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Kor SD, Chowdhury N, Keot AK, Yogendra K, Chikkaputtaiah C, Sudhakar Reddy P. RNA Pol III promoters-key players in precisely targeted plant genome editing. Front Genet 2023; 13:989199. [PMID: 36685866 PMCID: PMC9845283 DOI: 10.3389/fgene.2022.989199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/15/2022] [Indexed: 01/05/2023] Open
Abstract
The clustered regularly interspaced short palindrome repeat (CRISPR)/CRISPR-associated protein Cas) system is a powerful and highly precise gene-editing tool in basic and applied research for crop improvement programs. CRISPR/Cas tool is being extensively used in plants to improve crop yield, quality, and nutritional value and make them tolerant to environmental stresses. CRISPR/Cas system consists of a Cas protein with DNA endonuclease activity and one CRISPR RNA transcript that is processed to form one or several short guide RNAs that direct Cas9 to the target DNA sequence. The expression levels of Cas proteins and gRNAs significantly influence the editing efficiency of CRISPR/Cas-mediated genome editing. This review focuses on insights into RNA Pol III promoters and their types that govern the expression levels of sgRNA in the CRISPR/Cas system. We discussed Pol III promoters structural and functional characteristics and their comparison with Pol II promoters. Further, the use of synthetic promoters to increase the targeting efficiency and overcome the structural, functional, and expressional limitations of RNA Pol III promoters has been discussed. Our review reports various studies that illustrate the use of endogenous U6/U3 promoters for improving editing efficiency in plants and the applicative approach of species-specific RNA pol III promoters for genome editing in model crops like Arabidopsis and tobacco, cereals, legumes, oilseed, and horticultural crops. We further highlight the significance of optimizing these species-specific promoters' systematic identification and validation for crop improvement and biotic and abiotic stress tolerance through CRISPR/Cas mediated genome editing.
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Affiliation(s)
- Sakshi Dharmendra Kor
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Ajay Kumar Keot
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kalenahalli Yogendra
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Palakolanu Sudhakar Reddy
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India,*Correspondence: Palakolanu Sudhakar Reddy, ,
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Yan B, Tzertzinis G, Schildkraut I, Ettwiller L. Comprehensive determination of transcription start sites derived from all RNA polymerases using ReCappable-seq. Genome Res 2021; 32:162-174. [PMID: 34815308 PMCID: PMC8744680 DOI: 10.1101/gr.275784.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Determination of eukaryotic transcription start sites (TSSs) has been based on methods that require the cap structure at the 5' end of transcripts derived from Pol II RNA polymerase. Consequently, these methods do not reveal TSSs derived from the other RNA polymerases that also play critical roles in various cell functions. To address this limitation, we developed ReCappable-seq, which comprehensively identifies TSS for both Pol II and non-Pol II transcripts at single-nucleotide resolution. The method relies on specific enzymatic exchange of 5' m7G caps and 5' triphosphates with a selectable tag. When applied to human transcriptomes, ReCappable-seq identifies Pol II TSSs that are in agreement with orthogonal methods such as CAGE. Additionally, ReCappable-seq reveals a rich landscape of TSSs associated with Pol III transcripts that have not previously been amenable to study at genome-wide scale. Novel TSS from non-Pol II transcription can be located in the nuclear and mitochondrial genomes. ReCappable-seq interrogates the regulatory landscape of coding and noncoding RNA concurrently and enables the classification of epigenetic profiles associated with Pol II and non-Pol II TSS.
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Affiliation(s)
- Bo Yan
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
| | | | - Ira Schildkraut
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
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Patterson K, Shavarebi F, Magnan C, Chang I, Qi X, Baldi P, Bilanchone V, Sandmeyer SB. Local features determine Ty3 targeting frequency at RNA polymerase III transcription start sites. Genome Res 2019; 29:1298-1309. [PMID: 31249062 PMCID: PMC6673722 DOI: 10.1101/gr.240861.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 06/12/2019] [Indexed: 12/27/2022]
Abstract
Retroelement integration into host genomes affects chromosome structure and function. A goal of a considerable number of investigations is to elucidate features influencing insertion site selection. The Saccharomyces cerevisiae Ty3 retrotransposon inserts proximal to the transcription start sites (TSS) of genes transcribed by RNA polymerase III (RNAP3). In this study, differential patterns of insertion were profiled genome-wide using a random barcode-tagged Ty3. Saturation transposition showed that tRNA genes (tDNAs) are targeted at widely different frequencies even within isoacceptor families. Ectopic expression of Ty3 integrase (IN) showed that it localized to targets independent of other Ty3 proteins and cDNA. IN, RNAP3, and transcription factor Brf1 were enriched at tDNA targets with high frequencies of transposition. To examine potential effects of cis-acting DNA features on transposition, targeting was tested on high-copy plasmids with restricted amounts of 5′ flanking sequence plus tDNA. Relative activity of targets was reconstituted in these constructions. Weighting of genomic insertions according to frequency identified an A/T-rich sequence followed by C as the dominant site of strand transfer. This site lies immediately adjacent to the adenines previously implicated in the RNAP3 TSS motif (CAA). In silico DNA structural analysis upstream of this motif showed that targets with elevated DNA curvature coincide with reduced integration. We propose that integration mediated by the Ty3 intasome complex (IN and cDNA) is subject to inputs from a combination of host factor occupancy and insertion site architecture, and that this results in the wide range of Ty3 targeting frequencies.
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Affiliation(s)
- Kurt Patterson
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Farbod Shavarebi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Christophe Magnan
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Ivan Chang
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Xiaojie Qi
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Pierre Baldi
- School of Information and Computer Sciences, University of California, Irvine, Irvine, California 92697, USA
| | - Virginia Bilanchone
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
| | - Suzanne B Sandmeyer
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California 92697, USA
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4
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Hummel G, Warren J, Drouard L. The multi-faceted regulation of nuclear tRNA gene transcription. IUBMB Life 2019; 71:1099-1108. [PMID: 31241827 DOI: 10.1002/iub.2097] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/31/2022]
Abstract
Transfer RNAs are among the most ancient molecules of life on earth. Beyond their crucial role in protein synthesis as carriers of amino acids, they are also important players in a plethora of other biological processes. Many debates in term of biogenesis, regulation and function persist around these fascinating non-coding RNAs. Our review focuses on the first step of their biogenesis in eukaryotes, i.e. their transcription from nuclear genes. Numerous and complementary ways have emerged during evolution to regulate transfer RNA gene transcription. Here, we will summarize the different actors implicated in this process: cis-elements, trans-factors, genomic contexts, epigenetic environments and finally three-dimensional organization of nuclear genomes. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1099-1108, 2019.
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Affiliation(s)
- Guillaume Hummel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Jessica Warren
- Department of biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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Ohira T, Suzuki T. Precursors of tRNAs are stabilized by methylguanosine cap structures. Nat Chem Biol 2016; 12:648-55. [PMID: 27348091 DOI: 10.1038/nchembio.2117] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 05/20/2016] [Indexed: 01/30/2023]
Abstract
Efficient maturation of transfer RNAs (tRNAs) is required for rapid cell growth. However, the precise timing of tRNA processing in coordination with the order of tRNA modifications has not been thoroughly elucidated. To analyze the modification status of tRNA precursors (pre-tRNAs) during maturation, we isolated pre-tRNAs at various stages from Saccharomyces cerevisiae and subjected them to MS analysis. We detected methylated guanosine cap structures at the 5' termini of pre-tRNAs bearing 5' leader sequences. These capped pre-tRNAs accumulated substantially after inhibition of RNase P activity. Upon depletion of the capping enzyme Ceg1p, the steady state level of capped pre-tRNA was markedly reduced. In addition, a population of capped pre-tRNAs accumulated in strains in which 5' exonucleases were inhibited, indicating that the 5' cap structures protect pre-tRNAs from 5'-exonucleolytic degradation during maturation.
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Affiliation(s)
- Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
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Ido A, Iwata S, Iwata Y, Igarashi H, Hamada T, Sonobe S, Sugiura M, Yukawa Y. Arabidopsis Pol II-Dependent in Vitro Transcription System Reveals Role of Chromatin for Light-Inducible rbcS Gene Transcription. PLANT PHYSIOLOGY 2016; 170:642-52. [PMID: 26662274 PMCID: PMC4734572 DOI: 10.1104/pp.15.01614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/08/2015] [Indexed: 05/20/2023]
Abstract
In vitro transcription is an essential tool to study the molecular mechanisms of transcription. For over a decade, we have developed an in vitro transcription system from tobacco (Nicotiana tabacum)-cultured cells (BY-2), and this system supported the basic activities of the three RNA polymerases (Pol I, Pol II, and Pol III). However, it was not suitable to study photosynthetic genes, because BY-2 cells have lost their photosynthetic activity. Therefore, Arabidopsis (Arabidopsis thaliana) in vitro transcription systems were developed from green and etiolated suspension cells. Sufficient in vitro Pol II activity was detected after the minor modification of the nuclear soluble extracts preparation method; removal of vacuoles from protoplasts and L-ascorbic acid supplementation in the extraction buffer were particularly effective. Surprisingly, all four Arabidopsis Rubisco small subunit (rbcS-1A, rbcS-1B, rbcS-2B, and rbcS-3B) gene members were in vitro transcribed from the naked DNA templates without any light-dependent manner. However, clear light-inducible transcriptions were observed using chromatin template of rbcS-1A gene, which was prepared with a human nucleosome assembly protein 1 (hNAP1) and HeLa histones. This suggested that a key determinant of light-dependency through the rbcS gene transcription was a higher order of DNA structure (i.e. chromatin).
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Affiliation(s)
- Ayaka Ido
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Shinya Iwata
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Yuka Iwata
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Hisako Igarashi
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Takahiro Hamada
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Seiji Sonobe
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Masahiro Sugiura
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Mizuho, Nagoya 464-8501, Japan (A.I., S.I., Y.I., M.S., Y.Y.); andGraduate School of Life Science, University of Hyogo, Harima Science Park City, Hyogo 678-1297, Japan (H.I., T.H., S.S.)
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Yukawa Y, Akama K, Noguchi K, Komiya M, Sugiura M. The context of transcription start site regions is crucial for transcription of a plant tRNALys(UUU) gene group both in vitro and in vivo. Gene 2013; 512:286-93. [DOI: 10.1016/j.gene.2012.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 09/22/2012] [Accepted: 10/18/2012] [Indexed: 10/27/2022]
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Dieci G, Conti A, Pagano A, Carnevali D. Identification of RNA polymerase III-transcribed genes in eukaryotic genomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:296-305. [PMID: 23041497 DOI: 10.1016/j.bbagrm.2012.09.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/20/2012] [Accepted: 09/21/2012] [Indexed: 12/16/2022]
Abstract
The RNA polymerase (Pol) III transcription system is devoted to the production of short, generally abundant noncoding (nc) RNAs in all eukaryotic cells. Previously thought to be restricted to a few housekeeping genes easily detectable in genome sequences, the set of known Pol III-transcribed genes (class III genes) has been expanding in the last ten years, and the issue of their detection, annotation and actual expression has been stimulated and revived by the results of recent high-resolution genome-wide location analyses of the mammalian Pol III machinery, together with those of Pol III-centered computational studies and of ncRNA-focused transcriptomic approaches. In this article, we provide an outline of distinctive features of Pol III-transcribed genes that have allowed and currently allow for their detection in genome sequences, we critically review the currently practiced strategies for the identification of novel class III genes and transcripts, and we discuss emerging themes in Pol III transcription regulation which might orient future transcriptomic studies. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy.
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Wu J, Okada T, Fukushima T, Tsudzuki T, Sugiura M, Yukawa Y. A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis. RNA Biol 2012; 9:302-13. [PMID: 22336715 DOI: 10.4161/rna.19101] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recently, a large number of non-coding RNAs (ncRNAs) have been found in a wide variety of organisms, but their biological functions are poorly understood, except for several tiny RNAs. To identify novel ncRNAs with essential functions in flowering plants, we focused attention on RNA polymerase III (Pol III) and its transcriptional activity, because most Pol III-transcribed RNAs contribute to key processes relating to cell activities, and have highly conserved promoter elements: upstream sequence elements, a TATA-like sequence, and a poly(T) stretch as a transcription terminator. After in silico prediction from the Arabidopsis genome, 20 novel ncRNAs candidates were obtained. AtR8 RNA (approx. 260 nt) and AtR18 RNA (approx. 160 nt) were identified by efficient in vitro transcription by Pol III in tobacco nuclear extracts. AtR8 RNA was conserved among six additional taxa of Brassicaceae, and the secondary structure of the RNA was also conserved among the orthologs. Abundant accumulation of AtR8 RNA was observed in the plant roots and cytosol of cultured cells. The RNA was not processed into a smaller fragment and no short open reading frame was included. Remarkably, expression of the AtR8 RNA responded negatively to hypoxic stress, and this regulation evidently differed from that of U6 snRNA.
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Affiliation(s)
- Juan Wu
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
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Jeong JH, Kim HJ, Kim KH, Shin M, Hong Y, Rhee JH, Schneider TD, Choy HE. An unusual feature associated with LEE1 P1 promoters in enteropathogenic Escherichia coli (EPEC). Mol Microbiol 2012; 83:612-22. [PMID: 22229878 PMCID: PMC3480209 DOI: 10.1111/j.1365-2958.2011.07956.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Transcription start points in bacteria are influenced by the nature of the RNA polymerase·promoter interaction. For Escherichia coli RNA polymerase holoenzyme containing σ70, it is presumed that specific sequence in one or more of the -10, extended -10 and -35 elements of the promoter guides the RNAP to select the cognate start point. Here, we investigated the promoter driving expression of the LEE1 operon in enteropathogenic E. coli and found two promoters separated by 10 bp, LEE1 P1A (+1) and LEE1 P1B (+10) using various in vitro biochemical tools. A unique feature of P1B was the presence of multiple transcription starts from five neighbouring As at the initial transcribed region. The multiple products did not arise from stuttering synthesis. Analytical software based on information theory was employed to determine promoter elements. The concentration of the NTP pool altered the preferred transcription start points, albeit the underlying mechanism is elusive. Under in vivo conditions, dominant P1B, but not P1A, was subject to regulation by IHF.
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Affiliation(s)
- Jae-Ho Jeong
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Hyun-Ju Kim
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Kun-Hee Kim
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Minsang Shin
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Yeongjin Hong
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Joon Haeng Rhee
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
| | - Thomas D. Schneider
- National Cancer Institute, National Institutes of Health, Gene Regulation and Chromosome Biology Laboratory, Building 539, Room 129A, NCI-Frederick, Maryland, United States
| | - Hyon E. Choy
- Center for Host Defense against Enteropathogenic Bacteria Infection, Chonnam National University Medical School, Kwangju 501-746, South Korea
- Department of Microbiology, Chonnam National University Medical School, Kwangju 501-746, South Korea
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RNA polymerase III transcription control elements: themes and variations. Gene 2011; 493:185-94. [PMID: 21712079 DOI: 10.1016/j.gene.2011.06.015] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Revised: 06/06/2011] [Accepted: 06/09/2011] [Indexed: 11/22/2022]
Abstract
Eukaryotic genomes are punctuated by a multitude of tiny genetic elements, that share the property of being recognized and transcribed by the RNA polymerase (Pol) III machinery to produce a variety of small, abundant non-protein-coding (nc) RNAs (tRNAs, 5S rRNA, U6 snRNA and many others). The highly selective, efficient and localized action of Pol III at its minute genomic targets is made possible by a handful of cis-acting regulatory elements, located within the transcribed region (where they are bound by the multisubunit assembly factor TFIIIC) and/or upstream of the transcription start site. Most of them participate directly or indirectly in the ultimate recruitment of TFIIIB, a key multiprotein initiation factor able to direct, once assembled, multiple transcription cycles by Pol III. But the peculiar efficiency and selectivity of Pol III transcription also depends on its ability to recognize very simple and precisely positioned termination signals. Studies in the last few years have significantly expanded the set of known Pol III-associated loci in genomes and, concomitantly, have revealed unexpected features of Pol III cis-regulatory elements in terms of variety, function, genomic location and potential contribution to transcriptome complexity. Here we review, in a historical perspective, well established and newly acquired knowledge about Pol III transcription control elements, with the aim of providing a useful reference for future studies of the Pol III system, which we anticipate will be numerous and intriguing for years to come.
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