1
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Kim YW, Kang J, Kim A. Hematopoietic/erythroid enhancers activate nearby target genes by extending histone H3K27ac and transcribing intergenic RNA. FASEB J 2023; 37:e22870. [PMID: 36929052 DOI: 10.1096/fj.202201891r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
Enhancers activate gene transcription remotely, which requires tissue specific transcription factors binding to them. GATA1 and TAL1 are hematopoietic/erythroid-specific factors and often bind together to enhancers, activating target genes. Interestingly, we found that some hematopoietic/erythroid genes are transcribed in a GATA1-dependent but TAL1-independnet manner. They appear to have enhancers within a relatively short distance. In this study, we paired highly transcribed hematopoietic/erythroid genes with the nearest GATA1/TAL1-binding enhancers and analyzed these putative enhancer-gene pairs depending on distance between them. Enhancers located at various distances from genes in the pairs, which was not related to transcription level of the genes. However, genes with enhancers at short distances away tended to be transcriptionally unaffected by TAL1 depletion. Histone H3K27ac extended from the enhancers to target genes. The H3K27ac extension was maintained without TAL1, even though it disappeared owing to the loss of GATA1. Intergenic RNA was highly transcribed from the enhancers to nearby target genes, independent of TAL1. Taken together, TAL1-independent transcription of hematopoietic/erythroid genes appears to be promoted by enhancers present in a short distance. These enhancers are likely to activate nearby target genes by tracking the intervening regions.
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Affiliation(s)
- Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, South Korea
- Department of Biomedical Laboratory Science, College of Healthcare Medical Science and Engineering, Inje University, Gimhae, South Korea
| | - Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, South Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, South Korea
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2
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Kravatsky YV, Chechetkin VR, Tchurikov NA, Kravatskaya GI. Genome-Wide Study of Colocalization between Genomic Stretches: A Method and Applications to the Regulation of Gene Expression. BIOLOGY 2022; 11:1422. [PMID: 36290327 PMCID: PMC9598420 DOI: 10.3390/biology11101422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
In this paper, we describe a method for the study of colocalization effects between stretch-stretch and stretch-point genome tracks based on a set of indices varying within the (-1, +1) interval. The indices combine the distances between the centers of neighboring stretches and their lengths. The extreme boundaries of the interval correspond to the complete colocalization of the genome tracks or its complete absence. We also obtained the relevant criteria of statistical significance for such indices using the complete permutation test. The method is robust with respect to strongly inhomogeneous positioning and length distribution of the genome tracks. On the basis of this approach, we created command-line software, the Genome Track Colocalization Analyzer. The software was tested, compared with other available packages, and applied to particular problems related to gene expression. The package, Genome Track Colocalization Analyzer (GTCA), is freely available to the users. GTCA complements our previous software, the Genome Track Analyzer, intended for the search for pairwise correlations between point-like genome tracks (also freely available). The corresponding details are provided in Data Availability Statement at the end of the text.
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Affiliation(s)
- Yuri V. Kravatsky
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir R. Chechetkin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Nickolai A. Tchurikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
| | - Galina I. Kravatskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str., 32, 119991 Moscow, Russia
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3
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Monfils K, Barakat TS. Models behind the mystery of establishing enhancer-promoter interactions. Eur J Cell Biol 2021; 100:151170. [PMID: 34246183 DOI: 10.1016/j.ejcb.2021.151170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 10/20/2022] Open
Abstract
Enhancers and promoters are transcriptional regulatory elements whose facilitated interactions increase gene expression. Enhancer DNA sequences can be located far away from the promoter sequences that they regulate. Currently, the mechanism facilitating the establishment of enhancer-promoter interactions remains unclear. However, mutations causing errors in these interactions have been linked to cancer and disease, further conveying the need to understand the full mechanism. This review discusses multiple models that have been proposed to describe how enhancers go the distance to interact with promoters. Evidence supporting loop formation models is reviewed in addition to more complex hypotheses involving aspects of 3D chromatin organization and phase separation.
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Affiliation(s)
- Kathryn Monfils
- Department of Clinical Genetics, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, the Netherlands.
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4
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Fedoseeva DM, Kretova OV, Gorbacheva MA, Tchurikov NA. Individual effects of the copia and gypsy enhancer and insulator on chromatin marks, eRNA synthesis, and binding of insulator proteins in transfected genetic constructs. Gene 2018; 641:151-160. [PMID: 29045822 DOI: 10.1016/j.gene.2017.10.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 07/10/2017] [Accepted: 10/11/2017] [Indexed: 12/28/2022]
Abstract
Enhancers and insulators are involved in the regulation of gene expression, but the basic underlying mechanisms of action of these elements are unknown. We analyzed the individual effects of the enhancer and the insulator from Drosophila mobile elements copia [enh(copia)] and gypsy using transfected genetic constructs in S2 cells. This system excludes the influence of genomic cis regulatory elements. The enhancer-induced synthesis of 350-1050-nt-long enhancer RNAs (eRNAs) and H3K4me3 and H3K18ac marks, mainly in the region located about 300bp downstream of the enhancer. Insertion of the insulator between the enhancer and the promoter reduced these effects. We also observed the binding of dCTCF to the enhancer and to gypsy insulator. Our data indicate that a single gypsy insulator interacts with both the enhancer and the promoter, while two copies of the gypsy insulator preferentially interact with each other. Our results suggest the formation of chromatin loops that are shaped by the enhancer and the insulator.
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Affiliation(s)
| | - Olga V Kretova
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
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5
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Tchurikov NA, Fedoseeva DM, Gashnikova NM, Sosin DV, Gorbacheva MA, Alembekov IR, Chechetkin VR, Kravatsky YV, Kretova OV. Conserved sequences in the current strains of HIV-1 subtype A in Russia are effectively targeted by artificial RNAi in vitro. Gene 2016; 583:78-83. [PMID: 26947394 DOI: 10.1016/j.gene.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 10/25/2022]
Abstract
Highly active antiretroviral therapy has greatly reduced the morbidity and mortality of AIDS. However, many of the antiretroviral drugs are toxic with long-term use, and all currently used anti-HIV agents generate drug-resistant mutants. Therefore, there is a great need for new approaches to AIDS therapy. RNAi is a powerful means of inhibiting HIV-1 production in human cells. We propose to use RNAi for gene therapy of HIV/AIDS. Previously we identified a number of new biologically active siRNAs targeting several moderately conserved regions in HIV-1 transcripts. Here we analyze the heterogeneity of nucleotide sequences in three RNAi targets in sequences encoding the reverse transcriptase and integrase domains of current isolates of HIV-1 subtype A in Russia. These data were used to generate genetic constructs expressing short hairpin RNAs 28-30-bp in length that could be processed in cells into siRNAs. After transfection of the constructs we observed siRNAs that efficiently attacked the selected targets. We expect that targeting several viral genes important for HIV-1 reproduction will help overcome the problem of viral adaptation and will prevent the appearance of RNAi escape mutants in current virus strains, an important feature of gene therapy of HIV/AIDS.
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Affiliation(s)
| | | | | | - Dmitri V Sosin
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
| | | | | | | | - Yuri V Kravatsky
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
| | - Olga V Kretova
- Engelhardt Institute of Molecular Biology, Moscow 119334, Russia
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6
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Tikhonov M, Gasanov NB, Georgiev P, Maksimenko O. A Model System in S2 Cells to Test the Functional Activities of Drosophila Insulators. Acta Naturae 2015; 7:97-106. [PMID: 26798496 PMCID: PMC4717254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Insulators are a special class of regulatory elements that can regulate interactions between enhancers and promoters in the genome of high eukaryotes. To date, the mechanisms of insulator action remain unknown, which is primarily related to the lack of convenient model systems. We suggested studying a model system which is based on transient expression of a plasmid with an enhancer of the copia transposable element, in Drosophila embryonic cell lines. We demonstrated that during transient transfection of circle plasmids with a well-known Drosophila insulator from the gypsy retrotransposon, the insulator exhibits in an enhancer-blocking assay the same properties as in Drosophila stable transgenic lines. Therefore, the Drosophila cell line is suitable for studying the main activities of insulators, which provides additional opportunities for investigating the functional role of certain insulator proteins.
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Affiliation(s)
- M. Tikhonov
- Institute of Gene Biology Russian Academy of Sciences, Vavilova str., 34/5, 119334, Moscow, Russia
| | - N. B. Gasanov
- Institute of Gene Biology Russian Academy of Sciences, Vavilova str., 34/5, 119334, Moscow, Russia
| | - P. Georgiev
- Institute of Gene Biology Russian Academy of Sciences, Vavilova str., 34/5, 119334, Moscow, Russia
| | - O. Maksimenko
- Institute of Gene Biology Russian Academy of Sciences, Vavilova str., 34/5, 119334, Moscow, Russia
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7
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Kravatsky YV, Chechetkin VR, Tchurikov NA, Kravatskaya GI. Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression. DNA Res 2015; 22:109-19. [PMID: 25627242 PMCID: PMC4379982 DOI: 10.1093/dnares/dsu044] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The broad class of tasks in genetics and epigenetics can be reduced to the study of various features that are distributed over the genome (genome tracks). The rapid and efficient processing of the huge amount of data stored in the genome-scale databases cannot be achieved without the software packages based on the analytical criteria. However, strong inhomogeneity of genome tracks hampers the development of relevant statistics. We developed the criteria for the assessment of genome track inhomogeneity and correlations between two genome tracks. We also developed a software package, Genome Track Analyzer, based on this theory. The theory and software were tested on simulated data and were applied to the study of correlations between CpG islands and transcription start sites in the Homo sapiens genome, between profiles of protein-binding sites in chromosomes of Drosophila melanogaster, and between DNA double-strand breaks and histone marks in the H. sapiens genome. Significant correlations between transcription start sites on the forward and the reverse strands were observed in genomes of D. melanogaster, Caenorhabditis elegans, Mus musculus, H. sapiens, and Danio rerio. The observed correlations may be related to the regulation of gene expression in eukaryotes. Genome Track Analyzer is freely available at http://ancorr.eimb.ru/.
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Affiliation(s)
- Yuri V Kravatsky
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia
| | - Vladimir R Chechetkin
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia
| | - Nikolai A Tchurikov
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia
| | - Galina I Kravatskaya
- Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Moscow 119991, Russia
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8
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Korenjak M, Kwon E, Morris RT, Anderssen E, Amzallag A, Ramaswamy S, Dyson NJ. dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes. Nucleic Acids Res 2014; 42:8939-53. [PMID: 25053843 PMCID: PMC4132727 DOI: 10.1093/nar/gku609] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
dREAM complexes represent the predominant form of E2F/RBF repressor complexes in Drosophila. dREAM associates with thousands of sites in the fly genome but its mechanism of action is unknown. To understand the genomic context in which dREAM acts we examined the distribution and localization of Drosophila E2F and dREAM proteins. Here we report a striking and unexpected overlap between dE2F2/dREAM sites and binding sites for the insulator-binding proteins CP190 and Beaf-32. Genetic assays show that these components functionally co-operate and chromatin immunoprecipitation experiments on mutant animals demonstrate that dE2F2 is important for association of CP190 with chromatin. dE2F2/dREAM binding sites are enriched at divergently transcribed genes, and the majority of genes upregulated by dE2F2 depletion represent the repressed half of a differentially expressed, divergently transcribed pair of genes. Analysis of mutant animals confirms that dREAM and CP190 are similarly required for transcriptional integrity at these gene pairs and suggest that dREAM functions in concert with CP190 to establish boundaries between repressed/activated genes. Consistent with the idea that dREAM co-operates with insulator-binding proteins, genomic regions bound by dREAM possess enhancer-blocking activity that depends on multiple dREAM components. These findings suggest that dREAM functions in the organization of transcriptional domains.
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Affiliation(s)
- Michael Korenjak
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Eunjeong Kwon
- Massachusetts General Hospital, Cutaneous Biology Research Center, Charlestown, MA 02129, USA
| | - Robert T Morris
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Endre Anderssen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
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9
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Fedoseeva DM, Tchurikov NA. Analysis of insulator proteins binding in reporter genetic constructs transfected into Drosophila S2 cells. DOKL BIOCHEM BIOPHYS 2013; 451:198-202. [PMID: 23975400 DOI: 10.1134/s160767291304008x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Indexed: 11/23/2022]
Affiliation(s)
- D M Fedoseeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia
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10
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Fedoseeva DM, Kretova OV, Tchurikov NA. Molecular analysis of enhancer RNAs and chromatin modifications in the region of their synthesis in Drosophila cells possessing genetic constructs. DOKL BIOCHEM BIOPHYS 2012; 442:7-11. [PMID: 22419084 DOI: 10.1134/s1607672912010012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Indexed: 11/22/2022]
Affiliation(s)
- D M Fedoseeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow, 119991, Russia
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11
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Singer SD, Hily JM, Cox KD. Analysis of the enhancer-blocking function of the TBS element from Petunia hybrida in transgenic Arabidopsis thaliana and Nicotiana tabacum. PLANT CELL REPORTS 2011; 30:2013-25. [PMID: 21706298 DOI: 10.1007/s00299-011-1109-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/01/2011] [Accepted: 06/13/2011] [Indexed: 05/31/2023]
Abstract
Transcriptional enhancers possess the ability to override the tissue-specificity and efficiency of nearby promoters, which is of concern when generating transgenic constructs bearing multiple cassettes. One means of preventing these inappropriate interactions is through the use of enhancer-blocking insulators. The 2-kb transformation booster sequence (TBS) from Petunia hybrida has been shown previously to exhibit this function when inserted between an enhancer and promoter in transgenic Arabidopsis thaliana. In this study, we attempted to further characterize the ability of this fragment to impede enhancer-promoter interference through an analysis of transgenic Arabidopsis and Nicotiana tabacum lines bearing various permutations of the TBS element between the cauliflower mosaic virus (CaMV) 35S enhancer and an assortment of tissue-specific promoters fused to the β-glucuronidase (GUS) reporter gene. The full-length TBS fragment was found to function in both orientations, although to a significantly lesser degree in the reverse orientation, and was operational in both plant species tested. While multiple deletion fragments were found to exhibit activity, it appeared that several regions of the TBS were required for maximal enhancer-blocking function. Furthermore, we found that this element exhibited promoter-like activity, which has implications in terms of possible mechanisms behind its ability to impede enhancer-promoter communication in plants.
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Affiliation(s)
- Stacy D Singer
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456, USA
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12
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Vogelmann J, Valeri A, Guillou E, Cuvier O, Nollmann M. Roles of chromatin insulator proteins in higher-order chromatin organization and transcription regulation. Nucleus 2011; 2:358-69. [PMID: 21983085 DOI: 10.4161/nucl.2.5.17860] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Eukaryotic chromosomes are condensed into several hierarchical levels of complexity: DNA is wrapped around core histones to form nucleosomes, nucleosomes form a higher-order structure called chromatin, and chromatin is subsequently compartmentalized in part by the combination of multiple specific or unspecific long-range contacts. The conformation of chromatin at these three levels greatly influences DNA metabolism and transcription. One class of chromatin regulatory proteins called insulator factors may organize chromatin both locally, by setting up barriers between heterochromatin and euchromatin, and globally by establishing platforms for long-range interactions. Here, we review recent data revealing a global role of insulator proteins in the regulation of transcription through the formation of clusters of long-range interactions that impact different levels of chromatin organization.
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Affiliation(s)
- Jutta Vogelmann
- Centre de Biochimie Structurale, Centre National de la Recherche Scientifique and Institut National de la Santé et la Recherche Médicale, 29 rue de Navacelles, 34090, Montpellier, France
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13
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Tchurikov NA, Kretova OV. Both piRNA and siRNA pathways are silencing transcripts of the suffix element in the Drosophila melanogaster germline and somatic cells. PLoS One 2011; 6:e21882. [PMID: 21779345 PMCID: PMC3136478 DOI: 10.1371/journal.pone.0021882] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 06/10/2011] [Indexed: 01/22/2023] Open
Abstract
In the Drosophila melanogaster germline, the piRNA pathway silences retrotransposons as well as other transcribed repetitive elements. Suffix is an unusual short retroelement that was identified both as an actively transcribed repetitive element and also as an element at the 3' ends of the Drosophila non-LTR F element. The copies of suffix that are F element-independent are far more actively transcribed than their counterparts on the F element. We studied the patterns of small RNAs targeting both strands of suffix in Drosophila ovaries using an RNase protection assay and the analysis of the corresponding RNA sequences from the libraries of total small RNAs. Our results indicate that suffix sense and antisense transcripts are targeted mainly by 23-29 nucleotides in length piRNAs and also by 21 nucleotides in length siRNAs. Suffix sense transcripts actively form longer RNA species, corresponding either to partial digestion products of the RNAi and Piwi pathways or to another RNA silencing mechanism. Both sense and antisense suffix transcripts accumulated in the ovaries of homozygous spn-E, piwi and aub mutants. These results provide evidence that suffix sense and antisense transcripts in the germ line and soma are targeted by both RNAi and Piwi pathways and that a Dicer-independent pathway of biogenesis of siRNAs could exist in Drosophila cells.
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Affiliation(s)
- Nickolai A. Tchurikov
- Department of Genome Organization, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Olga V. Kretova
- Department of Genome Organization, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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14
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Moiseeva ED, Tchurikov NA. Study of the effects of enhancer and insulator on the chromatin structure in Drosophila melanogaster. DOKL BIOCHEM BIOPHYS 2011; 437:60-3. [PMID: 21590376 DOI: 10.1134/s1607672911020037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Indexed: 11/22/2022]
Affiliation(s)
- E D Moiseeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
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15
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Singer SD, Cox KD, Liu Z. Enhancer-promoter interference and its prevention in transgenic plants. PLANT CELL REPORTS 2011; 30:723-31. [PMID: 21170713 DOI: 10.1007/s00299-010-0977-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 12/07/2010] [Accepted: 12/07/2010] [Indexed: 05/22/2023]
Abstract
Biotechnology has several advantages over conventional breeding for the precise engineering of gene function and provides a powerful tool for the genetic improvement of agronomically important traits in crops. In particular, it has been exploited for the improvement of multiple traits through the simultaneous introduction or stacking of several genes driven by distinct tissue-specific promoters. Since transcriptional enhancer elements have been shown to override the specificity of nearby promoters in a position- and orientation-independent manner, the co-existence of multiple enhancers/promoters within a single transgenic construct could be problematic as it has the potential to cause the mis-expression of transgene product(s). In order to develop strategies with, which to prevent such interference, a clear understanding of the mechanisms underlying enhancer-mediated activation of target promoters, as well as the identification of DNA sequences that function to block these interactions in plants, will be necessary. To date, little is known concerning enhancer function in plants and only a very limited number of enhancer-blocking insulators that operate in plant species have been identified. In this review, we discuss the current knowledge surrounding enhancer-promoter interactions, as well as possible means of minimizing such interference during plant transformation experiments.
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Affiliation(s)
- Stacy D Singer
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV, 25430, USA
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16
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Fedoseeva DM, Kretova OV, Tchurikov NA. Molecular analysis of RNA induced by enhancer in Drosophila cells carrying reporter genetic constructs. DOKL BIOCHEM BIOPHYS 2010; 435:339-43. [PMID: 21184308 DOI: 10.1134/s1607672910060153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Indexed: 11/23/2022]
Affiliation(s)
- D M Fedoseeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, ul. Vavilova 32, Moscow 119991, Russia
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17
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Singer SD, Cox KD, Liu Z. Both the constitutive cauliflower mosaic virus 35S and tissue-specific AGAMOUS enhancers activate transcription autonomously in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2010; 74:293-305. [PMID: 20703807 DOI: 10.1007/s11103-010-9673-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 07/27/2010] [Indexed: 05/20/2023]
Abstract
The expression of eukaryotic genes from their cognate promoters is often regulated by the action of transcriptional enhancer elements that function in an orientation-independent manner either locally or at a distance within a genome. This interactive nature often provokes unexpected interference within transgenes in plants, as reflected by misexpression of the introduced gene and undesired phenotypes in transgenic lines. To gain a better understanding of the mechanism underlying enhancer/promoter interactions in a plant system, we analyzed the activation of a β-glucuronidase (GUS) reporter gene by enhancers contained within the AGAMOUS second intron (AGI) and the Cauliflower Mosaic Virus (CaMV) 35S promoter, respectively, in the presence and absence of a target promoter. Our results indicate that both the AGI and 35S enhancers, which differ significantly in their species of origin and in the pattern of expression that they induce, have the capacity to activate the expression of a nearby gene through the promoter-independent initiation of autonomous transcriptional events. Furthermore, we provide evidence that the 35S enhancer utilizes a mechanism resembling animal- and yeast-derived scanning or facilitated tracking models of long-distance enhancer action in its activation of a remote target promoter.
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Affiliation(s)
- Stacy D Singer
- USDA-ARS Appalachian Fruit Research Station, 2217 Wiltshire Road, Kearneysville, WV 25430, USA
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18
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Castano E, Philimonenko VV, Kahle M, Fukalová J, Kalendová A, Yildirim S, Dzijak R, Dingová-Krásna H, Hozák P. Actin complexes in the cell nucleus: new stones in an old field. Histochem Cell Biol 2010; 133:607-26. [PMID: 20443021 DOI: 10.1007/s00418-010-0701-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2010] [Indexed: 01/13/2023]
Abstract
Actin is a well-known protein that has shown a myriad of activities in the cytoplasm. However, recent findings of actin involvement in nuclear processes are overwhelming. Actin complexes in the nucleus range from very dynamic chromatin-remodeling complexes to structural elements of the matrix with single partners known as actin-binding proteins (ABPs). This review summarizes the recent findings of actin-containing complexes in the nucleus. Particular attention is given to key processes like chromatin remodeling, transcription, DNA replication, nucleocytoplasmic transport and to actin roles in nuclear architecture. Understanding the mechanisms involving ABPs will definitely lead us to the principles of the regulation of gene expression performed via concerting nuclear and cytoplasmic processes.
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Affiliation(s)
- E Castano
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the ASCR, Prague, Czech Republic
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