Similar studies for GEO DataSets (Select 200022067) - GEO DataSets

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Items: 20

Select item 2000220671.

Small RNA-based silencing strategies for transposons in the process of invading Drosophila species

(Submitter supplied) We investigated a pool of small RNAs derived from transposon Penelope to probe the evolution of small RNA pathways in response to the transposon challenge in natural (D. virilis) and experimentally induced (D. melanogaster) colonization processes. In both species, Penelope was predominantly targeted by endo-siRNAs rather than by piRNAs. Although we observed correlations between Penelope transcription and dysgenesis, we could not correlate differences in maternally deposited Penelope piRNAs with the sterility of progeny. more...

Organism:: Drosophila virilis; Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL9058 GPL10472
48 Samples

Download data: TXT

Series

Accession:: GSE22067

ID:: 200022067

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000419532.

Evolution and dynamics of small RNA response to a retroelement invasion in Drosphila

(Submitter supplied) Although small RNAs efficiently control transposition activity of most transposons in the host genome, such immune system is not always applicable against new transposon's invasions. Here we explored a possibility to introduce potentially mobile copy of the Penelope retroelement previously implicated in hybrid dysgenesis syndrome in Drosophila virilis into the genomes of two distant Drosophila species. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13304
3 Samples

Download data: XLSX

Series

Accession:: GSE41953

ID:: 200041953

PubMed Similar studies SRA Run Selector

Select item 2001607783.

Maternally inherited piRNAs direct transient heterochromatin formation at active transposons during early Drosophila embryogenesis

(Submitter supplied) The piRNA pathway controls transposon expression in animal germ cells, thereby ensuring genome stability over generations. piRNAs are maternally deposited and required for proper transposon silencing in adult offspring. However, a long-standing question in the field is the precise function of maternally deposited piRNAs and its associated factors during embryogenesis. Here, we probe the spatio-temporal expression patterns of several piRNA pathway components during early stages of development. more...

Organism:: Drosophila melanogaster

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platform:: GPL21306
62 Samples

Download data: BED, BW

Series

Accession:: GSE160778

ID:: 200160778

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Select item 2000318134.

Adaptation to transposon invasion in Drosophila melanogaster

(Submitter supplied) Transposons evolve rapidly and can mobilize and trigger genetic instability. piRNAs silence these genome pathogens, but it is unclear how the piRNA pathway adapts to new transposons. In Drosophila piRNAs, encoded by heterochromatic clusters are maternally deposited in the embryo. Paternally inherited P-element transposons thus escape silencing and trigger a genetic instability and sterility. We show that this syndrome, termed P-M hybrid dysgenesis, also disrupts the piRNA biogenesis machinery and activates resident transposons. more...

Organism:: Drosophila melanogaster

Type:: Genome variation profiling by genome tiling array

Platform:: GPL6629
9 Samples

Download data: CEL, TXT

Series

Accession:: GSE31813

ID:: 200031813

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Select item 2000151865.

Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary

(Submitter supplied) Here, we analyzed nine Drosophila piRNA pathway mutants for their impacts on both small RNA populations and the sub-cellular localization patterns of Piwi proteins. We find that distinct piRNA pathways with differing components function in ovarian germ and somatic cells. Keywords: Epigenetics

Organism:: Drosophila erecta; Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing; Other

Platforms:: GPL9321 GPL9061
20 Samples

Download data: CSV

Series

Accession:: GSE15186

ID:: 200015186

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 2000130816.

An epigenetic role for maternally inherited piRNAs in transposon silencing

(Submitter supplied) In plants and mammals, small RNAs indirectly mediate epigenetic inheritance by specifying cytosine methylation. Here, we find that small RNAs themselves serve as vectors for epigenetic information. Crosses between Drosophila strains that differ in the presence of a particular transposon can produce sterile progeny, a phenomenon called hybrid dysgenesis. This phenotype manifests itself only if the transposon is paternally inherited, suggesting maternal transmission of a factor that maintains fertility. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL9061
15 Samples

Download data: TXT

Series

Accession:: GSE13081

ID:: 200013081

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Select item 2000452907.

Transposon defense by endo-siRNAs, piRNAs and somatic pilRNAs: Roles of Loqs-PD and R2D2

(Submitter supplied) Transposable elements are a serious threat for genome integrity and their control via small RNA mediated silencing pathways is an ancient strategy. The fruit fly Drosophila melanogaster has two silencing mechanisms that repress TEs expression: endogenous siRNAs (esiRNAs or endo-siRNAs) and Piwi-interacting small RNAs (piRNAs). The biogenesis of endo-siRNAs involves Loqs-PD, which acts predominantly during processing of dsRNA by Dcr-2, and R2D2 that primarily helps to direct siRNAs for loading into Ago2. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL11203
16 Samples

Download data: TXT

Series

Accession:: GSE45290

ID:: 200045290

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Select item 2000091388.

PIWI-associated piRNA in Drosophila melanogaster ovary

(Submitter supplied) Heterochromatin, representing the silenced state of transcription, largely consists of transposon-enriched and highly repetitive sequences. Implicated in heterochromatin formation and transcriptional silencing in Drosophila are PIWI and repeat-associated small interfering RNAs (rasiRNAs). Despite this, the role of PIWI in rasiRNA expression and heterochromatic silencing remains unknown. Here we report the identification and characterization of 12,903 PIWI-interacting RNAs (piRNAs) in Drosophila, demonstrating that rasiRNAs represent a subset of piRNAs. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL5922
1 Sample

Download data: TXT

Series

Accession:: GSE9138

ID:: 200009138

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Select item 2000833169.

Natural variation of piRNA expression affects immunity to transposable elements

(Submitter supplied) In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13304
7 Samples

Download data: TXT

Series

Accession:: GSE83316

ID:: 200083316

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Select item 20010358210.

piRNA-mediated regulation of transposon alternative splicing in soma and germline

(Submitter supplied) Transposable elements can drive genome evolution, but their enhanced activity is detrimental to the host and therefore must be tightly regulated. The piwi-interacting small RNAs (piRNAs) pathway is critically important for transposable element regulation, by inducing transcriptional silencing or post-transcriptional decay of mRNAs. We show that piRNAs and piRNA biogenesis components regulate pre-mRNA splicing of P transposable element transcripts in vivo, leading to the production of the non-transposase-encoding mature mRNA isoform in germ cells. more...

Organism:: Drosophila melanogaster

Type:: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:: GPL17275
20 Samples

Download data: BEDGRAPH, BIGWIG

Series

Accession:: GSE103582

ID:: 200103582

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Select item 20012080211.

piRNA silencing contributes to interspecies hybrid sterility and reproductive isolation in Drosophila

(Submitter supplied) The piRNA pathway is an adaptive mechanism for maintaining the stability of the genome by repression selfish genomic elements such as transposons. As a host defense mechanism the piRNA pathway is rapidly evolving with different sets of piRNA silencing different targets in closely-related species. In male germline of D.melanogaster, repression of Stellate genes by piRNA generated from Supressor of Stellate, Su(Ste), locus is required for male fertility, but both Su(Ste) piRNA and their targets are absent in other Drosophila species. more...

Organism:: Drosophila mauritiana; Drosophila melanogaster x Drosophila mauritiana; Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL25638 GPL17275 GPL25637
7 Samples

Download data: TXT, XLSX

Series

Accession:: GSE120802

ID:: 200120802

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Select item 20007177512.

piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire

(Submitter supplied) PIWI-clade Argonaute proteins silence transposon expression in animal gonads. Their target specificity is defined by bound ~23-30nt piRNAs that are processed from single-stranded precursor transcripts via two distinct pathways. Primary piRNAs are defined by the endo-nuclease Zucchini, while biogenesis of secondary piRNAs depends on piRNA-guided transcript cleavage and results in piRNA amplification. more...

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13304
46 Samples

Download data: BW, TXT

Series

Accession:: GSE71775

ID:: 200071775

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Select item 20009863513.

Integrative analysis unveils new functions for the Drosophila Cutoff protein in non-coding RNA biogenesis and gene regulation

(Submitter supplied) Piwi-Interacting RNAs (piRNAs) are central components of the piRNA pathway, which directs transposon silencing and guarantees genome integrity in the germ cells of several metazoans. In Drosophila, piRNAs are produced from discrete regions of the genome termed piRNA clusters, whose expression relies on the RDC complex comprised of the core proteins Rhino, Deadlock and Cutoff. To date, the RDC complex has been exclusively implicated in the regulation of the piRNA loci. more...

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9061
17 Samples

Download data: BED, TXT

Series

Accession:: GSE98635

ID:: 200098635

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Select item 20013888614.

Epigenetic requirements for triggering heterochromatinization and Piwi-interacting RNA production from transgenes in the Drosophila germline

(Submitter supplied) Transgenes containing a fragment of I transposon represent a powerful model of piRNA cluster de novo formation in the Drosophila germline. We revealed that the same transgenes located at different genomic loci form piRNA clusters with various capacity of small RNA production. Transgenic piRNA clusters are not established in piRNA pathway mutants. However, in wild-type context, the endogenous ancestral I-related piRNAs are sufficient to heterochromatinize and convert the I-containing transgenes into piRNA-producing loci. more...

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Other

Platforms:: GPL25244 GPL17275
20 Samples

Download data: BW, TXT

Series

Accession:: GSE138886

ID:: 200138886

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Select item 20004059215.

Maternally deposited germline piRNAs silence the tirant retrotransposon in somatic cells

(Submitter supplied) Transposable elements (TEs), whose propagation can result in severe damage to the host genome, are silenced in the animal gonad by Piwi-interacting RNAs (piRNAs). piRNAs produced in the ovaries are deposited in the embryonic germline and initiate TE repression in the germline progeny. Whether the maternally transmitted piRNAs play a role in the silencing of somatic TEs is, however, unknown. Here we show that maternally transmitted piRNAs from the tirant retrotransposon in Drosophila are required for the somatic silencing of the TE and correlate with an increase in histone H3K9 trimethylation an active tirant copy.

Organism:: Drosophila simulans

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13306
4 Samples

Download data: TXT

Series

Accession:: GSE40592

ID:: 200040592

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Select item 20000673416.

piRNA libraries from Drosophila melanogaster ovaries

(Submitter supplied) Drosophila Piwi-family proteins have been implicated in transposon control. Here, we examine piwi-interacting RNAs (piRNAs) associated with each Drosophila Piwi protein and find that Piwi and Aubergine bind RNAs that are predominantly antisense to transposons, whereas Ago3 complexes contain predominantly sense piRNAs. As in mammals, the majority of Drosophila piRNAs are derived from discrete genomic loci. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL9058
4 Samples

Download data

Series

Accession:: GSE6734

ID:: 200006734

PubMed Similar studies

Select item 20007813517.

Telomeric retrotransposon HeT-A contains a bidirectional promoter that initiates divergent transcription of piRNA precursors in Drosophila germline

(Submitter supplied) PIWI-interacting (pi) RNAs provide silencing of transposable elements (TE) in the germline. Drosophila telomeres are maintained by transpositions of specialized telomeric retroelements. piRNAs generated from sense and antisense transcripts of telomeric elements provide telomere length control in the germline. Previously, we have found that antisense transcription of the major telomeric retroelement HeT-A is initiated upstream of the HeT-A sense transcription start site. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL13304
3 Samples

Download data: TXT

Series

Accession:: GSE78135

ID:: 200078135

PubMed Similar studies SRA Run Selector

Select item 20001513718.

FLX sequencing of Piwi-associated small RNAs extracted from Drosophila ovarian somatic cells (OSC)

(Submitter supplied) piRNAs function in silencing retrotransposons by associating with the PIWI proteins, AGO3, Aub, and Piwi, in Drosophila germlines. Bioinformatics analyses of piRNAs in Drosophila ovaries suggested that piRNAs are produced by two systems, the primary processing pathway and the amplification loop, from repetitive genes and piRNA clusters in the genome. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. more...

Organism:: Drosophila melanogaster

Type:: Non-coding RNA profiling by high throughput sequencing

Platform:: GPL9333
1 Sample

Download data

Series

Accession:: GSE15137

ID:: 200015137

PubMed Similar studies SRA Run Selector

Select item 20009393419.

Co-chaperone Hop/dSTIP1 is required for piRNA biogenesis and transposon silencing

(Submitter supplied) piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element silencing and maintenance of genome integrity. It has been shown that Drosophila Hsp70/90 Organizing Protein Homolog (Hop) – a co-chaperone interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. more...

Organism:: Drosophila melanogaster

Type:: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:: GPL17275
6 Samples

Download data: TXT

Series

Accession:: GSE93934

ID:: 200093934

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20001108620.

Deep sequencing of Drosophila melanogaster small RNAs

(Submitter supplied) High throughput seqeuncing of small RNAs (PAGE isolated from total RNA or Argonaute immunoprecipitates) from Drosophila melanogaster using the Illumina platform. Adapter ligation requires 5' monophosphate and 3' OH. Full analysis of all libraries in this set is published (Czech B. et al. 2008), leading to the description of endogenous siRNAs in flies. Keywords: Solexa sequences

Organism:: Drosophila melanogaster; Flock House virus

Type:: Non-coding RNA profiling by high throughput sequencing

Platforms:: GPL9058 GPL9402
9 Samples

Download data: TXT

Series

Accession:: GSE11086

ID:: 200011086

PubMed Full text in PMC Similar studies

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