1
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Wu AC, Vivori C, Patel H, Sideri T, Moretto F, van Werven FJ. RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription. Life Sci Alliance 2022; 5:e202201394. [PMID: 36114005 PMCID: PMC9481977 DOI: 10.26508/lsa.202201394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/02/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
The directionality of gene promoters-the ratio of protein-coding over divergent noncoding transcription-is highly variable. How promoter directionality is controlled remains poorly understood. Here, we show that the chromatin remodelling complex RSC and general regulatory factors (GRFs) dictate promoter directionality by attenuating divergent transcription relative to protein-coding transcription. At gene promoters that are highly directional, depletion of RSC leads to a relative increase in divergent noncoding transcription and thus to a decrease in promoter directionality. We find that RSC has a modest effect on nucleosome positioning upstream in promoters at the sites of divergent transcription. These promoters are also enriched for the binding of GRFs such as Reb1 and Abf1. Ectopic targeting of divergent transcription initiation sites with GRFs or the dCas9 DNA-binding protein suppresses divergent transcription. Our data suggest that RSC and GRFs play a pervasive role in limiting divergent transcription relative to coding direction transcription. We propose that any DNA-binding factor, when stably associated with cryptic transcription start sites, forms a barrier which represses divergent transcription, thereby promoting promoter directionality.
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Affiliation(s)
- Andrew Ck Wu
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Vivori
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Theodora Sideri
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
| | - Fabien Moretto
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Greece
| | - Folkert J van Werven
- Cell Fate and Gene Regulation Laboratory, The Francis Crick Institute, London, UK
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2
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Kang DH, Ko SC, Heo YB, Lee HJ, Woo HM. RoboMoClo: A Robotics-Assisted Modular Cloning Framework for Multiple Gene Assembly in Biofoundry. ACS Synth Biol 2022; 11:1336-1348. [PMID: 35167276 DOI: 10.1021/acssynbio.1c00628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Efficient and versatile DNA assembly frameworks have had an impact on promoting synthetic biology to build complex biological systems. To accelerate system development, laboratory automation (or biofoundry) provides an opportunity to construct organisms and DNA assemblies via computer-aided design. However, a modular cloning (MoClo) system for multiple DNA assemblies limits the biofoundry workflow in terms of simplicity and feasibility by preparing the number of cloning materials such as destination vectors prior to the automation process. Herein, we propose robot-assisted MoClo (RoboMoClo) to accelerate a synthetic biology project with multiple gene expressions at the biofoundry. The architecture of the RoboMoClo framework provides a hybrid strategy of hierarchical gene assembly and iterative gene assembly, and fewer destination vectors compared with other MoClo systems. An industrial bacterium, Corynebacterium glutamicum, was used as a model host for RoboMoClo. After building a biopart library (promoter and terminator; level 0) and evaluating its features (level 1), various transcriptional directions in multiple gene assemblies (level 2) were studied using the RoboMoClo vectors. Among the constructs, the convergent construct exhibited potential transcriptional interference through the collision of RNA polymerases. To study design of experiment-guided lycopene biosynthesis in C. glutamicum (levels 1, 2, and 3), the biofoundry-assisted multiple gene assembly was demonstrated as a proof-of-concept by constructing various sub-pathway units (level 2) and pathway units (level 3) for C. glutamicum. The RoboMoClo framework provides an improved MoClo toolkit for laboratory automation in a synthetic biology application.
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Affiliation(s)
- Dong Hun Kang
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sung Cheon Ko
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Hyun Jeong Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
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3
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Zou F, Bai L. Using time-lapse fluorescence microscopy to study gene regulation. Methods 2018; 159-160:138-145. [PMID: 30599195 DOI: 10.1016/j.ymeth.2018.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 12/20/2018] [Accepted: 12/27/2018] [Indexed: 12/20/2022] Open
Abstract
Time-lapse fluorescence microscopy is a powerful tool to study gene regulation. By probing fluorescent signals in single cells over extended period of time, this method can be used to study the dynamics, noise, movement, memory, inheritance, and coordination, of gene expression during cell growth, development, and differentiation. In combination with a flow-cell device, it can also measure gene regulation by external stimuli. Due to the single cell nature and the spatial/temporal capacity, this method can often provide information that is hard to get using other methods. Here, we review the standard experimental procedures and new technical developments in this field.
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Affiliation(s)
- Fan Zou
- Department of Physics, The Pennsylvania State University, University Park, PA 16802, United States; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, United States
| | - Lu Bai
- Department of Physics, The Pennsylvania State University, University Park, PA 16802, United States; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States; Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, United States.
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4
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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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5
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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: 53] [Impact Index Per Article: 8.8] [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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6
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Systematic Study of Nucleosome-Displacing Factors in Budding Yeast. Mol Cell 2018; 71:294-305.e4. [PMID: 30017582 DOI: 10.1016/j.molcel.2018.06.017] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/04/2018] [Accepted: 06/07/2018] [Indexed: 12/11/2022]
Abstract
Nucleosomes present a barrier for the binding of most transcription factors (TFs). However, special TFs known as nucleosome-displacing factors (NDFs) can access embedded sites and cause the depletion of the local nucleosomes as well as repositioning of the neighboring nucleosomes. Here, we developed a novel high-throughput method in yeast to identify NDFs among 104 TFs and systematically characterized the impact of orientation, affinity, location, and copy number of their binding motifs on the nucleosome occupancy. Using this assay, we identified 29 NDF motifs and divided the nuclear TFs into three groups with strong, weak, and no nucleosome-displacing activities. Further studies revealed that tight DNA binding is the key property that underlies NDF activity, and the NDFs may partially rely on the DNA replication to compete with nucleosome. Overall, our study presents a framework to functionally characterize NDFs and elucidate the mechanism of nucleosome invasion.
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7
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Ahmed V, Verma MK, Gupta S, Mandhan V, Chauhan NS. Metagenomic Profiling of Soil Microbes to Mine Salt Stress Tolerance Genes. Front Microbiol 2018; 9:159. [PMID: 29472909 PMCID: PMC5809485 DOI: 10.3389/fmicb.2018.00159] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022] Open
Abstract
Osmotolerance is one of the critical factors for successful survival and colonization of microbes in saline environments. Nonetheless, information about these osmotolerance mechanisms is still inadequate. Exploration of the saline soil microbiome for its community structure and novel genetic elements is likely to provide information on the mechanisms involved in osmoadaptation. The present study explores the saline soil microbiome for its native structure and novel genetic elements involved in osmoadaptation. 16S rRNA gene sequence analysis has indicated the dominance of halophilic/halotolerant phylotypes affiliated to Proteobacteria, Actinobacteria, Gemmatimonadetes, Bacteroidetes, Firmicutes, and Acidobacteria. A functional metagenomics approach led to the identification of osmotolerant clones SSR1, SSR4, SSR6, SSR2 harboring BCAA_ABCtp, GSDH, STK_Pknb, and duf3445 genes. Furthermore, transposon mutagenesis, genetic, physiological and functional studies in close association has confirmed the role of these genes in osmotolerance. Enhancement in host osmotolerance possibly though the cytosolic accumulation of amino acids, reducing equivalents and osmolytes involving BCAA-ABCtp, GSDH, and STKc_PknB. Decoding of the genetic elements prevalent within these microbes can be exploited either as such for ameliorating soils or their genetically modified forms can assist crops to resist and survive in saline environment.
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Affiliation(s)
- Vasim Ahmed
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Manoj K Verma
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Shashank Gupta
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Vibha Mandhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Nar S Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
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8
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Bunch H. Gene regulation of mammalian long non-coding RNA. Mol Genet Genomics 2017; 293:1-15. [PMID: 28894972 DOI: 10.1007/s00438-017-1370-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
Abstract
RNA polymerase II (Pol II) transcribes two classes of RNAs, protein-coding and non-protein-coding (ncRNA) genes. ncRNAs are also synthesized by RNA polymerases I and III (Pol I and III). In humans, the number of ncRNA genes exceeds more than twice that of protein-coding genes. However, the history of studying Pol II-synthesized ncRNA is relatively short. Since early 2000s, important biological and pathological functions of these ncRNA genes have begun to be discovered and intensively studied. And transcription mechanisms of long non-coding RNA (lncRNA) have been recently reported. Transcription of lncRNAs utilizes some transcription factors and mechanisms shared in that of protein-coding genes. In addition, tissue specificity in lncRNA gene expression has been shown. LncRNAs play essential roles in regulating the expression of neighboring or distal genes through different mechanisms. This leads to the implication of lncRNAs in a wide variety of biological pathways and pathological development. In this review, the newly discovered transcription mechanisms, characteristics, and functions of lncRNA are discussed.
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Affiliation(s)
- Heeyoun Bunch
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Agriculture & Life Sciences Building 1, Room 207, 80 Dae-Hak Ro, Daegu, Republic of Korea.
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9
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Bosio MC, Fermi B, Spagnoli G, Levati E, Rubbi L, Ferrari R, Pellegrini M, Dieci G. Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. Nucleic Acids Res 2017; 45:4493-4506. [PMID: 28158860 PMCID: PMC5416754 DOI: 10.1093/nar/gkx058] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 01/25/2017] [Indexed: 01/21/2023] Open
Abstract
Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. Two cis-acting elements called PAC and RRPE are known to mediate Ribi gene repression in response to nutritional downshift. Here, we show that most Ribi gene promoters also contain binding sites for one or more General Regulatory Factors (GRFs), most frequently Abf1 and Reb1, and that these factors are enriched in vivo at Ribi promoters. Abf1/Reb1/Tbf1 promoter association was required for full Ribi gene expression in rich medium and for its modulation in response to glucose starvation, characterized by a rapid drop followed by slow recovery. Such a response did not entail changes in Abf1 occupancy, but it was paralleled by a quick increase, followed by slow decrease, in Rpd3L histone deacetylase occupancy. Remarkably, Abf1 site disruption also abolished Rpd3L complex recruitment in response to starvation. Extensive mutational analysis of the DBP7 promoter revealed a complex interplay of Tbf1 sites, PAC and RRPE in the transcriptional regulation of this Ribi gene. Our observations point to GRFs as new multifaceted players in Ribi gene regulation both during exponential growth and under repressive conditions.
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Affiliation(s)
- Maria Cristina Bosio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Beatrice Fermi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Gloria Spagnoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Elisabetta Levati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Ludmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roberto Ferrari
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
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10
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Du M, Bai L. 3D clustering of co-regulated genes and its effect on gene expression. Curr Genet 2017; 63:1017-1021. [PMID: 28551816 DOI: 10.1007/s00294-017-0712-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 01/29/2023]
Abstract
There are extensive long-distance chromosomal interactions in eukaryotic genomes, but to what extent these interactions affect gene expression is not clear. Recent works have identified several cases where clustering of co-regulated genes leads to enhanced gene expression in budding yeast. Similar phenomenon was also observed in mammalian cells. These results challenge widely held views of gene regulation in yeast and further our understanding of how the 3D organization of the genome contribute to gene regulation in eukaryotes.
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Affiliation(s)
- Manyu Du
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, State College, PA, USA.,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, State College, PA, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, State College, PA, USA. .,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, State College, PA, USA. .,Department of Physics, The Pennsylvania State University, University Park, State College, PA, USA.
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11
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Fischl H, Howe FS, Furger A, Mellor J. Paf1 Has Distinct Roles in Transcription Elongation and Differential Transcript Fate. Mol Cell 2017; 65:685-698.e8. [PMID: 28190769 PMCID: PMC5316414 DOI: 10.1016/j.molcel.2017.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/22/2016] [Accepted: 01/05/2017] [Indexed: 12/12/2022]
Abstract
RNA polymerase II (Pol2) movement through chromatin and the co-transcriptional processing and fate of nascent transcripts is coordinated by transcription elongation factors (TEFs) such as polymerase-associated factor 1 (Paf1), but it is not known whether TEFs have gene-specific functions. Using strand-specific nucleotide resolution techniques, we show that levels of Paf1 on Pol2 vary between genes, are controlled dynamically by environmental factors via promoters, and reflect levels of processing and export factors on the encoded transcript. High levels of Paf1 on Pol2 promote transcript nuclear export, whereas low levels reflect nuclear retention. Strains lacking Paf1 show marked elongation defects, although low levels of Paf1 on Pol2 are sufficient for transcription elongation. Our findings support distinct Paf1 functions: a core general function in transcription elongation, satisfied by the lowest Paf1 levels, and a regulatory function in determining differential transcript fate by varying the level of Paf1 on Pol2.
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Affiliation(s)
- Harry Fischl
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Françoise S Howe
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Andre Furger
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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12
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Grünberg S, Henikoff S, Hahn S, Zentner GE. Mediator binding to UASs is broadly uncoupled from transcription and cooperative with TFIID recruitment to promoters. EMBO J 2016; 35:2435-2446. [PMID: 27797823 DOI: 10.15252/embj.201695020] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Accepted: 09/20/2016] [Indexed: 11/09/2022] Open
Abstract
Mediator is a conserved, essential transcriptional coactivator complex, but its in vivo functions have remained unclear due to conflicting data regarding its genome-wide binding pattern obtained by genome-wide ChIP Here, we used ChEC-seq, a method orthogonal to ChIP, to generate a high-resolution map of Mediator binding to the yeast genome. We find that Mediator associates with upstream activating sequences (UASs) rather than the core promoter or gene body under all conditions tested. Mediator occupancy is surprisingly correlated with transcription levels at only a small fraction of genes. Using the same approach to map TFIID, we find that TFIID is associated with both TFIID- and SAGA-dependent genes and that TFIID and Mediator occupancy is cooperative. Our results clarify Mediator recruitment and binding to the genome, showing that Mediator binding to UASs is widespread, partially uncoupled from transcription, and mediated in part by TFIID.
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Affiliation(s)
- Sebastian Grünberg
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Hahn
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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13
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Characterization of Five Novel Brevibacillus Bacteriophages and Genomic Comparison of Brevibacillus Phages. PLoS One 2016; 11:e0156838. [PMID: 27304881 PMCID: PMC4909266 DOI: 10.1371/journal.pone.0156838] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 05/20/2016] [Indexed: 12/31/2022] Open
Abstract
Brevibacillus laterosporus is a spore-forming bacterium that causes a secondary infection in beehives following European Foulbrood disease. To better understand the contributions of Brevibacillus bacteriophages to the evolution of their hosts, five novel phages (Jenst, Osiris, Powder, SecTim467, and Sundance) were isolated and characterized. When compared with the five Brevibacillus phages currently in NCBI, these phages were assigned to clusters based on whole genome and proteome synteny. Powder and Osiris, both myoviruses, were assigned to the previously described Jimmer-like cluster. SecTim467 and Jenst, both siphoviruses, formed a novel phage cluster. Sundance, a siphovirus, was assigned as a singleton phage along with the previously isolated singleton, Emery. In addition to characterizing the basic relationships between these phages, several genomic features were observed. A motif repeated throughout phages Jenst and SecTim467 was frequently upstream of genes predicted to function in DNA replication, nucleotide metabolism, and transcription, suggesting transcriptional co-regulation. In addition, paralogous gene pairs that encode a putative transcriptional regulator were identified in four Brevibacillus phages. These paralogs likely evolved to bind different DNA sequences due to variation at amino acid residues predicted to bind specific nucleotides. Finally, a putative transposable element was identified in SecTim467 and Sundance that carries genes homologous to those found in Brevibacillus chromosomes. Remnants of this transposable element were also identified in phage Jenst. These discoveries provide a greater understanding of the diversity of phages, their behavior, and their evolutionary relationships to one another and to their host. In addition, they provide a foundation with which further Brevibacillus phages can be compared.
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14
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Gadaleta MC, González-Medina A, Noguchi E. Timeless protection of telomeres. Curr Genet 2016; 62:725-730. [PMID: 27068713 DOI: 10.1007/s00294-016-0599-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Abstract
The DNA replication machinery encounters problems at numerous genomic regions that are inherently difficult to replicate. These genomic regions include telomeres, which contain repetitive DNA and telomere-binding proteins. If not properly regulated, replication of such genomic regions can result in DNA damage, leading to genomic instability. Studies implicated a role of Timeless-related proteins at difficult-to-replicate genomic regions, including telomeres. However, how these proteins maintain telomeres was elusive. In a recent report, we described the role of Swi1, a Timeless-related protein, in telomere maintenance in fission yeast. We demonstrated that Swi1 is required for proper replication of repeat DNA sequences at telomeres. We also showed that Swi1-deficient cells utilize recombination-based ALT (alternative lengthening of telomeres)-like mechanisms to maintain telomeres in the absence of telomerase. Here, we highlight these findings and present additional data to discuss the role of Swi1Timeless in telomere protection and ALT prevention.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Alberto González-Medina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.,Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA, 19102, USA.
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The Determinants of Directionality in Transcriptional Initiation. Trends Genet 2016; 32:322-333. [PMID: 27066865 DOI: 10.1016/j.tig.2016.03.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 03/11/2016] [Accepted: 03/16/2016] [Indexed: 01/20/2023]
Abstract
A new paradigm has emerged in recent years characterizing transcription initiation as a bidirectional process encompassing a larger proportion of the genome than previously thought. Past concepts of coding genes thinly scattered among a vast background of transcriptionally inert noncoding DNA have been abandoned. A richer picture has taken shape, integrating transcription of coding genes, enhancer RNAs (eRNAs), and various other noncoding transcriptional events. In this review we give an overview of recent studies detailing the mechanisms of RNA polymerase II (RNA Pol II)-based transcriptional initiation and discuss the ways in which transcriptional direction is established as well as its functional implications.
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16
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Regulation of cell-to-cell variability in divergent gene expression. Nat Commun 2016; 7:11099. [PMID: 27010670 PMCID: PMC4820839 DOI: 10.1038/ncomms11099] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/21/2016] [Indexed: 12/03/2022] Open
Abstract
Cell-to-cell variability (noise) is an important feature of gene expression that impacts cell fitness and development. The regulatory mechanism of this variability is not fully understood. Here we investigate the effect on gene expression noise in divergent gene pairs (DGPs). We generated reporters driven by divergent promoters, rearranged their gene order, and probed their expressions using time-lapse fluorescence microscopy and single-molecule fluorescence in situ hybridization (smFISH). We show that two genes in a co-regulated DGP have higher expression covariance compared with the separate, tandem and convergent configurations, and this higher covariance is caused by more synchronized firing of the divergent transcriptions. For differentially regulated DGPs, the regulatory signal of one gene can stochastically ‘leak' to the other, causing increased gene expression noise. We propose that the DGPs' function in limiting or promoting gene expression noise may enhance or compromise cell fitness, providing an explanation for the conservation pattern of DGPs. Gene expression noise affects cell fitness and development. Here, Yan et al. show that co-regulated divergent gene pairs (DGPs) suppress uncorrelated gene expression noise due to more synchronized transcription firing, and differentially regulated DGPs enhance gene expression noise due to transcription leakage.
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