 10.1016/j.molcel.2021.06.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/24/2021] [Accepted: 06/11/2021] [Indexed: 01/22/2023]
Abstract
SPT6 is a histone chaperone that tightly binds RNA polymerase II (RNAPII) during transcription elongation. However, its primary role in transcription is uncertain. We used targeted protein degradation to rapidly deplete SPT6 in human cells and analyzed defects in RNAPII behavior by a multi-omics approach and mathematical modeling. Our data indicate that SPT6 is a crucial factor for RNAPII processivity and is therefore required for the productive transcription of protein-coding genes. Unexpectedly, SPT6 also has a vital role in RNAPII termination, as acute depletion induced readthrough transcription for thousands of genes. Long-term depletion of SPT6 induced cryptic intragenic transcription, as observed earlier in yeast. However, this phenotype was not observed upon acute SPT6 depletion and therefore can be attributed to accumulated epigenetic perturbations in the prolonged absence of SPT6. In conclusion, targeted degradation of SPT6 allowed the temporal discrimination of its function as an epigenetic safeguard and RNAPII elongation factor. Auxin-inducible degradation discriminates direct roles of human SPT6 in transcription Acute loss of SPT6 globally impairs RNAPII processivity and speed SPT6 is required for efficient transcription termination on protein-coding genes Long-term loss of SPT6 ultimately results in cryptic intragenic transcription
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Affiliation(s)
- Ashwin Narain
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Bikash Adhikari
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Simone Backes
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Lars Dölken
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Straße 2, 97080 Würzburg, Germany
| | - Florian Erhard
- Computational Systems Virology and Bioinformatics, Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany.
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; Mildred Scheel Early Career Center, University of Würzburg, Beethovenstraße 1A, 97080 Würzburg, Germany.
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12
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Gordon MR, Zhu J, Qu V, Li R. A case of convergent-gene interference in the budding yeast knockout library causing chromosome instability. G3 (BETHESDA, MD.) 2021; 11:jkab084. [PMID: 33724427 PMCID: PMC8104933 DOI: 10.1093/g3journal/jkab084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 12/07/2020] [Indexed: 11/12/2022]
Abstract
To maintain genome stability, organisms depend on faithful chromosome segregation, a process affected by diverse genetic pathways, some of which are not directly linked to mitosis. In this study, we set out to explore one such pathway represented by an undercharacterized gene, SNO1, identified previously in screens of the yeast knockout (YKO) library for mitotic fidelity genes. We found that the causative factor increasing mitotic error rate in the sno1Δ mutant is not loss of the Sno1 protein, but rather perturbation to the mRNA of the neighboring convergent gene, CTF13, encoding an essential component for forming the yeast kinetochore. This is caused by a combination of the Kanamycin resistance gene and the transcriptional terminator used in the YKO library affecting the CTF13 mRNA level and quality . We further provide a list of gene pairs potentially subjected to this artifact, which may be useful for accurate phenotypic interpretation of YKO mutants.
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Affiliation(s)
- Molly R Gordon
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jin Zhu
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Victoria Qu
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rong Li
- Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore 117411, Singapore
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13
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Viktorovskaya O, Chuang J, Jain D, Reim NI, López-Rivera F, Murawska M, Spatt D, Churchman LS, Park PJ, Winston F. Essential histone chaperones collaborate to regulate transcription and chromatin integrity. Genes Dev 2021; 35:698-712. [PMID: 33888559 PMCID: PMC8091981 DOI: 10.1101/gad.348431.121] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/30/2021] [Indexed: 12/15/2022]
Abstract
Histone chaperones are critical for controlling chromatin integrity during transcription, DNA replication, and DNA repair. Three conserved and essential chaperones, Spt6, Spn1/Iws1, and FACT, associate with elongating RNA polymerase II and interact with each other physically and/or functionally; however, there is little understanding of their individual functions or their relationships with each other. In this study, we selected for suppressors of a temperature-sensitive spt6 mutation that disrupts the Spt6-Spn1 physical interaction and that also causes both transcription and chromatin defects. This selection identified novel mutations in FACT. Surprisingly, suppression by FACT did not restore the Spt6-Spn1 interaction, based on coimmunoprecipitation, ChIP, and mass spectrometry experiments. Furthermore, suppression by FACT bypassed the complete loss of Spn1. Interestingly, the FACT suppressor mutations cluster along the FACT-nucleosome interface, suggesting that they alter FACT-nucleosome interactions. In agreement with this observation, we showed that the spt6 mutation that disrupts the Spt6-Spn1 interaction caused an elevated level of FACT association with chromatin, while the FACT suppressors reduced the level of FACT-chromatin association, thereby restoring a normal Spt6-FACT balance on chromatin. Taken together, these studies reveal previously unknown regulation between histone chaperones that is critical for their essential in vivo functions.
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Affiliation(s)
- Olga Viktorovskaya
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James Chuang
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Natalia I Reim
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Francheska López-Rivera
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Magdalena Murawska
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dan Spatt
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fred Winston
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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14
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Formosa T, Winston F. The role of FACT in managing chromatin: disruption, assembly, or repair? Nucleic Acids Res 2020; 48:11929-11941. [PMID: 33104782 PMCID: PMC7708052 DOI: 10.1093/nar/gkaa912] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription) has long been considered to be a transcription elongation factor whose ability to destabilize nucleosomes promotes RNAPII progression on chromatin templates. However, this is just one function of this histone chaperone, as FACT also functions in DNA replication. While broadly conserved among eukaryotes and essential for viability in many organisms, dependence on FACT varies widely, with some differentiated cells proliferating normally in its absence. It is therefore unclear what the core functions of FACT are, whether they differ in different circumstances, and what makes FACT essential in some situations but not others. Here, we review recent advances and propose a unifying model for FACT activity. By analogy to DNA repair, we propose that the ability of FACT to both destabilize and assemble nucleosomes allows it to monitor and restore nucleosome integrity as part of a system of chromatin repair, in which disruptions in the packaging of DNA are sensed and returned to their normal state. The requirement for FACT then depends on the level of chromatin disruption occurring in the cell, and the cell's ability to tolerate packaging defects. The role of FACT in transcription would then be just one facet of a broader system for maintaining chromatin integrity.
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Affiliation(s)
- Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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15
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Reim NI, Chuang J, Jain D, Alver BH, Park PJ, Winston F. The conserved elongation factor Spn1 is required for normal transcription, histone modifications, and splicing in Saccharomyces cerevisiae. Nucleic Acids Res 2020; 48:10241-10258. [PMID: 32941642 PMCID: PMC7544207 DOI: 10.1093/nar/gkaa745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022] Open
Abstract
Spn1/Iws1 is a conserved protein involved in transcription and chromatin dynamics, yet its general in vivo requirement for these functions is unknown. Using a Spn1 depletion system in Saccharomyces cerevisiae, we demonstrate that Spn1 broadly influences several aspects of gene expression on a genome-wide scale. We show that Spn1 is globally required for normal mRNA levels and for normal splicing of ribosomal protein transcripts. Furthermore, Spn1 maintains the localization of H3K36 and H3K4 methylation across the genome and is required for normal histone levels at highly expressed genes. Finally, we show that the association of Spn1 with the transcription machinery is strongly dependent on its binding partner, Spt6, while the association of Spt6 and Set2 with transcribed regions is partially dependent on Spn1. Taken together, our results show that Spn1 affects multiple aspects of gene expression and provide additional evidence that it functions as a histone chaperone in vivo.
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Affiliation(s)
- Natalia I Reim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Dhawal Jain
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Burak H Alver
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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16
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Babaei M, Borja Zamfir GM, Chen X, Christensen HB, Kristensen M, Nielsen J, Borodina I. Metabolic Engineering of Saccharomyces cerevisiae for Rosmarinic Acid Production. ACS Synth Biol 2020; 9:1978-1988. [PMID: 32589831 PMCID: PMC8961883 DOI: 10.1021/acssynbio.0c00048] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Indexed: 02/08/2023]
Abstract
Rosmarinic acid is a hydroxycinnamic acid ester commonly found in the Boraginaceae and Lamiaceae plant families. It exhibits various biological activities, including antioxidant, anti-inflammatory, antibacterial, antiallergic, and antiviral properties. Rosmarinic acid is used as a food and cosmetic ingredient, and several pharmaceutical applications have been suggested as well. Rosmarinic acid is currently produced by extraction from plants or chemical synthesis; however, due to limited availability of the plant sources and the complexity of the chemical synthesis method, there is an increasing interest in producing this compound by microbial fermentation. In this study, we aimed to produce rosmarinic acid by engineered baker's yeast Saccharomyces cerevisiae. Multiple biosynthetic pathway variants, carrying only plant genes or a combination of plant and Escherichia coli genes, were implemented using a full factorial design of experiment. Through analysis of variances, the effect of each enzyme variant (factors), together with possible interactions between these factors, was assessed. The best pathway variant produced 2.95 ± 0.08 mg/L rosmarinic acid in mineral medium with glucose as the sole carbon source. Increasing the copy number of rosmarinic acid biosynthetic genes increased the titer to 5.93 ± 0.06 mg/L. The study shows the feasibility of producing rosmarinic acid by yeast fermentation.
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Affiliation(s)
- Mahsa Babaei
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Gheorghe M. Borja Zamfir
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Xiao Chen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Hanne Bjerre Christensen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Mette Kristensen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
| | - Jens Nielsen
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
- Department
of Biology and Biological Engineering, Chalmers
University of Technology, 412 96, Gothenburg, Sweden
- BioInnovation
Institute, Ole Måløes
Vej 3, 2200, Copenhagen
N, Denmark
| | - Irina Borodina
- The
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220, DK-2800 Kgs. Lyngby, Denmark
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17
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Jeronimo C, Poitras C, Robert F. Histone Recycling by FACT and Spt6 during Transcription Prevents the Scrambling of Histone Modifications. Cell Rep 2020; 28:1206-1218.e8. [PMID: 31365865 DOI: 10.1016/j.celrep.2019.06.097] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/28/2019] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
Genomic DNA is framed by additional layers of information, referred to as the epigenome. Epigenomic marks such as DNA methylation, histone modifications, and histone variants are concentrated on specific genomic sites, where they can both instruct and reflect gene expression. How this information is maintained, notably in the face of transcription, is not completely understood. Specifically, the extent to which modified histones themselves are retained through RNA polymerase II passage is unclear. Here, we show that several histone modifications are mislocalized when the transcription-coupled histone chaperones FACT or Spt6 are disrupted in Saccharomyces cerevisiae. In the absence of functional FACT or Spt6, transcription generates nucleosome loss, which is partially compensated for by the increased activity of non-transcription-coupled histone chaperones. The random incorporation of transcription-evicted modified histones scrambles epigenomic information. Our work highlights the importance of local recycling of modified histones by FACT and Spt6 during transcription in the maintenance of the epigenomic landscape.
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Affiliation(s)
- Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Christian Poitras
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC, Canada.
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18
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Genetic circuit design automation for yeast. Nat Microbiol 2020; 5:1349-1360. [DOI: 10.1038/s41564-020-0757-2] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/17/2020] [Indexed: 11/08/2022]
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19
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Transcriptional control of gene expression in Pichia pastoris by manipulation of terminators. Appl Microbiol Biotechnol 2020; 104:7841-7851. [DOI: 10.1007/s00253-020-10785-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/03/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022]
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20
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Dronamraju R, Kerschner JL, Peck SA, Hepperla AJ, Adams AT, Hughes KD, Aslam S, Yoblinski AR, Davis IJ, Mosley AL, Strahl BD. Casein Kinase II Phosphorylation of Spt6 Enforces Transcriptional Fidelity by Maintaining Spn1-Spt6 Interaction. Cell Rep 2019; 25:3476-3489.e5. [PMID: 30566871 PMCID: PMC6347388 DOI: 10.1016/j.celrep.2018.11.089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 10/22/2018] [Accepted: 11/21/2018] [Indexed: 02/07/2023] Open
Abstract
Spt6 is a histone chaperone that associates with RNA polymerase II and deposits nucleosomes in the wake of transcription. Although Spt6 has an essential function in nucleosome deposition, it is not known whether this function is influenced by post-translational modification. Here, we report that casein kinase II (CKII) phosphorylation of Spt6 is required for nucleosome occupancy at the 5′ ends of genes to prevent aberrant antisense transcription and enforce transcriptional directionality. Mechanistically, we show that CKII phosphorylation of Spt6 promotes the interaction of Spt6 with Spn1, a binding partner required for chromatin reassembly and full recruitment of Spt6 to genes. Our study defines a function for CKII phosphorylation in transcription and highlights the importance of post-translational modification in histone chaperone function. Dronamraju et al. show that the N terminus of Spt6 is phosphorylated by casein kinase II, which is required for proper Spt6-Spn1 interaction. CKII phosphorylation of Spt6 is pivotal to maintain nucleosome occupancy at the 5′ ends of genes, suppression of antisense transcription from the 5′ ends, and resistance to genotoxic agents.
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Affiliation(s)
- Raghuvar Dronamraju
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jenny L Kerschner
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Austin J Hepperla
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexander T Adams
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sadia Aslam
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Andrew R Yoblinski
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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21
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Gopalakrishnan R, Marr SK, Kingston RE, Winston F. A conserved genetic interaction between Spt6 and Set2 regulates H3K36 methylation. Nucleic Acids Res 2019; 47:3888-3903. [PMID: 30793188 PMCID: PMC6486648 DOI: 10.1093/nar/gkz119] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/05/2019] [Accepted: 02/13/2019] [Indexed: 12/28/2022] Open
Abstract
The transcription elongation factor Spt6 and the H3K36 methyltransferase Set2 are both required for H3K36 methylation and transcriptional fidelity in Saccharomyces cerevisiae. However, the nature of the requirement for Spt6 has remained elusive. By selecting for suppressors of a transcriptional defect in an spt6 mutant, we have isolated several highly clustered, dominant SET2 mutations (SET2sup mutations) in a region encoding a proposed autoinhibitory domain. SET2sup mutations suppress the H3K36 methylation defect in the spt6 mutant, as well as in other mutants that impair H3K36 methylation. We also show that SET2sup mutations overcome the requirement for certain Set2 domains for H3K36 methylation. In vivo, SET2sup mutants have elevated levels of H3K36 methylation and the purified Set2sup mutant protein has greater enzymatic activityin vitro. ChIP-seq studies demonstrate that the H3K36 methylation defect in the spt6 mutant, as well as its suppression by a SET2sup mutation, occurs at a step following the recruitment of Set2 to chromatin. Other experiments show that a similar genetic relationship between Spt6 and Set2 exists in Schizosaccharomyces pombe. Taken together, our results suggest a conserved mechanism by which the Set2 autoinhibitory domain requires multiple Set2 interactions to ensure that H3K36 methylation occurs specifically on actively transcribed chromatin.
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Affiliation(s)
| | - Sharon K Marr
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert E Kingston
- Department of Genetics, Harvard Medical School, Boston, MA, USA 02115.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA, USA 02115
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22
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Uchida N, Hsieh MM, Raines L, Haro-Mora JJ, Demirci S, Bonifacino AC, Krouse AE, Metzger ME, Donahue RE, Tisdale JF. Development of a forward-oriented therapeutic lentiviral vector for hemoglobin disorders. Nat Commun 2019; 10:4479. [PMID: 31578323 PMCID: PMC6775231 DOI: 10.1038/s41467-019-12456-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 09/11/2019] [Indexed: 02/06/2023] Open
Abstract
Hematopoietic stem cell (HSC) gene therapy is being evaluated for hemoglobin disorders including sickle cell disease (SCD). Therapeutic globin vectors have demanding requirements including high-efficiency transduction at the HSC level and high-level, erythroid-specific expression with long-term persistence. The requirement of intron 2 for high-level β-globin expression dictates a reverse-oriented globin-expression cassette to prevent its loss from RNA splicing. Current reverse-oriented globin vectors can drive phenotypic correction, but they are limited by low vector titers and low transduction efficiencies. Here we report a clinically relevant forward-oriented β-globin-expressing vector, which has sixfold higher vector titers and four to tenfold higher transduction efficiency for long-term hematopoietic repopulating cells in humanized mice and rhesus macaques. Insertion of Rev response element (RRE) allows intron 2 to be retained, and β-globin production is observed in transplanted macaques and human SCD CD34+ cells. These findings bring us closer to a widely applicable gene therapy for hemoglobin disorders.
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Affiliation(s)
- Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA.
- Cellular and Molecular Therapeutics Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA.
| | - Matthew M Hsieh
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Cellular and Molecular Therapeutics Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Lydia Raines
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Cellular and Molecular Therapeutics Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Juan J Haro-Mora
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Cellular and Molecular Therapeutics Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Cellular and Molecular Therapeutics Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Aylin C Bonifacino
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Allen E Krouse
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Mark E Metzger
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Robert E Donahue
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Cellular and Molecular Therapeutics Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, Maryland, USA
- Cellular and Molecular Therapeutics Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
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23
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Soudet J, Stutz F. Regulation of Gene Expression and Replication Initiation by Non‐Coding Transcription: A Model Based on Reshaping Nucleosome‐Depleted Regions. Bioessays 2019; 41:e1900043. [DOI: 10.1002/bies.201900043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/19/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Julien Soudet
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
| | - Françoise Stutz
- Department of Cell BiologyUniversity of Geneva 1211 Geneva Switzerland
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24
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Gouot E, Bhat W, Rufiange A, Fournier E, Paquet E, Nourani A. Casein kinase 2 mediated phosphorylation of Spt6 modulates histone dynamics and regulates spurious transcription. Nucleic Acids Res 2019; 46:7612-7630. [PMID: 29905868 PMCID: PMC6125631 DOI: 10.1093/nar/gky515] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022] Open
Abstract
CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. Interestingly, strand-specific RNA-seq analyses show that CK2 inhibits global cryptic promoters driving both sense and antisense transcription. This further indicates a role of CK2 in the modulation of chromatin during transcription. Next, we showed that CK2 interacts with the major histone chaperone Spt6, and phosphorylates it in vivo and in vitro. CK2 phosphorylation of Spt6 is required for its cellular levels, for the suppression of histone H3 turnover and for the inhibition of spurious transcription. Finally, we showed that CK2 and Spt6 phosphorylation sites are important to various transcriptional responses suggesting that cryptic intragenic and antisense transcript production are associated with a defective adaptation to environmental cues. Altogether, our data indicate that CK2 mediated phosphorylation of Spt6 regulates chromatin dynamics associated with transcription, and prevents aberrant transcription.
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Affiliation(s)
- Emmanuelle Gouot
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
| | - Wajid Bhat
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
| | - Anne Rufiange
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
| | - Eric Fournier
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada.,CHU de Quebec Research Center - Laval University, Endocrinology and Nephrology CHUL, Québec, Québec, Canada
| | - Eric Paquet
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada.,CHU de Quebec Research Center - Laval University, Endocrinology and Nephrology CHUL, Québec, Québec, Canada.,The Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amine Nourani
- Laval University Cancer Research Center, St-Patrick Research Group in Basic Oncology, Québec, Québec, Canada
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25
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Scandaglia M, Barco A. Contribution of spurious transcription to intellectual disability disorders. J Med Genet 2019; 56:491-498. [PMID: 30745423 DOI: 10.1136/jmedgenet-2018-105668] [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: 08/07/2018] [Revised: 12/17/2018] [Accepted: 01/18/2019] [Indexed: 12/31/2022]
Abstract
During the development of multicellular organisms, chromatin-modifying enzymes orchestrate the establishment of gene expression programmes that characterise each differentiated cell type. These enzymes also contribute to the maintenance of cell type-specific transcription profiles throughout life. But what happens when epigenomic regulation goes awry? Genomic screens in experimental models of intellectual disability disorders (IDDs) caused by mutations in epigenetic machinery-encoding genes have shown that transcriptional dysregulation constitutes a hallmark of these conditions. Here, we underscore the connections between a subset of chromatin-linked IDDs and spurious transcription in brain cells. We also propose that aberrant gene expression in neurons, including both the ectopic transcription of non-neuronal genes and the activation of cryptic promoters, may importantly contribute to the pathoaetiology of these disorders.
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Affiliation(s)
- Marilyn Scandaglia
- Molecular Neurobiology and Neuropathology Unit, Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante, Alicante, Spain
| | - Angel Barco
- Molecular Neurobiology and Neuropathology Unit, Instituto de Neurociencias (UMH-CSIC), San Juan de Alicante, Alicante, Spain
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26
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Soudet J, Gill JK, Stutz F. Noncoding transcription influences the replication initiation program through chromatin regulation. Genome Res 2018; 28:1882-1893. [PMID: 30401734 PMCID: PMC6280764 DOI: 10.1101/gr.239582.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023]
Abstract
In eukaryotic organisms, replication initiation follows a temporal program. Among the parameters that regulate this program in Saccharomyces cerevisiae, chromatin structure has been at the center of attention without considering the contribution of transcription. Here, we revisit the replication initiation program in the light of widespread genomic noncoding transcription. We find that noncoding RNA transcription termination in the vicinity of autonomously replicating sequences (ARSs) shields replication initiation from transcriptional readthrough. Consistently, high natural nascent transcription correlates with low ARS efficiency and late replication timing. High readthrough transcription is also linked to increased nucleosome occupancy and high levels of H3K36me3. Moreover, forcing ARS readthrough transcription promotes these chromatin features. Finally, replication initiation defects induced by increased transcriptional readthrough are partially rescued in the absence of H3K36 methylation. Altogether, these observations indicate that natural noncoding transcription into ARSs influences replication initiation through chromatin regulation.
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Affiliation(s)
- Julien Soudet
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Jatinder Kaur Gill
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Françoise Stutz
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
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27
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Mendoza-Ochoa GI, Barrass JD, Terlouw BR, Maudlin IE, de Lucas S, Sani E, Aslanzadeh V, Reid JAE, Beggs JD. A fast and tuneable auxin-inducible degron for depletion of target proteins in budding yeast. Yeast 2018; 36:75-81. [PMID: 30375036 PMCID: PMC6587778 DOI: 10.1002/yea.3362] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 12/11/2022] Open
Abstract
The auxin‐inducible degron (AID) is a useful technique to rapidly deplete proteins of interest in nonplant eukaryotes. Depletion is achieved by addition of the plant hormone auxin to the cell culture, which allows the auxin‐binding receptor, TIR1, to target the AID‐tagged protein for degradation by the proteasome. Fast depletion of the target protein requires good expression of TIR1 protein, but as we show here, high levels of TIR1 may cause uncontrolled depletion of the target protein in the absence of auxin. To enable conditional expression of TIR1 to a high level when required, we regulated the expression of TIR1 using the β‐estradiol expression system. This is a fast‐acting gene induction system that does not cause secondary effects on yeast cell metabolism. We demonstrate that combining the AID and β‐estradiol systems results in a tightly controlled and fast auxin‐induced depletion of nuclear target proteins. Moreover, we show that depletion rate can be tuned by modulating the duration of β‐estradiol preincubation. We conclude that TIR1 protein is a rate‐limiting factor for target protein depletion in yeast, and we provide new tools that allow tightly controlled, tuneable, and efficient depletion of essential proteins whereas minimising secondary effects.
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Affiliation(s)
- Gonzalo I Mendoza-Ochoa
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J David Barrass
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Barbara R Terlouw
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Isabella E Maudlin
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Susana de Lucas
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Emanuela Sani
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Vahid Aslanzadeh
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jane A E Reid
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Jean D Beggs
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Doris SM, Chuang J, Viktorovskaya O, Murawska M, Spatt D, Churchman LS, Winston F. Spt6 Is Required for the Fidelity of Promoter Selection. Mol Cell 2018; 72:687-699.e6. [PMID: 30318445 DOI: 10.1016/j.molcel.2018.09.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/20/2018] [Accepted: 08/31/2018] [Indexed: 01/06/2023]
Abstract
Spt6 is a conserved factor that controls transcription and chromatin structure across the genome. Although Spt6 is viewed as an elongation factor, spt6 mutations in Saccharomyces cerevisiae allow elevated levels of transcripts from within coding regions, suggesting that Spt6 also controls initiation. To address the requirements for Spt6 in transcription and chromatin structure, we have combined four genome-wide approaches. Our results demonstrate that Spt6 represses transcription initiation at thousands of intragenic promoters. We characterize these intragenic promoters and find sequence features conserved with genic promoters. Finally, we show that Spt6 also regulates transcription initiation at most genic promoters and propose a model of initiation site competition to account for this. Together, our results demonstrate that Spt6 controls the fidelity of transcription initiation throughout the genome.
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Affiliation(s)
- Stephen M Doris
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Chuang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | | | - Dan Spatt
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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29
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Vogl T, Kickenweiz T, Pitzer J, Sturmberger L, Weninger A, Biggs BW, Köhler EM, Baumschlager A, Fischer JE, Hyden P, Wagner M, Baumann M, Borth N, Geier M, Ajikumar PK, Glieder A. Engineered bidirectional promoters enable rapid multi-gene co-expression optimization. Nat Commun 2018; 9:3589. [PMID: 30181586 DOI: 10.1038/s41467-018-0591-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/25/2018] [Indexed: 05/22/2023] Open
Abstract
Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature's use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications.
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Affiliation(s)
- Thomas Vogl
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Thomas Kickenweiz
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Julia Pitzer
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | - Lukas Sturmberger
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | - Astrid Weninger
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Bradley W Biggs
- Manus Biosynthesis, 1030 Massachusetts Avenue, Suite 300, Cambridge, MA, 02138, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Eva-Maria Köhler
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Armin Baumschlager
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Jasmin Elgin Fischer
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Patrick Hyden
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Marlies Wagner
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Martina Geier
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010, Graz, Austria
| | | | - Anton Glieder
- Institute of Molecular Biotechnology, NAWI Graz, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
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30
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Engineered bidirectional promoters enable rapid multi-gene co-expression optimization. Nat Commun 2018; 9:3589. [PMID: 30181586 PMCID: PMC6123417 DOI: 10.1038/s41467-018-05915-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/25/2018] [Indexed: 01/24/2023] Open
Abstract
Numerous synthetic biology endeavors require well-tuned co-expression of functional components for success. Classically, monodirectional promoters (MDPs) have been used for such applications, but MDPs are limited in terms of multi-gene co-expression capabilities. Consequently, there is a pressing need for new tools with improved flexibility in terms of genetic circuit design, metabolic pathway assembly, and optimization. Here, motivated by nature’s use of bidirectional promoters (BDPs) as a solution for efficient gene co-expression, we generate a library of 168 synthetic BDPs in the yeast Komagataella phaffii (syn. Pichia pastoris), leveraging naturally occurring BDPs as a parts repository. This library of synthetic BDPs allows for rapid screening of diverse expression profiles and ratios to optimize gene co-expression, including for metabolic pathways (taxadiene, β-carotene). The modular design strategies applied for creating the BDP library could be relevant in other eukaryotic hosts, enabling a myriad of metabolic engineering and synthetic biology applications. Classic monodirectional promoters are of limited use for multiple gene co-expression. Here the authors generate a library of 168 bidirectional promoters for the yeast K. phaffii (syn. P. pastoris) with diverse expression profiles to optimize metabolic pathway design.
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31
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Krzyszton M, Zakrzewska-Placzek M, Kwasnik A, Dojer N, Karlowski W, Kufel J. Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1017-1031. [PMID: 29356198 DOI: 10.1111/tpj.13826] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/13/2017] [Accepted: 12/21/2017] [Indexed: 06/07/2023]
Abstract
Arabidopsis thaliana contains two nuclear XRN2/3 5'-3' exonucleases that are homologs of yeast and human Rat1/Xrn2 proteins involved in the processing and degradation of several classes of nuclear RNAs and in transcription termination of RNA polymerase II. Using strand-specific short read sequencing we show that knockdown of XRN3 leads to an altered expression of hundreds of genes and the accumulation of uncapped and polyadenylated read-through transcripts generated by inefficiently terminated Pol II. Our data support the notion that XRN3-mediated changes in the expression of a subset of genes are caused by upstream read-through transcription and these effects are enhanced by RNA-mRNA chimeras generated in xrn3 plants. In turn, read-through transcripts that are antisense to downstream genes may trigger production of siRNA. Our results highlight the importance of XRN3 exoribonuclease in Pol II transcription termination in plants and show that disturbance in this process may significantly alter gene expression.
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Affiliation(s)
- Michal Krzyszton
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Monika Zakrzewska-Placzek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Aleksandra Kwasnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Norbert Dojer
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097, Warsaw, Poland
| | - Wojciech Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland
| | - Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
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32
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Abstract
Most RNA polymerases can initiate transcription from diverse DNA template sequences with relatively few outright sequence restraints. Recent reports have demonstrated that failure to subdue the promiscuity of RNA polymerase in vivo can severely impede cell function. This phenomenon appears common to all cell types with undesirable effects ranging from growth inhibition in prokaryotes to cancer in higher organisms. Here we discuss similarities and differences in strategies employed by cells to minimise spurious transcription across life's domains.
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Affiliation(s)
- Joseph T Wade
- a Wadsworth Center , New York State Department of Health , Albany , NY , USA.,b Department of Biomedical Sciences , School of Public Health, University at Albany, SUNY , Albany , NY , USA
| | - David C Grainger
- c Institute of Microbiology and Infection, School of Biosciences, University of Birmingham , Edgbaston, Birmingham , UK
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33
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Robert F. Bidirectional terminators: an underestimated aspect of gene regulation. Curr Genet 2017; 64:389-391. [PMID: 29018946 DOI: 10.1007/s00294-017-0763-y] [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: 10/03/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 10/18/2022]
Abstract
Recent experimental and computational work revealed that transcriptional terminators in Saccharomyces cerevisiae can terminate transcription coming from both directions. This mechanism helps budding yeast cope with the pervasive nature of transcription by limiting aberrant transcription from invading neighboring genes.
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Affiliation(s)
- François Robert
- Institut de recherches cliniques de Montréal (IRCM), 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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