Mobile elements and transposition events in the cut locus of Drosophila melanogaster

Tchurikov, Nickolai A.; Gerasimova, T. I.; Johnson, Terrell K.; Barbakar, Nickolai I.; Kenzior, Alexander; Georgiev, G.P.

doi:10.1007/bf00261183

Cited by 24 publications

(25 citation statements)

References 15 publications

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“…In addition, we found that the heteroallelic combination ct A flam A /ct 6 flam 1 produced a low but significant increase of lethal ecdysis deficiency with respect to flam A /flam 1 , confirming the specificity of the genetic interaction ( Figure 2H). Since roo-specific small RNAs are not produced by the flamenco locus (Yang et al 2010), we explored whether the ct n allele, which is induced by insertion of a roo element (Tchurikov et al 1989), genetically interacts with flam 1 . The ct n flam 1 recombinant flies did not show an increased level of ecdysis failure with respect to flam 1 and ct n flies ( Figure 2G).…”

Section: Resultsmentioning

confidence: 99%

“…We also tried to confirm these data using two other ct alleles and the permissive flam 1 allele. To achieve this goal, the ct 6 allele, which is also induced by a gypsy insertion (Tchurikov et al 1989), was recombined with flam 1 . These recombinant flies (ct 6 flam 1 ) also showed an increased lethal ecdysis deficiency with respect to flam 1 and ct 6 flies ( Figure 2G).…”

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confidence: 99%

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Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster

et al. 2016

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Protective mechanisms based on RNA silencing directed against the propagation of transposable elements are highly conserved in eukaryotes. The control of transposable elements is mediated by small noncoding RNAs, which derive from transposonrich heterochromatic regions that function as small RNA-generating loci. These clusters are transcribed and the precursor transcripts are processed to generate Piwi-interacting RNAs (piRNAs) and endogenous small interfering RNAs (endo-siRNAs), which silence transposable elements in gonads and somatic tissues. The flamenco locus is a Drosophila melanogaster small RNA cluster that controls gypsy and other transposable elements, and has played an important role in understanding how small noncoding RNAs repress transposable elements. In this study, we describe a cosuppression mechanism triggered by new euchromatic gypsy insertions in genetic backgrounds carrying flamenco alleles defective in gypsy suppression. We found that the silencing of gypsy is accompanied by the silencing of other transposons regulated by flamenco, and of specific flamenco sequences from which small RNAs against gypsy originate. This cosuppression mechanism seems to depend on a post-transcriptional regulation that involves both endo-siRNA and piRNA pathways and is associated with the occurrence of developmental defects. In conclusion, we propose that new gypsy euchromatic insertions trigger a post-transcriptional silencing of gypsy sense and antisense sequences, which modifies the flamenco activity. This cosuppression mechanism interferes with some developmental processes, presumably by influencing the expression of specific genes. KEYWORDS transposon; small RNA; RNA silencing; primary transcript; ecdysis E UKARYOTIC genomes consist in part of sequences derived from a wide variety of transposable elements (TEs), some of which can mobilize to new genomic locations (de Koning et al. 2011). A genomic consequence of their mobilization is the induction of new mutations and chromosomal rearrangements that may have deleterious effects on fitness. However, they may also provide a fundamental contribution to genetic variation and evolutionary changes (Fedoroff 2012;Warren et al. 2015;Elbarbary et al. 2016;Mita and Boeke 2016). TE activation is suppressed by specific silencing mechanisms that act both at the transcriptional level, through chromatin modifications, and at the post-transcriptional level (Buchon and Vaury 2006). Piwi-interacting RNAs (piRNAs), a distinct class of 24-to 30-nt-long RNAs produced by a Dicer-independent biogenesis pathway, are involved in the recognition and selective silencing of transposons during gametogenesis (Sarot et al. 2004;Kalmykova et al. 2005). In the Drosophila ovary germline, the coordinated action of aubergine (aub), Argonaute 3 (AGO3), and piwi suppresses activity of a broad group of TEs through the formation of piRNAs involving both a primary processing and a secondary "ping-pong" amplification loop (Brennecke et al. 2007;Gunawardane et al. 2007;Li et al. 2009;Malone...

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Section: Resultsmentioning

confidence: 99%

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confidence: 99%

Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster

et al. 2016

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“…Fig. 5D shows a typical alignment of RT sequences (17) derived from VIPER, the Burdock LTRretrotransposon of Drosophila melanogaster (18) and the rice tungro bacilliform virus (RTBV) (19). Twenty of 183 residues are identical between the compared sequences ( * in Fig.…”

Section: Sire Is Related To Viper An Unusual Retroelementmentioning

confidence: 99%

The short interspersed repetitive element of Trypanosoma cruzi , SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons

Vázquez

Ben‐Dov

Lorenzi

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

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The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was first detected when comparing the sequences of loci that encode the TcP2␤ genes. It is present in about 1,500 -3,000 copies per genome, depending on the strain, and it is distributed in all chromosomes. An initial analysis of SIRE sequences from 21 genomic fragments allowed us to derive a consensus nucleotide sequence and structure for the element, consisting of three regions (I, II, and III) each harboring distinctive features. Analysis of 158 transcribed SIREs demonstrates that the consensus is highly conserved. The sequences of 51 cDNAs show that SIRE is included in the 3 end of several mRNAs, always transcribed from the sense strand, contributing the polyadenylation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroelement. VIPER's 5 end is formed by the first 182 bp of SIRE, whereas its 3 end is formed by the last 220 bp of the element. Both SIRE moieties are connected by a 1,924-bp-long fragment that carries a unique ORF encoding a complete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids derive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptaseRNase H shares significant homology to that of long terminal repeat retrotransposons. The fact that SIRE and VIPER sequences are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan parasite.

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“…Arabidopsis, tomato, and maize protoplasts were prepared as described (11 10 min, the reaction mixture was diluted to 500 ,ul and digested with EcoRI enzyme. The DNA was used for cloning in AL47.1 arms as described (12). For plating on 5-bromo4 chloro-3-indolyl /B-D-galactoside/isopropyl P-D-thiogalactoside agar, the 3103 E. coli lac7 amber recA host was used.…”

Section: Methodsmentioning

confidence: 99%

“…To understand further the nature of the sensitive regions, we attempted to map the f-DNA segment ends inside the Drosophila cut locus, which was cloned earlier in a region spanning 240 kb (12). The Southern blot containing EcoRI digestion fragments of A clones from this chromosomal walk was hybridized with the end-labeled Drosophila f-DNA probe.…”

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Detection of DNA domains in Drosophila, human, and plant chromosomes possessing mainly 50- to 150-kilobase stretches of DNA.

Tchurikov

Пономаренко

1992

Proc. Natl. Acad. Sci. U.S.A.

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We have used pulsed-field gel electrophoresis of undigested DNA prepared by cell lysis in agarose with proteinase K detergent treatment and found a resolvable DNA fraction, denoted forum DNA (f-DNA). By changing the pulsed-field gel pulse length from 25 to 4500 sec, to obtain optimal separation in different ranges, we have found f-DNA to occupy a rather broad zone from 2 megabases to 10 kilobases (kb), but mainly at a range between 50 and 150 kb. f-DNA seems to appear as a result of nonrandom spontaneous degradation during cell treatment. The terminal regions of f-DNA segments have been cloned by using a jumping library. The molecular analysis of unique DNA sequence from an anonymous Drosophila DNA segment led to the conclusion that f-DNA appears as a result of nonrandom chromosomal DNA cleavage within sensitive regions that occupy a few kilobases. This conclusion was confirmed by detection of rather discrete hybridization bands on pulsed-field gel Southern blots in a region of good separation of undigested f-DNA after hybridization with different unique and repetitive probes. We propose that f-DNA segments may correspond to some regular higher-order structures in the eukaryotic chromosomes.From general reasoning and some experimental evidence, it is believed that linear chromosomal DNA must be organized into some kind of superstructures. The string of nucleosomes could form several structural levels in the chromosome, reflecting different features in its organization and function (1). Analysis of these structures in higher eukaryotes is hampered by both the complexity of the chromosomal architecture and the lack of appropriate assay techniques for fine measurements of the basic elements involved.The study by DNase I treatment of structural changes in chromosomal organization occurring when a gene is activated led to detection of a preferential sensitivity to digestion that extends throughout the transcription unit (1). This sensitivity is specific to the chromosomal regions in which the gene is active. The second phenomenon detected by DNase I digestion is very local alterations in chromosomal structure, which makes it extremely sensitive to DNase I digestion (2). The local changes in structure at 5' and 3' regions of genes could be determined by stable sequestration of transcription factors onto promoters that may play a critical role in transcription activation (3).The study of DNA packaging in interphase and metaphase chromosomes of higher eukaryotes has revealed chromosomal loops to be formed by attachment of specific DNA sites on the nuclear scaffold (4-6). It has been proposed that nontranscribed scaffold binding regions located at the base of looped domains may play roles in chromosome segregation, transcription activation, and replication (4-8).Recent studies have revealed compositionally (measured as G+C percent) homogeneous vertebrate chromosomal DNA domains spanning several hundred kilobases-socalled isochores (9). In this paper, we report chromosomal DNA domains detected by pulsed-field gel ...

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Mobile elements and transposition events in the cut locus of Drosophila melanogaster

Cited by 24 publications

References 15 publications

Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster

Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster

The short interspersed repetitive element of Trypanosoma cruzi , SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons

Detection of DNA domains in Drosophila, human, and plant chromosomes possessing mainly 50- to 150-kilobase stretches of DNA.

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