1
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Diao AJ, Su BG, Vos SM. Pause Patrol: Negative Elongation Factor's Role in Promoter-Proximal Pausing and Beyond. J Mol Biol 2024:168779. [PMID: 39241983 DOI: 10.1016/j.jmb.2024.168779] [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: 06/28/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
Abstract
RNA polymerase (Pol) II is highly regulated to ensure appropriate gene expression. Early transcription elongation is associated with transient pausing of RNA Pol II in the promoter-proximal region. In multicellular organisms, this pausing is stabilized by the association of transcription elongation factors DRB-sensitivity inducing factor (DSIF) and Negative Elongation Factor (NELF). DSIF is a broadly conserved transcription elongation factor whereas NELF is mostly restricted to the metazoan lineage. Mounting evidence suggests that NELF association with RNA Pol II serves as checkpoint for either release into rapid and productive transcription elongation or premature termination at promoter-proximal pause sites. Here we summarize NELF's roles in promoter-proximal pausing, transcription termination, DNA repair, and signaling based on decades of cell biological, biochemical, and structural work and describe areas for future research.
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Affiliation(s)
- Annette J Diao
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, United States
| | - Bonnie G Su
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, United States
| | - Seychelle M Vos
- Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, United States; Howard Hughes Medical Institute, United States.
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2
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Fang C, Huang K, Wu X, Zhang H, Gu Z, Wang J, Zhang Y. Transcription elongation of the plant RNA polymerase IV is prone to backtracking. SCIENCE ADVANCES 2024; 10:eadq3087. [PMID: 39178250 PMCID: PMC11343019 DOI: 10.1126/sciadv.adq3087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/22/2024] [Indexed: 08/25/2024]
Abstract
RNA polymerase IV (Pol IV) forms a complex with RNA-directed RNA polymerase 2 (RDR2) to produce double-stranded RNA (dsRNA) precursors essential for plant gene silencing. In the "backtracking-triggered RNA channeling" model, Pol IV backtracks and delivers its transcript's 3' terminus to RDR2, which synthesizes dsRNA. However, the mechanisms underlying Pol IV backtracking and RNA protection from cleavage are unclear. Here, we determined cryo-electron microscopy structures of Pol IV elongation complexes at four states of its nucleotide addition cycle (NAC): posttranslocation, guanosine triphosphate-bound, pretranslocation, and backtracked states. The structures reveal that Pol IV maintains an open DNA cleft and kinked bridge helix in all NAC states, loosely interacts with the nucleoside triphosphate substrate, and barely contacts proximal backtracked nucleotides. Biochemical data indicate that Pol IV is inefficient in forward translocation and RNA cleavage. These findings suggest that Pol IV transcription elongation is prone to backtracking and incapable of RNA hydrolysis, ensuring efficient dsRNA production by Pol IV-RDR2.
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Affiliation(s)
- Chengli Fang
- Key Laboratory of Synthetic Biology, State 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 200032, China
| | - Kun Huang
- Key Laboratory of Synthetic Biology, State 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 200032, China
| | - Xiaoxian Wu
- Key Laboratory of Synthetic Biology, State 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 200032, China
| | - Hongwei Zhang
- Key Laboratory of Synthetic Biology, State 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 200032, China
| | - Zhanxi Gu
- Key Laboratory of Synthetic Biology, State 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 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, State 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 200032, China
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3
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Yang KB, Rasouly A, Epshtein V, Martinez C, Nguyen T, Shamovsky I, Nudler E. Persistence of backtracking by human RNA polymerase II. Mol Cell 2024; 84:897-909.e4. [PMID: 38340716 DOI: 10.1016/j.molcel.2024.01.019] [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: 08/25/2023] [Revised: 11/20/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024]
Abstract
RNA polymerase II (RNA Pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome-wide distribution of more persistent backtracking are unknown. Consequently, we developed a method to directly sequence the extruded, "backtracked" 3' RNA. Our data show that RNA Pol II slides backward more than 20 nt in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where RNA Pol II pauses near promoters and intron-exon junctions and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking can potentially affect diverse gene expression programs.
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Affiliation(s)
- Kevin B Yang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Aviram Rasouly
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Criseyda Martinez
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Thao Nguyen
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, NYU Langone Health, New York, NY 10016, USA.
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4
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Yang KB, Rasouly A, Epshtein V, Martinez C, Nguyen T, Shamovsky I, Nudler E. Persistence of backtracking by human RNA polymerase II. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571520. [PMID: 38168453 PMCID: PMC10760130 DOI: 10.1101/2023.12.13.571520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
RNA polymerase II (pol II) can backtrack during transcription elongation, exposing the 3' end of nascent RNA. Nascent RNA sequencing can approximate the location of backtracking events that are quickly resolved; however, the extent and genome wide distribution of more persistent backtracking is unknown. Consequently, we developed a novel method to directly sequence the extruded, "backtracked" 3' RNA. Our data shows that pol II slides backwards more than 20 nucleotides in human cells and can persist in this backtracked state. Persistent backtracking mainly occurs where pol II pauses near promoters and intron-exon junctions, and is enriched in genes involved in translation, replication, and development, where gene expression is decreased if these events are unresolved. Histone genes are highly prone to persistent backtracking, and the resolution of such events is likely required for timely expression during cell division. These results demonstrate that persistent backtracking has the potential to affect diverse gene expression programs.
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5
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Mermigka G, Michalopoulou VA, Amartolou A, Mentzelopoulou A, Astropekaki N, Sarris PF. Assassination tango: an NLR/NLR-ID immune receptors pair of rapeseed co-operates inside the nucleus to activate cell death. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1211-1222. [PMID: 36628462 DOI: 10.1111/tpj.16105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Plant immunity largely relies on intracellular nucleotide-binding domain leucine-rich repeat (NLR) immune receptors. Some plant NLRs carry integrated domains (IDs) that mimic authentic pathogen effector targets. We report here the identification of a genetically linked NLR-ID/NLR pair: BnRPR1 and BnRPR2 in Brassica napus. The NLR-ID carries two ID fusions and the mode of action of the pair conforms to the proposed "integrated sensor/decoy" model. The two NLRs interact and the heterocomplex localizes in the plant-cell nucleus and nucleolus. However, the BnRPRs pair does not operate through a negative regulation as it was previously reported for other NLR-IDs. Cell death is induced only upon co-expression of the two proteins and is dependent on the helper genes, EDS1 and NRG1. The nuclear localization of both proteins seems to be essential for cell death activation, while the IDs of BnRPR1 are dispensable for this purpose. In summary, we describe a new pair of NLR-IDs with interesting features in relation to its regulation and the cell death activation.
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Affiliation(s)
- Glykeria Mermigka
- Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, 70013, Crete, Heraklion, Greece
| | - Vassiliki A Michalopoulou
- Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, 70013, Crete, Heraklion, Greece
| | - Argyro Amartolou
- Department of Biology, University of Crete, Crete, 714 09 Heraklion, Greece
| | | | - Niki Astropekaki
- Department of Biology, University of Crete, Crete, 714 09 Heraklion, Greece
| | - Panagiotis F Sarris
- Foundation for Research and Technology-Hellas, Institute of Molecular Biology and Biotechnology, 70013, Crete, Heraklion, Greece
- Department of Biology, University of Crete, Crete, 714 09 Heraklion, Greece
- Biosciences, University of Exeter, EX4 4QD, Exeter, Geoffrey Pope Building, Stocker Road, UK
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6
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Mitra P, Banerjee S, Khandavalli C, Deshmukh AS. The role of Toxoplasma TFIIS-like protein in the early stages of mRNA transcription. Biochim Biophys Acta Gen Subj 2022; 1866:130240. [PMID: 36058424 DOI: 10.1016/j.bbagen.2022.130240] [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: 06/24/2022] [Revised: 08/25/2022] [Accepted: 08/28/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND The mRNA transcription is a multistep process involving distinct sets of proteins associated with RNA polymerase II (RNAPII) through various stages. Recent studies have highlighted the role of RNAPII-associated proteins in facilitating the assembly of functional complexes in a crowded nuclear milieu. RNAPII dynamics and gene expression regulation have been primarily studied in model eukaryotes like yeasts and mammals and remain largely unchartered in protozoan parasites like Toxoplasma gondii, where considerable gene expression changes accompany stage differentiations. Here we report a key modulator of RNAPII activity, TFIIS in Toxoplasma gondii (TgTFIIS). METHODS A Pull-down assay demonstrated that TgTFIIS binds to RNAPII subunit TgRPB1. Truncation mutants of TFIIS help us define the regions critical for its binding to TgRPB1. Co-immunoprecipitation analysis confirmed the interaction between the native TgTFIIS and TgRPB1. Confocal microscopy revealed a predominantly nuclear localization. Native TgTFIIS was able to bind promoter DNA which was consistent with the CHIP results. RESULTS TgTFIIS complements initiation defects in yeast mutants, and the regions implicated in RNAPII binding appeared essential for this function. Interestingly, the C-terminal zinc finger domain necessary for its potential elongation function is dispensable for TgRPB1 binding. TgTFIIS was found to be associated with the promoter region along with its association with the ORF on an RNAPII transcribed gene. CONCLUSION The observations were in line with the potential role of TgTFIIS in early events of RNAPII transcription in addition to elongation. GENERAL SIGNIFICANCE The study elucidates the potential role of RNAPII-associated proteins in multiple steps of transcription.
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Affiliation(s)
- Pallabi Mitra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India.
| | - Sneha Banerjee
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Chittiraju Khandavalli
- DBT-National Institute of Animal Biotechnology, Hyderabad, India; Dept. of Graduate Studies, Regional Centre for Biotechnology, Faridabad, Haryana, India
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7
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Fei J, Xu J, Li Z, Xu K, Wang D, Kassavetis GA, Kadonaga JT. NDF is a transcription factor that stimulates elongation by RNA polymerase II. Genes Dev 2022; 36:294-299. [PMID: 35273076 PMCID: PMC8973848 DOI: 10.1101/gad.349150.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022]
Abstract
Here, Fei et al. found that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. Their findings demonstrate that NDF is a Pol II binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans. RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we found that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than that used by transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.
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Affiliation(s)
- Jia Fei
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Ziwei Li
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Kevin Xu
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Cellular and Molecular Medicine, School of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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8
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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9
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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10
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Jacobs RQ, Ingram ZM, Lucius AL, Schneider DA. Defining the divergent enzymatic properties of RNA polymerases I and II. J Biol Chem 2021; 296:100051. [PMID: 33168625 PMCID: PMC7948988 DOI: 10.1074/jbc.ra120.015904] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/26/2020] [Accepted: 11/09/2020] [Indexed: 01/22/2023] Open
Abstract
Eukaryotes express at least three nuclear DNA-dependent RNA polymerases (Pols) responsible for synthesizing all RNA required by the cell. Despite sharing structural homology, they have functionally diverged to suit their distinct cellular roles. Although the Pols have been studied extensively, direct comparison of their enzymatic properties is difficult because studies are often conducted under disparate experimental conditions and techniques. Here, we directly compare and reveal functional differences between Saccharomyces cerevisiae Pols I and II using a series of quantitative in vitro transcription assays. We find that Pol I single-nucleotide and multinucleotide addition rate constants are faster than those of Pol II. Pol I elongation complexes are less stable than Pol II elongation complexes, and Pol I is more error prone than Pol II. Collectively, these data show that the enzymatic properties of the Pols have diverged over the course of evolution, optimizing these enzymes for their unique cellular responsibilities.
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Affiliation(s)
- Ruth Q Jacobs
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zachariah M Ingram
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama, USA.
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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11
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Rushworth LK, Harle V, Repiscak P, Clark W, Shaw R, Hall H, Bushell M, Leung HY, Patel R. In vivo CRISPR/Cas9 knockout screen: TCEAL1 silencing enhances docetaxel efficacy in prostate cancer. Life Sci Alliance 2020; 3:e202000770. [PMID: 33033111 PMCID: PMC7556750 DOI: 10.26508/lsa.202000770] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/22/2020] [Accepted: 09/25/2020] [Indexed: 01/03/2023] Open
Abstract
Docetaxel chemotherapy in metastatic prostate cancer offers only a modest survival benefit because of emerging resistance. To identify candidate therapeutic gene targets, we applied a murine prostate cancer orthograft model that recapitulates clinical invasive prostate cancer in a genome-wide CRISPR/Cas9 screen under docetaxel treatment pressure. We identified 17 candidate genes whose suppression may enhance the efficacy of docetaxel, with transcription elongation factor A-like 1 (Tceal1) as the top candidate. TCEAL1 function is not fully characterised; it may modulate transcription in a promoter dependent fashion. Suppressed TCEAL1 expression in multiple human prostate cancer cell lines enhanced therapeutic response to docetaxel. Based on gene set enrichment analysis from transcriptomic data and flow cytometry, we confirmed that loss of TCEAL1 in combination with docetaxel leads to an altered cell cycle profile compared with docetaxel alone, with increased subG1 cell death and increased polyploidy. Here, we report the first in vivo genome-wide treatment sensitisation CRISPR screen in prostate cancer, and present proof of concept data on TCEAL1 as a candidate for a combinational strategy with the use of docetaxel.
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Affiliation(s)
- Linda K Rushworth
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Victoria Harle
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Peter Repiscak
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Robin Shaw
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Holly Hall
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Martin Bushell
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Hing Y Leung
- Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
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12
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Abstract
More than 50 years after the identification of RNA polymerase II, the enzyme responsible for the transcription of most eukaryotic genes, studies have continued to reveal fresh aspects of its structure and regulation. New technologies, coupled with years of development of a vast catalog of RNA polymerase II accessory proteins and activities, have led to new revelations about the transcription process. The maturation of cryo-electron microscopy as a tool for unraveling the detailed structure of large molecular machines has provided numerous structures of the enzyme and its accessory factors. Advances in biophysical methods have enabled the observation of a single polymerase’s behavior, distinct from work on aggregate population averages. Other recent work has revealed new properties and activities of the general initiation factors that RNA polymerase II employs to accurately initiate transcription, as well as chromatin proteins that control RNA polymerase II’s firing frequency, and elongation factors that facilitate the enzyme’s departure from the promoter and which control sequential steps and obstacles that must be navigated by elongating RNA polymerase II. There has also been a growing appreciation of the physical properties conferred upon many of these proteins by regions of each polypeptide that are of low primary sequence complexity and that are often intrinsically disordered. This peculiar feature of a surprisingly large number of proteins enables a disordered region of the protein to morph into a stable structure and creates an opportunity for pathway participants to dynamically partition into subcompartments of the nucleus. These subcompartments host designated portions of the chemical reactions that lead to mRNA synthesis. This article highlights a selection of recent findings that reveal some of the resolved workings of RNA polymerase II and its ensemble of supporting factors.
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Affiliation(s)
- Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
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13
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The Regulatory Properties of the Ccr4-Not Complex. Cells 2020; 9:cells9112379. [PMID: 33138308 PMCID: PMC7692201 DOI: 10.3390/cells9112379] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
The mammalian Ccr4–Not complex, carbon catabolite repression 4 (Ccr4)-negative on TATA-less (Not), is a large, highly conserved, multifunctional assembly of proteins that acts at different cellular levels to regulate gene expression. In the nucleus, it is involved in the regulation of the cell cycle, chromatin modification, activation and inhibition of transcription initiation, control of transcription elongation, RNA export, nuclear RNA surveillance, and DNA damage repair. In the cytoplasm, the Ccr4–Not complex plays a central role in mRNA decay and affects protein quality control. Most of our original knowledge of the Ccr4–Not complex is derived, primarily, from studies in yeast. More recent studies have shown that the mammalian complex has a comparable structure and similar properties. In this review, we summarize the evidence for the multiple roles of both the yeast and mammalian Ccr4–Not complexes, highlighting their similarities.
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14
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Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina. Genes (Basel) 2020; 11:genes11091107. [PMID: 32967372 PMCID: PMC7564353 DOI: 10.3390/genes11091107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/18/2020] [Indexed: 11/17/2022] Open
Abstract
The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt ('Pt104') as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27-40 candidates and CNV analysis identified 14-31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available.
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Herzog JJ, Xu W, Deshpande M, Rahman R, Suib H, Rodal AA, Rosbash M, Paradis S. TDP-43 dysfunction restricts dendritic complexity by inhibiting CREB activation and altering gene expression. Proc Natl Acad Sci U S A 2020; 117:11760-11769. [PMID: 32393629 PMCID: PMC7260973 DOI: 10.1073/pnas.1917038117] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are two related neurodegenerative diseases that present with similar TDP-43 pathology in patient tissue. TDP-43 is an RNA-binding protein which forms aggregates in neurons of ALS and FTD patients as well as in a subset of patients diagnosed with other neurodegenerative diseases. Despite our understanding that TDP-43 is essential for many aspects of RNA metabolism, it remains obscure how TDP-43 dysfunction contributes to neurodegeneration. Interestingly, altered neuronal dendritic morphology is a common theme among several neurological disorders and is thought to precede neurodegeneration. We previously found that both TDP-43 overexpression (OE) and knockdown (KD) result in reduced dendritic branching of cortical neurons. In this study, we used TRIBE (targets of RNA-binding proteins identified by editing) as an approach to identify signaling pathways that regulate dendritic branching downstream of TDP-43. We found that TDP-43 RNA targets are enriched for pathways that signal to the CREB transcription factor. We further found that TDP-43 dysfunction inhibits CREB activation and CREB transcriptional output, and restoring CREB signaling rescues defects in dendritic branching. Finally, we demonstrate, using RNA sequencing, that TDP-43 OE and KD cause similar changes in the abundance of specific messenger RNAs, consistent with their ability to produce similar morphological defects. Our data therefore provide a mechanism by which TDP-43 dysfunction interferes with dendritic branching, and may define pathways for therapeutic intervention in neurodegenerative diseases.
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Affiliation(s)
- Josiah J Herzog
- Department of Biology, Brandeis University, Waltham, MA 02453
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
| | - Weijin Xu
- Department of Biology, Brandeis University, Waltham, MA 02453
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453
| | - Mugdha Deshpande
- Department of Biology, Brandeis University, Waltham, MA 02453
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
| | - Reazur Rahman
- Department of Biology, Brandeis University, Waltham, MA 02453
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453
| | - Hannah Suib
- Department of Biology, Brandeis University, Waltham, MA 02453
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
| | - Avital A Rodal
- Department of Biology, Brandeis University, Waltham, MA 02453
| | - Michael Rosbash
- Department of Biology, Brandeis University, Waltham, MA 02453;
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453
| | - Suzanne Paradis
- Department of Biology, Brandeis University, Waltham, MA 02453;
- Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453
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16
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Antosz W, Deforges J, Begcy K, Bruckmann A, Poirier Y, Dresselhaus T, Grasser KD. Critical Role of Transcript Cleavage in Arabidopsis RNA Polymerase II Transcriptional Elongation. THE PLANT CELL 2020; 32:1449-1463. [PMID: 32152189 PMCID: PMC7203918 DOI: 10.1105/tpc.19.00891] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/10/2020] [Accepted: 03/05/2020] [Indexed: 05/14/2023]
Abstract
Transcript elongation factors associate with elongating RNA polymerase II (RNAPII) to control the efficiency of mRNA synthesis and consequently modulate plant growth and development. Encountering obstacles during transcription such as nucleosomes or particular DNA sequences may cause backtracking and transcriptional arrest of RNAPII. The elongation factor TFIIS stimulates the intrinsic transcript cleavage activity of the polymerase, which is required for efficient rescue of backtracked/arrested RNAPII. A TFIIS mutant variant (TFIISmut) lacks the stimulatory activity to promote RNA cleavage, but instead efficiently inhibits unstimulated transcript cleavage by RNAPII. We could not recover viable Arabidopsis (Arabidopsis thaliana) tfIIs plants constitutively expressing TFIISmut. Induced, transient expression of TFIISmut in tfIIs plants provoked severe growth defects, transcriptomic changes and massive, transcription-related redistribution of elongating RNAPII within transcribed regions toward the transcriptional start site. The predominant site of RNAPII accumulation overlapped with the +1 nucleosome, suggesting that upon inhibition of RNA cleavage activity, RNAPII arrest prevalently occurs at this position. In the presence of TFIISmut, the amount of RNAPII was reduced, which could be reverted by inhibiting the proteasome, indicating proteasomal degradation of arrested RNAPII. Our findings suggest that polymerase backtracking/arrest frequently occurs in plant cells, and RNAPII-reactivation is essential for correct transcriptional output and proper growth/development.
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Affiliation(s)
- Wojciech Antosz
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Jules Deforges
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Kevin Begcy
- Environmental Horticulture Department, University of Florida, Gainesville, Florida 32611
| | - Astrid Bruckmann
- Department for Biochemistry I, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Yves Poirier
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Thomas Dresselhaus
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
| | - Klaus D Grasser
- Department of Cell Biology & Plant Biochemistry, Biochemistry Centre, University of Regensburg, D-93040 Regensburg, Germany
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17
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Kazim N, Adhikari A, Oh TJ, Davie J. The transcription elongation factor TCEA3 induces apoptosis in rhabdomyosarcoma. Cell Death Dis 2020; 11:67. [PMID: 31988307 PMCID: PMC6985194 DOI: 10.1038/s41419-020-2258-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/13/2022]
Abstract
TCEA3 is one of three genes representing the transcription elongation factor TFIIS family in vertebrates. TCEA3 is upregulated during skeletal muscle differentiation and acts to promote muscle specific gene expression during myogenesis. Rhabdomyosarcoma (RMS) is a pediatric cancer derived from the muscle lineage, but the expression or function of TCEA3 in RMS was uncharacterized. We found that TCEA3 expression was strongly inhibited in RMS cell lines representing both ERMS and ARMS subtypes of RMS. TCEA3 expression correlates with DNA methylation and we show that TBX2 is also involved in the repression of TCEA3 in RMS cell lines. Ectopic expression of TCEA3 inhibited proliferation of RMS cell lines and initiated apoptosis through both the intrinsic and extrinsic pathways. We found that only pan-caspase inhibitors could block apoptosis in the presence of TCEA3. While expression of TCEA3 is highest in skeletal muscle, expression has been detected in other tissues as well, including breast, ovarian and prostate. We found that ectopic expression of TCEA3 also promotes apoptosis in HeLa, MCF7, MDA-231, and PC3 cell lines, representing cervical, breast, and prostate cancer, respectively. Restoration of TCEA3 expression in RMS cell lines enhanced sensitivity to chemotherapeutic drugs, including TRAIL. Thus, TCEA3 presents a novel target for therapeutic strategies to promote apoptosis and enhance sensitivity to current chemotherapeutic drugs.
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Affiliation(s)
- Noor Kazim
- Department of Biomedical Science, Cornell University, Ithaca, NY, 14850, USA
| | - Abhinav Adhikari
- Department of Biochemistry and Molecular Biology and Simmons Cancer Institute, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA
| | - Teak Jung Oh
- Department of Biochemistry, University of Illinois Urbana, Champaign, IL, 61820, USA
| | - Judith Davie
- Department of Biochemistry and Molecular Biology and Simmons Cancer Institute, Southern Illinois University School of Medicine, Carbondale, IL, 62901, USA.
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18
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Peck SA, Hughes KD, Victorino JF, Mosley AL. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1529. [PMID: 30848101 PMCID: PMC6570551 DOI: 10.1002/wrna.1529] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 12/27/2018] [Accepted: 02/07/2019] [Indexed: 12/20/2022]
Abstract
Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Sarah A Peck
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Katlyn D Hughes
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jose F Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
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19
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Ge Y, Li S, Hu XY, Tong HL, Li SF, Yan YQ. TCEA3 promotes differentiation of C2C12 cells via an Annexin A1-mediated transforming growth factor-β signaling pathway. J Cell Physiol 2019; 234:10554-10565. [PMID: 30623413 DOI: 10.1002/jcp.27726] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 10/18/2018] [Indexed: 12/13/2022]
Abstract
TCEA3 is a member of the transcription elongation factor family that not only promotes transcription but may also participate in other cytoplasmic processes. However, its mechanisms of action remain unclear. Our previous study indicated that TCEA3 may affect muscle differentiation. In this study, we investigated the expression and localization of TCEA3 in C2C12 cells and examined the role of TCEA3 in differentiation, its interaction with other cell proteins, and mechanisms of action. We found that the expression of TCEA3 increased gradually with an increase in the number of differentiation days and that it is mainly expressed in the cytoplasm of C2C12 cells, of which it promotes differentiation. Coimmunoprecipitation experiments and western blot analysis revealed that TCEA3 interacts with Annexin A1 (ANXA1), which is located in the cytoplasm and also promotes cell differentiation. Collectively, our results indicate that TCEA3 promotes cell differentiation by interacting with ANXA1 and affecting transforming growth factor-β signaling pathways.
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Affiliation(s)
- Yao Ge
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, China
| | - Shuang Li
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, China
| | - Xiao-Yang Hu
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, China
| | - Hui-Li Tong
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, China
| | - Shu-Feng Li
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, China
| | - Yun-Qin Yan
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, China
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20
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TCEA1 regulates the proliferative potential of mouse myeloid cells. Exp Cell Res 2018; 370:551-560. [PMID: 30009791 DOI: 10.1016/j.yexcr.2018.07.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 01/15/2023]
Abstract
Leukemia is a malignance with complex pathogenesis and poor prognosis. Discovery of noval regulators amenable to leukemia could be of value to gain insight into the pathogenesis, diagnosis and prognosis of leukemia. Here, we conducted a large-scale shRNA library screening for functional regulators in the development of myeloid cells in primary cells. We identified eighteen candidate regulators in the primary screening. Those genes cover a wide range of cellular functions, including gene expression regulation, intracellular signaling transduction, nucleotide excision repair, cell cycle control and transcription regulation. In both primary screening and validation, shRNAs targeting Tcea1, encoding the transcription elongation factor A (SII) 1, exhibited the greatest influence on the proliferative potential of cells. Knocking down the expression of Tcea1 in the 32Dcl3 myeloid cell line led to enhanced proliferation of myeloid cells and blockage of myeloid differentiation induced by G-CSF. In addition, silence of Tcea1 inhibited apoptosis of myeloid cells. Thus, Tcea1 was identified as a gene which can influence the proliferative potential, survival and differentiation of myeloid cells. These findings have implications for how transcriptional elongation influences myeloid cell development and leukemic transformation.
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21
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Herzog JJ, Deshpande M, Shapiro L, Rodal AA, Paradis S. TDP-43 misexpression causes defects in dendritic growth. Sci Rep 2017; 7:15656. [PMID: 29142232 PMCID: PMC5688077 DOI: 10.1038/s41598-017-15914-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 11/03/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Dementia (FTD) share overlapping genetic causes and disease symptoms, and are linked neuropathologically by the RNA binding protein TDP-43 (TAR DNA binding protein-43 kDa). TDP-43 regulates RNA metabolism, trafficking, and localization of thousands of target genes. However, the cellular and molecular mechanisms by which dysfunction of TDP-43 contributes to disease pathogenesis and progression remain unclear. Severe changes in the structure of neuronal dendritic arbors disrupt proper circuit connectivity, which in turn could contribute to neurodegenerative disease. Although aberrant dendritic morphology has been reported in non-TDP-43 mouse models of ALS and in human ALS patients, this phenotype is largely unexplored with regards to TDP-43. Here we have employed a primary rodent neuronal culture model to study the cellular effects of TDP-43 dysfunction in hippocampal and cortical neurons. We show that manipulation of TDP-43 expression levels causes significant defects in dendritic branching and outgrowth, without an immediate effect on cell viability. The effect on dendritic morphology is dependent on the RNA-binding ability of TDP-43. Thus, this model system will be useful in identifying pathways downstream of TDP-43 that mediate dendritic arborization, which may provide potential new avenues for therapeutic intervention in ALS/FTD.
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Affiliation(s)
- Josiah J Herzog
- Department of Biology, Volen Center for Complex Systems, and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts, 02454, USA
| | - Mugdha Deshpande
- Department of Biology, Volen Center for Complex Systems, and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts, 02454, USA
| | - Leah Shapiro
- Department of Biology, Volen Center for Complex Systems, and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts, 02454, USA
| | - Avital A Rodal
- Department of Biology, Volen Center for Complex Systems, and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts, 02454, USA
| | - Suzanne Paradis
- Department of Biology, Volen Center for Complex Systems, and National Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts, 02454, USA.
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22
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Gali VK, Balint E, Serbyn N, Frittmann O, Stutz F, Unk I. Translesion synthesis DNA polymerase η exhibits a specific RNA extension activity and a transcription-associated function. Sci Rep 2017; 7:13055. [PMID: 29026143 PMCID: PMC5638924 DOI: 10.1038/s41598-017-12915-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/01/2017] [Indexed: 11/09/2022] Open
Abstract
Polymerase eta (Polη) is a low fidelity translesion synthesis DNA polymerase that rescues damage-stalled replication by inserting deoxy-ribonucleotides opposite DNA damage sites resulting in error-free or mutagenic damage bypass. In this study we identify a new specific RNA extension activity of Polη of Saccharomyces cerevisiae. We show that Polη is able to extend RNA primers in the presence of ribonucleotides (rNTPs), and that these reactions are an order of magnitude more efficient than the misinsertion of rNTPs into DNA. Moreover, during RNA extension Polη performs error-free bypass of the 8-oxoguanine and thymine dimer DNA lesions, though with a 103 and 102-fold lower efficiency, respectively, than it synthesizes opposite undamaged nucleotides. Furthermore, in vivo experiments demonstrate that the transcription of several genes is affected by the lack of Polη, and that Polη is enriched over actively transcribed regions. Moreover, inactivation of its polymerase activity causes similar transcription inhibition as the absence of Polη. In summary, these results suggest that the new RNA synthetic activity of Polη can have in vivo relevance.
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Affiliation(s)
- Vamsi K Gali
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary.,Institute of Medical Sciences Foresterhill, University of Aberdeen, Aberdeen, United Kingdom
| | - Eva Balint
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Nataliia Serbyn
- Department of Cell Biology, iGE3, University of Geneva, 1211, Geneva, Switzerland
| | - Orsolya Frittmann
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary
| | - Francoise Stutz
- Department of Cell Biology, iGE3, University of Geneva, 1211, Geneva, Switzerland
| | - Ildiko Unk
- The Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6726, Hungary.
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23
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Multisubunit DNA-Dependent RNA Polymerases from Vaccinia Virus and Other Nucleocytoplasmic Large-DNA Viruses: Impressions from the Age of Structure. Microbiol Mol Biol Rev 2017; 81:81/3/e00010-17. [PMID: 28701329 DOI: 10.1128/mmbr.00010-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The past 17 years have been marked by a revolution in our understanding of cellular multisubunit DNA-dependent RNA polymerases (MSDDRPs) at the structural level. A parallel development over the past 15 years has been the emerging story of the giant viruses, which encode MSDDRPs. Here we link the two in an attempt to understand the specialization of multisubunit RNA polymerases in the domain of life encompassing the large nucleocytoplasmic DNA viruses (NCLDV), a superclade that includes the giant viruses and the biochemically well-characterized poxvirus vaccinia virus. The first half of this review surveys the recently determined structural biology of cellular RNA polymerases for a microbiology readership. The second half discusses a reannotation of MSDDRP subunits from NCLDV families and the apparent specialization of these enzymes by virus family and by subunit with regard to subunit or domain loss, subunit dissociability, endogenous control of polymerase arrest, and the elimination/customization of regulatory interactions that would confer higher-order cellular control. Some themes are apparent in linking subunit function to structure in the viral world: as with cellular RNA polymerases I and III and unlike cellular RNA polymerase II, the viral enzymes seem to opt for speed and processivity and seem to have eliminated domains associated with higher-order regulation. The adoption/loss of viral RNA polymerase proofreading functions may have played a part in matching intrinsic mutability to genome size.
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24
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Myers RR, Smith TD, Elsawa SF, Puel O, Tadrist S, Calvo AM. rtfA controls development, secondary metabolism, and virulence in Aspergillus fumigatus. PLoS One 2017; 12:e0176702. [PMID: 28453536 PMCID: PMC5409149 DOI: 10.1371/journal.pone.0176702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/14/2017] [Indexed: 12/18/2022] Open
Abstract
Invasive aspergillosis by Aspergillus fumigatus is a leading cause of infection-related mortality in immune-compromised patients. In order to discover potential genetic targets to control A. fumigatus infections we characterized rtfA, a gene encoding a putative RNA polymerase II transcription elongation factor-like protein. Our recent work has shown that the rtfA ortholog in the model fungus Aspergillus nidulans regulates morphogenesis and secondary metabolism. The present study on the opportunistic pathogen A. fumigatus rtfA gene revealed that this gene influences fungal growth and conidiation, as well as production of the secondary metabolites tryptoquivaline F, pseurotin A, fumiquinazoline C, festuclavine, and fumigaclavines A, B and C. Additionally, rtfA influences protease activity levels, the sensitivity to oxidative stress and adhesion capacity, all factors important in pathogenicity. Furthermore, rtfA was shown to be indispensable for normal virulence using Galleria mellonella as well as murine infection model systems.
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Affiliation(s)
- Ryan R. Myers
- Department of Biological Sciences, Northern Illinois University, Dekalb, Illinois, United States of America
| | - Timothy D. Smith
- Department of Biological Sciences, Northern Illinois University, Dekalb, Illinois, United States of America
| | - Sherine F. Elsawa
- Department of Biological Sciences, Northern Illinois University, Dekalb, Illinois, United States of America
| | - Olivier Puel
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Souraia Tadrist
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Ana M. Calvo
- Department of Biological Sciences, Northern Illinois University, Dekalb, Illinois, United States of America
- * E-mail:
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25
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Zhu Y, Tong HL, Li SF, Yan YQ. Effect of TCEA3 on the differentiation of bovine skeletal muscle satellite cells. Biochem Biophys Res Commun 2017; 484:827-832. [PMID: 28161635 DOI: 10.1016/j.bbrc.2017.01.182] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 11/17/2022]
Abstract
Bovine muscle-derived satellite cells (MDSCs) are important for animal growth. In this study, the effect of transcription elongation factor A3 (TCEA3) on bovine MDSC differentiation was investigated. Western blotting, immunofluorescence assays, and cytoplasmic and nuclear protein isolation and purification techniques were used to determine the expression pattern and protein localization of TCEA3 in bovine MDSCs during in vitro differentiation. TCEA3 expression was upregulated using the CRISPR/Cas9 technique to study its effects on MDSC differentiation in vitro. TCEA3 expression gradually increased during the in vitro differentiation of bovine MDSCs and peaked on the 5th day of differentiation. TCEA3 was mainly localized in the cytoplasm of bovine MDSCs, and its expression was not detected in the nucleus. The level of TCEA3 was relatively higher in myotubes at a higher degree of differentiation than during early differentiation. After transfection with a TCEA3-activating plasmid vector (TCEA3 overexpression) for 24 h, the myotube fusion rate, number of myotubes, and expression levels of the muscle differentiation-related loci myogenin (MYOG) and myosin heavy chain 3 (MYH3) increased significantly during the in vitro differentiation of bovine MDSCs. After transfection with a TCEA3-inhibiting plasmid vector for 24 h, the myotube fusion rate, number of myotubes, and expression levels of MYOG and MYH3 decreased significantly. Our results indicated, for the first time, that TCEA3 promotes the differentiation of bovine MDSCs and have implications for meat production and animal rearing.
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Affiliation(s)
- Yue Zhu
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Hui-Li Tong
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Shu-Feng Li
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China
| | - Yun-Qin Yan
- The Laboratory of Cell and Development, Northeast Agricultural University, Harbin, Heilongjiang 150030, China.
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26
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Gómez-Navarro N, Peiró-Chova L, Estruch F. Iwr1 facilitates RNA polymerase II dynamics during transcription elongation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:803-811. [PMID: 28258010 DOI: 10.1016/j.bbagrm.2017.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 02/16/2017] [Accepted: 02/27/2017] [Indexed: 11/16/2022]
Abstract
Iwr1 is an RNA polymerase II (RNPII) interacting protein that directs nuclear import of the enzyme which has been previously assembled in the cytoplasm. Here we present genetic and molecular evidence that links Iwr1 with transcription. Our results indicate that Iwr1 interacts with RNPII during elongation and is involved in the disassembly of the enzyme from chromatin. This function is especially important in resolving problems posed by damage-arrested RNPII, as shown by the sensitivity of iwr1 mutants to genotoxic drugs and the Iwr1's genetic interactions with RNPII degradation pathway mutants. Moreover, absence of Iwr1 causes genome instability that is enhanced by defects in the DNA repair machinery.
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Affiliation(s)
- Natalia Gómez-Navarro
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Burjassot, Valencia 46100, Spain
| | - Lorena Peiró-Chova
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Burjassot, Valencia 46100, Spain
| | - Francisco Estruch
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Burjassot, Valencia 46100, Spain.
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27
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Uthe H, Vanselow JT, Schlosser A. Proteomic Analysis of the Mediator Complex Interactome in Saccharomyces cerevisiae. Sci Rep 2017; 7:43584. [PMID: 28240253 PMCID: PMC5327418 DOI: 10.1038/srep43584] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/25/2017] [Indexed: 12/02/2022] Open
Abstract
Here we present the most comprehensive analysis of the yeast Mediator complex interactome to date. Particularly gentle cell lysis and co-immunopurification conditions allowed us to preserve even transient protein-protein interactions and to comprehensively probe the molecular environment of the Mediator complex in the cell. Metabolic 15N-labeling thereby enabled stringent discrimination between bona fide interaction partners and nonspecifically captured proteins. Our data indicates a functional role for Mediator beyond transcription initiation. We identified a large number of Mediator-interacting proteins and protein complexes, such as RNA polymerase II, general transcription factors, a large number of transcriptional activators, the SAGA complex, chromatin remodeling complexes, histone chaperones, highly acetylated histones, as well as proteins playing a role in co-transcriptional processes, such as splicing, mRNA decapping and mRNA decay. Moreover, our data provides clear evidence, that the Mediator complex interacts not only with RNA polymerase II, but also with RNA polymerases I and III, and indicates a functional role of the Mediator complex in rRNA processing and ribosome biogenesis.
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Affiliation(s)
- Henriette Uthe
- Rudolf Virchow Center for Experimental Biomedicine, University of Wuerzburg, Josef-Schneider-Str. 2, 97080, Wuerzburg, Germany
| | - Jens T Vanselow
- Rudolf Virchow Center for Experimental Biomedicine, University of Wuerzburg, Josef-Schneider-Str. 2, 97080, Wuerzburg, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center for Experimental Biomedicine, University of Wuerzburg, Josef-Schneider-Str. 2, 97080, Wuerzburg, Germany
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28
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Distinct functions of human RecQ helicases during DNA replication. Biophys Chem 2016; 225:20-26. [PMID: 27876204 DOI: 10.1016/j.bpc.2016.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/13/2016] [Accepted: 11/13/2016] [Indexed: 12/31/2022]
Abstract
DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition.
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29
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He Y, Yan C, Fang J, Inouye C, Tjian R, Ivanov I, Nogales E. Near-atomic resolution visualization of human transcription promoter opening. Nature 2016; 533:359-65. [PMID: 27193682 PMCID: PMC4940141 DOI: 10.1038/nature17970] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/05/2016] [Indexed: 12/11/2022]
Abstract
In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.
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Affiliation(s)
- Yuan He
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Chunli Yan
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, USA
| | - Jie Fang
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA
| | - Carla Inouye
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, California 94720, USA
| | - Robert Tjian
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30302, USA
| | - Eva Nogales
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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30
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Liao JM, Cao B, Deng J, Zhou X, Strong M, Zeng S, Xiong J, Flemington E, Lu H. TFIIS.h, a new target of p53, regulates transcription efficiency of pro-apoptotic bax gene. Sci Rep 2016; 6:23542. [PMID: 27005522 PMCID: PMC4804275 DOI: 10.1038/srep23542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/03/2016] [Indexed: 11/09/2022] Open
Abstract
Tumor suppressor p53 transcriptionally regulates hundreds of genes involved in various cellular functions. However, the detailed mechanisms underlying the selection of p53 targets in response to different stresses are still elusive. Here, we identify TFIIS.h, a transcription elongation factor, as a new transcriptional target of p53, and also show that it can enhance the efficiency of transcription elongation of apoptosis-associated bax gene, but not cell cycle-associated p21 (CDKN1A) gene. TFIIS.h is revealed as a p53 target through microarray analysis of RNAs extracted from cells treated with or without inauhzin (INZ), a p53 activator, and further confirmed by RT-q-PCR, western blot, luciferase reporter, and ChIP assays. Interestingly, knocking down TFIIS.h impairs, but overexpressing TFIIS.h promotes, induction of bax, but not other p53 targets including p21, by p53 activation. In addition, overexpression of TFIIS.h induces cell death in a bax- dependent fashion. These findings reveal a mechanism by which p53 utilizes TFIIS.h to selectively promote the transcriptional elongation of the bax gene, upsurging cell death in response to severe DNA damage.
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Affiliation(s)
- Jun-Ming Liao
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Bo Cao
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Jun Deng
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA.,Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Xiang Zhou
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Michael Strong
- Department of Pathology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Shelya Zeng
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Jianping Xiong
- Department of Oncology, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Erik Flemington
- Department of Pathology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
| | - Hua Lu
- Department of Biochemistry &Molecular Biology and Cancer Center, Tulane University School of Medicine, 1430, Louisiana, LA 70112, USA
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31
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Collart MA. The Ccr4-Not complex is a key regulator of eukaryotic gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:438-54. [PMID: 26821858 PMCID: PMC5066686 DOI: 10.1002/wrna.1332] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 12/22/2022]
Abstract
The Ccr4‐Not complex is a multisubunit complex present in all eukaryotes that contributes to regulate gene expression at all steps, from production of messenger RNAs (mRNAs) in the nucleus to their degradation in the cytoplasm. In the nucleus it influences the post‐translational modifications of the chromatin template that has to be remodeled for transcription, it is present at sites of transcription and associates with transcription factors as well as with the elongating polymerase, it interacts with the factors that prepare the new transcript for export to the cytoplasm and finally is important for nuclear quality control and influences mRNA export. In the cytoplasm it is present in polysomes where mRNAs are translated and in RNA granules where mRNAs will be redirected upon inhibition of translation. It influences mRNA translatability, and is needed during translation, on one hand for co‐translational protein interactions and on the other hand to preserve translation that stalls. It is one of the relevant players during co‐translational quality control. It also interacts with factors that will repress translation or induce mRNA decapping when recruited to the translating template. Finally, Ccr4‐Not carries deadenylating enzymes and is a key player in mRNA decay, generic mRNA decay that follows normal translation termination, co‐translational mRNA decay of transcripts on which the ribosomes stall durably or which carry a non‐sense mutation and finally mRNA decay that is induced by external signaling for a change in genetic programming. Ccr4‐Not is a master regulator of eukaryotic gene expression. WIREs RNA 2016, 7:438–454. doi: 10.1002/wrna.1332 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Martine A Collart
- Department Microbiology and Molecular Medicine, CMU, Geneva, Switzerland.,Institute of Genetics and Genomics, Geneva, Switzerland
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32
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Wu J, Ye W, Yang J, Chen HF. Conformational selection and induced fit for RNA polymerase and RNA/DNA hybrid backtracked recognition. Front Mol Biosci 2015; 2:61. [PMID: 26594643 PMCID: PMC4633505 DOI: 10.3389/fmolb.2015.00061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/11/2015] [Indexed: 01/22/2023] Open
Abstract
RNA polymerase catalyzes transcription with a high fidelity. If DNA/RNA mismatch or DNA damage occurs downstream, a backtracked RNA polymerase can proofread this situation. However, the backtracked mechanism is still poorly understood. Here we have performed multiple explicit-solvent molecular dynamics (MD) simulations on bound and apo DNA/RNA hybrid to study backtracked recognition. MD simulations at room temperature suggest that specific electrostatic interactions play key roles in the backtracked recognition between the polymerase and DNA/RNA hybrid. Kinetics analysis at high temperature shows that bound and apo DNA/RNA hybrid unfold via a two-state process. Both kinetics and free energy landscape analyses indicate that bound DNA/RNA hybrid folds in the order of DNA/RNA contracting, the tertiary folding and polymerase binding. The predicted Φ-values suggest that C7, G9, dC12, dC15, and dT16 are key bases for the backtracked recognition of DNA/RNA hybrid. The average RMSD values between the bound structures and the corresponding apo ones and Kolmogorov-Smirnov (KS) P-test analyses indicate that the recognition between DNA/RNA hybrid and polymerase might follow an induced fit mechanism for DNA/RNA hybrid and conformation selection for polymerase. Furthermore, this method could be used to relative studies of specific recognition between nucleic acid and protein.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai, China
| | - Wei Ye
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai, China
| | - Jingxu Yang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai, China ; Shanghai Center for Bioinformation Technology Shanghai, China
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33
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Li J, Jin Y, Pan S, Chen Y, Wang K, Lin C, Jin S, Wu J. TCEA3 Attenuates Gastric Cancer Growth by Apoptosis Induction. Med Sci Monit 2015; 21:3241-6. [PMID: 26498664 PMCID: PMC4627366 DOI: 10.12659/msm.895860] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background The aim of this study was to investigate and interpret the expression level and potential function of TCEA3 in gastric cancer. Material/Methods qRT-PCR was used to determine the expression level of TCEA3 in gastric cancer tissues. Pearson χ2 test was performed to clarify the correlation between TCEA3 expression and patients’ clinicopathologic characteristics. Biological function of TCEA3 was tested by proliferation assay and colony formation assay. Flow cytometry was used to study the potential function of TCEA3 in apoptosis induction. Results TCEA3 expression was significantly downregulated in gastric cancer tissues compared with paired normal tissues. Poor prognoses were observed in the low TCEA3 expression group of patients in contrast to the high TCEA3 expression group. Functionally, upregulation of TCEA3 inhibited gastric cancer cell proliferation and colony formation. We also found that TCEA3 may attenuate cell growth through apoptosis induction. Conclusions Our findings suggest that TCEA3 attenuates the proliferation and induces apoptosis of gastric cancer cells.
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Affiliation(s)
- Jia Li
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Yin Jin
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Shuang Pan
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Yina Chen
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Kaijing Wang
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Chunjing Lin
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Shuqing Jin
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
| | - Jiansheng Wu
- Department of Gastroenterology, First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China (mainland)
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34
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Arimbasseri AG, Rijal K, Maraia RJ. Comparative overview of RNA polymerase II and III transcription cycles, with focus on RNA polymerase III termination and reinitiation. Transcription 2015; 5:e27639. [PMID: 25764110 DOI: 10.4161/trns.27369] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In eukaryotes, RNA polymerase (RNAP) III transcribes hundreds of genes for tRNAs and 5S rRNA, among others, which share similar promoters and stable transcription initiation complexes (TIC), which support rapid RNAP III recycling. In contrast, RNAP II transcribes a large number of genes with highly variable promoters and interacting factors, which exert fine regulatory control over TIC lability and modifications of RNAP II at different transitional points in the transcription cycle. We review data that illustrate a relatively smooth continuity of RNAP III initiation-elongation-termination and reinitiation toward its function to produce high levels of tRNAs and other RNAs that support growth and development.
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Affiliation(s)
- Aneeshkumar G Arimbasseri
- a Intramural Research Program; Eunice Kennedy Shriver National Institute of Child Health and Human Development; National Institutes of Health; Bethesda, MD USA
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35
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Zhou H, Liu Q, Shi T, Yu Y, Lu H. Genome-wide screen of fission yeast mutants for sensitivity to 6-azauracil, an inhibitor of transcriptional elongation. Yeast 2015; 32:643-55. [DOI: 10.1002/yea.3085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/23/2015] [Accepted: 06/26/2015] [Indexed: 01/10/2023] Open
Affiliation(s)
- Huan Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Qi Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Tianfang Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai People's Republic of China
- Shanghai Engineering Research Centre of Industrial Microorganisms; Shanghai 200438 People's Republic of China
- Shanghai Collaborative Innovation Centre for Biomanufacturing Technology; Shanghai 200237 People's Republic of China
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36
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Ccr4-Not and TFIIS Function Cooperatively To Rescue Arrested RNA Polymerase II. Mol Cell Biol 2015; 35:1915-25. [PMID: 25776559 DOI: 10.1128/mcb.00044-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/11/2015] [Indexed: 12/13/2022] Open
Abstract
Expression of the genome requires RNA polymerase II (RNAPII) to transcribe across many natural and unnatural barriers, and this transcription across barriers is facilitated by protein complexes called elongation factors (EFs). Genetic studies in Saccharomyces cerevisiae yeast suggest that multiple EFs collaborate to assist RNAPII in completing the transcription of genes, but the molecular mechanisms of how they cooperate to promote elongation are not well understood. The Ccr4-Not complex participates in multiple steps of mRNA metabolism and has recently been shown to be an EF. Here we describe how Ccr4-Not and TFIIS cooperate to stimulate elongation. We find that Ccr4-Not and TFIIS mutations show synthetically enhanced phenotypes, and biochemical analyses indicate that Ccr4-Not and TFIIS work synergistically to reactivate arrested RNAPII. Ccr4-Not increases the recruitment of TFIIS into elongation complexes and enhances the cleavage of the displaced transcript in backtracked RNAPII. This is mediated by an interaction between Ccr4-Not and the N terminus of TFIIS. In addition to revealing insights into how these two elongation factors cooperate to promote RNAPII elongation, our study extends the growing body of evidence suggesting that the N terminus of TFIIS acts as a docking/interacting site that allows it to synergize with other EFs to promote RNAPII transcription.
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37
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Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM. Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev 2014; 28:1957-75. [PMID: 25184681 PMCID: PMC4197947 DOI: 10.1101/gad.241620.114] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BRCA1 is a breast and ovarian tumor suppressor. Given its numerous incompletely understood functions and the possibility that more exist, we performed complementary systematic screens in search of new BRCA1 protein-interacting partners. New BRCA1 functions and/or a better understanding of existing ones were sought. Among the new interacting proteins identified, genetic interactions were detected between BRCA1 and four of the interactors: TONSL, SETX, TCEANC, and TCEA2. Genetic interactions were also detected between BRCA1 and certain interactors of TONSL, including both members of the FACT complex. From these results, a new BRCA1 function in the response to transcription-associated DNA damage was detected. Specifically, new roles for BRCA1 in the restart of transcription after UV damage and in preventing or repairing damage caused by stabilized R loops were identified. These roles are likely carried out together with some of the newly identified interactors. This new function may be important in BRCA1 tumor suppression, since the expression of several interactors, including some of the above-noted transcription proteins, is repeatedly aberrant in both breast and ovarian cancers.
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Affiliation(s)
- Sarah J Hill
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas Rolland
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Guillaume Adelmant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Xianfang Xia
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Matthew S Owen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Amélie Dricot
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Travis I Zack
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; The Broad Institute, Cambridge, Massachusetts 02142, USA
| | - Nidhi Sahni
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Yves Jacob
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, F-75015 Paris, France; UMR3569, Centre National de la Recherche Scientifique, F-75015 Paris, France; Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot, F-75015 Paris, France
| | - Tong Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Kristine M McKinney
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Allison P Clark
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Deepak Reyon
- Molecular Pathology Unit, Center for Computational and Integrative Biology, Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Shengdar Q Tsai
- Molecular Pathology Unit, Center for Computational and Integrative Biology, Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Computational and Integrative Biology, Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA; Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; The Broad Institute, Cambridge, Massachusetts 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Marc Vidal
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Suzanne Gaudet
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David E Hill
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David M Livingston
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
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Hall MP, Schneider LV. Isotope-differentiated binding energy shift tags (IDBEST™) for improved targeted biomarker discovery and validation. Expert Rev Proteomics 2014; 1:421-31. [PMID: 15966839 DOI: 10.1586/14789450.1.4.421] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Mass spectrometry has proved to be an important tool for protein biomarker discovery, identification and characterization. However, global proteomic profiling strategies often fail to identify known low-abundance biomarkers as a result of the limited dynamic range of mass spectrometry (two to three orders of magnitude) compared with the large dynamic range of protein concentrations in biologic fluids (11 to 12 orders of magnitude for serum). In addition, the number of peptides generated in such methods vastly overwhelms the resolution capacity of mass spectrometers, requiring extensive sample clean-up (e.g., affinity tag, retentate chromatography and/or high-performance liquid chromatography) before mass spectrometry analysis. Baiting and affinity pre-enrichment strategies, which overcome the dynamic range and sample complexity issues of global proteomic strategies, are very difficult to couple to mass spectrometry. This is due to the fact that it is nearly impossible to sort target peptides from those of the bait since there will be many cases of isobaric peptides. IDBEST (Target Discovery, Inc.) is a new tagging strategy that enables such pre-enrichment of specific proteins or protein classes as the resulting tagged peptides are distinguishable from those of the bait by a mass defect shift of approximately 0.1 atomic mass units. The special characteristics of these tags allow: resolution of tagged peptides from untagged peptides through incorporation of a mass defect element; high-precision quantitation of up- and downregulation by using stable isotope versions of the same tag; and potential analysis of protein isoforms through more complete peptide coverage from the proteins of interest.
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Affiliation(s)
- Michael P Hall
- Target Discovery, Inc., 4015 Fabian Way, Palo Alto, CA 94303, USA.
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Song P, Li L, Liu J. Proteomic analysis in nitrogen-deprived Isochrysis galbana during lipid accumulation. PLoS One 2013; 8:e82188. [PMID: 24340005 PMCID: PMC3855430 DOI: 10.1371/journal.pone.0082188] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 10/22/2013] [Indexed: 11/30/2022] Open
Abstract
The differentially co-expressed proteins in N-deprived and N-enriched I. galbana were comparatively analyzed by using two dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight-mass spectrometry (MALDI-TOF/TOF-MS) with the aim of better understanding lipid metabolism in this oleaginous microalga. Forty-five of the 900 protein spots showed dramatic changes in N-deprived I. galbana compared with the N-enriched cells. Of these, 36 protein spots were analyzed and 27 proteins were successfully identified. The identified proteins were classified into seven groups by their molecular functions, including the proteins related to energy production and transformation, substance metabolism, signal transduction, molecular chaperone, transcription and translation, immune defense and cytoskeleton. These altered proteins slowed cell growth and photosynthesis of I. galbana directly or indirectly, but at the same time increased lipid accumulation. Eight key enzymes involved in lipid metabolism via different pathways were identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), enolase, aspartate aminotransferase (AST), fumarate hydratase (FH), citrate synthase (CS), O-acetyl-serine lyase (OAS-L) and ATP sulfurylase (ATPS). The results suggested that the glycolytic pathway and citrate transport system might be the main routes for lipid anabolism in N-deprived I. galbana, and that the tricarboxylic acid (TCA) cycle, glyoxylate cycle and sulfur assimilation system might be the major pathways involved in lipid catabolism.
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Affiliation(s)
- Pingping Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Ling Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jianguo Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Mortensen SA, Grasser KD. The seed dormancy defect of Arabidopsis mutants lacking the transcript elongation factor TFIIS is caused by reduced expression of the DOG1 gene. FEBS Lett 2013; 588:47-51. [PMID: 24252221 DOI: 10.1016/j.febslet.2013.10.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 11/25/2022]
Abstract
TFIIS is a transcript elongation factor that facilitates transcription by RNA polymerase II, as it assists the enzyme to bypass blocks to mRNA synthesis. Previously, we have reported that Arabidopsis plants lacking TFIIS exhibit reduced seed dormancy. Among the genes differentially expressed in tfIIs seeds, the DOG1 gene was identified that is a known QTL for seed dormancy. Here we have analysed plants that overexpress TFIIS in wild type background, or that harbour an additional copy of DOG1 in tfIIs mutant background. These experiments demonstrate that the down-regulation of DOG1 expression causes the seed dormancy phenotype of tfIIs mutants.
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Affiliation(s)
- Simon A Mortensen
- Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg, Regensburg University, Universitätsstr. 31, D-93053 Regensburg, Germany; Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark
| | - Klaus D Grasser
- Cell Biology & Plant Biochemistry, Biochemie-Zentrum Regensburg, Regensburg University, Universitätsstr. 31, D-93053 Regensburg, Germany; Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000 Aalborg, Denmark.
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Kim N, Cho JE, Li YC, Jinks-Robertson S. RNA∶DNA hybrids initiate quasi-palindrome-associated mutations in highly transcribed yeast DNA. PLoS Genet 2013; 9:e1003924. [PMID: 24244191 PMCID: PMC3820800 DOI: 10.1371/journal.pgen.1003924] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/05/2013] [Indexed: 11/18/2022] Open
Abstract
RNase H enzymes promote genetic stability by degrading aberrant RNA∶DNA hybrids and by removing ribonucleotide monophosphates (rNMPs) that are present in duplex DNA. Here, we report that loss of RNase H2 in yeast is associated with mutations that extend identity between the arms of imperfect inverted repeats (quasi-palindromes or QPs), a mutation type generally attributed to a template switch during DNA synthesis. QP events were detected using frameshift-reversion assays and were only observed under conditions of high transcription. In striking contrast to transcription-associated short deletions that also are detected by these assays, QP events do not require Top1 activity. QP mutation rates are strongly affected by the direction of DNA replication and, in contrast to their elevation in the absence of RNase H2, are reduced when RNase H1 is additionally eliminated. Finally, transcription-associated QP events are limited by components of the nucleotide excision repair pathway and are promoted by translesion synthesis DNA polymerases. We suggest that QP mutations reflect either a transcription-associated perturbation of Okazaki-fragment processing, or the use of a nascent transcript to resume replication following a transcription-replication conflict. Mutation rates are correlated with the level of gene expression in budding yeast, demonstrating a link between transcription and stability of the underlying DNA template. In the current work, we describe a novel type of transcription-associated mutation that converts imperfect inverted repeats (quasi-palindromes or QPs) to perfect inverted repeats. Using appropriate mutation reporters, we demonstrate that QP mutations are strongly affected by the direction of DNA replication and have distinctive genetic requirements. Most notably, rates of transcription-associated QP events are regulated by the RNase H class of enzymes, which are specialized to process the RNA component of RNA∶DNA hybrids. The source of the RNA∶DNA hybrids that initiate QP mutations is unclear, but could reflect transcripts that remain stably base-paired with the DNA template, or aberrant processing of the RNA primers normally used to initiate DNA synthesis. These studies further expand the diverse ways that transcription affects the mutation landscape, and establish a novel way that RNA∶DNA hybrids can contribute to genetic instability. The high conservation of basic DNA-related metabolic processes suggests that results in yeast will be broadly applicable in higher eukaryotes.
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Affiliation(s)
- Nayun Kim
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jang-Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Yue C. Li
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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42
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Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue. Proc Natl Acad Sci U S A 2013; 110:15277-82. [PMID: 24003114 DOI: 10.1073/pnas.1311010110] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Bypass of Ess1 (Bye1) is a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. Here we show that Bye1 binds with its TFIIS-like domain (TLD) to RNA polymerase (Pol) II, and report crystal structures of the Bye1 TLD bound to Pol II and three different Pol II-nucleic acid complexes. Like TFIIS, Bye1 binds with its TLD to the Pol II jaw and funnel. In contrast to TFIIS, however, it neither alters the conformation nor the in vitro functions of Pol II. In vivo, Bye1 is recruited to chromatin via its TLD and occupies the 5'-region of active genes. A plant homeo domain (PHD) in Bye1 binds histone H3 tails with trimethylated lysine 4, and this interaction is enhanced by the presence of neighboring posttranslational modifications (PTMs) that mark active transcription and conversely is impaired by repressive PTMs. We identify putative human homologs of Bye1, the proteins PHD finger protein 3 and death-inducer obliterator, which are both implicated in cancer. These results establish Bye1 as the founding member of a unique family of chromatin transcription factors that link histones with active PTMs to transcribing Pol II.
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Park KS, Cha Y, Kim CH, Ahn HJ, Kim D, Ko S, Kim KH, Chang MY, Ko JH, Noh YS, Han YM, Kim J, Song J, Kim JY, Tesar PJ, Lanza R, Lee KA, Kim KS. Transcription elongation factor Tcea3 regulates the pluripotent differentiation potential of mouse embryonic stem cells via the Lefty1-Nodal-Smad2 pathway. Stem Cells 2013; 31:282-92. [PMID: 23169579 DOI: 10.1002/stem.1284] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/25/2012] [Indexed: 01/07/2023]
Abstract
Self-renewal and pluripotency are hallmark properties of pluripotent stem cells, including embryonic stem cells (ESCs) and iPS cells. Previous studies revealed the ESC-specific core transcription circuitry and showed that these core factors (e.g., Oct3/4, Sox2, and Nanog) regulate not only self-renewal but also pluripotent differentiation. However, it remains elusive how these two cell states are regulated and balanced during in vitro replication and differentiation. Here, we report that the transcription elongation factor Tcea3 is highly enriched in mouse ESCs (mESCs) and plays important roles in regulating the differentiation. Strikingly, altering Tcea3 expression in mESCs did not affect self-renewal under nondifferentiating condition; however, upon exposure to differentiating cues, its overexpression impaired in vitro differentiation capacity, and its knockdown biased differentiation toward mesodermal and endodermal fates. Furthermore, we identified Lefty1 as a downstream target of Tcea3 and showed that the Tcea3-Lefty1-Nodal-Smad2 pathway is an innate program critically regulating cell fate choices between self-replication and differentiation commitment. Together, we propose that Tcea3 critically regulates pluripotent differentiation of mESCs as a molecular rheostat of Nodal-Smad2/3 signaling.
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Affiliation(s)
- Kyung-Soon Park
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Korea.
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Kawauchi J, Inoue M, Fukuda M, Uchida Y, Yasukawa T, Conaway RC, Conaway JW, Aso T, Kitajima S. Transcriptional properties of mammalian elongin A and its role in stress response. J Biol Chem 2013; 288:24302-15. [PMID: 23828199 DOI: 10.1074/jbc.m113.496703] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Elongin A was shown previously to be capable of potently activating the rate of RNA polymerase II (RNAPII) transcription elongation in vitro by suppressing transient pausing by the enzyme at many sites along DNA templates. The role of Elongin A in RNAPII transcription in mammalian cells, however, has not been clearly established. In this report, we investigate the function of Elongin A in RNAPII transcription. We present evidence that Elongin A associates with the IIO form of RNAPII at sites of newly transcribed RNA and is relocated to dotlike domains distinct from those containing RNAPII when cells are treated with the kinase inhibitor 5,6-dichloro-1-β-d-ribofuranosylbenzimidazole. Significantly, Elongin A is required for maximal induction of transcription of the stress response genes ATF3 and p21 in response to several stimuli. Evidence from structure-function studies argues that Elongin A transcription elongation activity, but not its ubiquitination activity, is most important for its function in induction of transcription of ATF3 and p21. Taken together, our data provide new insights into the function of Elongin A in RNAPII transcription and bring to light a previously unrecognized role for Elongin A in the regulation of stress response genes.
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Affiliation(s)
- Junya Kawauchi
- Department of Biochemical Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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Kassube SA, Jinek M, Fang J, Tsutakawa S, Nogales E. Structural mimicry in transcription regulation of human RNA polymerase II by the DNA helicase RECQL5. Nat Struct Mol Biol 2013; 20:892-9. [PMID: 23748380 PMCID: PMC3702667 DOI: 10.1038/nsmb.2596] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/25/2013] [Indexed: 11/22/2022]
Abstract
RECQL5 is a member of the highly conserved RecQ family of DNA helicases involved in DNA repair. RECQL5 interacts with RNA polymerase II (Pol II) and inhibits transcription of protein-encoding genes by an unknown mechanism. We show that RECQL5 contacts the Rpb1 jaw domain of Pol II at a site that overlaps with the binding site for the transcription elongation factor TFIIS. Our cryo-EM structure of elongating Pol II arrested in complex with RECQL5 shows that the RECQL5 helicase domain is positioned to sterically block elongation. The crystal structure of the RECQL5 KIX domain reveals similarities with TFIIS, and binding of RECQL5 to Pol II interferes with the ability of TFIIS to promote transcriptional read-through in vitro. Together, our findings reveal a dual mode of transcriptional repression by RECQL5 that includes structural mimicry of the Pol II-TFIIS interaction.
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Affiliation(s)
- Susanne A. Kassube
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Martin Jinek
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jie Fang
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Susan Tsutakawa
- Life Science Division, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
| | - Eva Nogales
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Life Science Division, Lawrence Berkeley National Lab, Berkeley, CA 94720, USA
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46
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McKay BC, Cabrita MA. Arresting transcription and sentencing the cell: the consequences of blocked transcription. Mech Ageing Dev 2013; 134:243-52. [PMID: 23542592 DOI: 10.1016/j.mad.2013.03.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/16/2013] [Accepted: 03/16/2013] [Indexed: 10/27/2022]
Abstract
Bulky DNA adducts induced by agents like ultraviolet light, cisplatin and oxidative metabolism pose a block to elongation by RNA polymerase II (RNAPII). The arrested RNAPII can initiate the repair of transcription-blocking DNA lesions by transcription-coupled nucleotide excision repair (TC-NER) to permit efficient recovery of mRNA synthesis while widespread sustained transcription blocks lead to apoptosis. Therefore, RNAPII serves as a processive DNA damage sensor that identifies transcription-blocking DNA lesions. Cockayne syndrome (CS) is an autosomal recessive disorder characterized by a complex phenotype that includes clinical photosensitivity, progressive neurological degeneration and premature-aging. CS is associated with defects in TC-NER and the recovery of mRNA synthesis, making CS cells exquisitely sensitive to a variety of DNA damaging agents. These defects in the coupling of repair and transcription appear to underlie some of the complex clinical features of CS. Recent insight into the consequences of blocked transcription and their relationship to CS will be discussed.
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Affiliation(s)
- Bruce C McKay
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Canada.
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47
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Cha Y, Kim DK, Hyun J, Kim SJ, Park KS. TCEA3 binds to TGF-beta receptor I and induces Smad-independent, JNK-dependent apoptosis in ovarian cancer cells. Cell Signal 2013; 25:1245-51. [PMID: 23357533 DOI: 10.1016/j.cellsig.2013.01.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/31/2012] [Accepted: 01/21/2013] [Indexed: 12/21/2022]
Abstract
TFIIS is a transcription elongation factor conserved in frog, mouse and human. Recently, knockdown of TCEA1, the most well-characterized isoform of TFIIS, by RNA silencing was reported to inhibit cancer cell proliferation and induce apoptosis in breast, lung and pancreatic cancer cell lines through activation of p53 (Hubbard et al., 2008 [1]). However, the functions of other TFIIS isoforms are poorly defined. The present study shows that TCEA3, an isoform of TFIIS, can trigger ovarian cancer-specific cell death by activating the JNK signaling pathway. TCEA3 expression is low in ovarian cancer cell lines compared to noncancerous ovarian epithelial cells. Suppression of TCEA3 in noncancerous ovarian epithelial cells promotes cell growth whereas ectopic expression of TCEA3 in ovarian cancer cell lines induces the caspase-dependent mitochondrial cell death pathway. Molecular and chemical inhibition assays show that the interaction of TCEA3 with TGFβ receptor I induces cell death in ovarian cancer cell through Smad-independent activation of the JNK pathway. These results reveal that TCEA3 induces a novel apoptotic mechanism in OEC, which provides TCEA3 as a novel target to develop therapeutics of ovarian cancer.
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Affiliation(s)
- Young Cha
- Department of Biomedical Science, College of Life Science, CHA University, Seoul, Republic of Korea
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Herriges JC, Yi L, Hines EA, Harvey JF, Xu G, Gray P, Ma Q, Sun X. Genome-scale study of transcription factor expression in the branching mouse lung. Dev Dyn 2012; 241:1432-53. [PMID: 22711520 PMCID: PMC3529173 DOI: 10.1002/dvdy.23823] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2012] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Mammalian lung development consists of a series of precisely choreographed events that drive the progression from simple lung buds to the elaborately branched organ that fulfills the vital function of gas exchange. Strict transcriptional control is essential for lung development. Among the large number of transcription factors encoded in the mouse genome, only a small portion of them are known to be expressed and function in the developing lung. Thus a systematic investigation of transcription factors expressed in the lung is warranted. RESULTS To enrich for genes that may be responsible for regional growth and patterning, we performed a screen using RNA in situ hybridization to identify genes that show restricted expression patterns in the embryonic lung. We focused on the pseudoglandular stage during which the lung undergoes branching morphogenesis, a cardinal event of lung development. Using a genome-scale probe set that represents over 90% of the transcription factors encoded in the mouse genome, we identified 62 transcription factor genes with localized expression in the epithelium, mesenchyme, or both. Many of these genes have not been previously implicated in lung development. CONCLUSIONS Our findings provide new starting points for the elucidation of the transcriptional circuitry that controls lung development.
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Affiliation(s)
- John C. Herriges
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Lan Yi
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Elizabeth A. Hines
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Julie F. Harvey
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
| | - Guoliang Xu
- Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China 200031
| | - Paul Gray
- Department of Anatomy and Neurobiology, Washington University, St. Louis, MO 63110
| | - Qiufu Ma
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115
| | - Xin Sun
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706
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Regulation of mammalian transcription by Gdown1 through a novel steric crosstalk revealed by cryo-EM. EMBO J 2012; 31:3575-87. [PMID: 22850672 DOI: 10.1038/emboj.2012.205] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 07/03/2012] [Indexed: 01/24/2023] Open
Abstract
In mammals, a distinct RNA polymerase II form, RNAPII(G) contains a novel subunit Gdown1 (encoded by POLR2M), which represses gene activation, only to be reversed by the multisubunit Mediator co-activator. Here, we employed single-particle cryo-electron microscopy (cryo-EM) to disclose the architectures of RNAPII(G), RNAPII and RNAPII in complex with the transcription initiation factor TFIIF, all to ~19 Å. Difference analysis mapped Gdown1 mostly to the RNAPII Rpb5 shelf-Rpb1 jaw, supported by antibody labelling experiments. These structural features correlate with the moderate increase in the efficiency of RNA chain elongation by RNAP II(G). In addition, our updated RNAPII-TFIIF map showed that TFIIF tethers multiple regions surrounding the DNA-binding cleft, in agreement with cross-linking and biochemical mapping. Gdown1's binding sites overlap extensively with those of TFIIF, with Gdown1 sterically excluding TFIIF from RNAPII, herein demonstrated by competition assays using size exclusion chromatography. In summary, our work establishes a structural basis for Gdown1 impeding initiation at promoters, by obstruction of TFIIF, accounting for an additional dependent role of Mediator in activated transcription.
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50
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Sekine SI, Tagami S, Yokoyama S. Structural basis of transcription by bacterial and eukaryotic RNA polymerases. Curr Opin Struct Biol 2012; 22:110-8. [DOI: 10.1016/j.sbi.2011.11.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 11/14/2011] [Accepted: 11/16/2011] [Indexed: 01/22/2023]
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