1
|
Yoth M, Maupetit-Méhouas S, Akkouche A, Gueguen N, Bertin B, Jensen S, Brasset E. Reactivation of a somatic errantivirus and germline invasion in Drosophila ovaries. Nat Commun 2023; 14:6096. [PMID: 37773253 PMCID: PMC10541861 DOI: 10.1038/s41467-023-41733-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/15/2023] [Indexed: 10/01/2023] Open
Abstract
Most Drosophila transposable elements are LTR retrotransposons, some of which belong to the genus Errantivirus and share structural and functional characteristics with vertebrate endogenous retroviruses. Like endogenous retroviruses, it is unclear whether errantiviruses retain some infectivity and transposition capacity. We created conditions where control of the Drosophila ZAM errantivirus through the piRNA pathway was abolished leading to its de novo reactivation in somatic gonadal cells. After reactivation, ZAM invaded the oocytes and severe fertility defects were observed. While ZAM expression persists in the somatic gonadal cells, the germline then set up its own adaptive genomic immune response by producing piRNAs against the constantly invading errantivirus, restricting invasion. Our results suggest that although errantiviruses are continuously repressed by the piRNA pathway, they may retain their ability to infect the germline and transpose, thus allowing them to efficiently invade the germline if they are expressed.
Collapse
Affiliation(s)
- Marianne Yoth
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | | | - Abdou Akkouche
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Nathalie Gueguen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Benjamin Bertin
- LIMAGRAIN EUROPE, Centre de recherche, 63720, Chappes, France
| | - Silke Jensen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
| |
Collapse
|
2
|
Franco G, Taillebourg E, Delfino E, Homolka D, Gueguen N, Brasset E, Pandey RR, Pillai RS, Fauvarque MO. The catalytic-dead Pcif1 regulates gene expression and fertility in Drosophila. RNA 2023; 29:609-619. [PMID: 36754578 PMCID: PMC10158991 DOI: 10.1261/rna.079192.122] [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: 04/12/2022] [Accepted: 01/09/2023] [Indexed: 05/06/2023]
Abstract
Eukaryotic mRNAs are modified at the 5' end with a methylated guanosine (m7G) that is attached to the transcription start site (TSS) nucleotide. The TSS nucleotide is 2'-O-methylated (Nm) by CMTR1 in organisms ranging from insects to human. In mammals, the TSS adenosine can be further N 6 -methylated by RNA polymerase II phosphorylated CTD-interacting factor 1 (PCIF1) to create m6Am. Curiously, the fly ortholog of mammalian PCIF1 is demonstrated to be catalytic-dead, and its functions are not known. Here, we show that Pcif1 mutant flies display a reduced fertility which is particularly marked in females. Deep sequencing analysis of Pcif1 mutant ovaries revealed transcriptome changes with a notable increase in expression of genes belonging to the mitochondrial ATP synthetase complex. Furthermore, the Pcif1 protein is distributed along euchromatic regions of polytene chromosomes, and the Pcif1 mutation behaved as a modifier of position-effect-variegation (PEV) suppressing the heterochromatin-dependent silencing of the white gene. Similar or stronger changes in the transcriptome and PEV phenotype were observed in flies that expressed a cytosolic version of Pcif1. These results point to a nuclear cotranscriptional gene regulatory role for the catalytic-dead fly Pcif1 that is probably based on its conserved ability to interact with the RNA polymerase II carboxy-terminal domain.
Collapse
Affiliation(s)
- Giulia Franco
- Université Grenoble Alpes, CEA, INSERM, BGE, F-38000 Grenoble, France
| | | | - Elena Delfino
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Nathalie Gueguen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Radha Raman Pandey
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, CH-1211 Geneva 4, Switzerland
| | | |
Collapse
|
3
|
Casier K, Autaa J, Gueguen N, Delmarre V, Marie PP, Ronsseray S, Carré C, Brasset E, Teysset L, Boivin A. The histone demethylase Kdm3 prevents auto-immune piRNAs production in Drosophila. Sci Adv 2023; 9:eade3872. [PMID: 37027460 PMCID: PMC10081847 DOI: 10.1126/sciadv.ade3872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Genome integrity of the animal germline is protected from transposable element activity by PIWI-interacting RNAs (piRNAs). While piRNA biogenesis is intensively explored, little is known about the genetical determination of piRNA clusters, the genomic sources of piRNAs. Using a bimodal epigenetic state piRNA cluster (BX2), we identified the histone demethylase Kdm3 as being able to prevent a cryptic piRNA production. In the absence of Kdm3, dozens of coding gene-containing regions become genuine germline dual-strand piRNA clusters. Eggs laid by Kdm3 mutant females show developmental defects phenocopying loss of function of genes embedded into the additional piRNA clusters, suggesting an inheritance of functional ovarian "auto-immune" piRNAs. Antagonizing piRNA cluster determination through chromatin modifications appears crucial to prevent auto-immune genic piRNAs production.
Collapse
Affiliation(s)
- Karine Casier
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Julie Autaa
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Nathalie Gueguen
- iGReD, CNRS, INSERM, Faculté de Médecine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Valérie Delmarre
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Pauline P. Marie
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Stéphane Ronsseray
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Clément Carré
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Emilie Brasset
- iGReD, CNRS, INSERM, Faculté de Médecine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France
| | - Laure Teysset
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| | - Antoine Boivin
- Transgenerational Epigenetics and Small RNA Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, F-75005 Paris, France
| |
Collapse
|
4
|
Akkouche A, Brasset E. More than just an inert dense region. eLife 2022; 11:83076. [PMID: 36239700 PMCID: PMC9566848 DOI: 10.7554/elife.83076] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A newly discovered protein helps define a subset of heterochromatin regions that can silence harmful mobile genetic elements in the genome of fruit flies.
Collapse
Affiliation(s)
- Abdou Akkouche
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, Clermont-Ferrand, France
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, Clermont-Ferrand, France
| |
Collapse
|
5
|
Yoth M, Jensen S, Brasset E. The Intricate Evolutionary Balance between Transposable Elements and Their Host: Who Will Kick at Goal and Convert the Next Try? Biology (Basel) 2022; 11:710. [PMID: 35625438 PMCID: PMC9138309 DOI: 10.3390/biology11050710] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
Abstract
Transposable elements (TEs) are mobile DNA sequences that can jump from one genomic locus to another and that have colonized the genomes of all living organisms. TE mobilization and accumulation are an important source of genomic innovations that greatly contribute to the host species evolution. To ensure their maintenance and amplification, TE transposition must occur in the germ cell genome. As TE transposition is also a major threat to genome integrity, the outcome of TE mobility in germ cell genomes could be highly dangerous because such mutations are inheritable. Thus, organisms have developed specialized strategies to protect the genome integrity from TE transposition, particularly in germ cells. Such effective TE silencing, together with ongoing mutations and negative selection, should result in the complete elimination of functional TEs from genomes. However, TEs have developed efficient strategies for their maintenance and spreading in populations, particularly by using horizontal transfer to invade the genome of novel species. Here, we discuss how TEs manage to bypass the host's silencing machineries to propagate in its genome and how hosts engage in a fightback against TE invasion and propagation. This shows how TEs and their hosts have been evolving together to achieve a fine balance between transposition and repression.
Collapse
Affiliation(s)
| | | | - Emilie Brasset
- iGReD, CNRS, INSERM, Faculté de Médecine, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (M.Y.); (S.J.)
| |
Collapse
|
6
|
Molla Herman A, Brasset E. Rhino breaks the deadlock in Drosophila testis. PLoS Genet 2021; 17:e1009702. [PMID: 34473721 PMCID: PMC8412255 DOI: 10.1371/journal.pgen.1009702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anahi Molla Herman
- Collège de France, CIRB, CNRS INSERM UMR 7241, PSL Research University, Paris, France
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, Clermont-Ferrand, France
| |
Collapse
|
7
|
Dennis C, Brasset E, Vaury C. flam piRNA precursors channel from the nucleus to the cytoplasm in a temporally regulated manner along Drosophila oogenesis. Mob DNA 2019; 10:28. [PMID: 31312260 PMCID: PMC6612187 DOI: 10.1186/s13100-019-0170-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 04/04/2019] [Accepted: 06/25/2019] [Indexed: 02/08/2023] Open
Abstract
Background PIWI-interacting RNAs (piRNAs) are the effectors of transposable element silencing in the reproductive apparatus. In Drosophila ovarian somatic cells, piRNAs arise from long RNA precursors presumably processed within cytoplasmic Yb-bodies. Results Here we show that the nucleo-cytoplasmic traffic of piRNA precursors encoded by the flamenco locus is subjected to a spatio-temporal regulation. Precursor RNAs first gather in a single nuclear focus, Dot COM, close to the nuclear periphery, and transit through the membrane before being delivered to the cytoplasmic Yb-bodies. Early in oogenesis, flamenco transcripts are rapidly transferred to the cytoplasm making their initial nuclear gathering in Dot COM too transient to be visualized. As oogenesis proceeds, the cytoplasmic delivery steadily decreases concomitantly with the decrease in the protein levels of Armi and Yb, two components of the Yb-bodies. Both events lead to a reduction of Yb-body assembly in late stages of oogenesis, which likely results in a drop in piRNA production. Conclusion Our findings show a spatio-temporal regulation of the piRNA biogenesis in the follicle cells of Drosophila ovaries, that involves coordinated control of both piRNA precursors and components of the piRNA processing machinery. This newly unveiled regulation establishes another level of complexity in the production of piRNAs and suggests a stage-dependent involvement of the piRNA biogenesis in the mechanism of transposable elements silencing along oogenesis. Electronic supplementary material The online version of this article (10.1186/s13100-019-0170-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cynthia Dennis
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| |
Collapse
|
8
|
Théron E, Maupetit-Mehouas S, Pouchin P, Baudet L, Brasset E, Vaury C. The interplay between the Argonaute proteins Piwi and Aub within Drosophila germarium is critical for oogenesis, piRNA biogenesis and TE silencing. Nucleic Acids Res 2019; 46:10052-10065. [PMID: 30113668 PMCID: PMC6212714 DOI: 10.1093/nar/gky695] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 07/20/2018] [Indexed: 11/28/2022] Open
Abstract
Transposable elements (TEs) have invaded most genomes and constitute up to 50% of the human genome. Machinery based on small non-coding piRNAs has evolved to inhibit their expression at the transcriptional and post-transcriptional levels. Surprisingly, this machinery is weakened during specific windows of time in mice, flies or plants, allowing the expression of TEs in germline cells. The function of this de-repression remains unknown. In Drosophila, we have previously shown that this developmental window is characterized by a reduction of Piwi expression in dividing germ cells. Here, we show that the unique knock-down of Aub in these cells leads to female sterility. It correlates with defects in piRNA amplification, an increased Piwi expression and an increased silencing of transcriptionally silenced TEs. These defects are similar to those observed when Aub is depleted in the whole germline which underlies the crucial role of this developmental window for both oogenesis and TE silencing. We further show that, with age, some fertility is recovered which is concomitant to a decrease of Piwi and TE silencing. These data pinpoint the Pilp as a tremendously important step for female fertility and genome stability. They further show that such a restricted developmental niche of germ cells may sense environmental changes, such as aging, to protect the germline all along the life.
Collapse
Affiliation(s)
- Emmanuelle Théron
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Stéphanie Maupetit-Mehouas
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Pierre Pouchin
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Laura Baudet
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| | - Chantal Vaury
- GReD laboratory, Université Clermont Auvergne, CNRS, Inserm, Faculté de Médecine, CRBC, F-63000 Clermont-Ferrand, France
| |
Collapse
|
9
|
Duc C, Yoth M, Jensen S, Mouniée N, Bergman CM, Vaury C, Brasset E. Trapping a somatic endogenous retrovirus into a germline piRNA cluster immunizes the germline against further invasion. Genome Biol 2019; 20:127. [PMID: 31227013 PMCID: PMC6587276 DOI: 10.1186/s13059-019-1736-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND For species survival, the germline must faithfully transmit genetic information to the progeny. Transposable elements (TEs) constitute a significant threat to genome stability due to their mobility. In the metazoan germline, their mobilization is limited by a class of small RNAs called PIWI-interacting RNAs (piRNAs) produced by dedicated genomic loci called piRNA clusters. Although the piRNA pathway is an adaptive genomic immunity system, it remains unclear how the germline gains protection from a new transposon invasion. RESULTS To address this question, we analyze Drosophila melanogaster lines harboring a deletion within flamenco, a major piRNA cluster specifically expressed in somatic follicular cells. This deletion leads to derepression of the retrotransposon ZAM in the somatic follicular cells and subsequent germline genome invasion. In this mutant line, we identify de novo production of sense and antisense ZAM-derived piRNAs that display a germinal molecular signature. These piRNAs originated from a new ZAM insertion into a germline dual-strand piRNA cluster and silence ZAM expression specifically in germ cells. Finally, we find that ZAM trapping in a germinal piRNA cluster is a frequent event that occurs early during the isolation of the mutant line. CONCLUSIONS Transposons can hijack the host developmental process to propagate whenever their silencing is lost. Here, we show that the germline can protect itself by trapping invading somatic-specific TEs into germline piRNA clusters. This is the first demonstration of "auto-immunization" of a germline endangered by mobilization of a surrounding somatic TE.
Collapse
Affiliation(s)
- Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
- Present address: UFIP UMR-CNRS 6286, Epigénétique: prolifération et différenciation, Faculté des Sciences et des Techniques, 2 rue de la Houssinière, 44322 Nantes, France
| | - Marianne Yoth
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Silke Jensen
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Nolwenn Mouniée
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Casey M. Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, 120 E. Green St, Athens, GA 30602 USA
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000 Clermont-Ferrand, France
| |
Collapse
|
10
|
Casier K, Delmarre V, Gueguen N, Hermant C, Viodé E, Vaury C, Ronsseray S, Brasset E, Teysset L, Boivin A. Environmentally-induced epigenetic conversion of a piRNA cluster. eLife 2019; 8:39842. [PMID: 30875295 PMCID: PMC6420265 DOI: 10.7554/elife.39842] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/04/2018] [Accepted: 03/06/2019] [Indexed: 01/02/2023] Open
Abstract
Transposable element (TE) activity is repressed in animal gonads by PIWI-interacting RNAs (piRNAs) produced by piRNA clusters. Current models in flies propose that germinal piRNA clusters are functionally defined by the maternal inheritance of piRNAs produced during the previous generation. Taking advantage of an inactive, but ready to go, cluster of P-element derived transgene insertions in Drosophila melanogaster, we show here that raising flies at high temperature (29°C) instead of 25°C triggers the stable conversion of this locus from inactive into actively producing functional piRNAs. The increase of antisense transcripts from the cluster at 29°C combined with the requirement of transcription of euchromatic homologous sequences, suggests a role of double stranded RNA in the production of de novo piRNAs. This report describes the first case of the establishment of an active piRNA cluster by environmental changes in the absence of maternal inheritance of homologous piRNAs. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Collapse
Affiliation(s)
- Karine Casier
- Laboratoire Biologie du Développement, UMR7622, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Valérie Delmarre
- Laboratoire Biologie du Développement, UMR7622, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Nathalie Gueguen
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, Clermont-Ferrand, France
| | - Catherine Hermant
- Laboratoire Biologie du Développement, UMR7622, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Elise Viodé
- Laboratoire Biologie du Développement, UMR7622, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, Clermont-Ferrand, France
| | - Stéphane Ronsseray
- Laboratoire Biologie du Développement, UMR7622, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, Clermont-Ferrand, France
| | - Laure Teysset
- Laboratoire Biologie du Développement, UMR7622, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| | - Antoine Boivin
- Laboratoire Biologie du Développement, UMR7622, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Paris, France
| |
Collapse
|
11
|
Pogorelcnik R, Vaury C, Pouchin P, Jensen S, Brasset E. sRNAPipe: a Galaxy-based pipeline for bioinformatic in-depth exploration of small RNAseq data. Mob DNA 2018; 9:25. [PMID: 30079119 PMCID: PMC6069783 DOI: 10.1186/s13100-018-0130-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 05/18/2018] [Accepted: 07/16/2018] [Indexed: 12/12/2022] Open
Abstract
Background The field of small RNA is one of the most investigated research areas since they were shown to regulate transposable elements and gene expression and play essential roles in fundamental biological processes. Small RNA deep sequencing (sRNA-seq) is now routinely used for large-scale analyses of small RNA. Such high-throughput sequencing typically produces several millions reads. Results Here we present a computational pipeline (sRNAPipe: small RNA pipeline) based on the Galaxy framework that takes as input a fastq file of small RNA-seq reads and performs successive steps of mapping to categories of genomic sequences: transposable elements, gene transcripts, microRNAs, small nuclear RNAs, ribosomal RNAs and transfer RNAs. It also provides individual mapping and counting for chromosomes, transposable elements and gene transcripts, normalization, small RNA length analysis and plotting of the data along genomic coordinates to build publication-quality graphs and figures. sRNAPipe evaluates 10-nucleotide 5′-overlaps of reads on opposite strands to test ping-pong amplification for putative PIWI-interacting RNAs, providing counts of overlaps and corresponding z-scores. Conclusions sRNAPipe is easy to use and does not require command-line or coding knowledge. This pipeline gives quick visual and quantitative results, which are usable for publications. sRNAPipe is freely available as a Galaxy tool and via GitHub. Electronic supplementary material The online version of this article (10.1186/s13100-018-0130-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Romain Pogorelcnik
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Chantal Vaury
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Pierre Pouchin
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Silke Jensen
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| | - Emilie Brasset
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 10448, 63001 Clermont-Ferrand, France
| |
Collapse
|
12
|
George P, Jensen S, Pogorelcnik R, Lee J, Xing Y, Brasset E, Vaury C, Sharakhov IV. Increased production of piRNAs from euchromatic clusters and genes in Anopheles gambiae compared with Drosophila melanogaster. Epigenetics Chromatin 2015; 8:50. [PMID: 26617674 PMCID: PMC4662822 DOI: 10.1186/s13072-015-0041-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/04/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Specific genomic loci, termed Piwi-interacting RNA (piRNA) clusters, manufacture piRNAs that serve as guides for the inactivation of complementary transposable elements (TEs). The piRNA pathway has been accurately detailed in Drosophila melanogaster, while it remains poorly examined in other insects. This pathway is increasingly recognized as critical for germline development and reproduction. Understanding of the piRNA functions in mosquitoes could offer an opportunity for disease vector control by the reduction of their reproductive potential. RESULTS To analyze the similarities and differences in this pathway between Drosophila and mosquito, we performed an in-depth analysis of the genomic loci producing piRNAs and their targets in the African malaria vector Anopheles gambiae. We identified 187 piRNA clusters in the An. gambiae genome and 155 piRNA clusters in the D. melanogaster genome. We demonstrate that many more piRNA clusters in the mosquito compared with the fruit fly are uni-directionally transcribed and are located outside pericentromeric heterochromatin. About 11 % of the An. gambiae piRNA population map to gene transcripts. This is a noticeable increase compared with the ~6 % of the piRNA population mapped to genes in D. melanogaster. A subset of the piRNA-enriched genes in An. gambiae has functions related to reproduction and development. At least 24 and 65 % of the mapped piRNAs correspond to genomic TE sequences in An. gambiae and D. melanogaster, respectively. DNA transposons and non-LTR retrotransposons are more abundant in An. gambiae, while LTR retrotransposons are more abundant in D. melanogaster. Yet, piRNAs predominantly target LTR retrotransposons in both species, which may point to a distinct feature of these elements compared to the other classes of TEs concerning their silencing by the piRNA pathway. CONCLUSIONS Here, we demonstrate that piRNA-producing loci have more ubiquitous distribution in the An. gambiae genome than in the genome of D. melanogaster. Also, protein-coding genes have an increased role in production of piRNAs in the germline of this mosquito. Genes involved in germline and embryonic development of An. gambiae generate a substantial portion of piRNAs, suggesting a role of the piRNA pathway in the epigenetic regulation of the reproductive processes in the African malaria vector.
Collapse
Affiliation(s)
- Phillip George
- />Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Silke Jensen
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Romain Pogorelcnik
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Jiyoung Lee
- />The PhD Program in Genomics Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Yi Xing
- />The PhD Program in Genomics Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Emilie Brasset
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Chantal Vaury
- />Laboratoire Génétique, Reproduction, et Développement, Clermont Université, Université d’Auvergne, BP 38, 63001 Clermont-Ferrand, France
- />Institut National de la Santé et de la Recherche Médicale, U 1103, BP 38, 63001 Clermont-Ferrand, France
- />Centre National de Recherche Scientifique, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Igor V. Sharakhov
- />Department of Entomology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
- />The PhD Program in Genomics Bioinformatics and Computational Biology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| |
Collapse
|
13
|
Théron E, Dennis C, Brasset E, Vaury C. Distinct features of the piRNA pathway in somatic and germ cells: from piRNA cluster transcription to piRNA processing and amplification. Mob DNA 2014; 5:28. [PMID: 25525472 PMCID: PMC4269861 DOI: 10.1186/s13100-014-0028-y] [Citation(s) in RCA: 22] [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: 09/19/2014] [Accepted: 11/12/2014] [Indexed: 02/05/2023] Open
Abstract
Transposable elements (TEs) are major components of genomes. Their mobilization may affect genomic expression and be a threat to genetic stability. This is why they have to be tightly regulated by a dedicated system. In the reproductive tissues of a large range of organisms, they are repressed by a subclass of small interfering RNAs called piRNAs (PIWI interacting RNAs). In Drosophila melanogaster, piRNAs are produced both in the ovarian germline cells and in their surrounding somatic cells. Accumulating evidence suggests that germinal and somatic piRNA pathways are far more different than previously thought. Here we review the current knowledge on piRNA production in both these cell types, and explore their similarities and differences.
Collapse
Affiliation(s)
- Emmanuelle Théron
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Cynthia Dennis
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Emilie Brasset
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| | - Chantal Vaury
- Laboratoire GReD, Faculté de Médecine, Clermont Université, Université d'Auvergne, 28 Place H Dunant, 63000 Clermont-Ferrand, France.,Inserm, U 1103, F-63001 Clermont-Ferrand, France.,CNRS, UMR 6293, F-63001 Clermont-Ferrand, France
| |
Collapse
|
14
|
Parisot N, Pelin A, Gasc C, Polonais V, Belkorchia A, Panek J, El Alaoui H, Biron DG, Brasset E, Vaury C, Peyret P, Corradi N, Peyretaillade É, Lerat E. Microsporidian genomes harbor a diverse array of transposable elements that demonstrate an ancestry of horizontal exchange with metazoans. Genome Biol Evol 2014; 6:2289-300. [PMID: 25172905 PMCID: PMC4202319 DOI: 10.1093/gbe/evu178] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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] [Indexed: 12/16/2022] Open
Abstract
Microsporidian genomes are the leading models to understand the streamlining in response to a pathogenic lifestyle; they are gene-poor and often possess small genomes. In this study, we show a feature of microsporidian genomes that contrasts this pattern of genome reduction. Specifically, genome investigations targeted at Anncaliia algerae, a human pathogen with a genome size of 23 Mb, revealed the presence of a hitherto undetected diversity in transposable elements (TEs). A total of 240 TE families per genome were identified, exceeding that found in many free-living fungi, and searches of microsporidian species revealed that these mobile elements represent a significant portion of their coding repertoire. Their phylogenetic analysis revealed that many cases of ancestry involve recent and bidirectional horizontal transfers with metazoans. The abundance and horizontal transfer origin of microsporidian TEs highlight a novel dimension of genome evolution in these intracellular pathogens, demonstrating that factors beyond reduction are at play in their diversification.
Collapse
Affiliation(s)
- Nicolas Parisot
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France CNRS, UMR 6023, LMGE, Aubière, France
| | - Adrian Pelin
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ontario, Canada
| | - Cyrielle Gasc
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Valérie Polonais
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Abdel Belkorchia
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Johan Panek
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Hicham El Alaoui
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - David G Biron
- CNRS, UMR 6023, LMGE, Aubière, France Clermont Université, Université d'Auvergne, Laboratoire "Microorganismes: Génome et Environnement," Clermont-Ferrand, France
| | - Emilie Brasset
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm; U 1103, Clermont-Ferrand, France, CNRS; UMR 6293, Clermont-Ferrand, France
| | - Chantal Vaury
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm; U 1103, Clermont-Ferrand, France, CNRS; UMR 6293, Clermont-Ferrand, France
| | - Pierre Peyret
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Nicolas Corradi
- Canadian Institute for Advanced Research, Department of Biology, University of Ottawa, Ontario, Canada
| | - Éric Peyretaillade
- Clermont Université, Université d'Auvergne, EA 4678 CIDAM, Clermont-Ferrand, France
| | - Emmanuelle Lerat
- Université de Lyon; Université Lyon 1; CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622 Villeurbanne, France
| |
Collapse
|
15
|
Goriaux C, Théron E, Brasset E, Vaury C. History of the discovery of a master locus producing piRNAs: the flamenco/COM locus in Drosophila melanogaster. Front Genet 2014; 5:257. [PMID: 25136352 PMCID: PMC4120762 DOI: 10.3389/fgene.2014.00257] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 05/06/2014] [Accepted: 07/12/2014] [Indexed: 11/14/2022] Open
Abstract
The discovery of transposable elements (TEs) in the 1950s by B. McClintock implied the existence of cellular regulatory systems controlling TE activity. The discovery of flamenco (flam) an heterochromatic locus from Drosophila melanogaster and its ability to survey several TEs such as gypsy, ZAM, and Idefix contributed to peer deeply into the mechanisms of the genetic and epigenetic regulation of TEs. flam was the first cluster producing small RNAs to be discovered long before RNAi pathways were identified in 1998. As a result of the detailed genetic analyses performed by certain laboratories and of the sophisticated genetic tools they developed, this locus has played a major role in our understanding of piRNA mediated TE repression in animals. Here we review the first discovery of this locus and retrace decades of studies that led to our current understanding of the relationship between genomes and their TE targets.
Collapse
Affiliation(s)
- Coline Goriaux
- Laboratoire GReD, Faculté de Médecine, Clermont Université - Université d'Auvergne, Clermont-Ferrand France ; INSERM, U 1103, Clermont-Ferrand France ; CNRS, UMR 6293, Clermont-Ferrand France
| | - Emmanuelle Théron
- Laboratoire GReD, Faculté de Médecine, Clermont Université - Université d'Auvergne, Clermont-Ferrand France ; INSERM, U 1103, Clermont-Ferrand France ; CNRS, UMR 6293, Clermont-Ferrand France
| | - Emilie Brasset
- Laboratoire GReD, Faculté de Médecine, Clermont Université - Université d'Auvergne, Clermont-Ferrand France ; INSERM, U 1103, Clermont-Ferrand France ; CNRS, UMR 6293, Clermont-Ferrand France
| | - Chantal Vaury
- Laboratoire GReD, Faculté de Médecine, Clermont Université - Université d'Auvergne, Clermont-Ferrand France ; INSERM, U 1103, Clermont-Ferrand France ; CNRS, UMR 6293, Clermont-Ferrand France
| |
Collapse
|
16
|
Mteirek R, Gueguen N, Jensen S, Brasset E, Vaury C. Drosophila heterochromatin: structure and function. Curr Opin Insect Sci 2014; 1:19-24. [PMID: 32846725 DOI: 10.1016/j.cois.2014.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 06/11/2023]
Abstract
Heterochromatic domains, which are enriched in repetitive sequences and packaged in a higher-order chromatin folding, carry the potential to epigenetically inactivate a euchromatic gene that has been moved in close proximity. The discovery that these domains encode non-coding RNAs involved in RNA-silencing mechanisms has recently contributed to a better understanding of the mechanisms of the epigenetic repression established by heterochromatic domains. In this review, we will consider the repeated nature of their DNA sequence, the successive steps in heterochromatin assembly, starting with the decision process, the higher order state assembly and its epigenetic propagation. Recent findings provide new insights into the cellular functions of heterochromatin, notably its major contribution to genome stability and chromosome integrity.
Collapse
Affiliation(s)
- Rana Mteirek
- Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 38, 63001 Clermont-Ferrand, France; Inserm, U 1103, BP 38, 63001 Clermont-Ferrand, France; CNRS, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Nathalie Gueguen
- Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 38, 63001 Clermont-Ferrand, France; Inserm, U 1103, BP 38, 63001 Clermont-Ferrand, France; CNRS, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Silke Jensen
- Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 38, 63001 Clermont-Ferrand, France; Inserm, U 1103, BP 38, 63001 Clermont-Ferrand, France; CNRS, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Emilie Brasset
- Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 38, 63001 Clermont-Ferrand, France; Inserm, U 1103, BP 38, 63001 Clermont-Ferrand, France; CNRS, UMR 6293, BP 38, 63001 Clermont-Ferrand, France
| | - Chantal Vaury
- Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 38, 63001 Clermont-Ferrand, France; Inserm, U 1103, BP 38, 63001 Clermont-Ferrand, France; CNRS, UMR 6293, BP 38, 63001 Clermont-Ferrand, France.
| |
Collapse
|
17
|
Abstract
In Drosophila, the piRNA cluster, flamenco, produces most of the piRNAs (PIWI-interacting RNAs) that silence transposable elements in the somatic follicle cells during oogenesis. These piRNAs are thought to be processed from a long single-stranded precursor transcript. Here, we demonstrate that flamenco transcription is initiated from an RNA polymerase II promoter containing an initiator motif (Inr) and downstream promoter element (DPE) and requires the transcription factor, Cubitus interruptus. We show that the flamenco precursor transcript undergoes differential alternative splicing to generate diverse RNA precursors that are processed to piRNAs. Our data reveal dynamic processing steps giving rise to piRNA cluster precursors.
Collapse
Affiliation(s)
- Coline Goriaux
- Clermont Université Université d'Auvergne, Clermont-Ferrand, France
| | | | | | | | | |
Collapse
|
18
|
Dufourt J, Dennis C, Boivin A, Gueguen N, Théron E, Goriaux C, Pouchin P, Ronsseray S, Brasset E, Vaury C. Spatio-temporal requirements for transposable element piRNA-mediated silencing during Drosophila oogenesis. Nucleic Acids Res 2013; 42:2512-24. [PMID: 24288375 PMCID: PMC3936749 DOI: 10.1093/nar/gkt1184] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During Drosophila oogenesis, transposable element (TE) repression involves the Piwi-interacting RNA (piRNA) pathway which ensures genome integrity for the next generation. We developed a transgenic model to study repression of the Idefix retrotransposon in the germline. Using a candidate gene KD-approach, we identified differences in the spatio-temporal requirements of the piRNA pathway components for piRNA-mediated silencing. Some of them (Aub, Vasa, Spn-E) are necessary in very early stages of oogenesis within the germarium and appear to be less important for efficient TE silencing thereafter. Others (Piwi, Ago3, Mael) are required at all stages of oogenesis. Moreover, during early oogenesis, in the dividing cysts within the germarium, Idefix anti-sense transgenes escape host control, and this is associated with very low piwi expression. Silencing of P-element-based transgenes is also strongly weakened in these cysts. This region, termed the 'Piwiless pocket' or Pilp, may ensure that new TE insertions occur and are transmitted to the next generation, thereby contributing to genome dynamics. In contrast, piRNA-mediated silencing is strong in germline stem cells in which TE mobilization is tightly repressed ensuring the continued production of viable germline cysts.
Collapse
Affiliation(s)
- Jérémy Dufourt
- Inserm, UMR1103, F-63001 Clermont-Ferrand, France, CNRS, UMR6293, F-63001 Clermont-Ferrand, France, Clermont Université, Université d'Auvergne, Laboratoire GReD, BP 10448, F-63000 Clermont-Ferrand, France, Laboratoire Biologie du Développement, UMR7622, CNRS-Université Pierre et Marie Curie, 9 quai Saint Bernard, 75005 Paris, France and CHU, F-63001 Clermont-Ferrand, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Dennis C, Zanni V, Brasset E, Eymery A, Zhang L, Mteirek R, Jensen S, Rong YS, Vaury C. "Dot COM", a nuclear transit center for the primary piRNA pathway in Drosophila. PLoS One 2013; 8:e72752. [PMID: 24039799 PMCID: PMC3767702 DOI: 10.1371/journal.pone.0072752] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 07/18/2013] [Indexed: 01/15/2023] Open
Abstract
The piRNA pathway protects genomes by silencing mobile elements. Despite advances in understanding the processing events that generate piRNAs for silencing, little is known about how primary transcripts are transported from their genomic clusters to their processing centers. Using a model of the Drosophila COM/flamenco locus in ovarian somatic cells, we identified a prominent nuclear structure called Dot COM, which is enriched in long transcripts from piRNA clusters but located far from their transcription sites. Remarkably, transcripts from multiple clusters accumulate at Dot COM, which is often juxtaposed with Yb-bodies, the cytoplasmic processing centers for cluster transcripts. Genetic evidence suggests that the accumulation of precursor transcripts at Dot COM represents one of the most upstream events in the piRNA pathway. Our results provide new insights into the initial steps of the piRNA pathway, and open up a new research area important for a complete understanding of this conserved pathway.
Collapse
Affiliation(s)
- Cynthia Dennis
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm, U 1103, Clermont-Ferrand, France, CNRS, UMR 6293, Clermont-Ferrand, France
| | - Vanessa Zanni
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm, U 1103, Clermont-Ferrand, France, CNRS, UMR 6293, Clermont-Ferrand, France
- UMR 1318, INRA-AgroParisTech, Versailles, France
| | - Emilie Brasset
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm, U 1103, Clermont-Ferrand, France, CNRS, UMR 6293, Clermont-Ferrand, France
| | - Angeline Eymery
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm, U 1103, Clermont-Ferrand, France, CNRS, UMR 6293, Clermont-Ferrand, France
| | - Liang Zhang
- LBMB, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rana Mteirek
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm, U 1103, Clermont-Ferrand, France, CNRS, UMR 6293, Clermont-Ferrand, France
| | - Silke Jensen
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm, U 1103, Clermont-Ferrand, France, CNRS, UMR 6293, Clermont-Ferrand, France
| | - Yikang S. Rong
- LBMB, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (CV); (YSR)
| | - Chantal Vaury
- Clermont Université, Université d'Auvergne, Clermont-Ferrand, France, Inserm, U 1103, Clermont-Ferrand, France, CNRS, UMR 6293, Clermont-Ferrand, France
- * E-mail: (CV); (YSR)
| |
Collapse
|
20
|
Abstract
A report on the 'Non-coding RNA, epigenetics and transgenerational inheritance' meeting, Churchill College, Cambridge, UK, 11-12 April 2013.
Collapse
|
21
|
Abstract
UNLABELLED BACKGROUND High-throughput deep-sequencing technology has generated an unprecedented number of expressed sequence reads that offer the opportunity to get insight into biological systems. Several databases report the sequence of small regulatory RNAs which play a prominent role in the control of transposable elements (TE). However, the huge amount of data reported in these databases remains mostly unexplored because the available tools are hard for biologists to use. RESULTS Here we report NucBase, a new program designed to make an exhaustive search for sequence matches and to align short sequence reads from large nucleic acid databases to genomes or input sequences. NucBase includes a graphical interface which allows biologists to align sequences with ease and immediately visualize matched sequences, their number and their genomic position. NucBase identifies nucleic motives with strict identity to input sequences, and it capably finds candidates with one or several mismatches. It offers the opportunity to identify "core sequences" comprised of a chosen number of consecutive matching nucleotides. This software can be run locally on any Windows, Linux or Mac OS computer with 32-bit architecture compatibility. CONCLUSIONS Since this software is easy to use and can detect reads that were undetected by other software, we believe that it will be useful for biologists involved in the field of TE silencing by small non-coding RNAs. We hope NucBase will be useful for a larger community of researchers, since it makes exploration of small nucleic sequences in any organism much easier.
Collapse
Affiliation(s)
- Jeremy Dufourt
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
| | - Pierre Pouchin
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
- CHRU, F-63001, Clermont-Ferrand, France
| | - Pierre Peyret
- EA4678, Université d’Auvergne, F-63001, Clermont-Ferrand, France
| | - Emilie Brasset
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
| | - Chantal Vaury
- Clermont Université, Université d’Auvergne, Laboratoire GReD, BP 38, F-63001 Clermont-Ferrand, France
- Inserm U 1103, F-63001, Clermont-Ferrand, France
- CNRS, UMR 6293, F-63001, Clermont-Ferrand, France
| |
Collapse
|
22
|
Dufourt J, Brasset E, Desset S, Pouchin P, Vaury C. Polycomb group-dependent, heterochromatin protein 1-independent, chromatin structures silence retrotransposons in somatic tissues outside ovaries. DNA Res 2011; 18:451-61. [PMID: 21908513 PMCID: PMC3223077 DOI: 10.1093/dnares/dsr031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Somatic cells are equipped with different silencing mechanisms that protect the genome against retrotransposons. In Drosophila melanogaster, a silencing pathway implicating the argonaute protein PIWI represses retrotransposons in cells surrounding the oocyte, whereas a PIWI-independent pathway is involved in other somatic tissues. Here, we show that these two silencing mechanisms result in distinct chromatin structures. Using sensor transgenes, we found that, in somatic tissues outside of the ovaries, these transgenes adopt a heterochromatic configuration implicating hypermethylation of H3K9 and K27. We identified the Polycomb repressive complexes (PRC1 and 2), but not heterochromatin protein 1 to be necessary factors for silencing. Once established, the compact structure is stably maintained through cell divisions. By contrast, in cells where the silencing is PIWI-dependent, the transgenes display an open and labile chromatin structure. Our data suggest that a post-transcriptional gene silencing (PTGS) mechanism is responsible for the repression in the ovarian somatic cells, whereas a mechanism that couples PTGS to transcriptional gene silencing operates to silence retrotransposons in the other somatic tissues.
Collapse
Affiliation(s)
- J Dufourt
- Clermont Université, Université d'Auvergne, France
| | | | | | | | | |
Collapse
|
23
|
Brasset E, Hermant C, Jensen S, Vaury C. The Idefix enhancer-blocking insulator also harbors barrier activity. Gene 2010; 450:25-31. [PMID: 19819312 DOI: 10.1016/j.gene.2009.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 09/04/2009] [Accepted: 09/10/2009] [Indexed: 01/08/2023]
|
24
|
Fablet M, Lerat E, Rebollo R, Horard B, Burlet N, Martinez S, Brasset E, Gilson E, Vaury C, Vieira C. Genomic environment influences the dynamics of the tirant LTR retrotransposon in Drosophila. FASEB J 2009; 23:1482-9. [PMID: 19141532 DOI: 10.1096/fj.08-123513] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Combining genome sequence analysis and functional analysis, we show that some full-length copies of tirant are present in heterochromatic regions in Drosophila simulans and that when tested in vitro, these copies have a functional promoter. However, when inserted in heterochromatic regions, tirant copies are inactive in vivo, and only transcription of euchromatic copies can be detected. Thus, our data indicate that the localization of the element is a hallmark of its activity in vivo and raise the question of genomic invasions by transposable elements and the importance of their genomic integration sites.
Collapse
Affiliation(s)
- Marie Fablet
- Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Faye B, Arnaud F, Peyretaillade E, Brasset E, Dastugue B, Vaury C. Functional characteristics of a highly specific integrase encoded by an LTR-retrotransposon. PLoS One 2008; 3:e3185. [PMID: 18784842 PMCID: PMC2527525 DOI: 10.1371/journal.pone.0003185] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Accepted: 08/03/2008] [Indexed: 12/18/2022] Open
Abstract
Background The retroviral Integrase protein catalyzes the insertion of linear viral DNA into host cell DNA. Although different retroviruses have been shown to target distinctive chromosomal regions, few of them display a site-specific integration. ZAM, a retroelement from Drosophila melanogaster very similar in structure and replication cycle to mammalian retroviruses is highly site-specific. Indeed, ZAM copies target the genomic 5′-CGCGCg-3′ consensus-sequences. To enlighten the determinants of this high integration specificity, we investigated the functional properties of its integrase protein denoted ZAM-IN. Principal Findings Here we show that ZAM-IN displays the property to nick DNA molecules in vitro. This endonuclease activity targets specific sequences that are present in a 388 bp fragment taken from the white locus and known to be a genomic ZAM integration site in vivo. Furthermore, ZAM-IN displays the unusual property to directly bind specific genomic DNA sequences. Two specific and independent sites are recognized within the 388 bp fragment of the white locus: the CGCGCg sequence and a closely apposed site different in sequence. Conclusion This study strongly argues that the intrinsic properties of ZAM-IN, ie its binding properties and its endonuclease activity, play an important part in ZAM integration specificity. Its ability to select two binding sites and to nick the DNA molecule reminds the strategy used by some site-specific recombination enzymes and forms the basis for site-specific integration strategies potentially useful in a broad range of genetic engineering applications.
Collapse
Affiliation(s)
- Babacar Faye
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Frederick Arnaud
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Eric Peyretaillade
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Emilie Brasset
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Bernard Dastugue
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
| | - Chantal Vaury
- UMR/CNRS 6247, Clermont Université, INSERM, U931, Faculté de Médecine, Clermont-Ferrand, France
- * E-mail:
| |
Collapse
|
26
|
Guelen L, Pagie L, Brasset E, Meuleman W, Faza MB, Talhout W, Eussen BH, de Klein A, Wessels L, de Laat W, van Steensel B. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 2008; 453:948-51. [PMID: 18463634 DOI: 10.1038/nature06947] [Citation(s) in RCA: 1339] [Impact Index Per Article: 83.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 03/28/2008] [Indexed: 12/13/2022]
Abstract
The architecture of human chromosomes in interphase nuclei is still largely unknown. Microscopy studies have indicated that specific regions of chromosomes are located in close proximity to the nuclear lamina (NL). This has led to the idea that certain genomic elements may be attached to the NL, which may contribute to the spatial organization of chromosomes inside the nucleus. However, sequences in the human genome that interact with the NL in vivo have not been identified. Here we construct a high-resolution map of the interaction sites of the entire genome with NL components in human fibroblasts. This map shows that genome-lamina interactions occur through more than 1,300 sharply defined large domains 0.1-10 megabases in size. These lamina-associated domains (LADs) are typified by low gene-expression levels, indicating that LADs represent a repressive chromatin environment. The borders of LADs are demarcated by the insulator protein CTCF, by promoters that are oriented away from LADs, or by CpG islands, suggesting possible mechanisms of LAD confinement. Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus.
Collapse
Affiliation(s)
- Lars Guelen
- Division of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Palstra RJ, Simonis M, Klous P, Brasset E, Eijkelkamp B, de Laat W. Maintenance of long-range DNA interactions after inhibition of ongoing RNA polymerase II transcription. PLoS One 2008; 3:e1661. [PMID: 18286208 PMCID: PMC2243019 DOI: 10.1371/journal.pone.0001661] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Accepted: 01/21/2008] [Indexed: 01/07/2023] Open
Abstract
A relationship exists between nuclear architecture and gene activity and it has been proposed that the activity of ongoing RNA polymerase II transcription determines genome organization in the mammalian cell nucleus. Recently developed 3C and 4C technology allowed us to test the importance of transcription for nuclear architecture. We demonstrate that upon transcription inhibition binding of RNA polymerase II to gene regulatory elements is severely reduced. However, contacts between regulatory DNA elements and genes in the β-globin locus are unaffected and the locus still interacts with the same genomic regions elsewhere on the chromosome. This is a general phenomenon since the great majority of intra- and interchromosomal interactions with the ubiquitously expressed Rad23a gene are also not affected. Our data demonstrate that without transcription the organization and modification of nucleosomes at active loci and the local binding of specific trans-acting factors is unaltered. We propose that these parameters, more than transcription or RNA polymerase II binding, determine the maintenance of long-range DNA interactions.
Collapse
Affiliation(s)
- Robert-Jan Palstra
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Marieke Simonis
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Petra Klous
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Emilie Brasset
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Bart Eijkelkamp
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Wouter de Laat
- Department of Cell Biology and Genetics, Erasmus MC, Rotterdam, The Netherlands
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
28
|
Abstract
Insulators play important roles in controlling gene activity and maintaining regulatory independence between neighbouring genes. In this article, we show that the enhancer-blocking activity of the insulator present within the LTR retrotransposon Idefix can be abolished if two copies of the region containing the insulator—specifically, the long terminal repeat (LTR)—are fused to the retrotransposon's 5′ untranslated region (5′ UTR). The presence of this combination of two [LTR-5′ UTR] modules is a prerequisite for the loss of enhancer-blocking activity. We further show that the 5′ UTR causes flanking genomic sequences to be displaced to the nuclear periphery, which is not observed when two insulators are present by themselves. This study thus provides a functional link between insulators and independent genomic modules, which may cooperate to allow the specific regulation of defined genomic loci via nuclear repositioning. It further illustrates the complexity of genomic regulation within a chromatic environment with multiple functional elements.
Collapse
Affiliation(s)
- E. Brasset
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - F. Bantignies
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - F. Court
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - S. Cheresiz
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - C. Conte
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
| | - C. Vaury
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France, Institut de Génétique Humaine, UPR 1142 – CNRS, 34396 Montpellier, France, Institute of Cytology and Genetics, Novosibirsk, Russia and INSERM, U589, 31432 Toulouse, France
- *To whom correspondence should be addressed 33 4 73 17 81 7133 4 73 27 61 32
| |
Collapse
|
29
|
Brasset E, Taddei AR, Arnaud F, Faye B, Fausto AM, Mazzini M, Giorgi F, Vaury C. Viral particles of the endogenous retrovirus ZAM from Drosophila melanogaster use a pre-existing endosome/exosome pathway for transfer to the oocyte. Retrovirology 2006; 3:25. [PMID: 16684341 PMCID: PMC1524798 DOI: 10.1186/1742-4690-3-25] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2006] [Accepted: 05/09/2006] [Indexed: 12/27/2022] Open
Abstract
Background Retroviruses have evolved various mechanisms to optimize their transfer to new target cells via late endosomes. Here, we analyzed the transfer of ZAM, a retroelement from Drosophila melanogaster, from ovarian follicle cells to the oocyte at stage 9–10 of oogenesis, when an active yolk transfer is occurring between these two cell types. Results Combining genetic and microscopic approaches, we show that a functional secretory apparatus is required to tether ZAM to endosomal vesicles and to direct its transport to the apical side of follicle cells. There, ZAM egress requires an intact follicular epithelium communicating with the oocyte. When gap junctions are inhibited or yolk receptors mutated, ZAM particles fail to sort out the follicle cells. Conclusion Overall, our results indicate that retrotransposons do not exclusively perform intracellular replication cycles but may usurp exosomal/endosomal traffic to be routed from one cell to another.
Collapse
Affiliation(s)
- E Brasset
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France
| | - AR Taddei
- Centre of Electron Microscopy, Department of Environmental Sciences, Tuscia, University Viterbo, Italy
| | - F Arnaud
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France
| | - B Faye
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France
| | - AM Fausto
- Centre of Electron Microscopy, Department of Environmental Sciences, Tuscia, University Viterbo, Italy
| | - M Mazzini
- Centre of Electron Microscopy, Department of Environmental Sciences, Tuscia, University Viterbo, Italy
| | - F Giorgi
- Centre of Electron Microscopy, Department of Environmental Sciences, Tuscia, University Viterbo, Italy
| | - C Vaury
- INSERM, U384, Faculté de Médecine, BP38, 63001 Clermont-Ferrand, France
| |
Collapse
|
30
|
Abstract
The properties of cis-regulatory elements able to influence gene transcription over large distances have led to the hypothesis that elements called insulators should exist to limit the action of enhancers and silencers. During the last decades, insulators have been identified in many eukaryotes from yeast to human. Insulators possess two main properties: (i) they can block enhancer-promoter communication ('enhancer blocker activity'), and (ii) they can prevent the spread of repressive chromatin ('barrier activity'). This review focuses on recent studies designed to elucidate the molecular mechanisms of the insulator function, and gives an overview of the critical role of insulators in nuclear organization and functional identity of chromatin.
Collapse
Affiliation(s)
- E Brasset
- INSERM U384, Faculté de Médecine, BP38, Clermont-Ferrand 63001, France
| | | |
Collapse
|
31
|
Zhao BY, Ardales E, Brasset E, Claflin LE, Leach JE, Hulbert SH. The Rxo1/ Rba1 locus of maize controls resistance reactions to pathogenic and non-host bacteria. Theor Appl Genet 2004; 109:71-79. [PMID: 15114472 DOI: 10.1007/s00122-004-1623-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2001] [Accepted: 01/29/2004] [Indexed: 05/24/2023]
Abstract
Infiltration of different maize lines with a variety of bacterial pathogens of maize, rice and sorghum identified qualitative differences in resistant reactions. Isolates from two bacterial species induced rapid hypersensitive reactions (HR) in some maize lines, but not others. All isolates of the non-host pathogen Xanthomonas oryzae pv. oryzicola (bacterial leaf streak disease of rice) and some isolates of the pathogenic bacterium Burkholderia andropogonis induced HR when infiltrated into maize line B73, but not Mo17. Genetic control of the HR to both bacteria segregated as a single dominant gene. Surprisingly, both phenotypes mapped to the same locus, indicating they are either tightly linked or controlled by the same gene. The locus maps on the short arm of maize chromosome six near several other disease-resistance genes. Results indicate the same type of genes may contribute to both non-host resistance and resistance to pathogens.
Collapse
Affiliation(s)
- B Y Zhao
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66502, USA
| | | | | | | | | | | |
Collapse
|