1
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van Breugel ME, Gerber A, van Leeuwen F. The choreography of chromatin in RNA polymerase III regulation. Biochem Soc Trans 2024; 52:1173-1189. [PMID: 38666598 DOI: 10.1042/bst20230770] [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: 03/07/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/27/2024]
Abstract
Regulation of eukaryotic gene expression involves a dynamic interplay between the core transcriptional machinery, transcription factors, and chromatin organization and modification. While this applies to transcription by all RNA polymerase complexes, RNA polymerase III (RNAPIII) seems to be atypical with respect to its mechanisms of regulation. One distinctive feature of most RNAPIII transcribed genes is that they are devoid of nucleosomes, which relates to the high levels of transcription. Moreover, most of the regulatory sequences are not outside but within the transcribed open chromatin regions. Yet, several lines of evidence suggest that chromatin factors affect RNAPIII dynamics and activity and that gene sequence alone does not explain the observed regulation of RNAPIII. Here we discuss the role of chromatin modification and organization of RNAPIII transcribed genes and how they interact with the core transcriptional RNAPIII machinery and regulatory DNA elements in and around the transcribed genes.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
| | - Alan Gerber
- Department of Neurosurgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam 1081HV, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, The Netherlands
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2
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Zeng Y, Zhang HW, Wu XX, Zhang Y. Structural basis of exoribonuclease-mediated mRNA transcription termination. Nature 2024; 628:887-893. [PMID: 38538796 DOI: 10.1038/s41586-024-07240-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/26/2024] [Indexed: 04/06/2024]
Abstract
Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II)1-5. Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5'-to-3' exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5' terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes.
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MESH Headings
- Cryoelectron Microscopy
- Exoribonucleases/chemistry
- Exoribonucleases/metabolism
- Exoribonucleases/ultrastructure
- Models, Molecular
- Protein Binding
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA Polymerase II/ultrastructure
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/ultrastructure
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/metabolism
- RNA-Binding Proteins/ultrastructure
- Saccharomyces cerevisiae/chemistry
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae/ultrastructure
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/metabolism
- Saccharomyces cerevisiae Proteins/ultrastructure
- Transcription Termination, Genetic
- Transcriptional Elongation Factors/chemistry
- Transcriptional Elongation Factors/metabolism
- Transcriptional Elongation Factors/ultrastructure
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosomal Proteins, Non-Histone/ultrastructure
- Protein Domains
- RNA, Fungal/biosynthesis
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/ultrastructure
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Affiliation(s)
- Yuan Zeng
- Key Laboratory of Synthetic Biology, National Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong-Wei Zhang
- Key Laboratory of Synthetic Biology, National Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiao-Xian Wu
- Key Laboratory of Synthetic Biology, National Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, National Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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3
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Liu X, Chen H, Li Z, Yang X, Jin W, Wang Y, Zheng J, Li L, Xuan C, Yuan J, Yang Y. InPACT: a computational method for accurate characterization of intronic polyadenylation from RNA sequencing data. Nat Commun 2024; 15:2583. [PMID: 38519498 PMCID: PMC10960005 DOI: 10.1038/s41467-024-46875-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Alternative polyadenylation can occur in introns, termed intronic polyadenylation (IPA), has been implicated in diverse biological processes and diseases, as it can produce noncoding transcripts or transcripts with truncated coding regions. However, a reliable method is required to accurately characterize IPA. Here, we propose a computational method called InPACT, which allows for the precise characterization of IPA from conventional RNA-seq data. InPACT successfully identifies numerous previously unannotated IPA transcripts in human cells, many of which are translated, as evidenced by ribosome profiling data. We have demonstrated that InPACT outperforms other methods in terms of IPA identification and quantification. Moreover, InPACT applied to monocyte activation reveals temporally coordinated IPA events. Further application on single-cell RNA-seq data of human fetal bone marrow reveals the expression of several IPA isoforms in a context-specific manner. Therefore, InPACT represents a powerful tool for the accurate characterization of IPA from RNA-seq data.
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Affiliation(s)
- Xiaochuan Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Hao Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zekun Li
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Xiaoxiao Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Wen Jin
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jian Zheng
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Long Li
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Chenghao Xuan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, The Second Hospital of Tianjin Medical University, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
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4
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Viera T, Abfalterer Q, Neal A, Trujillo R, Patidar PL. Molecular Basis of XRN2-Deficient Cancer Cell Sensitivity to Poly(ADP-ribose) Polymerase Inhibition. Cancers (Basel) 2024; 16:595. [PMID: 38339346 PMCID: PMC10854503 DOI: 10.3390/cancers16030595] [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: 12/21/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
R-loops (RNA-DNA hybrids with displaced single-stranded DNA) have emerged as a potent source of DNA damage and genomic instability. The termination of defective RNA polymerase II (RNAPII) is one of the major sources of R-loop formation. 5'-3'-exoribonuclease 2 (XRN2) promotes genome-wide efficient RNAPII termination, and XRN2-deficient cells exhibit increased DNA damage emanating from elevated R-loops. Recently, we showed that DNA damage instigated by XRN2 depletion in human fibroblast cells resulted in enhanced poly(ADP-ribose) polymerase 1 (PARP1) activity. Additionally, we established a synthetic lethal relationship between XRN2 and PARP1. However, the underlying cellular stress response promoting this synthetic lethality remains elusive. Here, we delineate the molecular consequences leading to the synthetic lethality of XRN2-deficient cancer cells induced by PARP inhibition. We found that XRN2-deficient lung and breast cancer cells display sensitivity to two clinically relevant PARP inhibitors, Rucaparib and Olaparib. At a mechanistic level, PARP inhibition combined with XRN2 deficiency exacerbates R-loop and DNA double-strand break formation in cancer cells. Consistent with our previous findings using several different siRNAs, we also show that XRN2 deficiency in cancer cells hyperactivates PARP1. Furthermore, we observed enhanced replication stress in XRN2-deficient cancer cells treated with PARP inhibitors. Finally, the enhanced stress response instigated by compromised PARP1 catalytic function in XRN2-deficient cells activates caspase-3 to initiate cell death. Collectively, these findings provide mechanistic insights into the sensitivity of XRN2-deficient cancer cells to PARP inhibition and strengthen the underlying translational implications for targeted therapy.
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Affiliation(s)
| | | | | | | | - Praveen L. Patidar
- Department of Chemistry, New Mexico Institute of Mining and Technology, Socorro, NM 87801, USA
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5
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Carminati M, Rodríguez-Molina JB, Manav MC, Bellini D, Passmore LA. A direct interaction between CPF and RNA Pol II links RNA 3' end processing to transcription. Mol Cell 2023; 83:4461-4478.e13. [PMID: 38029752 PMCID: PMC10783616 DOI: 10.1016/j.molcel.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Transcription termination by RNA polymerase II (RNA Pol II) is linked to RNA 3' end processing by the cleavage and polyadenylation factor (CPF or CPSF). CPF contains endonuclease, poly(A) polymerase, and protein phosphatase activities, which cleave and polyadenylate pre-mRNAs and dephosphorylate RNA Pol II to control transcription. Exactly how the RNA 3' end processing machinery is coupled to transcription remains unclear. Here, we combine in vitro reconstitution, structural studies, and genome-wide analyses to show that yeast CPF physically and functionally interacts with RNA Pol II. Surprisingly, CPF-mediated dephosphorylation promotes the formation of an RNA Pol II stalk-to-stalk homodimer in vitro. This dimer is compatible with transcription but not with the binding of transcription elongation factors. Disruption of the dimerization interface in cells causes transcription defects, including altered RNA Pol II abundance on protein-coding genes, tRNA genes, and intergenic regions. We hypothesize that RNA Pol II dimerization may provide a mechanistic basis for the allosteric model of transcription termination.
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Affiliation(s)
| | | | - M Cemre Manav
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Dom Bellini
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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6
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Liu L, Yu AM, Wang X, Soles LV, Teng X, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, England W, Spitale R, Yu Z, Marazzi I, Qiao F, Li W, Seelig G, Shi Y. The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. Nat Struct Mol Biol 2023; 30:1947-1957. [PMID: 38087090 DOI: 10.1038/s41594-023-01161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
JTE-607 is an anticancer and anti-inflammatory compound and its active form, compound 2, directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-messenger RNA (pre-mRNA) 3' processing. Surprisingly, compound 2-mediated inhibition of pre-mRNA cleavage is sequence specific and the drug sensitivity is predominantly determined by sequences flanking the cleavage site (CS). Using massively parallel in vitro assays, we identified key sequence features that determine drug sensitivity. We trained a machine learning model that can predict poly(A) site (PAS) relative sensitivity to compound 2 and provide the molecular basis for understanding the impact of JTE-607 on PAS selection and transcription termination genome wide. We propose that CPSF73 and associated factors bind to the CS region in a sequence-dependent manner and the interaction affinity determines compound 2 sensitivity. These results have not only elucidated the mechanism of action of JTE-607, but also unveiled an evolutionarily conserved sequence specificity of the mRNA 3' processing machinery.
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Affiliation(s)
- Liang Liu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Center for Virus Research, University of California, Irvine, Irvine, CA, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Seattle, WA, USA
| | - Xiuye Wang
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
- Guangzhou Laboratory, Guangdong, China
| | - Lindsey V Soles
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Xueyi Teng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yiling Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yoseop Yoon
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kristianna S K Sarkan
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Marielle Cárdenas Valdez
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Johannes Linder
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Whitney England
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
| | - Robert Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA, USA
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Zhaoxia Yu
- Department of Statistics, University of California, Irvine, Irvine, CA, USA
| | - Ivan Marazzi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Feng Qiao
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, Seattle, WA, USA.
- Paul G Allen School of Computer Science and Engineering, University of Washington, Seattle, Seattle, WA, USA.
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA, USA.
- Center for Virus Research, University of California, Irvine, Irvine, CA, USA.
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7
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Stroup EK, Ji Z. Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease. Nat Commun 2023; 14:7378. [PMID: 37968271 PMCID: PMC10651852 DOI: 10.1038/s41467-023-43266-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023] Open
Abstract
The genomic distribution of cleavage and polyadenylation (polyA) sites should be co-evolutionally optimized with the local gene structure. Otherwise, spurious polyadenylation can cause premature transcription termination and generate aberrant proteins. To obtain mechanistic insights into polyA site optimization across the human genome, we develop deep/machine learning models to identify genome-wide putative polyA sites at unprecedented nucleotide-level resolution and calculate their strength and usage in the genomic context. Our models quantitatively measure position-specific motif importance and their crosstalk in polyA site formation and cleavage heterogeneity. The intronic site expression is governed by the surrounding splicing landscape. The usage of alternative polyA sites in terminal exons is modulated by their relative locations and distance to downstream genes. Finally, we apply our models to reveal thousands of disease- and trait-associated genetic variants altering polyadenylation activity. Altogether, our models represent a valuable resource to dissect molecular mechanisms mediating genome-wide polyA site expression and characterize their functional roles in human diseases.
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Affiliation(s)
- Emily Kunce Stroup
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL, 60628, USA.
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8
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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9
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Stroup EK, Ji Z. Delineating yeast cleavage and polyadenylation signals using deep learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.10.561764. [PMID: 37873420 PMCID: PMC10592759 DOI: 10.1101/2023.10.10.561764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
3'-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared to well-defined regulatory elements in mammals. Especially, recent deep sequencing experiments showed extensive cleavage heterogeneity for some mRNAs in Saccharomyces cerevisiae and uncovered the polyA motif differences between S. cerevisiae vs. Schizosaccharomyces pombe . The findings raised the fundamental question of how polyadenylation signals are formed in yeast. Here we addressed this question by developing deep learning models to deconvolute degenerate cis -regulatory elements and quantify their positional importance in mediating yeast polyA site formation, cleavage heterogeneity, and strength. In S. cerevisiae , cleavage heterogeneity is promoted by the depletion of U-rich elements around polyA sites as well as multiple occurrences of upstream UA-rich elements. Sites with high cleavage heterogeneity show overall lower strength. The site strength and tandem site distances modulate alternative polyadenylation (APA) under the diauxic stress. Finally, we developed a deep learning model to reveal the distinct motif configuration of S. pombe polyA sites which show more precise cleavage than S. cerevisiae . Altogether, our deep learning models provide unprecedented insights into polyA site formation across yeast species.
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10
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Liu L, Yu AM, Wang X, Soles LV, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, Marazzi I, Yu Z, Qiao F, Li W, Seelig G, Shi Y. The anti-cancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.11.536453. [PMID: 37090613 PMCID: PMC10120630 DOI: 10.1101/2023.04.11.536453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
JTE-607 is a small molecule compound with anti-inflammation and anti-cancer activities. Upon entering the cell, it is hydrolyzed to Compound 2, which directly binds to and inhibits CPSF73, the endonuclease for the cleavage step in pre-mRNA 3' processing. Although CPSF73 is universally required for mRNA 3' end formation, we have unexpectedly found that Compound 2- mediated inhibition of pre-mRNA 3' processing is sequence-specific and that the sequences flanking the cleavage site (CS) are a major determinant for drug sensitivity. By using massively parallel in vitro assays, we have measured the Compound 2 sensitivities of over 260,000 sequence variants and identified key sequence features that determine drug sensitivity. A machine learning model trained on these data can predict the impact of JTE-607 on poly(A) site (PAS) selection and transcription termination genome-wide. We propose a biochemical model in which CPSF73 and other mRNA 3' processing factors bind to RNA of the CS region in a sequence-specific manner and the affinity of such interaction determines the Compound 2 sensitivity of a PAS. As the Compound 2-resistant CS sequences, characterized by U/A-rich motifs, are prevalent in PASs from yeast to human, the CS region sequence may have more fundamental functions beyond determining drug resistance. Together, our study not only characterized the mechanism of action of a compound with clinical implications, but also revealed a previously unknown and evolutionarily conserved sequence-specificity of the mRNA 3' processing machinery.
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11
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Suzuki H, Furugori K, Abe R, Ogawa S, Ito S, Akiyama T, Horiuchi K, Takahashi H. MED26-containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies. Bioessays 2023; 45:e2200178. [PMID: 36852638 DOI: 10.1002/bies.202200178] [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: 09/07/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
Mediator is a coregulatory complex that plays essential roles in multiple processes of transcription regulation. One of the human Mediator subunits, MED26, has a role in recruitment of the super elongation complex (SEC) to polyadenylated genes and little elongation complex (LEC) to non-polyadenylated genes, including small nuclear RNAs (snRNAs) and replication-dependent histone (RDH) genes. MED26-containing Mediator plays a role in 3' Pol II pausing at the proximal region of transcript end sites in RDH genes through recruitment of Cajal bodies (CBs) to histone locus bodies (HLBs). This finding suggests that Mediator is involved in the association of CBs with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing by supplying 3'-end processing factors from CBs. Thus, we argue the possibility that Mediator is involved in the organization of nuclear bodies to orchestrate multiple processes of gene transcription.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
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12
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Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. A CpG island-encoded mechanism protects genes from premature transcription termination. Nat Commun 2023; 14:726. [PMID: 36759609 PMCID: PMC9911701 DOI: 10.1038/s41467-023-36236-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
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Affiliation(s)
- Amy L Hughes
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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13
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Kor SD, Chowdhury N, Keot AK, Yogendra K, Chikkaputtaiah C, Sudhakar Reddy P. RNA Pol III promoters-key players in precisely targeted plant genome editing. Front Genet 2023; 13:989199. [PMID: 36685866 PMCID: PMC9845283 DOI: 10.3389/fgene.2022.989199] [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: 07/08/2022] [Accepted: 11/15/2022] [Indexed: 01/05/2023] Open
Abstract
The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters' systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
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Affiliation(s)
- Sakshi Dharmendra Kor
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Ajay Kumar Keot
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kalenahalli Yogendra
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India,*Correspondence: Palakolanu Sudhakar Reddy, ,
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14
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Khajuria DK, Nowak I, Leung M, Karuppagounder V, Imamura Y, Norbury CC, Kamal F, Elbarbary RA. Transcript shortening via alternative polyadenylation promotes gene expression during fracture healing. Bone Res 2023; 11:5. [PMID: 36596777 PMCID: PMC9810729 DOI: 10.1038/s41413-022-00236-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/15/2022] [Accepted: 10/12/2022] [Indexed: 01/04/2023] Open
Abstract
Maturation of the 3' end of almost all eukaryotic messenger RNAs (mRNAs) requires cleavage and polyadenylation. Most mammalian mRNAs are polyadenylated at different sites within the last exon, generating alternative polyadenylation (APA) isoforms that have the same coding region but distinct 3' untranslated regions (UTRs). The 3'UTR contains motifs that regulate mRNA metabolism; thus, changing the 3'UTR length via APA can significantly affect gene expression. Endochondral ossification is a central process in bone healing, but the impact of APA on gene expression during this process is unknown. Here, we report the widespread occurrence of APA, which impacts multiple pathways that are known to participate in bone healing. Importantly, the progression of endochondral ossification involves global 3'UTR shortening, which is coupled with an increased abundance of shortened transcripts relative to other transcripts; these results highlight the role of APA in promoting gene expression during endochondral bone formation. Our mechanistic studies of transcripts that undergo APA in the fracture callus revealed an intricate regulatory network in which APA enhances the expression of the collagen, type I, alpha 1 (Col1a1) and Col1a2 genes, which encode the 2 subunits of the abundantly expressed protein collagen 1. APA exerts this effect by shortening the 3'UTRs of the Col1a1 and Col1a2 mRNAs, thus removing the binding sites of miR-29a-3p, which would otherwise strongly promote the degradation of both transcripts. Taken together, our study is the first to characterize the crucial roles of APA in regulating the 3'UTR landscape and modulating gene expression during fracture healing.
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Affiliation(s)
- Deepak Kumar Khajuria
- grid.29857.310000 0001 2097 4281Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Irena Nowak
- grid.29857.310000 0001 2097 4281Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Ming Leung
- grid.240473.60000 0004 0543 9901Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Vengadeshprabhu Karuppagounder
- grid.29857.310000 0001 2097 4281Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Yuka Imamura
- grid.240473.60000 0004 0543 9901Institute for Personalized Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Christopher C. Norbury
- grid.29857.310000 0001 2097 4281Department of Microbiology and Immunology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Fadia Kamal
- grid.29857.310000 0001 2097 4281Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA
| | - Reyad A. Elbarbary
- grid.29857.310000 0001 2097 4281Department of Orthopaedics and Rehabilitation, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Center for Orthopaedic Research and Translational Science (CORTS), The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033 USA ,grid.29857.310000 0001 2097 4281Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802 USA
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15
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Hu LF, Li YX, Wang JZ, Zhao YT, Wang Y. Controlling CRISPR-Cas9 by guide RNA engineering. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1731. [PMID: 35393779 DOI: 10.1002/wrna.1731] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/15/2022] [Indexed: 01/31/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is a product of million years of evolution by microbes to fight against invading genetic materials. Around 10 years ago, scientists started to repurpose the CRISPR as genetic tools by molecular engineering approaches. The guide RNA provides a versatile and unique platform for the innovation to improve and expand the application of CRISPR-Cas9 system. In this review, we will first introduce the basic sequence and structure of guide RNA and its role during the function of CRISPR-Cas9. We will then summarize recent progress on the development of various guide RNA engineering strategies. These strategies have been dedicated to improve the performance of CRISPR-Cas9, to achieve precise spatiotemporal control of CRISPR-Cas9, and to broaden the application of CRISPR-Cas9. Finally, we will briefly discuss the uniqueness and advantage of guide RNA-engineering based systems versus those with engineered Cas9 proteins and speculate potential future directions in guide RNA engineering. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Methods > RNA Nanotechnology Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Lu-Feng Hu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yu-Xuan Li
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Jia-Zhen Wang
- College of Life Sciences, Peking University, Beijing, China
| | - Yu-Ting Zhao
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
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16
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Slight Variations in the Sequence Downstream of the Polyadenylation Signal Significantly Increase Transgene Expression in HEK293T and CHO Cells. Int J Mol Sci 2022; 23:ijms232415485. [PMID: 36555130 PMCID: PMC9779314 DOI: 10.3390/ijms232415485] [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: 10/14/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Compared to transcription initiation, much less is known about transcription termination. In particular, large-scale mutagenesis studies have, so far, primarily concentrated on promoter and enhancer, but not terminator sequences. Here, we used a massively parallel reporter assay (MPRA) to systematically analyze the influence of short (8 bp) sequence variants (mutations) located downstream of the polyadenylation signal (PAS) on the steady-state mRNA level of the upstream gene, employing an eGFP reporter and human HEK293T cells as a model system. In total, we evaluated 227,755 mutations located at different overlapping positions within +17..+56 bp downstream of the PAS for their ability to regulate the reporter gene expression. We found that the positions +17..+44 bp downstream of the PAS are more essential for gene upregulation than those located more distal to the PAS, and that the mutation sequences ensuring high levels of eGFP mRNA expression are extremely T-rich. Next, we validated the positive effect of a couple of mutations identified in the MPRA screening on the eGFP and luciferase protein expression. The most promising mutation increased the expression of the reporter proteins 13-fold and sevenfold on average in HEK293T and CHO cells, respectively. Overall, these findings might be useful for further improving the efficiency of production of therapeutic products, e.g., recombinant antibodies.
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17
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Tynkevich YO, Novikov AV, Chorney II, Volkov RA. Organization of the 5S rDNA Intergenic Spacer and Its Use in the Molecular Taxonomy of the Genus Aconitum L. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722060111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Girbig M, Xie J, Grötsch H, Libri D, Porrua O, Müller CW. Architecture of the yeast Pol III pre-termination complex and pausing mechanism on poly(dT) termination signals. Cell Rep 2022; 40:111316. [PMID: 36070694 DOI: 10.1016/j.celrep.2022.111316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/01/2022] [Accepted: 08/15/2022] [Indexed: 12/20/2022] Open
Abstract
RNA polymerase (Pol) III is specialized to transcribe short, abundant RNAs, for which it terminates transcription on polythymine (dT) stretches on the non-template (NT) strand. When Pol III reaches the termination signal, it pauses and forms the pre-termination complex (PTC). Here, we report cryoelectron microscopy (cryo-EM) structures of the yeast Pol III PTC and complementary functional states at resolutions of 2.7-3.9 Å. Pol III recognizes the poly(dT) termination signal with subunit C128 that forms a hydrogen-bond network with the NT strand and, thereby, induces pausing. Mutating key interacting residues interferes with transcription termination in vitro, impairs yeast growth, and causes global termination defects in vivo, confirming our structural results. Additional cryo-EM analysis reveals that C53-C37, a Pol III subcomplex and key termination factor, participates indirectly in Pol III termination. We propose a mechanistic model of Pol III transcription termination and rationalize why Pol III, unlike Pol I and Pol II, terminates on poly(dT) signals.
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Affiliation(s)
- Mathias Girbig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Juanjuan Xie
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Helga Grötsch
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Odil Porrua
- Université de Paris, CNRS, Institut Jacques Monod, 75006 Paris, France
| | - Christoph W Müller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany.
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19
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Suzuki H, Abe R, Shimada M, Hirose T, Hirose H, Noguchi K, Ike Y, Yasui N, Furugori K, Yamaguchi Y, Toyoda A, Suzuki Y, Yamamoto T, Saitoh N, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Takahashi H. The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies' association with histone locus bodies. Nat Commun 2022; 13:2905. [PMID: 35614107 PMCID: PMC9133132 DOI: 10.1038/s41467-022-30632-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Abstract
Non-polyadenylated mRNAs of replication-dependent histones (RDHs) are synthesized by RNA polymerase II (Pol II) at histone locus bodies (HLBs). HLBs frequently associate with Cajal bodies (CBs), in which 3'-end processing factors for RDH genes are enriched; however, this association's role in transcription termination of RDH genes remains unclear. Here, we show that Pol II pauses immediately upstream of transcript end sites of RDH genes and Mediator plays a role in this Pol II pausing through CBs' association with HLBs. Disruption of the Mediator docking site for Little elongation complex (LEC)-Cap binding complex (CBC)-Negative elongation factor (NELF), components of CBs, interferes with CBs' association with HLBs and 3' Pol II pausing, resulting in increased aberrant unprocessed RDH gene transcripts. Our findings suggest Mediator's involvement in CBs' association with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing of RDH genes by supplying 3'-end processing factors.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Miho Shimada
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Tomonori Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Hiroko Hirose
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Keisuke Noguchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yoko Ike
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Nanami Yasui
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama, Kanagawa, 226-8501, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
| | - Tatsuro Yamamoto
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Shigeo Sato
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA
| | - Chieri Tomomori-Sato
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA.,Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000E 50th Street, Kansas City, MO, 64110, USA.,Department of Biochemistry & Molecular Biology, University of Kansas Medical Center, Kansas City, MO, 66160, USA
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
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20
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Beyond the canonical role of TFIIB in eukaryotic transcription. Curr Genet 2021; 68:61-67. [PMID: 34797379 PMCID: PMC8602988 DOI: 10.1007/s00294-021-01223-x] [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: 09/10/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/06/2023]
Abstract
The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies demonstrating binding of TFIIB to both the 5’ and 3’ ends of genes in a diverse set of eukaryotes strongly suggested a rather unexpected role of the factor in termination. TFIIB indeed plays a role in termination of transcription. TFIIB occupancy of the 3’ end is possibly due to its interaction with the termination factors residing there. Interaction of the promoter-bound TFIIB with factors occupying the 3’ end of a gene may be the basis of transcription-dependent gene looping. The proximity of the terminator-bound factors with the promoter in a gene loop has the potential to terminate promoter-initiated upstream anti-sense transcription thereby conferring promoter directionality. TFIIB, therefore, is emerging as a factor with pleiotropic roles in the transcription cycle. This could be the reason for preferential targeting of TFIIB by viruses. Further studies are needed to understand the critical role of TFIIB in viral pathogenesis in the context of its newly identified roles in termination, gene looping and promoter directionality.
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21
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Hou H, Li Y, Wang M, Liu A, Yu Z, Chen K, Zhao D, Xu Y. Structural insights into RNA polymerase III-mediated transcription termination through trapping poly-deoxythymidine. Nat Commun 2021; 12:6135. [PMID: 34675218 PMCID: PMC8531034 DOI: 10.1038/s41467-021-26402-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/24/2021] [Indexed: 01/11/2023] Open
Abstract
Termination of the RNA polymerase III (Pol III)-mediated transcription requires the conversion of an elongation complex (EC) to a pre-termination complex (PTC) on poly-deoxythymidine (dT)-containing non-template strand, a mechanism distinct from Pol I and Pol II. Here, our in vitro transcription elongation assay showed that 5-7 dT-containing DNA template led to transcription termination of Pol III, but not Pol I or Pol II. We assembled human Pol III PTC on a 7 dT-containing DNA template and determined the structure at 3.6 Å resolution. The structure reveals that poly-dT are trapped in a narrow exit tunnel formed by RPC2. A hydrophobic gate of the exit tunnel separates the bases of two connected deoxythymidines and may prevent translocation of the non-template strand. The fork loop 2 stabilizes both template and non-template strands around the transcription fork, and may further prevent strand translocation. Our study shows that the Pol III-specific exit tunnel and FL2 allow for efficient translocation of non-poly-dT sequence during transcription elongation but trap poly-dT to promote DNA retention of Pol III, revealing molecular mechanism of poly-dT-dependent transcription termination of Pol III.
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Affiliation(s)
- Haifeng Hou
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yan Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Mo Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Aijun Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Zishuo Yu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Ke Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Dan Zhao
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.
- Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock School of Life Sciences, Inner Mongolia University, Hohhot, 010070, P. R. China.
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22
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Deligianni E, Kiamos IS. Gene editing in Plasmodium berghei made easy: Development of a CRISPR/Cas9 protocol using linear donor template and ribozymes for sgRNA generation. Mol Biochem Parasitol 2021; 246:111415. [PMID: 34537287 DOI: 10.1016/j.molbiopara.2021.111415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 10/20/2022]
Abstract
Efficient reverse genetics approaches are critical for the study of many organisms. The CRISPR/Cas9 gene editing system has led to a plethora of new tools for geneticists. Here, we successfully established a simplified CRISPR/Cas9 system for the malaria model parasite Plasmodium berghei. The homologous directed repair (HDR) template is provided as a linear template with homologous arms of 600-700bp while the CRISPR elements sgRNA and Cas9 are encoded from a single plasmid utilizing the Ribozyme-Guide-Ribozyme (RGR) expression strategy. Our approach eliminates the need for negative selection markers since the plasmid cannot be incorporated into the genome. As a test case we inserted the FLAG encoding sequence into the ACT2 locus using this new approach. We showed that the genetic modification of this locus had no adverse effects on the completion of the P. berghei life cycle, including transmission through the mosquito.
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Affiliation(s)
- Elena Deligianni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece.
| | - Inga Siden Kiamos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion, Greece
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23
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You J, Song Z, Lin J, Jia R, Xia F, Li Z, Huang C. RNAi-directed knockdown induces nascent transcript degradation and premature transcription termination in the nucleus. Cell Discov 2021; 7:79. [PMID: 34489400 PMCID: PMC8421446 DOI: 10.1038/s41421-021-00297-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 06/30/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Jin You
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Ruirui Jia
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Fei Xia
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China. .,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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24
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Woo HH, Chambers SK. Regulation of closely juxtaposed proto-oncogene c-fms and HMGXB3 gene expression by mRNA 3' end polymorphism in breast cancer cells. RNA (NEW YORK, N.Y.) 2021; 27:1068-1081. [PMID: 34155128 PMCID: PMC8370744 DOI: 10.1261/rna.078749.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Sense-antisense mRNA pairs generated by convergent transcription is a way of gene regulation. c-fms gene is closely juxtaposed to the HMGXB3 gene in the opposite orientation, in chromosome 5. The intergenic region (IR) between c-fms and HMGXB3 genes is 162 bp. We found that a small portion (∼4.18%) of HMGXB3 mRNA is transcribed further downstream, including the end of the c-fms gene generating antisense mRNA against c-fms mRNA. Similarly, a small portion (∼1.1%) of c-fms mRNA is transcribed further downstream, including the end of the HMGXB3 gene generating antisense mRNA against the HMGXB3 mRNA. Insertion of the strong poly(A) signal sequence in the IR results in decreased c-fms and HMGXB3 antisense mRNAs, resulting in up-regulation of both c-fms and HMGXB3 mRNA expression. miR-324-5p targets HMGXB3 mRNA 3' UTR, and as a result, regulates c-fms mRNA expression. HuR stabilizes c-fms mRNA, and as a result, down-regulates HMGXB3 mRNA expression. UALCAN analysis indicates that the expression pattern between c-fms and HMGXB3 proteins are opposite in vivo in breast cancer tissues. Together, our results indicate that the mRNA encoded by the HMGXB3 gene can influence the expression of adjacent c-fms mRNA, or vice versa.
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MESH Headings
- 3' Untranslated Regions
- CRISPR-Cas Systems
- Cell Line, Tumor
- Chromosomes, Human, Pair 5
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- ELAV-Like Protein 1/genetics
- ELAV-Like Protein 1/metabolism
- Female
- Gene Editing
- Gene Expression Regulation, Neoplastic
- Genes, fms
- High Mobility Group Proteins/genetics
- High Mobility Group Proteins/metabolism
- Humans
- Mammary Glands, Human/metabolism
- Mammary Glands, Human/pathology
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Polymorphism, Genetic
- Proto-Oncogene Mas
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- Signal Transduction
- Transcription, Genetic
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Affiliation(s)
- Ho-Hyung Woo
- The University of Arizona Cancer Center, Tucson, Arizona 85724, USA
| | - Setsuko K Chambers
- The University of Arizona Cancer Center, Tucson, Arizona 85724, USA
- Department of Obstetrics and Gynecology, College of Medicine, The University of Arizona, Tucson, Arizona 85724, USA
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25
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A BRD4-mediated elongation control point primes transcribing RNA polymerase II for 3'-processing and termination. Mol Cell 2021; 81:3589-3603.e13. [PMID: 34324863 DOI: 10.1016/j.molcel.2021.06.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 04/14/2021] [Accepted: 06/22/2021] [Indexed: 12/15/2022]
Abstract
Transcription elongation has emerged as a regulatory hub in gene expression of metazoans. A major control point occurs during early elongation before RNA polymerase II (Pol II) is released into productive elongation. Prior research has linked BRD4 with transcription elongation. Here, we use rapid BET protein and BRD4-selective degradation along with quantitative genome-wide approaches to investigate direct functions of BRD4 in Pol II transcription regulation. Notably, as an immediate consequence of acute BRD4 loss, promoter-proximal pause release is impaired, and transcriptionally engaged Pol II past this checkpoint undergoes readthrough transcription. An integrated proteome-wide analysis uncovers elongation and 3'-RNA processing factors as core BRD4 interactors. BRD4 ablation disrupts the recruitment of general 3'-RNA processing factors at the 5'-control region, which correlates with RNA cleavage and termination defects. These studies, performed in human cells, reveal a BRD4-mediated checkpoint and begin to establish a molecular link between 5'-elongation control and 3'-RNA processing.
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26
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Porter JJ, Heil CS, Lueck JD. Therapeutic promise of engineered nonsense suppressor tRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1641. [PMID: 33567469 PMCID: PMC8244042 DOI: 10.1002/wrna.1641] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022]
Abstract
Nonsense mutations change an amino acid codon to a premature termination codon (PTC) generally through a single-nucleotide substitution. The generation of a PTC results in a defective truncated protein and often in severe forms of disease. Because of the exceedingly high prevalence of nonsense-associated diseases and a unifying mechanism, there has been a concerted effort to identify PTC therapeutics. Most clinical trials for PTC therapeutics have been conducted with small molecules that promote PTC read through and incorporation of a near-cognate amino acid. However, there is a need for PTC suppression agents that recode PTCs with the correct amino acid while being applicable to PTC mutations in many different genomic landscapes. With these characteristics, a single therapeutic will be able to treat several disease-causing PTCs. In this review, we will focus on the use of nonsense suppression technologies, in particular, suppressor tRNAs (sup-tRNAs), as possible therapeutics for correcting PTCs. Sup-tRNAs have many attractive qualities as possible therapeutic agents although there are knowledge gaps on their function in mammalian cells and technical hurdles that need to be overcome before their promise is realized. This article is categorized under: RNA Processing > tRNA Processing Translation > Translation Regulation.
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Affiliation(s)
- Joseph J. Porter
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - Christina S. Heil
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
| | - John D. Lueck
- Department of Pharmacology and PhysiologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
- Department of NeurologyUniversity of Rochester Medical CenterRochesterNew YorkUSA
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27
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Fütterer A, Talavera-Gutiérrez A, Pons T, de Celis J, Gutiérrez J, Domínguez Plaza V, Martínez-A C. Impaired stem cell differentiation and somatic cell reprogramming in DIDO3 mutants with altered RNA processing and increased R-loop levels. Cell Death Dis 2021; 12:637. [PMID: 34155199 PMCID: PMC8217545 DOI: 10.1038/s41419-021-03906-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 02/08/2023]
Abstract
Embryonic stem cell (ESC) differentiation and somatic cell reprogramming are biological processes governed by antagonistic expression or repression of a largely common set of genes. Accurate regulation of gene expression is thus essential for both processes, and alterations in RNA processing are predicted to negatively affect both. We show that truncation of the DIDO gene alters RNA splicing and transcription termination in ESC and mouse embryo fibroblasts (MEF), which affects genes involved in both differentiation and reprogramming. We combined transcriptomic, protein interaction, and cellular studies to identify the underlying molecular mechanism. We found that DIDO3 interacts with the helicase DHX9, which is involved in R-loop processing and transcription termination, and that DIDO3-exon16 deletion increases nuclear R-loop content and causes DNA replication stress. Overall, these defects result in failure of ESC to differentiate and of MEF to be reprogrammed. MEF immortalization restored impaired reprogramming capacity. We conclude that DIDO3 has essential functions in ESC differentiation and somatic cell reprogramming by supporting accurate RNA metabolism, with its exon16-encoded domain playing the main role.
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Affiliation(s)
- Agnes Fütterer
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Amaia Talavera-Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Tirso Pons
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Jesús de Celis
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Julio Gutiérrez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain
| | - Verónica Domínguez Plaza
- Transgenesis Unit, CNB & Centro de Biología Molecular Severo Ochoa, CSIC-Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Carlos Martínez-A
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), 28049, Madrid, Spain.
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28
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Wu Y, Yang Q, Wang M, Chen S, Jia R, Yang Q, Zhu D, Liu M, Zhao X, Zhang S, Huang J, Ou X, Mao S, Gao Q, Sun D, Tian B, Cheng A. Multifaceted Roles of ICP22/ORF63 Proteins in the Life Cycle of Human Herpesviruses. Front Microbiol 2021; 12:668461. [PMID: 34163446 PMCID: PMC8215345 DOI: 10.3389/fmicb.2021.668461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/05/2021] [Indexed: 01/03/2023] Open
Abstract
Herpesviruses are extremely successful parasites that have evolved over millions of years to develop a variety of mechanisms to coexist with their hosts and to maintain host-to-host transmission and lifelong infection by regulating their life cycles. The life cycle of herpesviruses consists of two phases: lytic infection and latent infection. During lytic infection, active replication and the production of numerous progeny virions occur. Subsequent suppression of the host immune response leads to a lifetime latent infection of the host. During latent infection, the viral genome remains in an inactive state in the host cell to avoid host immune surveillance, but the virus can be reactivated and reenter the lytic cycle. The balance between these two phases of the herpesvirus life cycle is controlled by broad interactions among numerous viral and cellular factors. ICP22/ORF63 proteins are among these factors and are involved in transcription, nuclear budding, latency establishment, and reactivation. In this review, we summarized the various roles and complex mechanisms by which ICP22/ORF63 proteins regulate the life cycle of human herpesviruses and the complex relationships among host and viral factors. Elucidating the role and mechanism of ICP22/ORF63 in virus-host interactions will deepen our understanding of the viral life cycle. In addition, it will also help us to understand the pathogenesis of herpesvirus infections and provide new strategies for combating these infections.
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Affiliation(s)
- Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiqi Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Dekang Zhu
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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29
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Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021; 17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022] Open
Abstract
The eukaryotic transcription cycle consists of three main steps: initiation, elongation, and cleavage of the nascent RNA transcript. Although each of these steps can be regulated as well as coupled with each other, their in vivo dissection has remained challenging because available experimental readouts lack sufficient spatiotemporal resolution to separate the contributions from each of these steps. Here, we describe a novel application of Bayesian inference techniques to simultaneously infer the effective parameters of the transcription cycle in real time and at the single-cell level using a two-color MS2/PP7 reporter gene and the developing fruit fly embryo as a case study. Our method enables detailed investigations into cell-to-cell variability in transcription-cycle parameters as well as single-cell correlations between these parameters. These measurements, combined with theoretical modeling, suggest a substantial variability in the elongation rate of individual RNA polymerase molecules. We further illustrate the power of this technique by uncovering a novel mechanistic connection between RNA polymerase density and nascent RNA cleavage efficiency. Thus, our approach makes it possible to shed light on the regulatory mechanisms in play during each step of the transcription cycle in individual, living cells at high spatiotemporal resolution.
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Affiliation(s)
- Jonathan Liu
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
| | - Donald Hansen
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Elizabeth Eck
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Yang Joon Kim
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Meghan Turner
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
| | - Simon Alamos
- Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, United States of America
| | - Hernan G. Garcia
- Department of Physics, University of California at Berkeley, Berkeley, California, United States of America
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California, United States of America
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California, United States of America
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30
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Wang X, Liu L, Whisnant AW, Hennig T, Djakovic L, Haque N, Bach C, Sandri-Goldin RM, Erhard F, Friedel CC, Dölken L, Shi Y. Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation. PLoS Genet 2021; 17:e1009263. [PMID: 33684133 PMCID: PMC7971895 DOI: 10.1371/journal.pgen.1009263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 03/18/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic gene expression is extensively regulated by cellular stress and pathogen infections. We have previously shown that herpes simplex virus 1 (HSV-1) and several cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes and that the viral immediate early factor ICP27 plays an important role in HSV-1-induced DoTT. Here, we show that HSV-1 infection also leads to widespread changes in alternative polyadenylation (APA) of host mRNAs. In the majority of cases, polyadenylation shifts to upstream poly(A) sites (PAS), including many intronic PAS. Mechanistically, ICP27 contributes to HSV-1-mediated APA regulation. HSV-1- and ICP27-induced activation of intronic PAS is sequence-dependent and does not involve general inhibition of U1 snRNP. HSV1-induced intronic polyadenylation is accompanied by early termination of RNAPII. HSV-1-induced mRNAs polyadenylated at intronic PAS (IPA) are exported into the cytoplasm while APA isoforms with extended 3' UTRs are sequestered in the nuclei, both preventing the expression of the full-length gene products. Finally we provide evidence that HSV-induced IPA isoforms are translated. Together with other recent studies, our results suggest that viral infection and cellular stresses induce a multi-faceted host response that includes DoTT and changes in APA profiles.
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Affiliation(s)
- Xiuye Wang
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States America
| | - Liang Liu
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States America
| | - Adam W. Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Germany
| | - Lara Djakovic
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Germany
| | - Nabila Haque
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States America
| | - Cindy Bach
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States America
| | - Rozanne M. Sandri-Goldin
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States America
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Germany
| | | | - Lars Dölken
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research, Würzburg, Germany
| | - Yongsheng Shi
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, California, United States America
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31
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Research Progress in the Molecular Functions of Plant mTERF Proteins. Cells 2021; 10:cells10020205. [PMID: 33494215 PMCID: PMC7909791 DOI: 10.3390/cells10020205] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/16/2021] [Accepted: 01/18/2021] [Indexed: 12/16/2022] Open
Abstract
Present-day chloroplast and mitochondrial genomes contain only a few dozen genes involved in ATP synthesis, photosynthesis, and gene expression. The proteins encoded by these genes are only a small fraction of the many hundreds of proteins that act in chloroplasts and mitochondria. Hence, the vast majority, including components of organellar gene expression (OGE) machineries, are encoded by nuclear genes, translated into the cytosol and imported to these organelles. Consequently, the expression of nuclear and organellar genomes has to be very precisely coordinated. Furthermore, OGE regulation is crucial to chloroplast and mitochondria biogenesis, and hence, to plant growth and development. Notwithstanding, the molecular mechanisms governing OGE are still poorly understood. Recent results have revealed the increasing importance of nuclear-encoded modular proteins capable of binding nucleic acids and regulating OGE. Mitochondrial transcription termination factor (mTERF) proteins are a good example of this category of OGE regulators. Plant mTERFs are located in chloroplasts and/or mitochondria, and have been characterized mainly from the isolation and analyses of Arabidopsis and maize mutants. These studies have revealed their fundamental roles in different plant development aspects and responses to abiotic stress. Fourteen mTERFs have been hitherto characterized in land plants, albeit to a different extent. These numbers are limited if we consider that 31 and 35 mTERFs have been, respectively, identified in maize and Arabidopsis. Notwithstanding, remarkable progress has been made in recent years to elucidate the molecular mechanisms by which mTERFs regulate OGE. Consequently, it has been experimentally demonstrated that plant mTERFs are required for the transcription termination of chloroplast genes (mTERF6 and mTERF8), transcriptional pausing and the stabilization of chloroplast transcripts (MDA1/mTERF5), intron splicing in chloroplasts (BSM/RUG2/mTERF4 and Zm-mTERF4) and mitochondria (mTERF15 and ZmSMK3) and very recently, also in the assembly of chloroplast ribosomes and translation (mTERF9). This review aims to provide a detailed update of current knowledge about the molecular functions of plant mTERF proteins. It principally focuses on new research that has made an outstanding contribution to unravel the molecular mechanisms by which plant mTERFs regulate the expression of chloroplast and mitochondrial genomes.
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32
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Kjellin J, Avesson L, Reimegård J, Liao Z, Eichinger L, Noegel A, Glöckner G, Schaap P, Söderbom F. Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas. Genome Res 2021; 31:436-447. [PMID: 33479022 PMCID: PMC7919456 DOI: 10.1101/gr.272856.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/15/2021] [Indexed: 01/26/2023]
Abstract
Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.
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Affiliation(s)
- Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
| | - Lotta Avesson
- Department of Molecular Biology, Biomedical Center, Swedish University of Agricultural Sciences, Uppsala S-75124, Sweden
| | - Johan Reimegård
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala S-75124, Sweden
| | - Zhen Liao
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
| | - Ludwig Eichinger
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Angelika Noegel
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Gernot Glöckner
- Centre for Biochemistry, Institute of Biochemistry I, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Pauline Schaap
- College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Uppsala University, Uppsala S-75124, Sweden
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33
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Feng G, Li X, Wang W, Deng L, Zeng K. Effects of Peptide Thanatin on the Growth and Transcriptome of Penicillium digitatum. Front Microbiol 2020; 11:606482. [PMID: 33381100 PMCID: PMC7767931 DOI: 10.3389/fmicb.2020.606482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/09/2020] [Indexed: 11/28/2022] Open
Abstract
Penicillium digitatum is the most damaging pathogen provoking green mold in citrus fruit during storage, and there is an urgent need for novel antifungal agents with high efficiency. The aim of this study was to investigate the antifungal effects of peptide thanatin against P. digitatum and the molecular mechanisms. Results showed that peptide thanatin had a prominent inhibitory effect on P. digitatum by in vitro and in vivo test. A total of 938 genes, including 556 downregulated and 382 upregulated genes, were differentially expressed, as revealed by RNA-seq of whole P. digitatum genomes analysis with or without thanatin treatment. The downregulated genes mainly encoded RNA polymerase, ribosome biogenesis, amino acid metabolism, and major facilitator superfamily. The genes associated with heat shock proteins and antioxidative systems were widely expressed in thanatin-treated group. DNA, RNA, and the protein content of P. digitatum were significantly decreased after thanatin treatment. In conclusion, thanatin could inhibit the growth of P. digitatum, and the underlying mechanism might be the genetic information processing and stress response were affected. The research will provide more precise and directional clues to explore the inhibitory mechanism of thanatin on growth of P. digitatum.
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Affiliation(s)
- Guirong Feng
- College of Food Science, Southwest University, Chongqing, China
| | - Xindan Li
- College of Food Science, Southwest University, Chongqing, China
| | - Wenjun Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Lili Deng
- College of Food Science, Southwest University, Chongqing, China.,Research Center of Food Storage and Logistics, Southwest University, Chongqing, China
| | - Kaifang Zeng
- College of Food Science, Southwest University, Chongqing, China.,Research Center of Food Storage and Logistics, Southwest University, Chongqing, China
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34
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Al-Husini N, Medler S, Ansari A. Crosstalk of promoter and terminator during RNA polymerase II transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194657. [PMID: 33246184 DOI: 10.1016/j.bbagrm.2020.194657] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
The transcription cycle of RNAPII is comprised of three consecutive steps; initiation, elongation and termination. It has been assumed that the initiation and termination steps occur in spatial isolation, essentially as independent events. A growing body of evidence, however, has challenged this dogma. First, factors involved in initiation and termination exhibit both a genetic and a physical interaction during transcription. Second, the initiation and termination factors have been found to occupy both ends of a transcribing gene. Third, physical interaction of initiation and termination factors occupying distal ends of a gene sometime results in the entire terminator region of a genes looping back and contact its cognate promoter, thereby forming a looped gene architecture during transcription. A logical interpretation of these findings is that the initiation and termination steps of transcription do not occur in isolation. There is extensive communication of factors occupying promoter and terminator ends of a gene during transcription cycle. This review entails a discussion of the promoter-terminator crosstalk and its implication in the context of transcription.
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Affiliation(s)
- Nadra Al-Husini
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Scott Medler
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America
| | - Athar Ansari
- Department of Biological Science, Wayne State University, Detroit, MI, United States of America.
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35
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XRN2 interactome reveals its synthetic lethal relationship with PARP1 inhibition. Sci Rep 2020; 10:14253. [PMID: 32859985 PMCID: PMC7455564 DOI: 10.1038/s41598-020-71203-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/11/2020] [Indexed: 12/17/2022] Open
Abstract
Persistent R-loops (RNA-DNA hybrids with a displaced single-stranded DNA) create DNA damage and lead to genomic instability. The 5'-3'-exoribonuclease 2 (XRN2) degrades RNA to resolve R-loops and promotes transcription termination. Previously, XRN2 was implicated in DNA double strand break (DSB) repair and in resolving replication stress. Here, using tandem affinity purification-mass spectrometry, bioinformatics, and biochemical approaches, we found that XRN2 associates with proteins involved in DNA repair/replication (Ku70-Ku80, DNA-PKcs, PARP1, MCM2-7, PCNA, RPA1) and RNA metabolism (RNA helicases, PRP19, p54(nrb), splicing factors). Novel major pathways linked to XRN2 include cell cycle control of chromosomal replication and DSB repair by non-homologous end joining. Investigating the biological implications of these interactions led us to discover that XRN2 depletion compromised cell survival after additional knockdown of specific DNA repair proteins, including PARP1. XRN2-deficient cells also showed enhanced PARP1 activity. Consistent with concurrent depletion of XRN2 and PARP1 promoting cell death, XRN2-deficient fibroblast and lung cancer cells also demonstrated sensitivity to PARP1 inhibition. XRN2 alterations (mutations, copy number/expression changes) are frequent in cancers. Thus, PARP1 inhibition could target cancers exhibiting XRN2 functional loss. Collectively, our data suggest XRN2's association with novel protein partners and unravel synthetic lethality between XRN2 depletion and PARP1 inhibition.
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36
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Vo TV, Dhakshnamoorthy J, Larkin M, Zofall M, Thillainadesan G, Balachandran V, Holla S, Wheeler D, Grewal SIS. CPF Recruitment to Non-canonical Transcription Termination Sites Triggers Heterochromatin Assembly and Gene Silencing. Cell Rep 2020; 28:267-281.e5. [PMID: 31269446 DOI: 10.1016/j.celrep.2019.05.107] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/16/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023] Open
Abstract
In eukaryotic genomes, heterochromatin is targeted by RNAi machinery and/or by pathways requiring RNA elimination and transcription termination factors. However, a direct connection between termination machinery and RNA polymerase II (RNAPII) transcriptional activity at heterochromatic loci has remained elusive. Here, we show that, in fission yeast, the conserved cleavage and polyadenylation factor (CPF) is a key component involved in RNAi-independent assembly of constitutive and facultative heterochromatin domains and that CPF is broadly required to silence genes regulated by Clr4SUV39H. Remarkably, CPF is recruited to non-canonical termination sites within the body of genes by the YTH family RNA-binding protein Mmi1 and is required for RNAPII transcription termination and facultative heterochromatin assembly. CPF loading by Mmi1 also promotes the selective termination of long non-coding RNAs that regulate gene expression in cis. These analyses delineate a mechanism in which CPF loaded onto non-canonical termination sites specifies targets of heterochromatin assembly and gene silencing.
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Affiliation(s)
- Tommy V Vo
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jothy Dhakshnamoorthy
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Madeline Larkin
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Martin Zofall
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Gobi Thillainadesan
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Vanivilasini Balachandran
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sahana Holla
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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37
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Sharma M, Wente SR. Nucleocytoplasmic shuttling of Gle1 impacts DDX1 at transcription termination sites. Mol Biol Cell 2020; 31:2398-2408. [PMID: 32755435 PMCID: PMC7851961 DOI: 10.1091/mbc.e20-03-0215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gle1 is a nucleocytoplasmic shuttling protein with well-documented cytoplasmic roles as a modulator of ATP-dependent DEAD-box RNA helicases involved in messenger (m)RNA export, translation initiation and termination, and stress granule dynamics. Here, we identify a novel nuclear role for Gle1 during transcription termination. In HeLa cells treated with a peptide that disrupts Gle1 nucleocytoplasmic shuttling, we detected nuclear accumulation of specific mRNAs with elongated 3′-UTR (untranslated region). Enriched mRNAs were nascently transcribed and accumulated in the nucleus due to a change in transcription state and not due to altered nuclear export. Whereas Gle1 shuttling inhibition did not appear to perturb nuclear DDX19 functions, it did result in increased DDX1 nucleoplasmic localization and decreased DDX1 interactions with Gle1 and the pre-mRNA cleavage stimulation factor CstF-64. An increase in nuclear R-loop signal intensity was also observed with diminished Gle1 shuttling, as well as colocalization of Gle1 at R-loops. Taken together, these studies reveal a nuclear role for Gle1 in coordinating DDX1 function in transcription termination complexes.
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Affiliation(s)
- Manisha Sharma
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN 37240
| | - Susan R Wente
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN 37240
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38
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Zheng N, Jiang S, He Y, Chen Y, Zhang C, Guo X, Ma L, Xiao D. Production of low-alcohol Huangjiu with improved acidity and reduced levels of higher alcohols by fermentation with scarless ALD6 overexpression yeast. Food Chem 2020; 321:126691. [DOI: 10.1016/j.foodchem.2020.126691] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/29/2020] [Accepted: 03/23/2020] [Indexed: 10/24/2022]
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39
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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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40
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LaBella ML, Hujber EJ, Moore KA, Rawson RL, Merrill SA, Allaire PD, Ailion M, Hollien J, Bastiani MJ, Jorgensen EM. Casein Kinase 1δ Stabilizes Mature Axons by Inhibiting Transcription Termination of Ankyrin. Dev Cell 2020; 52:88-103.e18. [PMID: 31910362 DOI: 10.1016/j.devcel.2019.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 01/19/2023]
Abstract
After axon outgrowth and synapse formation, the nervous system transitions to a stable architecture. In C. elegans, this transition is marked by the appearance of casein kinase 1δ (CK1δ) in the nucleus. In CK1δ mutants, neurons continue to sprout growth cones into adulthood, leading to a highly ramified nervous system. Nervous system architecture in these mutants is completely restored by suppressor mutations in ten genes involved in transcription termination. CK1δ prevents termination by phosphorylating and inhibiting SSUP-72. SSUP-72 would normally remodel the C-terminal domain of RNA polymerase in anticipation of termination. The antitermination activity of CK1δ establishes the mature state of a neuron by promoting the expression of the long isoform of a single gene, the cytoskeleton protein Ankyrin.
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Affiliation(s)
- Matthew L LaBella
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Edward J Hujber
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Kristin A Moore
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Randi L Rawson
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Sean A Merrill
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Patrick D Allaire
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Julie Hollien
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | | | - Erik M Jorgensen
- Department of Biology, Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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41
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Senturk N, Ergoren MC. Developing an Online Portal for Determining the Genomic Signature of Archaic DNA that are Associated to Modern Human Genetic Diseases: A Meta-Analysis Study. Eurasian J Med 2020; 52:153-160. [PMID: 32612423 DOI: 10.5152/eurasianjmed.2019.18424] [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: 01/09/2019] [Accepted: 08/22/2019] [Indexed: 11/22/2022] Open
Abstract
Objective Mutations or introgression can cause and rise adaptive alleles of which some can be beneficial. Archaic humans lived more than 200,000 years ago in Europe and Western Asia. They were adapted to the environment and pathogens that prevailed in these locations. It can therefore be thought that modern humans obtained significant immune advantage from the archaic alleles. Materials and Methods First, data were collected by meta-analysis from previously identified genetic diseases caused by alleles that were introgressed from archaics. Second, the in silico model portal (http://www.archaics2phenotype.xxx.edu.tr) was designed to trace the history of the Neanderthal allele. The portal also shows the current distribution of the genotypes of the selected alleles within different populations and correlates with the individuals phenotype. Results Our developed model provides a better understanding for the origin of genetic diseases or traits that are associated with the Neanderthal genome. Conclusion The developed medicine model will help individuals and their populations to receive the best treatment. It also clarifies why there are differences in disease phenotypes in modern humans.
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Affiliation(s)
- Niyazi Senturk
- Department of Biomedical Engineering, Near East University Faculty of Engineering, Nicosia, Cyprus
| | - Mahmut Cerkez Ergoren
- Department of Medical Biology, Near East University School of Medicine, Nicosia, Cyprus.,DESAM Institute, Near East University, Nicosia, Cyprus
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42
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More DA, Kumar A. SRSF3: Newly discovered functions and roles in human health and diseases. Eur J Cell Biol 2020; 99:151099. [PMID: 32800280 DOI: 10.1016/j.ejcb.2020.151099] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/29/2020] [Indexed: 12/21/2022] Open
Abstract
The serine/arginine rich proteins (SR proteins) are members of a family of RNA binding proteins involved in regulating various features of RNA metabolism, including pre-mRNA constitutive and alternative splicing. In humans, a total of 12 SR splicing factors (SRSFs) namely SRSF1-SRSF12 have been reported. SRSF3, the smallest member of the SR family and the focus of this review, regulates critical steps in mRNA metabolism and has been shown to have mRNA-independent functions as well. Recent studies on SRSF3 have uncovered its role in a wide array of complex biological processes. We have also reviewed the involvement of SRSF3 in disease conditions like cancer, ageing, neurological and cardiac disorders. Finally, we have discussed in detail the autoregulation of SRSF3 and its implications in cancer and commented on the potential of SRSF3 as a therapeutic target, especially in the context of cancer.
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Affiliation(s)
- Dhanashree Anil More
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Arun Kumar
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India.
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43
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Fischer J, Song YS, Yosef N, di Iulio J, Churchman LS, Choder M. The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions. J Biol Chem 2020; 295:11435-11454. [PMID: 32518159 DOI: 10.1074/jbc.ra120.013426] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/05/2020] [Indexed: 11/06/2022] Open
Abstract
mRNA levels are determined by the balance between mRNA synthesis and decay. Protein factors that mediate both processes, including the 5'-3' exonuclease Xrn1, are responsible for a cross-talk between the two processes that buffers steady-state mRNA levels. However, the roles of these proteins in transcription remain elusive and controversial. Applying native elongating transcript sequencing (NET-seq) to yeast cells, we show that Xrn1 functions mainly as a transcriptional activator and that its disruption manifests as a reduction of RNA polymerase II (Pol II) occupancy downstream of transcription start sites. By combining our sequencing data and mathematical modeling of transcription, we found that Xrn1 modulates transcription initiation and elongation of its target genes. Furthermore, Pol II occupancy markedly increased near cleavage and polyadenylation sites in xrn1Δ cells, whereas its activity decreased, a characteristic feature of backtracked Pol II. We also provide indirect evidence that Xrn1 is involved in transcription termination downstream of polyadenylation sites. We noted that two additional decay factors, Dhh1 and Lsm1, seem to function similarly to Xrn1 in transcription, perhaps as a complex, and that the decay factors Ccr4 and Rpb4 also perturb transcription in other ways. Interestingly, the decay factors could differentiate between SAGA- and TFIID-dominated promoters. These two classes of genes responded differently to XRN1 deletion in mRNA synthesis and were differentially regulated by mRNA decay pathways, raising the possibility that one distinction between these two gene classes lies in the mechanisms that balance mRNA synthesis with mRNA decay.
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Affiliation(s)
- Jonathan Fischer
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA.,Chan Zuckerberg BioHub, San Francisco, California, USA
| | - Nir Yosef
- Chan Zuckerberg BioHub, San Francisco, California, USA.,Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, USA
| | - Julia di Iulio
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Mordechai Choder
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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44
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Roth SJ, Heinz S, Benner C. ARTDeco: automatic readthrough transcription detection. BMC Bioinformatics 2020; 21:214. [PMID: 32456667 PMCID: PMC7249449 DOI: 10.1186/s12859-020-03551-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Mounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription past the 3' end of genes, which can result in novel transcripts, changes in epigenetic states and altered 3D genome structure. RESULTS We developed Automatic Readthrough Transcription Detection (ARTDeco), a tool to detect and analyze multiple features of readthrough transcription from RNA-seq and other next-generation sequencing (NGS) assays that profile transcriptional activity. ARTDeco robustly quantifies the global severity of readthrough phenotypes, and reliably identifies individual genes that fail to terminate (readthrough genes), are aberrantly transcribed due to upstream termination failure (read-in genes), and novel transcripts created as a result of readthrough (downstream of gene or DoG transcripts). We used ARTDeco to characterize readthrough transcription observed during influenza A virus (IAV) infection, validating its specificity and sensitivity by comparing its performance in samples infected with a mutant virus that fails to block transcription termination. We verify ARTDeco's ability to detect readthrough as well as identify read-in genes from different experimental assays across multiple experimental systems with known defects in transcriptional termination, and show how these results can be leveraged to improve the interpretation of gene expression and downstream analysis. Applying ARTDeco to a gene expression data set from IAV-infected monocytes from different donors, we find strong evidence that read-in gene-associated expression quantitative trait loci (eQTLs) likely regulate genes upstream of read-in genes. This indicates that taking readthrough transcription into account is important for the interpretation of eQTLs in systems where transcription termination is blocked. CONCLUSIONS ARTDeco aids researchers investigating readthrough transcription in a variety of systems and contexts.
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Affiliation(s)
- Samuel J Roth
- Bioinformatics and Systems Biology Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA
| | - Sven Heinz
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA
| | - Christopher Benner
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0640, USA.
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45
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Wu Y, Chen H, Chen Y, Qu L, Zhang E, Wang Z, Wu Y, Yang R, Mao R, Lu C, Fan Y. HPV shapes tumor transcriptome by globally modifying the pool of RNA binding protein-binding motif. Aging (Albany NY) 2020; 11:2430-2446. [PMID: 31039132 PMCID: PMC6520004 DOI: 10.18632/aging.101927] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/19/2019] [Indexed: 12/15/2022]
Abstract
Human papillomavirus (HPV) positive head and neck cancer displayed specific transcription landscape but the underlying molecular mechanisms are not fully determined. Here, we interestingly found that HPV infection could globally elongate the 3’-untranslated regions (3’UTRs) in the majority of alternative polyadenylation (APA)-containing genes. Counterintuitively, the 3’UTR elongation does not affect their resident gene expression. Rather, they significantly increase the number of binding sites for RNA-binding proteins (RBPs) and subsequently upregulate a group of oncogenic genes by absorbing RBPs. A significant fraction of HPV affected genes are regulated through such mechanism that is 3’UTR-mediated recruitment of RBPs. As an example, we observed that HPV infection increases the length of 3’UTR of RBM25 transcript and hence recruits much more RNA binding protein including FUS and DGCR8. Consequently, in the absence of FUS and DGCR8 regulation, PD-1 was rescued and up-regulated after HPV infection. Taken together, our findings not only suggest a novel paradigm of how oncogenic viruses shape tumor transcriptome by modifying the 3’UTR, but also present a previously unrecognized layer of APA—RBP interplay in this molecular hierarchy. Modification of the pool of RBP-binding motif might expand our understandings into virus-associated carcinogenesis.
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Affiliation(s)
- Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Hao Chen
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Yuyan Chen
- Department of Surgery, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Lishuai Qu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Erhao Zhang
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Zhou Wang
- School of Life Sciences, Nantong University, Jiangsu 226001, China
| | - Yuanyuan Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Riyun Yang
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu 226001, China
| | - Cuihua Lu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu 226001, China.,Department of Immunology, School of Medicine, Nantong University, Jiangsu 226001, China
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46
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Lyons DE, McMahon S, Ott M. A combinatorial view of old and new RNA polymerase II modifications. Transcription 2020; 11:66-82. [PMID: 32401151 DOI: 10.1080/21541264.2020.1762468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The production of mRNA is a dynamic process that is highly regulated by reversible post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II. The CTD is a highly repetitive domain consisting mostly of the consensus heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. Phosphorylation of serine residues within this repeat sequence is well studied, but modifications of all residues have been described. Here, we focus on integrating newly identified and lesser-studied CTD post-translational modifications into the existing framework. We also review the growing body of work demonstrating crosstalk between different CTD modifications and the functional consequences of such crosstalk on the dynamics of transcriptional regulation.
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Affiliation(s)
- Danielle E Lyons
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
| | - Sarah McMahon
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco , San Francisco, CA, USA
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47
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Kwon SW, Paari KA, Malaviya A, Jang YS. Synthetic Biology Tools for Genome and Transcriptome Engineering of Solventogenic Clostridium. Front Bioeng Biotechnol 2020; 8:282. [PMID: 32363182 PMCID: PMC7181999 DOI: 10.3389/fbioe.2020.00282] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
Strains of Clostridium genus are used for production of various value-added products including fuels and chemicals. Development of any commercially viable production process requires a combination of both strain and fermentation process development strategies. The strain development in Clostridium sp. could be achieved by random mutagenesis, and targeted gene alteration methods. However, strain improvement in Clostridium sp. by targeted gene alteration method was challenging due to the lack of efficient tools for genome and transcriptome engineering in this organism. Recently, various synthetic biology tools have been developed to facilitate the strain engineering of solventogenic Clostridium. In this review, we consolidated the recent advancements in toolbox development for genome and transcriptome engineering in solventogenic Clostridium. Here we reviewed the genome-engineering tools employing mobile group II intron, pyrE alleles exchange, and CRISPR/Cas9 with their application for strain development of Clostridium sp. Next, transcriptome engineering tools such as untranslated region (UTR) engineering and synthetic sRNA techniques were also discussed in context of Clostridium strain engineering. Application of any of these discussed techniques will facilitate the metabolic engineering of clostridia for development of improved strains with respect to requisite functional attributes. This might lead to the development of an economically viable butanol production process with improved titer, yield and productivity.
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Affiliation(s)
- Seong Woo Kwon
- Department of Agricultural Chemistry and Food Science Technology, Division of Applied Life Science (BK21 Plus Program), Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
| | | | - Alok Malaviya
- Applied and Industrial Biotechnology Laboratory (AIBL), Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru, India
| | - Yu-Sin Jang
- Department of Agricultural Chemistry and Food Science Technology, Division of Applied Life Science (BK21 Plus Program), Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju, South Korea
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48
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The transcription and export complex THO/TREX contributes to transcription termination in plants. PLoS Genet 2020; 16:e1008732. [PMID: 32282821 PMCID: PMC7179932 DOI: 10.1371/journal.pgen.1008732] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 04/23/2020] [Accepted: 03/22/2020] [Indexed: 11/23/2022] Open
Abstract
Transcription termination has important regulatory functions, impacting mRNA stability, localization and translation potential. Failure to appropriately terminate transcription can also lead to read-through transcription and the synthesis of antisense RNAs which can have profound impact on gene expression. The Transcription-Export (THO/TREX) protein complex plays an important role in coupling transcription with splicing and export of mRNA. However, little is known about the role of the THO/TREX complex in the control of transcription termination. In this work, we show that two proteins of the THO/TREX complex, namely TREX COMPONENT 1 (TEX1 or THO3) and HYPER RECOMBINATION1 (HPR1 or THO1) contribute to the correct transcription termination at several loci in Arabidopsis thaliana. We first demonstrate this by showing defective termination in tex1 and hpr1 mutants at the nopaline synthase (NOS) terminator present in a T-DNA inserted between exon 1 and 3 of the PHO1 locus in the pho1-7 mutant. Read-through transcription beyond the NOS terminator and splicing-out of the T-DNA resulted in the generation of a near full-length PHO1 mRNA (minus exon 2) in the tex1 pho1-7 and hpr1 pho1-7 double mutants, with enhanced production of a truncated PHO1 protein that retained phosphate export activity. Consequently, the strong reduction of shoot growth associated with the severe phosphate deficiency of the pho1-7 mutant was alleviated in the tex1 pho1-7 and hpr1 pho1-7 double mutants. Additionally, we show that RNA termination defects in tex1 and hpr1 mutants leads to 3’UTR extensions in several endogenous genes. These results demonstrate that THO/TREX complex contributes to the regulation of transcription termination. Production of messenger RNAs (mRNAs) involves numerous steps including initiation of transcription, elongation, splicing, termination, as well as export out of the nucleus. All these steps are highly coordinated and failure in any steps has a profound impact on the level and identity of mRNAs produced. The THO/TREX protein complex is associated with nascent RNAs and contributes to several mRNA biogenesis steps, including splicing and export. However, the contribution of the THO/TREX complex to mRNA termination was poorly defined. We have identified a role for two components of the THO/TREX complex, namely the proteins TEX1 and HPR1, in the control of transcription termination in the plant Arabidopsis thaliana. We show that the tex1 and hpr1 mutants have defects in terminating mRNA at the nopaline synthase (NOS) terminator found in a T-DNA insertion mutant leading to the transcriptional read-through pass the NOS terminator. We also show that tex1 and hpr1 mutants have defects in mRNA termination at several endogenous genes, leading to the production of 3’UTR extensions. Together, these results highlight a role for the THO/TREX complex in mRNA termination.
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49
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Lee KY, Chopra A, Burke GL, Chen Z, Greenblatt JF, Biggar KK, Meneghini MD. A crucial RNA-binding lysine residue in the Nab3 RRM domain undergoes SET1 and SET3-responsive methylation. Nucleic Acids Res 2020; 48:2897-2911. [PMID: 31960028 PMCID: PMC7102954 DOI: 10.1093/nar/gkaa029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/07/2020] [Accepted: 01/18/2020] [Indexed: 11/13/2022] Open
Abstract
The Nrd1-Nab3-Sen1 (NNS) complex integrates molecular cues to direct termination of noncoding transcription in budding yeast. NNS is positively regulated by histone methylation as well as through Nrd1 binding to the initiating form of RNA PolII. These cues collaborate with Nrd1 and Nab3 binding to target RNA sequences in nascent transcripts through their RRM RNA recognition motifs. In this study, we identify nine lysine residues distributed amongst Nrd1, Nab3 and Sen1 that are methylated, suggesting novel molecular inputs for NNS regulation. We identify mono-methylation of one these residues (Nab3-K363me1) as being partly dependent on the H3K4 methyltransferase, Set1, a known regulator of NNS function. Moreover, the accumulation of Nab3-K363me1 is essentially abolished in strains lacking SET3, a SET domain containing protein that is positively regulated by H3K4 methylation. Nab3-K363 resides within its RRM and physically contacts target RNA. Mutation of Nab3-K363 to arginine (Nab3-K363R) decreases RNA binding of the Nab3 RRM in vitro and causes transcription termination defects and slow growth. These findings identify SET3 as a potential contextual regulator of Nab3 function through its role in methylation of Nab3-K363. Consistent with this hypothesis, we report that SET3 exhibits genetic activation of NAB3 that is observed in a sensitized context.
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Affiliation(s)
- Kwan Yin Lee
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Anand Chopra
- Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Giovanni L Burke
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Ziyan Chen
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
| | - Jack F Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada.,Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Kyle K Biggar
- Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Marc D Meneghini
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G 1M1, Canada
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50
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Roy KR, Chanfreau GF. Robust mapping of polyadenylated and non-polyadenylated RNA 3' ends at nucleotide resolution by 3'-end sequencing. Methods 2020; 176:4-13. [PMID: 31128237 PMCID: PMC6874744 DOI: 10.1016/j.ymeth.2019.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/10/2019] [Accepted: 05/20/2019] [Indexed: 10/26/2022] Open
Abstract
3'-end poly(A)+ sequencing is an efficient and economical method for global measurement of mRNA levels and alternative poly(A) site usage. A common method involves oligo(dT)19V reverse-transcription (RT)-based library preparation and high-throughput sequencing with a custom primer ending in (dT)19. While the majority of library products have the first sequenced nucleotide reflect the bona fide poly(A) site (pA), a substantial fraction of sequencing reads arise from various mis-priming events. These can result in incorrect pA site calls anywhere from several nucleotides downstream to several kilobases upstream from the bona fide pA site. While these mis-priming events can be mitigated by increasing annealing stringency (e.g. increasing temperature from 37 °C to 42 °C), they still persist at an appreciable level (∼10%) and computational methods must be used to prevent artifactual calls. Here we present a bioinformatics workflow for precise mapping of poly(A)+ 3' ends and handling of artifacts due to oligo(dT) mis-priming and sample polymorphisms. We test pA site calling with three different read mapping programs (STAR, BWA, and BBMap), and show that the way in which each handles terminal mismatches and soft clipping has a substantial impact on identifying correct pA sites, with BWA requiring the least post-processing to correct artifacts. We demonstrate the use of this pipeline for mapping pA sites in the model eukaryote S. cerevisiae, and further apply this technology to non-polyadenylated transcripts by employing in vitro polyadenylation prior to library prep (IVP-seq). As proof of principle, we show that a fraction of tRNAs harbor CCU 3' tails instead of the canonical CCA tail, and globally identify 3' ends of splicing intermediates arising from inefficiently spliced transcripts.
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Affiliation(s)
- Kevin R Roy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1570, United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095-1569, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095-1570, United States.
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