151
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Transfer RNA-derived small RNAs in plants. SCIENCE CHINA-LIFE SCIENCES 2017; 61:155-161. [PMID: 29170889 DOI: 10.1007/s11427-017-9167-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/12/2017] [Indexed: 12/31/2022]
Abstract
Rather than random degradation products, the 18 to 40 nucleotides (nt) transfer RNA-derived small RNAs (tsRNAs) are RNA species generated specifically from pre-RNAs or mature tRNAs in archaea, bacteria and eukaryotes. Recent studies from animal systems have shown that tsRNAs are important non-coding RNAs that regulate gene expression at the transcriptional and/or post-transcriptional levels. They are involved in various biological processes, such as cell proliferation, tumor genesis, stress response and intergenerational epigenetic inheritance. In this review, we will summarize the discovery, biogenesis, and function of tsRNAs in higher plants. In addition, analysis on tsRNAs from lower plants is shown.
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152
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Kögler A, Schmidt T, Wenke T. Evolutionary modes of emergence of short interspersed nuclear element (SINE) families in grasses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:676-695. [PMID: 28857316 DOI: 10.1111/tpj.13676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11 052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species-specific diversification and amplification. We found that Poaceae SINEs (PoaS) fall into two length categories: simple SINEs of up to 180 bp and dimeric SINEs larger than 240 bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty-eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5' or 3' regions, across Poaceae species and share large sequence stretches with one or more other PoaS families.
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Affiliation(s)
- Anja Kögler
- Institute of Botany, Technische Universität Dresden, Dresden, 01069, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, 01069, Germany
| | - Torsten Wenke
- Institute of Botany, Technische Universität Dresden, Dresden, 01069, Germany
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153
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WITHDRAWN: Abnormal expression of TFIIIB subunits and RNA Pol III genes is associated with hepatocellular carcinoma. LIVER RESEARCH 2017. [DOI: 10.1016/j.livres.2017.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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154
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Park JL, Lee YS, Kunkeaw N, Kim SY, Kim IH, Lee YS. Epigenetic regulation of noncoding RNA transcription by mammalian RNA polymerase III. Epigenomics 2017; 9:171-187. [PMID: 28112569 DOI: 10.2217/epi-2016-0108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
RNA polymerase III (Pol III) synthesizes a range of medium-sized noncoding RNAs (collectively 'Pol III genes') whose early established biological roles were so essential that they were considered 'housekeeping genes'. Besides these fundamental functions, diverse unconventional roles of mammalian Pol III genes have recently been recognized and their expression must be exquisitely controlled. In this review, we summarize the epigenetic regulation of Pol III genes by chromatin structure, histone modification and CpG DNA methylation. We also recapitulate the association between dysregulation of Pol III genes and diseases such as cancer and neurological disorders. Additionally, we will discuss why in-depth molecular studies of Pol III genes have not been attempted and how nc886, a Pol III gene, may resolve this issue.
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Affiliation(s)
- Jong-Lyul Park
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 305-806, Korea.,Department of Functional Genomics, University of Science & Technology, Daejeon 305-806, Korea
| | - Yeon-Su Lee
- Cancer Genomics Branch, Research Institute, National Cancer Center, Goyang 10408, Korea
| | - Nawapol Kunkeaw
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1072, USA.,Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 305-806, Korea.,Department of Functional Genomics, University of Science & Technology, Daejeon 305-806, Korea
| | - In-Hoo Kim
- Graduate School of Cancer Science & Policy, National Cancer Center, Goyang 10408, Korea
| | - Yong Sun Lee
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555-1072, USA.,Graduate School of Cancer Science & Policy, National Cancer Center, Goyang 10408, Korea
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155
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Lei J, Chen S, Zhong S. Abnormal expression of TFIIIB subunits and RNA Pol III genes is associated with hepatocellular carcinoma. LIVER RESEARCH 2017; 1:112-120. [PMID: 29276645 PMCID: PMC5739085 DOI: 10.1016/j.livres.2017.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The levels of the products of RNA polymerase III-dependent genes (Pol III genes), including tRNAs and 5S rRNA, are elevated in transformed and tumor cells, which potentiate tumorigenesis. TFIIB-related factor 1 (Brf1) is a key transcription factor and specifically regulates the transcription of Pol III genes. In vivo and in vitro studies have demonstrated that a decrease in Brf1 reduces Pol III gene transcription and is sufficient for inhibiting cell transformation and tumor formation. Emerging evidence indicates that dysregulation of Brf1 and Pol III genes is linked to the development of hepatocellular carcinoma (HCC) in humans and animals. We have reported that Brf1 is overexpressed in human liver cancer patients and that those with high Brf1 levels have shorter survivals. This review summarizes the effects of dysregulation of these genes on HCC and their regulation by signaling pathways and epigenetics. These novel data should help us determine the molecular mechanisms of HCC from a different perspective and guide the development of therapeutic approaches for HCC patients.
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Affiliation(s)
- Junxia Lei
- School of medicine, South china university of technology, China
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Songlin Chen
- Department of Cardiothoracic Surgery, Xiamen University Affiliated Southeast Hospital, China
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shuping Zhong
- Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Corresponding author. Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA. (S. Zhong)
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156
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Gouge J, Vannini A. New tricks for an old dog: Brf2-dependent RNA Polymerase III transcription in oxidative stress and cancer. Transcription 2017; 9:61-66. [PMID: 28854119 PMCID: PMC5791813 DOI: 10.1080/21541264.2017.1335269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 01/07/2023] Open
Abstract
Here, we discuss the role of Brf2, an RNA Polymerase III core transcription factor, as a master switch of the oxidative stress response. We highlight the interplay of Brf2 with the Nrf2/Keap1 pathway, as well as the role of Brf2 in cancer and other possible regulations.
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157
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Park JL, Lee YS, Song MJ, Hong SH, Ahn JH, Seo EH, Shin SP, Lee SJ, Johnson BH, Stampfer MR, Kim HP, Kim SY, Lee YS. Epigenetic regulation of RNA polymerase III transcription in early breast tumorigenesis. Oncogene 2017; 36:6793-6804. [PMID: 28846112 DOI: 10.1038/onc.2017.285] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Revised: 06/13/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023]
Abstract
RNA polymerase III (Pol III) transcribes medium-sized non-coding RNAs (collectively termed Pol III genes). Emerging diverse roles of Pol III genes suggest that individual Pol III genes are exquisitely regulated by transcription and epigenetic factors. Here we report global Pol III expression/methylation profiles and molecular mechanisms of Pol III regulation that have not been as extensively studied, using nc886 as a representative Pol III gene. In a human mammary epithelial cell system that recapitulates early breast tumorigenesis, the fraction of actively transcribed Pol III genes increases reaching a plateau during immortalization. Hyper-methylation of Pol III genes inhibits Pol III binding to DNA via inducing repressed chromatin and is a determinant for the Pol III repertoire. When Pol III genes are hypo-methylated, MYC amplifies their transcription, regardless of its recognition DNA motif. Thus, Pol III expression during tumorigenesis is delineated by methylation and magnified by MYC.
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Affiliation(s)
- J-L Park
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Y-S Lee
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - M-J Song
- Department of Environmental Medical Biology, Yonsei University College of Medicine, Seoul, Korea
| | - S-H Hong
- Rare Cancer Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - J-H Ahn
- Department of Life and Nanopharmaceutical Sciences and Department of Oriental Pharmacy, Kyung Hee University, Seoul, Korea
| | - E-H Seo
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - S-P Shin
- Immunotherapeutics Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - S-J Lee
- Immunotherapeutics Branch, Research Institute, National Cancer Center, Goyang-si, Korea
| | - B H Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA
| | - M R Stampfer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - H-P Kim
- Department of Environmental Medical Biology, Yonsei University College of Medicine, Seoul, Korea.,Institute of Tropical Medicine, Yonsei University College of Medicine, Seoul, Korea.,Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - S-Y Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, Korea.,Department of Functional Genomics, University of Science and Technology, Daejeon, Korea
| | - Y S Lee
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, USA.,Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
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158
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Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Res 2017; 24:251-260. [PMID: 28338834 PMCID: PMC5499648 DOI: 10.1093/dnares/dsx002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/21/2017] [Indexed: 11/14/2022] Open
Abstract
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments. Overall, the 15 ncRNAs that were found shared between Encephalitozoon and Nosema spp. may represent the minimal core set required for parasitic life. Interestingly, the systematic presence of a CCC- or GGG-like motif in 5' of all ncRNA and mRNA gene transcripts regardless of the RNA polymerase involved suggests that the RNA polymerase machineries in microsporidia species could use common factors. Our data provide additional insights in accordance with the simplification processes observed in these reduce genomes and underline the usefulness of sequencing closely related species to help identify highly divergent ncRNAs in these parasites.
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Affiliation(s)
- Abdel Belkorchia
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | | | - Valérie Polonais
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | - Nicolas Parisot
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Frédéric Delbac
- Laboratoire "Microorganismes: Génome et Environnement", Université Clermont Auvergne, BP 10448, F-63000 Clermont-Ferrand, France.,CNRS, UMR 6023, LMGE, F-63171 Aubière, France
| | - Jean-François Brugère
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | - Pierre Peyret
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
| | | | - Eric Peyretaillade
- Université Clermont Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France
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159
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Kim Y, Lee J, Shin H, Jang S, Kim SC, Lee Y. Biosynthesis of brain cytoplasmic 200 RNA. Sci Rep 2017; 7:6884. [PMID: 28761139 PMCID: PMC5537265 DOI: 10.1038/s41598-017-05097-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/10/2017] [Indexed: 12/13/2022] Open
Abstract
Brain cytoplasmic 200 RNA (BC200 RNA), a neuron-specific non-coding RNA, is also highly expressed in a number of tumors of non-neuronal origin. However, the biosynthesis of BC200 RNA remains poorly understood. In this study, we show that the efficient transcription of BC200 RNA requires both internal and upstream promoter elements in cancer cells. The transcription complex seems to interact with a broad range of sequences within the upstream 100-bp region. The cellular levels and half-lives of BC200 RNA were found to differ across various cancer cell types, but there was no significant correlation between these parameters. Exogenously expressed BC200 RNA had a shorter half-life than that observed for the endogenous version in cancer cells, suggesting that BC200 RNA might be protected by some limiting factor(s) in cancer cells. Transient transfection experiments showed that the transcriptional activity of the exogenous BC200 RNA promoter element varied depending on the cancer cell type. However, the promoter activities together with the half-life data could not explain the differences in the levels of BC200 RNA among different cell types, suggesting that there is another level of transcriptional regulation beyond that detected by our transient transfection experiments.
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Affiliation(s)
- Youngmi Kim
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Jungmin Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Heegwon Shin
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Seonghui Jang
- Department of Chemistry, KAIST, Daejeon, 34141, Korea
| | - Sun Chang Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Korea
| | - Younghoon Lee
- Department of Chemistry, KAIST, Daejeon, 34141, Korea.
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160
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Gouge J, Guthertz N, Kramm K, Dergai O, Abascal-Palacios G, Satia K, Cousin P, Hernandez N, Grohmann D, Vannini A. Molecular mechanisms of Bdp1 in TFIIIB assembly and RNA polymerase III transcription initiation. Nat Commun 2017; 8:130. [PMID: 28743884 PMCID: PMC5526994 DOI: 10.1038/s41467-017-00126-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Initiation of gene transcription by RNA polymerase (Pol) III requires the activity of TFIIIB, a complex formed by Brf1 (or Brf2), TBP (TATA-binding protein), and Bdp1. TFIIIB is required for recruitment of Pol III and to promote the transition from a closed to an open Pol III pre-initiation complex, a process dependent on the activity of the Bdp1 subunit. Here, we present a crystal structure of a Brf2-TBP-Bdp1 complex bound to DNA at 2.7 Å resolution, integrated with single-molecule FRET analysis and in vitro biochemical assays. Our study provides a structural insight on how Bdp1 is assembled into TFIIIB complexes, reveals structural and functional similarities between Bdp1 and Pol II factors TFIIA and TFIIF, and unravels essential interactions with DNA and with the upstream factor SNAPc. Furthermore, our data support the idea of a concerted mechanism involving TFIIIB and RNA polymerase III subunits for the closed to open pre-initiation complex transition.Transcription initiation by RNA polymerase III requires TFIIIB, a complex formed by Brf1/Brf2, TBP and Bdp1. Here, the authors describe the crystal structure of a Brf2-TBP-Bdp1 complex bound to a DNA promoter and characterize the role of Bdp1 in TFIIIB assembly and pre-initiation complex formation.
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Affiliation(s)
- Jerome Gouge
- The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Kevin Kramm
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, 93053, Regensburg, Germany
| | - Oleksandr Dergai
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | | | | | - Pascal Cousin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015, Lausanne, Switzerland
| | - Dina Grohmann
- Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, University of Regensburg, 93053, Regensburg, Germany
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161
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Gao Z, Harwig A, Berkhout B, Herrera-Carrillo E. Mutation of nucleotides around the +1 position of type 3 polymerase III promoters: The effect on transcriptional activity and start site usage. Transcription 2017; 8:275-287. [PMID: 28598252 PMCID: PMC5703244 DOI: 10.1080/21541264.2017.1322170] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 04/18/2017] [Accepted: 04/18/2017] [Indexed: 11/24/2022] Open
Abstract
Type 3 RNA polymerase III (Pol III) promoters are widely used for the expression of small RNAs such as short hairpin RNA and guide RNA in the popular RNAi and CRISPR-Cas gene regulation systems. Although it is generally believed that type 3 Pol III promoters use a defined transcription start site (+1 position), most man-made promoter constructs contain local sequence alterations of which the impact on transcription efficiency and initiation accuracy is not known. For three human type 3 Pol III promoters (7SK, U6, and H1), we demonstrated that the nucleotides around the +1 position affect both the transcriptional efficiency and start site selection. Human 7SK and U6 promoters with A or G at the +1 position efficiently produced small RNAs with a precise +1 start site. The human H1 promoter with +1A or G also efficiently produced small RNAs but from multiple start sites in the -3/-1 window. These results provide new insights for the design of vectors for accurate expression of designed small RNAs for research and therapeutic purposes.
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Affiliation(s)
- Zongliang Gao
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Elena Herrera-Carrillo
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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162
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Carnevali D, Conti A, Pellegrini M, Dieci G. Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines. DNA Res 2017; 24:59-69. [PMID: 28028040 PMCID: PMC5381342 DOI: 10.1093/dnares/dsw048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 10/09/2016] [Indexed: 01/06/2023] Open
Abstract
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority of Pol III-transcribed MIR elements are cell-specific, we discovered a small set of ubiquitously transcribed MIRs mapping within Pol II-transcribed genes in antisense orientation that could influence the expression of the overlapping gene. We also identified novel Pol III-transcribed ncRNAs, deriving from transcription of annotated MIR fragments flanked by unique MIR-unrelated sequences, and confirmed the role of Pol III-specific internal promoter elements in MIR transcription. Besides demonstrating widespread transcription at these retrotranspositionally inactive elements in human cells, the ability to profile MIR expression at single-locus resolution will facilitate their study in different cell types and states including pathological alterations.
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Affiliation(s)
| | - Anastasia Conti
- Department of Life Sciences, University of Parma, Parma, Italy
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095 723, USA
| | - Giorgio Dieci
- Department of Life Sciences, University of Parma, Parma, Italy
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163
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Ustyantsev IG, Golubchikova JS, Borodulina OR, Kramerov DA. Canonical and noncanonical RNA polyadenylation. Mol Biol 2017. [DOI: 10.1134/s0026893317010186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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164
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A new role of GCN2 in the nucleolus. Biochem Biophys Res Commun 2017; 485:484-491. [DOI: 10.1016/j.bbrc.2017.02.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 02/07/2017] [Indexed: 01/06/2023]
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165
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Locati MD, Pagano JFB, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Zhu K, Spaink HP, Girard G, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons. RNA (NEW YORK, N.Y.) 2017; 23:446-456. [PMID: 28003516 PMCID: PMC5340908 DOI: 10.1261/rna.059642.116] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/03/2016] [Indexed: 05/31/2023]
Abstract
5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci.
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Affiliation(s)
- Mauro D Locati
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Johanna F B Pagano
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Wim A Ensink
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Marina van Olst
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Selina van Leeuwen
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Ulrike Nehrdich
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands
| | - Kongju Zhu
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands
| | - Herman P Spaink
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands
| | - Geneviève Girard
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Han Rauwerda
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Rob J Dekker
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Timo M Breit
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
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166
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Parvovirus Expresses a Small Noncoding RNA That Plays an Essential Role in Virus Replication. J Virol 2017; 91:JVI.02375-16. [PMID: 28122984 DOI: 10.1128/jvi.02375-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/20/2017] [Indexed: 12/11/2022] Open
Abstract
Human bocavirus 1 (HBoV1) belongs to the species Primate bocaparvovirus of the genus Bocaparvovirus of the Parvoviridae family. HBoV1 causes acute respiratory tract infections in young children and has a selective tropism for the apical surface of well-differentiated human airway epithelia (HAE). In this study, we identified an additional HBoV1 gene, bocavirus-transcribed small noncoding RNA (BocaSR), within the 3' noncoding region (nucleotides [nt] 5199 to 5338) of the viral genome of positive sense. BocaSR is transcribed by RNA polymerase III (Pol III) from an intragenic promoter at levels similar to that of the capsid protein-coding mRNA and is essential for replication of the viral DNA in both transfected HEK293 and infected HAE cells. Mechanistically, we showed that BocaSR regulates the expression of HBoV1-encoded nonstructural proteins NS1, NS2, NS3, and NP1 but not NS4. BocaSR is similar to the adenovirus-associated type I (VAI) RNA in terms of both nucleotide sequence and secondary structure but differs from it in that its regulation of viral protein expression is independent of RNA-activated protein kinase (PKR) regulation. Notably, BocaSR accumulates in the viral DNA replication centers within the nucleus and likely plays a direct role in replication of the viral DNA. Our findings reveal BocaSR to be a novel viral noncoding RNA that coordinates the expression of viral proteins and regulates replication of viral DNA within the nucleus. Thus, BocaSR may be a target for antiviral therapies for HBoV and may also have utility in the production of recombinant HBoV vectors.IMPORTANCE Human bocavirus 1 (HBoV1) is pathogenic to humans, causing acute respiratory tract infections in young children. In this study, we identified a novel HBoV1 gene that lies in the 3' noncoding region of the viral positive-sense genome and is transcribed by RNA polymerase III into a noncoding RNA of 140 nt. This bocavirus-transcribed small RNA (BocaSR) diverges from both adenovirus-associated (VA) RNAs and Epstein-Barr virus-encoded small RNAs (EBERs) with respect to RNA sequence, representing a third species of this kind of Pol III-dependent viral noncoding RNA and the first noncoding RNA identified in autonomous parvoviruses. Unlike the VA RNAs, BocaSR localizes to the viral DNA replication centers of the nucleus and is essential for expression of viral nonstructural proteins independent of RNA-activated protein kinase R and replication of HBoV1 genomes. The identification of BocaSR and its role in virus DNA replication reveals potential avenues for developing antiviral therapies.
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167
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Sin O, de Jong T, Mata-Cabana A, Kudron M, Zaini MA, Aprile FA, Seinstra RI, Stroo E, Prins RW, Martineau CN, Wang HH, Hogewerf W, Steinhof A, Wanker EE, Vendruscolo M, Calkhoven CF, Reinke V, Guryev V, Nollen EAA. Identification of an RNA Polymerase III Regulator Linked to Disease-Associated Protein Aggregation. Mol Cell 2017; 65:1096-1108.e6. [PMID: 28306505 PMCID: PMC5364375 DOI: 10.1016/j.molcel.2017.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 01/05/2017] [Accepted: 02/22/2017] [Indexed: 11/24/2022]
Abstract
Protein aggregation is associated with age-related neurodegenerative disorders, such as Alzheimer's and polyglutamine diseases. As a causal relationship between protein aggregation and neurodegeneration remains elusive, understanding the cellular mechanisms regulating protein aggregation will help develop future treatments. To identify such mechanisms, we conducted a forward genetic screen in a C. elegans model of polyglutamine aggregation and identified the protein MOAG-2/LIR-3 as a driver of protein aggregation. In the absence of polyglutamine, MOAG-2/LIR-3 regulates the RNA polymerase III-associated transcription of small non-coding RNAs. This regulation is lost in the presence of polyglutamine, which mislocalizes MOAG-2/LIR-3 from the nucleus to the cytosol. We then show biochemically that MOAG-2/LIR-3 can also catalyze the aggregation of polyglutamine-expanded huntingtin. These results suggest that polyglutamine can induce an aggregation-promoting activity of MOAG-2/LIR-3 in the cytosol. The concept that certain aggregation-prone proteins can convert other endogenous proteins into drivers of aggregation and toxicity adds to the understanding of how cellular homeostasis can be deteriorated in protein misfolding diseases.
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Affiliation(s)
- Olga Sin
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands; Graduate Program in Areas of Basic and Applied Biology, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Tristan de Jong
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Alejandro Mata-Cabana
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Michelle Kudron
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mohamad Amr Zaini
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | | | - Renée I Seinstra
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Esther Stroo
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Roméo Willinge Prins
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Céline N Martineau
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Hai Hui Wang
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Wytse Hogewerf
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Anne Steinhof
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Erich E Wanker
- Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | | | - Cornelis F Calkhoven
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands
| | - Valerie Reinke
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands.
| | - Ellen A A Nollen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, 9700 AD Groningen, the Netherlands.
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168
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Paraboschi EM, Cardamone G, Rimoldi V, Duga S, Soldà G, Asselta R. miR-634 is a Pol III-dependent intronic microRNA regulating alternative-polyadenylated isoforms of its host gene PRKCA. Biochim Biophys Acta Gen Subj 2017; 1861:1046-1056. [PMID: 28212793 DOI: 10.1016/j.bbagen.2017.02.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 02/02/2017] [Accepted: 02/13/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND The protein kinase C alpha (PRKCA) gene, coding for a Th17-cell-selective kinase, shows a complex splicing pattern, with at least 2 stable alternative transcripts characterized by an alternative upstream polyadenylation site. Polymorphisms in this gene were associated with several conditions, including multiple sclerosis, asthma, schizophrenia, and cancer. The presence of a microRNA (miRNA), i.e. miR-634, within intron 15 of the PRKCA gene, suggests the intriguing possibility that this miRNA might play a role in the susceptibility to these pathologies. METHODS Here, we characterized miR-634 expression profile and searched for its putative targets using a combination of RT-PCR and gene reporter assays. RESULTS The quantitative analysis of PRKCA and miR-634 transcripts in a panel of human tissues and cell lines revealed discordant expression profiles, suggesting the presence of an independent miR-634 promoter and/or a possible direct role of miR-634 in modulating PRKCA expression. Functional studies demonstrated the existence of a miRNA-specific promoter, which was shown to be Pol-III-dependent. Furthermore, transfection experiments showed that miR-634 is able to target its host gene by specifically down-regulating the shorter alternative-polyadenylated isoforms. CONCLUSIONS MiR-634 is a Pol III-dependent intronic miRNA, which could target its host gene through a "first-order" negative feedback. GENERAL SIGNIFICANCE MiR-634 is one of the few characterized examples of Pol-III-dependent intronic miRNAs. Its independent transcription from the host gene suggests caution in using expression profiles of host genes as proxies for the expression of the corresponding intronic miRNAs.
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Affiliation(s)
- Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089, Rozzano, Milan, Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089, Rozzano, Milan, Italy.
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169
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Helbo AS, Lay FD, Jones PA, Liang G, Grønbæk K. Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters. Sci Rep 2017; 7:41947. [PMID: 28176797 PMCID: PMC5296907 DOI: 10.1038/srep41947] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 01/03/2017] [Indexed: 12/20/2022] Open
Abstract
Chromatin is structurally involved in the transcriptional regulation of all genes. While the nucleosome positioning at RNA polymerase II (pol II) promoters has been extensively studied, less is known about the chromatin structure at pol III promoters in human cells. We use a high-resolution analysis to show substantial differences in chromatin structure of pol II and pol III promoters, and between subtypes of pol III genes. Notably, the nucleosome depleted region at the transcription start site of pol III genes extends past the termination sequences, resulting in nucleosome free gene bodies. The +1 nucleosome is located further downstream than at pol II genes and furthermore displays weak positioning. The variable position of the +1 location is seen not only within individual cell populations and between cell types, but also between different pol III promoter subtypes, suggesting that the +1 nucleosome may be involved in the transcriptional regulation of pol III genes. We find that expression and DNA methylation patterns correlate with distinct accessibility patterns, where DNA methylation associates with the silencing and inaccessibility at promoters. Taken together, this study provides the first high-resolution map of nucleosome positioning and occupancy at human pol III promoters at specific loci and genome wide.
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Affiliation(s)
- Alexandra Søgaard Helbo
- Department of Hematology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Fides D Lay
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA
| | - Peter A Jones
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA.,Van Andel Research Institute, Grand Rapids, 49503, USA
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, 90089, USA
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Copenhagen, 2100, Denmark
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170
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Akhoundi M, Downing T, Votýpka J, Kuhls K, Lukeš J, Cannet A, Ravel C, Marty P, Delaunay P, Kasbari M, Granouillac B, Gradoni L, Sereno D. Leishmania infections: Molecular targets and diagnosis. Mol Aspects Med 2017; 57:1-29. [PMID: 28159546 DOI: 10.1016/j.mam.2016.11.012] [Citation(s) in RCA: 189] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 11/08/2016] [Accepted: 11/28/2016] [Indexed: 12/15/2022]
Abstract
Progress in the diagnosis of leishmaniases depends on the development of effective methods and the discovery of suitable biomarkers. We propose firstly an update classification of Leishmania species and their synonymies. We demonstrate a global map highlighting the geography of known endemic Leishmania species pathogenic to humans. We summarize a complete list of techniques currently in use and discuss their advantages and limitations. The available data highlights the benefits of molecular markers in terms of their sensitivity and specificity to quantify variation from the subgeneric level to species complexes, (sub) species within complexes, and individual populations and infection foci. Each DNA-based detection method is supplied with a comprehensive description of markers and primers and proposal for a classification based on the role of each target and primer in the detection, identification and quantification of leishmaniasis infection. We outline a genome-wide map of genes informative for diagnosis that have been used for Leishmania genotyping. Furthermore, we propose a classification method based on the suitability of well-studied molecular markers for typing the 21 known Leishmania species pathogenic to humans. This can be applied to newly discovered species and to hybrid strains originating from inter-species crosses. Developing more effective and sensitive diagnostic methods and biomarkers is vital for enhancing Leishmania infection control programs.
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Affiliation(s)
- Mohammad Akhoundi
- Service de Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France; MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France.
| | - Tim Downing
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Jan Votýpka
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Parasitology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Katrin Kuhls
- Division of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czech Republic; Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic; Canadian Institute for Advanced Research, Toronto, Canada
| | - Arnaud Cannet
- Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Université de Nice-Sophia Antipolis, Nice, France
| | - Christophe Ravel
- French National Reference Centre on Leishmaniasis, Montpellier University, Montpellier, France
| | - Pierre Marty
- Service de Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France; Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Université de Nice-Sophia Antipolis, Nice, France
| | - Pascal Delaunay
- Service de Parasitologie-Mycologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France; Inserm U1065, Centre Méditerranéen de Médecine Moléculaire, Université de Nice-Sophia Antipolis, Nice, France; MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France
| | - Mohamed Kasbari
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, ANSES, Laboratoire de Santé Animale, Maisons-Alfort, Cedex, France
| | - Bruno Granouillac
- IRD/UMI 233, INSERM U1175, Montpellier University, Montpellier, France; MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France
| | - Luigi Gradoni
- Unit of Vector-borne Diseases and International Health, Istituto Superiore di Sanità, Rome, Italy
| | - Denis Sereno
- MIVEGEC, UMR CNRS5290-IRD224-Université de Montpellier Centre IRD, Montpellier, France; Intertryp UMR IRD177, Centre IRD de Montpellier, Montpellier, France
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171
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Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome. Mol Genet Genomics 2016; 292:53-61. [PMID: 27714457 DOI: 10.1007/s00438-016-1255-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Abstract
Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in plants.
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172
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Molecular characterization of 5S ribosomal RNA genes and transcripts in the protozoan parasite Leishmania major. Parasitology 2016; 143:1917-1929. [PMID: 27707420 DOI: 10.1017/s0031182016001712] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Eukaryotic 5S rRNA, synthesized by RNA polymerase III (Pol III), is an essential component of the large ribosomal subunit. Most organisms contain hundreds of 5S rRNA genes organized into tandem arrays. However, the genome of the protozoan parasite Leishmania major contains only 11 copies of the 5S rRNA gene, which are interspersed and associated with other Pol III-transcribed genes. Here we report that, in general, the number and order of the 5S rRNA genes is conserved between different species of Leishmania. While in most organisms 5S rRNA genes are normally associated with the nucleolus, combined fluorescent in situ hybridization and indirect immunofluorescence experiments showed that 5S rRNA genes are mainly located at the nuclear periphery in L. major. Similarly, the tandemly repeated 5S rRNA genes in Trypanosoma cruzi are dispersed throughout the nucleus. In contrast, 5S rRNA transcripts in L. major were localized within the nucleolus, and scattered throughout the cytoplasm, where mature ribosomes are located. Unlike other rRNA species, stable antisense RNA complementary to 5S rRNA is not detected in L. major.
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173
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Abstract
The structures of RNA Polymerase (Pol) II pre-initiation complexes (PIC) have recently been determined at near-atomic resolution, elucidating unprecedented mechanistic details of promoter opening during transcription initiation. The key structural features of promoter opening are summarized here. Structural knowledge of Pol I and III PIC is also briefly discussed.
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Affiliation(s)
- Yan Han
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA,CONTACT Yan Han , Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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174
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Sagi D, Rak R, Gingold H, Adir I, Maayan G, Dahan O, Broday L, Pilpel Y, Rechavi O. Tissue- and Time-Specific Expression of Otherwise Identical tRNA Genes. PLoS Genet 2016; 12:e1006264. [PMID: 27560950 PMCID: PMC4999229 DOI: 10.1371/journal.pgen.1006264] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/27/2016] [Indexed: 11/18/2022] Open
Abstract
Codon usage bias affects protein translation because tRNAs that recognize synonymous codons differ in their abundance. Although the current dogma states that tRNA expression is exclusively regulated by intrinsic control elements (A- and B-box sequences), we revealed, using a reporter that monitors the levels of individual tRNA genes in Caenorhabditis elegans, that eight tryptophan tRNA genes, 100% identical in sequence, are expressed in different tissues and change their expression dynamically. Furthermore, the expression levels of the sup-7 tRNA gene at day 6 were found to predict the animal's lifespan. We discovered that the expression of tRNAs that reside within introns of protein-coding genes is affected by the host gene's promoter. Pairing between specific Pol II genes and the tRNAs that are contained in their introns is most likely adaptive, since a genome-wide analysis revealed that the presence of specific intronic tRNAs within specific orthologous genes is conserved across Caenorhabditis species.
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Affiliation(s)
- Dror Sagi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Roni Rak
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Hila Gingold
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Idan Adir
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Gadi Maayan
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Orna Dahan
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Limor Broday
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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175
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Guizetti J, Barcons-Simon A, Scherf A. Trans-acting GC-rich non-coding RNA at var expression site modulates gene counting in malaria parasite. Nucleic Acids Res 2016; 44:9710-9718. [PMID: 27466391 PMCID: PMC5175341 DOI: 10.1093/nar/gkw664] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/14/2022] Open
Abstract
Monoallelic expression of the var multigene family enables immune evasion of the malaria parasite Plasmodium falciparum in its human host. At a given time only a single member of the 60-member var gene family is expressed at a discrete perinuclear region called the 'var expression site'. However, the mechanism of var gene counting remains ill-defined. We hypothesize that activation factors associating specifically with the expression site play a key role in this process. Here, we investigate the role of a GC-rich non-coding RNA (ncRNA) gene family composed of 15 highly homologous members. GC-rich genes are positioned adjacent to var genes in chromosome-central gene clusters but are absent near subtelomeric var genes. Fluorescence in situ hybridization demonstrates that GC-rich ncRNA localizes to the perinuclear expression site of central and subtelomeric var genes in trans. Importantly, overexpression of distinct GC-rich ncRNA members disrupts the gene counting process at the single cell level and results in activation of a specific subset of var genes in distinct clones. We identify the first trans-acting factor targeted to the elusive perinuclear var expression site and open up new avenues to investigate ncRNA function in antigenic variation of malaria and other protozoan pathogens.
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Affiliation(s)
- Julien Guizetti
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75724, France .,INSERM U1201, F-75724 Paris, France.,CNRS ERL9195, F-75724 Paris, France
| | - Anna Barcons-Simon
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75724, France.,INSERM U1201, F-75724 Paris, France.,CNRS ERL9195, F-75724 Paris, France
| | - Artur Scherf
- Unité de Biologie des Interactions Hôte-Parasite, Institut Pasteur, Paris, 75724, France .,INSERM U1201, F-75724 Paris, France.,CNRS ERL9195, F-75724 Paris, France
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176
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Tramantano M, Sun L, Au C, Labuz D, Liu Z, Chou M, Shen C, Luk E. Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex. eLife 2016; 5. [PMID: 27438412 PMCID: PMC4995100 DOI: 10.7554/elife.14243] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 07/12/2016] [Indexed: 12/17/2022] Open
Abstract
The assembly of the preinitiation complex (PIC) occurs upstream of the +1 nucleosome which, in yeast, obstructs the transcription start site and is frequently assembled with the histone variant H2A.Z. To understand the contribution of the transcription machinery in the disassembly of the +1 H2A.Z nucleosome, conditional mutants were used to block PIC assembly. A quantitative ChIP-seq approach, which allows detection of global occupancy change, was employed to measure H2A.Z occupancy. Blocking PIC assembly resulted in promoter-specific H2A.Z accumulation, indicating that the PIC is required to evict H2A.Z. By contrast, H2A.Z eviction was unaffected upon depletion of INO80, a remodeler previously reported to displace nucleosomal H2A.Z. Robust PIC-dependent H2A.Z eviction was observed at active and infrequently transcribed genes, indicating that constitutive H2A.Z turnover is a general phenomenon. Finally, sites with strong H2A.Z turnover precisely mark transcript starts, providing a new metric for identifying cryptic and alternative sites of initiation. DOI:http://dx.doi.org/10.7554/eLife.14243.001 To fit the genetic information of an animal, yeast or other eukaryote into cells, DNA is tightly wound around proteins called histones to form repeating units known as nucleosomes. However, this tight winding prevents proteins from accessing the DNA, and so prevents gene transcription – the first stage of producing the molecules encoded by a gene. For transcription to take place, nucleosomes at DNA sequences called promoters must be reorganized and disassembled, thereby allowing proteins to bind to and engage these sequences and to turn nearby genes on. H2A is a histone protein that is found in the majority of nucleosomes in yeast cells. A different form of this histone – called H2A.Z – is found in nucleosomes near the promoter of almost every gene. It is thought that nucleosomes that contain H2A.Z are recognized and disassembled as the gene turns on, but it is unclear how this happens. To investigate how H2A.Z nucleosomes are disassembled, Tramantano et al. depleted yeast cells of various proteins thought to play a role in the disassembly process. This indicated that the proteins that transcribe genes play crucial roles in the process of disassembling the H2A.Z nucleosomes, because H2A.Z accumulated at promoters in cells that are depleted of these proteins. Further investigation revealed that disassembled H2A.Z nucleosomes are reassembled with H2A histones, before being converted back to the H2A.Z form by an enzyme called SWR1. This turnover of H2A.Z was seen at active genes and those that are infrequently transcribed, suggesting that it is a general phenomenon. Tramantano et al. also found that the turnover rate of H2A.Z can be used to accurately predict the sites in the DNA where transcription starts. This observation could therefore help to identify previously unknown transcription start sites. Future work could address further questions about how H2A.Z nucleosomes are disassembled. For example, what is the mechanical force that drives this process? And at what step of the transcription process does it occur? DOI:http://dx.doi.org/10.7554/eLife.14243.002
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Affiliation(s)
- Michael Tramantano
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Lu Sun
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Christy Au
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Daniel Labuz
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Zhimin Liu
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Mindy Chou
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Chen Shen
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, United States
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177
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Hoffmann NA, Sadian Y, Tafur L, Kosinski J, Müller CW. Specialization versus conservation: How Pol I and Pol III use the conserved architecture of the pre-initiation complex for specialized transcription. Transcription 2016; 7:127-32. [PMID: 27327079 PMCID: PMC4984676 DOI: 10.1080/21541264.2016.1203628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Here, we discuss the overall architecture of the RNA polymerase I (Pol I) and III (Pol III) core enzymes and their associated general transcription factors in the context of models of the Pol I and Pol III pre-initiation complexes, thereby highlighting potential functional adaptations of the Pol I and Pol III enzymes to their respective transcription tasks. Several new insights demonstrate the great degree of specialization of each of the eukaryotic RNA polymerases that is only beginning to be revealed as the structural and functional characterization of all eukaryotic RNA polymerases and their pre-initiation complexes progresses.
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Affiliation(s)
- Niklas A Hoffmann
- a European Molecular Biology Laboratory (EMBL) , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Yashar Sadian
- a European Molecular Biology Laboratory (EMBL) , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Lucas Tafur
- a European Molecular Biology Laboratory (EMBL) , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Jan Kosinski
- a European Molecular Biology Laboratory (EMBL) , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Christoph W Müller
- a European Molecular Biology Laboratory (EMBL) , Structural and Computational Biology Unit , Heidelberg , Germany
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178
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Midgley AC, Morris G, Phillips AO, Steadman R. 17β-estradiol ameliorates age-associated loss of fibroblast function by attenuating IFN-γ/STAT1-dependent miR-7 upregulation. Aging Cell 2016; 15:531-41. [PMID: 26931423 PMCID: PMC4854905 DOI: 10.1111/acel.12462] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/10/2016] [Indexed: 12/20/2022] Open
Abstract
Age‐related defects in fibroblast differentiation and functionality were previously shown to be associated with impaired hyaluronan (HA) synthase 2 (HAS2) and epidermal growth factor receptor (EGFR) function, as a result of upregulated microRNA‐7 (miR‐7) expression. In aging fibroblasts, inhibiting miR‐7 prevented the dysregulation of the HA‐mediated CD44/EGFR signaling pathway. Here, we investigated transcriptional upregulation of miR‐7 and implicated the age‐associated over‐activation of JAK/STAT1 as a primary candidate. STAT1 binding sites were identified on the putative miR‐7 promoter and stimulation of fibroblasts with the inflammatory cytokine, interferon‐γ (IFN‐γ), significantly increased miR‐7 transcriptional activity and resulted in upregulated miR‐7 and loss of EGFR. Additionally, we demonstrated a role for the anti‐inflammatory steroid, 17β‐estradiol (E2), in the attenuation of miR‐7 expression. E2 stimulation promoted estrogen receptor (ER) interactions with the miR‐7 putative promoter and suppressed miR‐7 expression. E2 also attenuated STAT1 expression and activity. Furthermore, treatments with E2 restored fibroblast functionality, including proliferation, migration and differentiation, key events in effective wound healing. In light of our findings, we propose that the regulation of miR‐7 by pro‐ and anti‐inflammatory mediators plays a wider role than previously thought. The modulation of fibroblast functions and ultimately wound healing by miR‐7 activators or inhibitors could provide realistic targets for the restoration of chronic wound healing capabilities in the elderly.
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Affiliation(s)
- Adam C. Midgley
- Institute of Nephrology, Wales Kidney Research Unit; Division of Infection and Immunity; Cardiff University; College of Biomedical and Life Sciences; University Hospital of Wales; Heath Park Wales CF14 4XN UK
| | - Glyn Morris
- Institute of Nephrology, Wales Kidney Research Unit; Division of Infection and Immunity; Cardiff University; College of Biomedical and Life Sciences; University Hospital of Wales; Heath Park Wales CF14 4XN UK
| | - Aled O. Phillips
- Institute of Nephrology, Wales Kidney Research Unit; Division of Infection and Immunity; Cardiff University; College of Biomedical and Life Sciences; University Hospital of Wales; Heath Park Wales CF14 4XN UK
| | - Robert Steadman
- Institute of Nephrology, Wales Kidney Research Unit; Division of Infection and Immunity; Cardiff University; College of Biomedical and Life Sciences; University Hospital of Wales; Heath Park Wales CF14 4XN UK
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179
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Matsutani S. Possible interaction between the bacterial transcription factor ArtA and the eukaryotic RNA polymerase III promoter. Genetica 2016; 144:361-74. [PMID: 27178279 DOI: 10.1007/s10709-016-9905-2] [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: 07/01/2015] [Accepted: 05/07/2016] [Indexed: 11/26/2022]
Abstract
Eukaryotic RNA polymerase III (RNAP III) transcribes tRNA genes and short interspersed elements that have internal promoters consisting of A- and B-blocks. The B-block binding subunit of the transcription initiation factor TFIIIC binds to the B-block. The mobile bacterial insertion sequence (IS) 1 contains a RNAP III promoter-like sequence, which stimulates bacterial transcription along with the bacterial ArtA protein. Here, the DNA-binding ability of ArtA was examined in vitro using a simple, newly developed method. Various DNA fragments, including RNAP III promoter fragments, were separately incubated with purified ArtA, and then loaded onto a polyacrylamide gel. Since DNAs bound by ArtA remain in the gel wells during electrophoresis, SDS was added into the wells at the electrophoresis halfway point. It was hypothesized that SDS would dissociate the DNA-ArtA complexes in the wells, and then the DNAs would begin to migrate. In fact, new bands appeared in all of the lanes at similar intensities, indicating that ArtA binds nonspecifically to DNA. Therefore, labeled wild-type RNAP III promoter fragments were incubated with either the unlabeled wild-type or mutant fragments and ArtA, and electrophoresed. The B-block(-like) sequences of IS1, a human Alu element, and an anuran tRNA gene were important for binding to ArtA. Additionally, in silico analyses revealed the presence of the RNAP III promoter-like structures in the IS1 isoforms and the IS3 family elements. These results suggest the presence of parts of the RNAP III transcription machinery in bacteria, and might imply that its prototype existed in the common ancestor.
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Affiliation(s)
- Sachiko Matsutani
- Division of Microbiology, National Institute of Health Sciences, Tokyo, 158-8501, Japan.
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180
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Diette N, Koo J, Cabarcas-Petroski S, Schramm L. Gender Specific Differences in RNA Polymerase III Transcription. ACTA ACUST UNITED AC 2016; 7. [PMID: 27158556 DOI: 10.4172/2157-2518.1000251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND RNA polymerase (pol) III transcribes a variety of untranslated RNAs responsible for regulating cellular growth and is deregulated in a variety of cancers. In this study, we examined gender differences in RNA pol III transcription in vitro and in vivo. METHODS Expression levels of U6 snRNA, tMet, and known modulators of RNA pol III transcription were assayed in male and female derived adenocarcinoma (AC) lung cancer cell lines and male and female C57BL/6J mice using real time quantitative PCR. Methylation status of the U6 snRNA promoter was determined for lung and liver tissue isolated from male and female C57BL/6J mice by digesting genomic DNA with methylation sensitive restriction enzymes and digestion profiles were analyzed by qPCR using primers spanning the U6 promoter. RESULTS Here, we demonstrate that RNA pol III transcription is differentially regulated by EGCG in male and female derived AC lung cancer cell lines. Basal RNA pol III transcript levels are significantly different in male and female derived AC lung cancer cell lines. These data prompted an investigation of gender specific differences in RNA pol III transcription in vivo in lung and liver tissue. Herein, we report that U6 snRNA RNA pol III transcription is significantly stimulated in the liver tissue of male C57BL/6J mice. Further, the increase in U6 transcription correlates with a significant inhibition in the expression of p53, a negative regulator of RNA pol III transcription, and demethylation of the U6 promoter in the liver tissue of male C57BL/6J mice. CONCLUSIONS To the best of our knowledge, this is the first study demonstrating gender specific differences in RNA pol III transcription both in vivo and in vitro and further highlights the need to include both male and female cell lines and animals in experimental design.
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Affiliation(s)
- N Diette
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - J Koo
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - S Cabarcas-Petroski
- Pennsylvania State University, Beaver Campus, Monaca, Pennsylvania, 15061 USA
| | - L Schramm
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
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181
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Kang JJ, Kang YS, Stumph WE. TFIIIB subunit locations on U6 gene promoter DNA mapped by site-specific protein-DNA photo-cross-linking. FEBS Lett 2016; 590:1488-97. [PMID: 27112515 DOI: 10.1002/1873-3468.12185] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/05/2022]
Abstract
RNA polymerase III-transcribed U6 snRNA genes have gene-external promoters that contain TATA boxes. U6 TATA sequences are bound by TFIIIB that in Drosophila contains the three subunits TBP, Brf1, and Bdp1. The overall structure of TFIIIB is still not well understood. We have therefore studied the mode of TFIIIB binding to DNA by site-specific protein-DNA photo-cross-linking. The results indicate that a portion of Brf1 is sandwiched between Bdp1 and TBP upstream of the TATA box. Furthermore, Bdp1 traverses the DNA under the N-terminal stirrup of TBP to interact with the DNA (and very likely Brf1) downstream of the TATA sequence.
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Affiliation(s)
- Jin Joo Kang
- Department of Chemistry and Biochemistry, San Diego State University, CA, USA
| | - Yoon Soon Kang
- Department of Chemistry and Biochemistry, San Diego State University, CA, USA
| | - William E Stumph
- Department of Chemistry and Biochemistry, San Diego State University, CA, USA
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182
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RNA Polymerase III Advances: Structural and tRNA Functional Views. Trends Biochem Sci 2016; 41:546-559. [PMID: 27068803 DOI: 10.1016/j.tibs.2016.03.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 12/25/2022]
Abstract
RNA synthesis in eukaryotes is divided among three RNA polymerases (RNAPs). RNAP III transcribes hundreds of tRNA genes and fewer additional short RNA genes. We survey recent work on transcription by RNAP III including an atomic structure, mechanisms of action, interactions with chromatin and retroposons, and a conserved link between its activity and a tRNA modification that enhances mRNA decoding. Other new work suggests important mechanistic connections to oxidative stress, autoimmunity and cancer, embryonic stem cell pluripotency, and tissue-specific developmental effects. We consider that, for some of its complex functions, variation in RNAP III activity levels lead to nonuniform changes in tRNAs that can shift the translation profiles of key codon-biased mRNAs with resultant phenotypes or disease states.
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183
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Gouge J, Satia K, Guthertz N, Widya M, Thompson AJ, Cousin P, Dergai O, Hernandez N, Vannini A. Redox Signaling by the RNA Polymerase III TFIIB-Related Factor Brf2. Cell 2016; 163:1375-87. [PMID: 26638071 PMCID: PMC4671959 DOI: 10.1016/j.cell.2015.11.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/14/2015] [Accepted: 10/23/2015] [Indexed: 01/06/2023]
Abstract
TFIIB-related factor 2 (Brf2) is a member of the family of TFIIB-like core transcription factors. Brf2 recruits RNA polymerase (Pol) III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. Found only in vertebrates, Brf2 has been linked to tumorigenesis but the underlying mechanisms remain elusive. We have solved crystal structures of a human Brf2-TBP complex bound to natural promoters, obtaining a detailed view of the molecular interactions occurring at Brf2-dependent Pol III promoters and highlighting the general structural and functional conservation of human Pol II and Pol III pre-initiation complexes. Surprisingly, our structural and functional studies unravel a Brf2 redox-sensing module capable of specifically regulating Pol III transcriptional output in living cells. Furthermore, we establish Brf2 as a central redox-sensing transcription factor involved in the oxidative stress pathway and provide a mechanistic model for Brf2 genetic activation in lung and breast cancer. Architectural conservation of TFIIB and TFIIB-related factors Brf2 is a redox-sensing RNA polymerase III core transcription factor Brf2 regulates cellular responses to oxidative stress Brf2 amplification enables cancer cells to evade oxidative stress-induced apoptosis
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Affiliation(s)
- Jerome Gouge
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Karishma Satia
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Nicolas Guthertz
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Marcella Widya
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Andrew James Thompson
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Pascal Cousin
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Oleksandr Dergai
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nouria Hernandez
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK.
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184
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Chan Z, Wang Y, Cao M, Gong Y, Mu Z, Wang H, Hu Y, Deng X, He XJ, Zhu JK. RDM4 modulates cold stress resistance in Arabidopsis partially through the CBF-mediated pathway. THE NEW PHYTOLOGIST 2016; 209:1527-39. [PMID: 26522658 PMCID: PMC5515388 DOI: 10.1111/nph.13727] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/25/2015] [Indexed: 05/20/2023]
Abstract
The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. How the CBF genes themselves are activated after cold acclimation remains poorly understood. In this study, we characterized cold tolerance of null mutant of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol V and Pol II, and is required for RNA-directed DNA methylation (RdDM) in Arabidopsis. The results showed that dysfunction of RDM4 reduced cold tolerance, as evidenced by decreased survival and increased electrolyte leakage. Mutation of RDM4 resulted in extensive transcriptomic reprogramming. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 constitutively increased the expression of CBFs and regulon genes and decreased cold-induced membrane injury. A great proportion of genes affected by rdm4 overlapped with those affected by CBFs. Chromatin immunoprecipitation results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF2 and CBF3. We present evidence of a considerable role for RDM4 in regulating gene expression at low temperature, including the CBF pathway in Arabidopsis.
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Affiliation(s)
- Zhulong Chan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yanping Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
| | - Minjie Cao
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuehua Gong
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- College of Life Science and Food Engineering, Yibin University, Yibin, Sichuan 644000, China
| | - Zixin Mu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- College of Life Science, Northwest A&F University, Yangling, Shaan’xi 712100, China
| | - Haiqing Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China
| | - Yuanlei Hu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- College of Life Sciences, Peking University, Beijing 100871, China
| | - Xin Deng
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA
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185
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Filonov GS, Kam CW, Song W, Jaffrey SR. In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. ACTA ACUST UNITED AC 2016; 22:649-60. [PMID: 26000751 DOI: 10.1016/j.chembiol.2015.04.018] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 04/14/2015] [Accepted: 04/20/2015] [Indexed: 11/18/2022]
Abstract
RNA aptamers can be expressed in cells to influence and image cellular processes. Aptamer folding is maintained by inserting the aptamers into highly structured RNA scaffolds. Here, we show that commonly used RNA scaffolds exhibit unexpected instability and cleavage in bacterial and mammalian cells. Using an in-gel staining approach for rapid and simple detection of Spinach- or Broccoli-tagged RNAs in cells, we monitored the processing of RNAs tagged with scaffolded aptamers, revealing endonucleolytic cleavage, RNA instability, and poor expression. We reengineered a natural three-way junction structure to generate an alternative scaffold that enables stable aptamer expression in cells. This scaffold was used to create cassettes containing up to four Broccoli units, markedly enhancing the brightness of mammalian cells expressing cassette-tagged RNAs. These experiments describe methods for screening RNA cleavage events in cells and identify cell-compatible scaffolds that enable efficient tagging of RNAs with aptamers for cellular expression.
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Affiliation(s)
- Grigory S Filonov
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Christina W Kam
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Wenjiao Song
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College, Cornell University, New York, NY 10065, USA.
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186
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de Lima Neto QA, Duarte Junior FF, Bueno PSA, Seixas FAV, Kowalski MP, Kheir E, Krude T, Fernandez MA. Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells: identification, molecular dynamics simulations and DNA replication initiation assays. BMC Mol Biol 2016; 17:1. [PMID: 26733090 PMCID: PMC4702372 DOI: 10.1186/s12867-015-0053-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/21/2015] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is available about Y RNAs in Chinese hamster cells, which have already been used to detect replication origins and alternative DNA structures around these sites. Here, we report the gene sequences and predicted structural characteristics of the Chinese hamster Y RNAs, and analyze their ability to support the initiation of chromosomal DNA replication in vitro. RESULTS We identified DNA sequences in the Chinese hamster genome of four Y RNAs (chY1, chY3, chY4 and chY5) with upstream promoter sequences, which are homologous to the four main types of vertebrate Y RNAs. The chY1, chY3 and chY5 genes were highly conserved with their vertebrate counterparts, whilst the chY4 gene showed a relatively high degree of diversification from the other vertebrate Y4 genes. Molecular dynamics simulations suggest that chY4 RNA is structurally stable despite its evolutionarily divergent predicted stem structure. Of the four Y RNA genes present in the hamster genome, we found that only the chY1 and chY3 RNA were strongly expressed in the Chinese hamster GMA32 cell line, while expression of the chY4 and chY5 RNA genes was five orders of magnitude lower, suggesting that they may in fact not be expressed. We synthesized all four chY RNAs and showed that any of these four could support the initiation of DNA replication in an established human cell-free system. CONCLUSIONS These data therefore establish that non-coding chY RNAs are stable structures and can substitute for human Y RNAs in a reconstituted cell-free DNA replication initiation system. The pattern of Y RNA expression and functionality is consistent with Y RNAs of other rodents, including mouse and rat.
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Affiliation(s)
- Quirino Alves de Lima Neto
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil.
| | - Francisco Ferreira Duarte Junior
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil.
| | | | | | | | - Eyemen Kheir
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | - Torsten Krude
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK.
| | - Maria Aparecida Fernandez
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Av. Colombo 5790, Maringá, Paraná, 87020-900, Brazil.
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187
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Wei Y, Xu J, Zhang W, Wen Z, Liu F. RNA polymerase III component Rpc9 regulates hematopoietic stem and progenitor cell maintenance in zebrafish. Development 2016; 143:2103-10. [DOI: 10.1242/dev.126797] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 04/25/2016] [Indexed: 12/18/2022]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are capable of self-renewal and replenishing all lineages of blood cells throughout the lifetime and thus critical for tissue homeostasis. However, the mechanism regulating HSPC development is still incompletely understood. Here, we isolate a zebrafish mutant with defective T lymphopoiesis and positional cloning identifies that Rpc9, a component of DNA-directed RNA polymerase III (Pol III) complex, is responsible for the mutant phenotype. Further analysis shows that rpc9-deficiency leads to the impairment of HSPCs and their derivatives in zebrafish embryos. Excessive apoptosis is observed in the caudal hematopoietic tissue (CHT, the equivalent of fetal liver in mammals) of rpc9−/− embryos and the hematopoietic defects in rpc9−/− embryos can be fully rescued by suppression of p53. Thus, our work illustrate that Rpc9, a component of Pol III, plays an important tissue-specific role in HSPC maintenance during zebrafish embryogenesis and that it might be conserved across vertebrates including mammals.
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Affiliation(s)
- Yonglong Wei
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Xu
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Wenqing Zhang
- Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, Southern Medical University, Guangzhou 510515, China
| | - Zilong Wen
- State Key Laboratory of Molecular Neuroscience, Center of Systems Biology and Human Health, Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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188
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Hoffmann NA, Jakobi AJ, Moreno-Morcillo M, Glatt S, Kosinski J, Hagen WJH, Sachse C, Müller CW. Molecular structures of unbound and transcribing RNA polymerase III. Nature 2015; 528:231-6. [PMID: 26605533 PMCID: PMC4681132 DOI: 10.1038/nature16143] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/13/2015] [Indexed: 12/11/2022]
Abstract
Transcription of genes encoding small structured RNAs such as transfer RNAs, spliceosomal U6 small nuclear RNA and ribosomal 5S RNA is carried out by RNA polymerase III (Pol III), the largest yet structurally least characterized eukaryotic RNA polymerase. Here we present the cryo-electron microscopy structures of the Saccharomyces cerevisiae Pol III elongating complex at 3.9 Å resolution and the apo Pol III enzyme in two different conformations at 4.6 and 4.7 Å resolution, respectively, which allow the building of a 17-subunit atomic model of Pol III. The reconstructions reveal the precise orientation of the C82-C34-C31 heterotrimer in close proximity to the stalk. The C53-C37 heterodimer positions residues involved in transcription termination close to the non-template DNA strand. In the apo Pol III structures, the stalk adopts different orientations coupled with closed and open conformations of the clamp. Our results provide novel insights into Pol III-specific transcription and the adaptation of Pol III towards its small transcriptional targets.
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Affiliation(s)
- Niklas A. Hoffmann
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Arjen J. Jakobi
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestr. 85, 22607 Hamburg, Germany
| | - Maria Moreno-Morcillo
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Sebastian Glatt
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jan Kosinski
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Wim J. H. Hagen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence and requests for materials should be addressed to C.S. () or C.W.M. ()
| | - Christoph W. Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Correspondence and requests for materials should be addressed to C.S. () or C.W.M. ()
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189
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Koo J, Cabarcas-Petroski S, Petrie JL, Diette N, White RJ, Schramm L. Induction of proto-oncogene BRF2 in breast cancer cells by the dietary soybean isoflavone daidzein. BMC Cancer 2015; 15:905. [PMID: 26573593 PMCID: PMC4647806 DOI: 10.1186/s12885-015-1914-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/06/2015] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND BRF2 is a transcription factor required for synthesis of a small group of non-coding RNAs by RNA polymerase III. Overexpression of BRF2 can transform human mammary epithelial cells. In both breast and lung cancers, the BRF2 gene is amplified and overexpressed and may serve as an oncogenic driver. Furthermore, elevated BRF2 can be independently prognostic of unfavorable survival. Dietary soy isoflavones increase metastasis to lungs in a model of breast cancer and a recent study reported significantly increased cell proliferation in breast cancer patients who used soy supplementation. The soy isoflavone daidzein is a major food-derived phytoestrogen that is structurally similar to estrogen. The putative estrogenic effect of soy raises concern that high consumption of soy foods by breast cancer patients may increase tumor growth. METHODS Expression of BRF2 RNA and protein was assayed in ER-positive or -negative human breast cancer cells after exposure to daidzein. We also measured mRNA stability, promoter methylation and response to the demethylating agent 5-azacytidine. In addition, expression was compared between mice fed diets enriched or deprived of isoflavones. RESULTS We demonstrate that the soy isoflavone daidzein specifically stimulates expression of BRF2 in ER-positive breast cancer cells, as well as the related factor BRF1. Induction is accompanied by increased levels of non-coding RNAs that are regulated by BRF2 and BRF1. Daidzein treatment stabilizes BRF2 and BRF1 mRNAs and selectively decreases methylation of the BRF2 promoter. Functional significance of demethylation is supported by induction of BRF2 by the methyltransferase inhibitor 5-azacytidine. None of these effects are observed in an ER-negative breast cancer line, when tested in parallel with ER-positive breast cancer cells. In vivo relevance is suggested by the significantly elevated levels of BRF2 mRNA detected in female mice fed a high-isoflavone commercial diet. In striking contrast, BRF2 and BRF1 mRNA levels are suppressed in matched male mice fed the same isoflavone-enriched diet. CONCLUSIONS The BRF2 gene that is implicated in cancer can be induced in human breast cancer cells by the isoflavone daidzein, through promoter demethylation and/or mRNA stabilization. Dietary isoflavones may also induce BRF2 in female mice, whereas the converse occurs in males.
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Affiliation(s)
- Jana Koo
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | | | - John L Petrie
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Nicole Diette
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA
| | - Robert J White
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Laura Schramm
- Department of Biological Sciences, St. John's University, Queens, New York, 11439, USA.
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190
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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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191
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Castro SI, Hleap JS, Cárdenas H, Blouin C. Molecular organization of the 5S rDNA gene type II in elasmobranchs. RNA Biol 2015; 13:391-9. [PMID: 26488198 PMCID: PMC4841605 DOI: 10.1080/15476286.2015.1100796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/21/2015] [Indexed: 10/22/2022] Open
Abstract
The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT4 sequence as stop signal, however in Rajiformes this signal was doubled in length to dT8. This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.
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Affiliation(s)
- Sergio I. Castro
- Grupo de Estudios en Genética Ecología Molecular y Fisiología Animal, Universidad del Valle, Cali, Colombia
- Fundación Colombiana para la Investigación y Conservación de Tiburones y Rayas, SQUALUS. Cali, Colombia
| | - Jose S. Hleap
- Grupo de Estudios en Genética Ecología Molecular y Fisiología Animal, Universidad del Valle, Cali, Colombia
- Fundación Colombiana para la Investigación y Conservación de Tiburones y Rayas, SQUALUS. Cali, Colombia
- Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Heiber Cárdenas
- Grupo de Estudios en Genética Ecología Molecular y Fisiología Animal, Universidad del Valle, Cali, Colombia
| | - Christian Blouin
- Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Computer Science, Dalhousie University, Halifax, Canada
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192
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Abstract
Reuter et al. show that Nab2, a poly(A)-binding protein important for correct poly(A) tail length and nuclear mRNA export, is present at all RNA polymerase III (RNAPIII) transcribed genes. Nab2 is required for the occupancy of RNAPIII and TFIIIB at target genes. RNA polymerase III (RNAPIII) synthesizes most small RNAs, the most prominent being tRNAs. Although the basic mechanism of RNAPIII transcription is well understood, recent evidence suggests that additional proteins play a role in RNAPIII transcription. Here, we discovered by a genome-wide approach that Nab2, a poly(A)-binding protein important for correct poly(A) tail length and nuclear mRNA export, is present at all RNAPIII transcribed genes. The occupancy of Nab2 at RNAPIII transcribed genes is dependent on transcription. Using a novel temperature-sensitive allele of NAB2, nab2-34, we show that Nab2 is required for the occupancy of RNAPIII and TFIIIB at target genes. Furthermore, Nab2 interacts with RNAPIII, TFIIIB, and RNAPIII transcripts. Importantly, impairment of Nab2 function causes an RNAPIII transcription defect in vivo and in vitro. Taken together, we establish Nab2, an important mRNA biogenesis factor, as a novel player required for RNAPIII transcription by stabilizing TFIIIB and RNAPIII at promoters.
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Affiliation(s)
- L Maximilian Reuter
- Institute of Biochemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Dominik M Meinel
- Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany
| | - Katja Sträßer
- Institute of Biochemistry, Justus Liebig University Giessen, 35392 Giessen, Germany; Gene Center, Ludwig-Maximilians-University Munich, 81377 Munich, Germany; Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-University Munich, 81377 Munich, Germany
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193
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Varshney D, Vavrova-Anderson J, Oler AJ, Cairns BR, White RJ. Selective repression of SINE transcription by RNA polymerase III. Mob Genet Elements 2015; 5:86-91. [PMID: 26942044 DOI: 10.1080/2159256x.2015.1096997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 10/23/2022] Open
Abstract
A million copies of the Alu short interspersed nuclear element (SINE) are scattered throughout the human genome, providing ∼11% of our total DNA. SINEs spread by retrotransposition, using a transcript generated by RNA polymerase (pol) III from an internal promoter. Levels of these pol III-dependent Alu transcripts are far lower than might be expected from the abundance of the template. This was believed to reflect transcriptional suppression through DNA methylation, denying pol III access to most SINEs through chromatin-mediated effects. Contrary to expectations, our recent study found no evidence that methylation of SINE DNA reduces its occupancy or expression by pol III. However, histone H3 associated with SINEs is prominently methylated on lysine 9, a mark that correlates with transcriptional silencing. The SUV39 methyltransferases that deposit this mark can be found at many SINEs. Furthermore, a selective inhibitor of SUV39 stimulates pol III recruitment to these loci, as well as SINE expression. These data suggest that methylation of histone H3 rather than DNA may mediate repression of SINE transcription by pol III, at least under the conditions we studied.
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Affiliation(s)
- Dhaval Varshney
- Centre for Gene Regulation and Expression; University of Dundee ; Dundee, UK
| | - Jana Vavrova-Anderson
- College of Medical; Veterinary and Life Sciences; University of Glasgow ; Glasgow, UK
| | - Andrew J Oler
- Bioinformatics and Computational Biosciences Branch; Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases; National Institutes of Health ; Bethesda, MD USA
| | - Bradley R Cairns
- Department of Oncological Sciences; Huntsman Cancer Institute; University of Utah School of Medicine; Salt Lake City, UT USA; Howard Hughes Medical Institute; University of Utah School of Medicine; Salt Lake City, UT USA
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194
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BRF1, a subunit of RNA polymerase III transcription factor TFIIIB, is essential for cell growth of Trypanosoma brucei. Parasitology 2015; 142:1563-73. [PMID: 26337955 DOI: 10.1017/s0031182015001122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RNA polymerase III (Pol III) synthesizes small RNA molecules that are essential for cell viability. Accurate initiation of transcription by Pol III requires general transcription factor TFIIIB, which is composed of three subunits: TFIIB-related factor BRF1, TATA-binding protein and BDP1. Here we report the molecular characterization of BRF1 in Trypanosoma brucei (TbBRF1), a parasitic protozoa that shows distinctive transcription characteristics. In silico analysis allowed the detection in TbBRF1 of the three conserved domains located in the N-terminal region of all BRF1 orthologues, namely a zinc ribbon motif and two cyclin repeats. Homology modelling suggested that, similarly to other BRF1 and TFIIB proteins, the TbBRF1 cyclin repeats show the characteristic structure of five α-helices per repeat, connected by a short random-coiled linker. As expected for a transcription factor, TbBRF1 was localized in the nucleus. Knock-down of TbBRF1 by RNA interference (RNAi) showed that this protein is essential for the viability of procyclic forms of T. brucei, since ablation of TbBRF1 led to growth arrest of the parasites. Nuclear run-on and quantitative real-time PCR analyses demonstrated that transcription of all the Pol III-dependent genes analysed was reduced, at different levels, after RNAi induction.
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195
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Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis. Mol Cell Biol 2015; 35:2278-94. [PMID: 25918241 DOI: 10.1128/mcb.00076-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To further our understanding of the RNAi machinery within the human nucleus, we analyzed the chromatin and RNA binding of Argonaute 2 (AGO2) within human cancer cell lines. Our data indicated that AGO2 binds directly to nascent tRNA and 5S rRNA, and to the genomic loci from which these RNAs are transcribed, in a small RNA- and DICER-independent manner. AGO2 chromatin binding was not observed at non-TFIIIC-dependent RNA polymerase III (Pol III) genes or at extra-TFIIIC (ETC) sites, indicating that the interaction is specific for TFIIIC-dependent Pol III genes. A genome-wide analysis indicated that loss of AGO2 caused a global increase in mRNA expression level among genes that flank AGO2-bound tRNA genes. This effect was shown to be distinct from that of the disruption of DICER, DROSHA, or CTCF. We propose that AGO2 binding to tRNA genes has a novel and important regulatory role in human cells.
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196
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Architecture of TFIIIC and its role in RNA polymerase III pre-initiation complex assembly. Nat Commun 2015; 6:7387. [PMID: 26060179 PMCID: PMC4490372 DOI: 10.1038/ncomms8387] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/04/2015] [Indexed: 02/05/2023] Open
Abstract
In eukaryotes, RNA Polymerase III (Pol III) is specifically responsible for transcribing genes encoding tRNAs and other short non-coding RNAs. The recruitment of Pol III to tRNA-encoding genes requires the transcription factors (TF) IIIB and IIIC. TFIIIC has been described as a conserved, multi-subunit protein complex composed of two subcomplexes, called τA and τB. How these two subcomplexes are linked and how their interaction affects the formation of the Pol III pre-initiation complex (PIC) is poorly understood. Here we use chemical crosslinking mass spectrometry and determine the molecular architecture of TFIIIC. We further report the crystal structure of the essential TPR array from τA subunit τ131 and characterize its interaction with a central region of τB subunit τ138. The identified τ131–τ138 interacting region is essential in vivo and overlaps with TFIIIB-binding sites, revealing a crucial interaction platform for the regulation of tRNA transcription initiation. TFIIIC is a RNA polymerase III-specific general transcription factor complex essential for tRNA synthesis. Here the authors combine chemical crosslinking/mass spectrometry and X-ray crystallography to define the architecture of TFIIIC and suggest a model for the assembly of pre-initiation complexes at tRNA genes.
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197
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A Region of Bdp1 Necessary for Transcription Initiation That Is Located within the RNA Polymerase III Active Site Cleft. Mol Cell Biol 2015; 35:2831-40. [PMID: 26055328 DOI: 10.1128/mcb.00263-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/01/2015] [Indexed: 02/02/2023] Open
Abstract
The RNA polymerase III (Pol III)-specific transcription factor Bdp1 is crucial to Pol III recruitment and promoter opening in transcription initiation, yet structural information is sparse. To examine its protein-binding targets within the preinitiation complex at the residue level, photoreactive amino acids were introduced into Saccharomyces cerevisiae Bdp1. Mutations within the highly conserved SANT domain cross-linked to the transcription factor IIB (TFIIB)-related transcription factor Brf1, consistent with the findings of previous studies. In addition, we identified an essential N-terminal region that cross-linked with the Pol III catalytic subunit C128 as well as Brf1. Closer examination revealed that this region interacted with the C128 N-terminal region, the N-terminal half of Brf1, and the C-terminal domain of the C37 subunit, together positioning this region within the active site cleft of the preinitiation complex. With our functional data, our analyses identified an essential region of Bdp1 that is positioned within the active site cleft of Pol III and necessary for transcription initiation.
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198
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Almuzzaini B, Sarshad AA, Farrants AKÖ, Percipalle P. Nuclear myosin 1 contributes to a chromatin landscape compatible with RNA polymerase II transcription activation. BMC Biol 2015; 13:35. [PMID: 26044184 PMCID: PMC4486089 DOI: 10.1186/s12915-015-0147-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 06/02/2015] [Indexed: 12/11/2022] Open
Abstract
Background Nuclear myosin 1c (NM1) is emerging as a regulator of transcription and chromatin organization. Results Using chromatin immunoprecipitation and deep sequencing (ChIP-Seq) in combination with molecular analyses, we investigated the global association of NM1 with the mammalian genome. Analysis of the ChIP-Seq data demonstrates that NM1 binds across the entire mammalian genome with occupancy peaks correlating with distributions of RNA Polymerase II (Pol II) and active epigenetic marks at class II gene promoters. In mouse embryonic fibroblasts subjected to RNAi mediated NM1 gene silencing, we show that NM1 synergizes with polymerase-associated actin to maintain active Pol II at the promoter. NM1 also co-localizes with the nucleosome remodeler SNF2h at class II promoters where they assemble together with WSTF as part of the B-WICH complex. A high resolution micrococcal nuclease (MNase) assay and quantitative real time PCR shows that this mechanism is required for local chromatin remodeling. Following B-WICH assembly, NM1 mediates physical recruitment of the histone acetyl transferase PCAF and the histone methyl transferase Set1/Ash2 to maintain and preserve H3K9acetylation and H3K4trimethylation for active transcription. Conclusions We propose a novel genome-wide mechanism where myosin synergizes with Pol II-associated actin to link the polymerase machinery with permissive chromatin for transcription activation. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0147-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bader Almuzzaini
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden.
| | - Aishe A Sarshad
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden. .,Present address: National Institute of Health, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD, 20892-3675, USA.
| | - Ann-Kristin Östlund Farrants
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Piergiorgio Percipalle
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77, Stockholm, Sweden.
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199
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Liu C, Li S, Dai X, Ma J, Wan J, Jiang H, Wang P, Liu Z, Zhang H. PRC2 regulates RNA polymerase III transcribed non-translated RNA gene transcription through EZH2 and SUZ12 interaction with TFIIIC complex. Nucleic Acids Res 2015; 43:6270-84. [PMID: 26038315 PMCID: PMC4513857 DOI: 10.1093/nar/gkv574] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/20/2015] [Indexed: 11/12/2022] Open
Abstract
Polycomb repression complex 2 (PRC2) component EZH2 tri-methylates H3K27 and exerts epigenetic repression on target gene expression. EZH2-mediated epigenetic control of RNA polymerase II (Pol II) transcribed coding gene transcription has been well established. However, little is known about EZH2-mediated epigenetic regulation of RNA polymerase III (Pol III) transcription. Here we present a paradigm that EZH2 is involved in the repression of Pol III transcription via interaction with transcriptional factor complex IIIC (TFIIIC). EZH2 and H3K27me3 co-occupy the promoter of tRNATyr, 5S rRNA and 7SL RNA genes. Depletion of EZH2 or inhibition of EZH2 methyltransferase activity led to upregulation of Pol III target gene transcription. EZH2-mediated repression of Pol III transcribed gene expression requires presence of SUZ12. SUZ12 was able to interact with TFIIIC complex and knockdown of SUZ12 decreased occupancy of EZH2 and H3K27me3 at the promoter of Pol III target genes. Our findings pointed out a previously unidentified role of PRC2 complex in suppressing transcription of Pol III transcribed non-translated RNA genes, putting Pol III on a new layer of epigenetic regulation.
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Affiliation(s)
- Chang Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Shuai Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Xiaoyan Dai
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Ji Ma
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Junhu Wan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hao Jiang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Peng Wang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Zhaoli Liu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
| | - Hongquan Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China Laboratory of Molecular Cell Biology and Tumor Biology, Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University Health Science Center, #38 Xue Yuan Road, Beijing 100191, China
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200
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Serruya R, Orlovetskie N, Reiner R, Dehtiar-Zilber Y, Wesolowski D, Altman S, Jarrous N. Human RNase P ribonucleoprotein is required for formation of initiation complexes of RNA polymerase III. Nucleic Acids Res 2015; 43:5442-50. [PMID: 25953854 PMCID: PMC4477669 DOI: 10.1093/nar/gkv447] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 04/24/2015] [Indexed: 12/12/2022] Open
Abstract
Human RNase P is implicated in transcription of small non-coding RNA genes by RNA polymerase III (Pol III), but the precise role of this ribonucleoprotein therein remains unknown. We here show that targeted destruction of HeLa nuclear RNase P inhibits transcription of 5S rRNA genes in whole cell extracts, if this precedes the stage of initiation complex formation. Biochemical purification analyses further reveal that this ribonucleoprotein is recruited to 5S rRNA genes as a part of proficient initiation complexes and the activity persists at reinitiation. Knockdown of RNase P abolishes the assembly of initiation complexes by preventing the formation of the initiation sub-complex of Pol III. Our results demonstrate that the structural intactness, but not the endoribonucleolytic activity per se, of RNase P is critical for the function of Pol III in cells and in extracts.
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Affiliation(s)
- Raphael Serruya
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Natalie Orlovetskie
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Robert Reiner
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yana Dehtiar-Zilber
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Donna Wesolowski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Sidney Altman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Nayef Jarrous
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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