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Yang EJY, Maranas CJ, Nemhauser JL. A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture. G3 (Bethesda) 2023; 13:jkad206. [PMID: 37697043 PMCID: PMC10627262 DOI: 10.1093/g3journal/jkad206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/13/2023]
Abstract
Promoters regulate both the amplitude and pattern of gene expression-key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters that lack any known promoter elements, thus designated as Coreless, tend to be expressed more uniformly. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression pattern. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.
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Affiliation(s)
- Eric J Y Yang
- Department of Biology, University of Washington, Seattle, WA 98105-1800, USA
| | - Cassandra J Maranas
- Department of Biology, University of Washington, Seattle, WA 98105-1800, USA
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2
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Lu J, Lu L, Yao F, Fang M, Ma X, Meng J, Shao K. Dicarboxylic Amino Acid Permease 7219 Regulates Fruiting Body Type of Auricularia heimuer. J Fungi (Basel) 2023; 9:876. [PMID: 37754984 PMCID: PMC10532715 DOI: 10.3390/jof9090876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/28/2023] Open
Abstract
Auricularia heimuer is a widely cultivated jelly mushroom. The fruiting bodies are categorized into cluster and chrysanthemum types. With changing consumer demands and the need to reduce bio-waste, the demand for clustered fruiting bodies is increasing. Therefore, gene mining for fruiting body types is a matter of urgency. We determined that the A. heimuer locus for fruiting body type was located at one end of the genetic linkage map. The locus was localized between the markers D23860 and D389 by increasing the density of the genetic linkage map. BlastN alignment showed that the marker SCL-18 was also located between D23860 and D389, and a total of 25 coding genes were annotated within this interval. Through parental transcriptome analysis and qRT-PCR verification, the locus g7219 was identified as the gene controlling the fruiting body type. A single-nucleotide substitution in the TATA box of g7219 was detected between the parents. By PCR amplification of the promoter region of g7219, the TATA-box sequences of the cluster- and chrysanthemum-type strains were found to be CATAAAA and TATAAAA, respectively. This study provides a foundation for the breeding of fruiting body types and strain improvement of A. heimuer.
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Affiliation(s)
- Jia Lu
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
- Guizhou Key Laboratory of Edible Fungi Breeding, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Lixin Lu
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Fangjie Yao
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Ming Fang
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Xiaoxu Ma
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
| | - Jingjing Meng
- College of Horticulture, Jilin Agricultural University, Changchun 130118, China; (L.L.); (M.F.); (J.M.)
| | - Kaisheng Shao
- Engineering Research Center of Ministry of Education of China for Food and Medicine, Jilin Agricultural University, Changchun 130118, China; (J.L.); (X.M.); (K.S.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nguyen-Vo TH, Trinh QH, Nguyen L, Nguyen-Hoang PU, Rahardja S, Nguyen BP. iPromoter-Seqvec: identifying promoters using bidirectional long short-term memory and sequence-embedded features. BMC Genomics 2022; 23:681. [PMID: 36192696 PMCID: PMC9531353 DOI: 10.1186/s12864-022-08829-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/30/2022] Open
Abstract
Background Promoters, non-coding DNA sequences located at upstream regions of the transcription start site of genes/gene clusters, are essential regulatory elements for the initiation and regulation of transcriptional processes. Furthermore, identifying promoters in DNA sequences and genomes significantly contributes to discovering entire structures of genes of interest. Therefore, exploration of promoter regions is one of the most imperative topics in molecular genetics and biology. Besides experimental techniques, computational methods have been developed to predict promoters. In this study, we propose iPromoter-Seqvec – an efficient computational model to predict TATA and non-TATA promoters in human and mouse genomes using bidirectional long short-term memory neural networks in combination with sequence-embedded features extracted from input sequences. The promoter and non-promoter sequences were retrieved from the Eukaryotic Promoter database and then were refined to create four benchmark datasets. Results The area under the receiver operating characteristic curve (AUCROC) and the area under the precision-recall curve (AUCPR) were used as two key metrics to evaluate model performance. Results on independent test sets showed that iPromoter-Seqvec outperformed other state-of-the-art methods with AUCROC values ranging from 0.85 to 0.99 and AUCPR values ranging from 0.86 to 0.99. Models predicting TATA promoters in both species had slightly higher predictive power compared to those predicting non-TATA promoters. With a novel idea of constructing artificial non-promoter sequences based on promoter sequences, our models were able to learn highly specific characteristics discriminating promoters from non-promoters to improve predictive efficiency. Conclusions iPromoter-Seqvec is a stable and robust model for predicting both TATA and non-TATA promoters in human and mouse genomes. Our proposed method was also deployed as an online web server with a user-friendly interface to support research communities. Links to our source codes and web server are available at https://github.com/mldlproject/2022-iPromoter-Seqvec. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08829-6.
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Affiliation(s)
- Thanh-Hoang Nguyen-Vo
- School of Mathematics and Statistics, Victoria University of Wellington, Gate 7, Kelburn Parade, 6140, Wellington, New Zealand
| | - Quang H Trinh
- School of Information and Communication Technology, Hanoi University of Science and Technology, 1 Dai Co Viet, 100000, Hanoi, Vietnam
| | - Loc Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Gate 7, Kelburn Parade, 6140, Wellington, New Zealand
| | - Phuong-Uyen Nguyen-Hoang
- Computational Biology Center, International University - VNU HCMC, Quarter 6, Linh Trung Ward, Thu Duc District, 700000, Ho Chi Minh City, Vietnam
| | - Susanto Rahardja
- School of Marine Science and Technology, Northwestern Polytechnical University, 127 West Youyi Road, 710072, Xi'an, China. .,Infocomm Technology Cluster, Singapore Institute of Technology, 10 Dover Drive, 138683, Singapore, Singapore.
| | - Binh P Nguyen
- School of Mathematics and Statistics, Victoria University of Wellington, Gate 7, Kelburn Parade, 6140, Wellington, New Zealand.
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Bondar EI, Troukhan ME, Krutovsky KV, Tatarinova TV. Genome-Wide Prediction of Transcription Start Sites in Conifers. Int J Mol Sci 2022; 23:1735. [PMID: 35163661 DOI: 10.3390/ijms23031735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/30/2022] [Accepted: 02/01/2022] [Indexed: 02/04/2023] Open
Abstract
The identification of promoters is an essential step in the genome annotation process, providing a framework for gene regulatory networks and their role in transcription regulation. Despite considerable advances in the high-throughput determination of transcription start sites (TSSs) and transcription factor binding sites (TFBSs), experimental methods are still time-consuming and expensive. Instead, several computational approaches have been developed to provide fast and reliable means for predicting the location of TSSs and regulatory motifs on a genome-wide scale. Numerous studies have been carried out on the regulatory elements of mammalian genomes, but plant promoters, especially in gymnosperms, have been left out of the limelight and, therefore, have been poorly investigated. The aim of this study was to enhance and expand the existing genome annotations using computational approaches for genome-wide prediction of TSSs in the four conifer species: loblolly pine, white spruce, Norway spruce, and Siberian larch. Our pipeline will be useful for TSS predictions in other genomes, especially for draft assemblies, where reliable TSS predictions are not usually available. We also explored some of the features of the nucleotide composition of the predicted promoters and compared the GC properties of conifer genes with model monocot and dicot plants. Here, we demonstrate that even incomplete genome assemblies and partial annotations can be a reliable starting point for TSS annotation. The results of the TSS prediction in four conifer species have been deposited in the Persephone genome browser, which allows smooth visualization and is optimized for large data sets. This work provides the initial basis for future experimental validation and the study of the regulatory regions to understand gene regulation in gymnosperms.
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Shen CZ, Chen J, Zhang CJ, Rao GY, Guo YP. Dysfunction of CYC2g is responsible for the evolutionary shift from radiate to disciform flowerheads in the Chrysanthemum group (Asteraceae: Anthemideae). Plant J 2021; 106:1024-1038. [PMID: 33638198 DOI: 10.1111/tpj.15216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/11/2021] [Indexed: 05/26/2023]
Abstract
Evolutionary shifts among radiate, disciform and discoid flowerheads have occurred repeatedly in a number of major lineages across the Asteraceae phylogeny; such transitions may also appear within evolutionarily young groups. Although several studies have demonstrated that CYC2 genes partake in regulating floral morphogenesis in Asteraceae, the evolution of capitulum forms within a recently diverging lineage has remained poorly understood. Here, we study the molecular regulation of the shift from a radiate to a disciform capitulum within the Chrysanthemum group. This is a recently radiating group mainly comprising two genera, Chrysanthemum and Ajania, that are phylogenetically intermingled but distinct in flowerhead morphology: Chrysanthemum spp. with radiate capitula and Ajania spp. with disciform capitula. We found that the morphogenesis of zygomorphy in the marginal floret in Ajania was disrupted soon after floral primordium emergence; CYC2g, one of the CYC2 copies that was expressed prominently in the ray floret of Chrysanthemum was not expressed in flowerheads of Ajania. Weakening the expression of ClCYC2g in Chrysanthemum lavandulifolium led to the gradual transition of a ray flower toward the disc-like form. Molecular evolutionary analyses indicated that the disciform capitulum might have evolved only once, approximately 8 Mya, arising from dysfunction of the CYC2g orthologs. A 20-nt deletion, including a putative TATA-box of the Ajania-type CYC2g promoter, appeared to inhibit the expression of the gene. Considering the divergent habitats of Chrysanthemum and Ajania, we propose that the shift from radiate to disciform capitulum must have been related to changes in pollination strategies under selective pressure.
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Affiliation(s)
- Chu-Ze Shen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, and College of Life Sciences, Beijing Normal University, Beijing, 100875, China
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jie Chen
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chu-Jie Zhang
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Guang-Yuan Rao
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan-Ping Guo
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, and College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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Parra-Marín O, López-Pacheco K, Hernández R, López-Villaseñor I. The highly diverse TATA box-binding proteins among protists: A review. Mol Biochem Parasitol 2020; 239:111312. [PMID: 32771681 DOI: 10.1016/j.molbiopara.2020.111312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 06/28/2020] [Accepted: 07/22/2020] [Indexed: 10/23/2022]
Abstract
Transcription is the first step of gene expression regulation and is a fundamental mechanism for establishing the viability and development of a cell. The TATA box-binding protein (TBP) interaction with a TATA box in a promoter is one of the best studied mechanisms in transcription initiation. TBP is a transcription factor that is highly conserved from archaea to humans and is essential for the transcription initiated by each of the three RNA polymerases. In addition, the discovery of TBP-related factor 1 (TRF1) and other factors related to TBP shed light on the variability among transcription initiation complexes, thus demonstrating that the compositions of these complexes are, in fact, more complicated than originally believed. Despite these facts, the majority of studies on transcription have been performed on animal, plant and fungal cells, which serve as canonical models, and information regarding protist cells is relatively scarce. The aim of this work is to review the diversity of the TBPs that have been documented in protists and describe some of the specific features that differentiate them from their counterparts in higher eukaryotes.
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Affiliation(s)
- Olivia Parra-Marín
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Karla López-Pacheco
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Roberto Hernández
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Imelda López-Villaseñor
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico.
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Chadaeva I, Ponomarenko P, Rasskazov D, Sharypova E, Kashina E, Kleshchev M, Ponomarenko M, Naumenko V, Savinkova L, Kolchanov N, Osadchuk L, Osadchuk A. Natural Selection Equally Supports the Human Tendencies in Subordination and Domination: A Genome-Wide Study With in silico Confirmation and in vivo Validation in Mice. Front Genet 2019; 10:73. [PMID: 30873204 PMCID: PMC6404730 DOI: 10.3389/fgene.2019.00073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/28/2019] [Indexed: 12/29/2022] Open
Abstract
We proposed the following heuristic decision-making rule: "IF {an excess of a protein relating to the nervous system is an experimentally known physiological marker of low pain sensitivity, fast postinjury recovery, or aggressive, risk/novelty-seeking, anesthetic-like, or similar agonistic-intolerant behavior} AND IF {a single nucleotide polymorphism (SNP) causes overexpression of the gene encoding this protein} THEN {this SNP can be a SNP marker of the tendency in dominance} WHILE {underexpression corresponds to subordination} AND vice versa." Using this decision-making rule, we analyzed 231 human genes of neuropeptidergic, non-neuropeptidergic, and neurotrophinergic systems that encode neurotrophic and growth factors, interleukins, neurotransmitters, receptors, transporters, and enzymes. These proteins are known as key factors of human social behavior. We analyzed all the 5,052 SNPs within the 70 bp promoter region upstream of the position where the protein-coding transcript starts, which were retrieved from databases Ensembl and dbSNP using our previously created public Web service SNP_TATA_Comparator (http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan/start.pl). This definition of the promoter region includes all TATA-binding protein (TBP)-binding sites. A total of 556 and 552 candidate SNP markers contributing to the dominance and the subordination, respectively, were uncovered. On this basis, we determined that 231 human genes under study are subject to natural selection against underexpression (significance p < 0.0005), which equally supports the human tendencies in domination and subordination such as the norm of a reaction (plasticity) of the human social hierarchy. These findings explain vertical transmission of domination and subordination traits previously observed in rodent models. Thus, the results of this study equally support both sides of the century-old unsettled scientific debate on whether both aggressiveness and the social hierarchy among humans are inherited (as suggested by Freud and Lorenz) or are due to non-genetic social education, when the children are influenced by older individuals across generations (as proposed by Berkowitz and Fromm).
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Affiliation(s)
- Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | | | | | | | - Maxim Kleshchev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Vladimir Naumenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Nikolay Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Ludmila Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexandr Osadchuk
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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Tjitro R, Campbell LA, Basova L, Johnson J, Najera JA, Lindsey A, Marcondes MCG. Modeling the Function of TATA Box Binding Protein in Transcriptional Changes Induced by HIV-1 Tat in Innate Immune Cells and the Effect of Methamphetamine Exposure. Front Immunol 2019; 9:3110. [PMID: 30778358 PMCID: PMC6369711 DOI: 10.3389/fimmu.2018.03110] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/17/2018] [Indexed: 01/24/2023] Open
Abstract
Innate immune cells are targets of HIV-1 infection in the Central Nervous System (CNS), generating neurological deficits. Infected individuals with substance use disorders as co-morbidities, are more likely to have aggravated neurological disorders, higher CNS viral load and inflammation. Methamphetamine (Meth) is an addictive stimulant drug, commonly among HIV+ individuals. The molecular basis of HIV direct effects and its interactions with Meth in host response, at the gene promoter level, are not well understood. The main HIV-1 peptide acting on transcription is the transactivator of transcription (Tat), which promotes replication by recruiting a Tata-box binding protein (TBP) to the virus long-terminal repeat (LTR). We tested the hypothesis that Tat can stimulate host gene expression through its ability to increase TBP, and thus promoting its binding to promoters that bear Tata-box binding motifs. Genes with Tata-box domains are mainly inducible, early response, and involved in inflammation, regulation and metabolism, relevant in HIV pathogenesis. We also tested whether Tat and Meth interact to trigger the expression of Tata-box bearing genes. The THP1 macrophage cell line is a well characterized innate immune cell system for studying signal transduction in inflammation. These cells are responsive to Tat, as well as to Meth, by recruiting RNA Polymerase (RNA Pol) to inflammatory gene promoters, within 15 min of stimulation (1). THP-1 cells, including their genetically engineered derivatives, represent valuable tools for investigating monocyte structure and function in both health and disease, as a consistent system (2). When differentiated, they mimic several aspects of the response of macrophages, and innate immune cells that are the main HIV-1 targets within the Central Nervous System (CNS). THP1 cells have been used to characterize the impact of Meth and resulting neurotransmitters on HIV entry (1), mimicking the CNS micro-environment. Integrative consensus sequence analysis in genes with enriched RNA Pol, revealed that TBP was a major transcription factor in Tat stimulation, while the co-incubation with Meth shifted usage to a distinct and diversified pattern. For validating these findings, we engineered a THP1 clone to be deficient in the expression of all major TBP splice variants, and tested its response to Tat stimulation, in the presence or absence of Meth. Transcriptional patterns in TBP-sufficient and deficient clones confirmed TBP as a dominant transcription factor in Tat stimulation, capable of inducing genes with no constitutive expression. However, in the presence of Meth, TBP was no longer necessary to activate the same genes, suggesting promoter plasticity. These findings demonstrate TBP as mechanism of host-response activation by HIV-1 Tat, and suggest that promoter plasticity is a challenge imposed by co-morbid factors such as stimulant drug addiction. This may be one mechanism responsible for limited efficacy of therapeutic approaches in HIV+ Meth abusers.
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Affiliation(s)
- Ryan Tjitro
- Department of Neurosciences, The Scripps Research Institute, La Jolla, CA, United States
| | - Lee A Campbell
- LAC Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD, United States
| | - Liana Basova
- Department of Neurosciences, The Scripps Research Institute, La Jolla, CA, United States.,San Diego Biomedical Research Institute, San Diego, CA, United States
| | - Jessica Johnson
- Department of Neurosciences, The Scripps Research Institute, La Jolla, CA, United States
| | - Julia A Najera
- Department of Neurosciences, The Scripps Research Institute, La Jolla, CA, United States
| | - Alexander Lindsey
- San Diego Biomedical Research Institute, San Diego, CA, United States
| | - Maria Cecilia Garibaldi Marcondes
- Department of Neurosciences, The Scripps Research Institute, La Jolla, CA, United States.,San Diego Biomedical Research Institute, San Diego, CA, United States
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Zhao B, Cao J, Hu G, Chen Z, Wang L, Shangguan X, Wang L, Mao Y, Zhang T, Wendel JF, Chen X. Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation. New Phytol 2018; 218:1061-1075. [PMID: 29465754 PMCID: PMC6079642 DOI: 10.1111/nph.15063] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 01/17/2018] [Indexed: 05/18/2023]
Abstract
Cotton cultivars have evolved to produce extensive, long, seed-born fibers important for the textile industry, but we know little about the molecular mechanism underlying spinnable fiber formation. Here, we report how PACLOBUTRAZOL RESISTANCE 1 (PRE1) in cotton, which encodes a basic helix-loop-helix (bHLH) transcription factor, is a target gene of spinnable fiber evolution. Differential expression of homoeologous genes in polyploids is thought to be important to plant adaptation and novel phenotypes. PRE1 expression is specific to cotton fiber cells, upregulated during their rapid elongation stage and A-homoeologous biased in allotetraploid cultivars. Transgenic studies demonstrated that PRE1 is a positive regulator of fiber elongation. We determined that the natural variation of the canonical TATA-box, a regulatory element commonly found in many eukaryotic core promoters, is necessary for subgenome-biased PRE1 expression, representing a mechanism underlying the selection of homoeologous genes. Thus, variations in the promoter of the cell elongation regulator gene PRE1 have contributed to spinnable fiber formation in cotton. Overexpression of GhPRE1 in transgenic cotton yields longer fibers with improved quality parameters, indicating that this bHLH gene is useful for improving cotton fiber quality.
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Affiliation(s)
- Bo Zhao
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Jun‐Feng Cao
- Plant Stress Biology CenterInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
- Plant Science Research CenterShanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai201602China
| | - Guan‐Jing Hu
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Zhi‐Wen Chen
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Lu‐Yao Wang
- Nanjing Agricultural UniversityNanjingJiangsu210095China
| | - Xiao‐Xia Shangguan
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Ling‐Jian Wang
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Ying‐Bo Mao
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
| | - Tian‐Zhen Zhang
- Nanjing Agricultural UniversityNanjingJiangsu210095China
- Zhejiang UniversityHangzhouZhejiang310058China
| | - Jonathan F. Wendel
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Xiao‐Ya Chen
- National Key Laboratory of Plant Molecular GeneticsNational Center for Plant Gene ResearchInstitute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesUniversity of CASChinese Academy of SciencesShanghai200032China
- Plant Science Research CenterShanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai201602China
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Danks GB, Navratilova P, Lenhard B, Thompson EM. Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate. BMC Genomics 2018; 19:164. [PMID: 29482522 PMCID: PMC6389100 DOI: 10.1186/s12864-018-4504-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/28/2018] [Indexed: 01/28/2023] Open
Abstract
Background Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. Results Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. Conclusions Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa. Electronic supplementary material The online version of this article (10.1186/s12864-018-4504-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma B Danks
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway.
| | - Pavla Navratilova
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway
| | - Boris Lenhard
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway.,Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London, W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, United Kingdom
| | - Eric M Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5006, Norway. .,Department of Biology, University of Bergen, Bergen, N-5006, Norway.
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12
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Samanta S, Raghunathan D, Mukherjee S. Effect of temperature on the structure and hydration layer of TATA-box DNA: A molecular dynamics simulation study. J Mol Graph Model 2016; 66:9-19. [PMID: 27017424 DOI: 10.1016/j.jmgm.2016.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 01/25/2023]
Abstract
DNA within the living cells experiences a diverse range of temperature, ranging from freezing condition to hot spring water. How the structure, the mechanical properties of DNA, and the solvation dynamics around DNA changes with the temperature is important to understand the functionality of DNA under those acute temperature conditions. In that notion, we have carried out molecular dynamics simulations of a DNA oligomer, containing TATA-box sequence for three different temperatures (250K, 300K and 350K). We observed that the structure of the DNA, in terms of backbone torsion angles, sugar pucker, base pair parameters, and base pair step parameters, did not show any unusual properties within the studied range of temperatures, but significant structural alteration was noticed between BI and BII forms at higher temperature. As expected, the flexibility of the DNA, in terms of the torsional rigidity and the bending rigidity is highly temperature dependent, confirming that flexibility increases with increase in temperature. Additionally, the groove widths of the studied DNA showed temperature sensitivity, specifically, the major groove width decreases and the minor groove width increases, respectively, with the increase in temperature. We observed that at higher temperature, water around both the major and the minor groove of the DNA is less structured. However, the water dynamics around the minor groove of the DNA is more restricted as compared to the water around the major groove throughout the studied range of temperatures, without any anomalous behavior.
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Affiliation(s)
- Sudipta Samanta
- BioSystems and Micromechanics IRG (BioSyM), Singapore-MIT Alliance for Research and Technology (SMART), 1 Create Way, 117543, Republic of Singapore; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Devanathan Raghunathan
- Prochem Solutions Pte. Ltd., 89C Science Park Drive, The Rutherford, # 04-13, Singapore Science Park 1, 118261, Singapore
| | - Sanchita Mukherjee
- Indian Institute of Science Education and Research, Kolkata, Mohanpur, West Bengal, 741246, India
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Itokawa K, Komagata O, Kasai S, Tomita T. A single nucleotide change in a core promoter is involved in the progressive overexpression of the duplicated CYP9M10 haplotype lineage in Culex quinquefasciatus. Insect Biochem Mol Biol 2015; 66:96-102. [PMID: 26494013 DOI: 10.1016/j.ibmb.2015.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 06/05/2023]
Abstract
Although the importance of cis-acting mutations on detoxification enzyme genes for insecticide resistance is widely accepted, only a few of them have been determined as concrete mutations present in genomic DNA till date. The overexpression of a cytochrome P450 gene, CYP9M10, is associated with pyrethroid resistance in the southern house mosquito Culex quinquefasciatus. The haplotypes of CYP9M10 exhibiting overexpression (resistant haplotypes) belong to one specific phylogenetic lineage that shares high nucleotide sequence homology and the same insertion of a transposable element. Among the resistant haplotypes, allelic progression involving an additional cis-acting mutation and gene duplication evolved a CYP9M10 haplotype associated with extremely high transcription and strong pyrethroid resistance. Here we show that a single nucleotide substitution G-27A, which is located near the transcription start site of CYP9M10, is involved in the progression of the duplicated haplotype lineage. The deletion of a 7-bp AT-rich sequence that includes nucleotide -27 inhibited the initiation of transcription from the original transcriptional initiation site. The mutation was suspected to reside within a core promoter, TATA-box, of CYP9M10.
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Affiliation(s)
- Kentaro Itokawa
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, Japan; Japan Agency for Medical Research and Development, 20F Yomiuri Shimbun Bldg., 1-7-1 Otemachi, Chiyoda-ku, Tokyo, Japan
| | - Osamu Komagata
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Shinji Kasai
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, Japan
| | - Takashi Tomita
- Department of Medical Entomology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, Japan.
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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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Srivastava R, Rai KM, Srivastava M, Kumar V, Pandey B, Singh SP, Bag SK, Singh BD, Tuli R, Sawant SV. Distinct role of core promoter architecture in regulation of light-mediated responses in plant genes. Mol Plant 2014; 7:626-41. [PMID: 24177688 DOI: 10.1093/mp/sst146] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In the present study, we selected four distinct classes of light-regulated promoters. The light-regulated promoters can be distinctly grouped into either TATA-box-containing or TATA-less (initiator-containing) promoters. Further, using either native promoters or their swapped versions of core promoter elements, we established that TATA-box and Inr (Initiator) elements have distinct mechanisms which are involved in light-mediated regulation, and these elements are not swappable. We identified that mutations in either functional TATA-box or Inr elements lead to the formation of nucleosomal structure. The nucleotide diversity in either the TATA-box or Inr element in Arabidopsis ecotypes proposes that the nucleotide variation in core promoters can alter the gene expression. We show that motif overrepresentation in light-activated promoters encompasses different specific regulatory motifs present downstream of TSS (transcription start site), and this might serve as a key factor in regulating light promoters which are parallel with these elements. Finally, we conclude that the TATA-box or Inr element does not act in isolation, but our results clearly suggests the probable involvement of other distinct core promoter elements in concurrence with the TATA-box or Inr element to impart selectivity to light-mediated transcription.
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Affiliation(s)
- Rakesh Srivastava
- Plant Molecular Biology and Genetic Engineering Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow-226001 (U.P.), India
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Abstract
Products of the myc gene family integrate extracellular signals by modulating a wide range of their targets involved in cellular biogenesis and metabolism; the purpose of this integration is to regulate cell death, proliferation, and differentiation. However, understanding the regulation of myc at the transcription level remains a challenge. We performed rapid amplification of dmyc cDNA ends (5' RACE) and mapped the transcription start site at P1 promoter, 18 base pairs upstream of the start of the known EST GM01143 and within the 5' UTR. Our data show that the first TATA box, previously computationally predicted, is utilized to generate dmyc full length mRNA. The largest transcript contains all three exons, generated after the removal of the introns by constitutively regulated splicing events. Further investigation of Downstream Promoter Element (DPE) was achieved by studying lacZ reporter activity; investigation revealed that this element and its upstream cluster of binding sites are required for the dmyc intron 2 activity. These findings may provide valuable tools for further analysis of dmyc cis-elements.
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Affiliation(s)
- Jasmine Kharazmi
- Bio-Technopark Zurich, Molecular Biology Laboratory, Zurich, Switzerland. ; Institute of Molecular Life Sciences, University of Zurich-Irchel, Zurich, Switzerland
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Bird DM, Kaloshian I, Molinari S. Promoter Structure of the RNA Polymerase II Large Subunit Gene in Caenorhabditis elegans and C. briggsae. J Nematol 1997; 29:144-152. [PMID: 19274143 PMCID: PMC2619764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
The 5'-end of the Caenorhabditis elegans ama-1 gene transcript, which encodes the largest subunit of RNA polymerase II, was cloned. Sequencing revealed that the message is trans-spliced. To characterize the Ce-ama-1 promoter, DNA sequence spanning 3 kb upstream from the initiation codon was determined. Typical elements, such as TATA and Spl sites, were absent. The homologue of ama-1 in C. briggsae, Cb-ama-1, was isolated and its 5' flanking sequence compared with that of Ce-ama-1, revealing only limited similarity, although both sequences included a potential initiator-class transcriptional regulator and phased repeats of an ATC motif. The latter elements are postulated to facilitate DNA bending and may play a role in transcription regulation.
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