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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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A rapid and scalable system for studying gene function in mice using conditional RNA interference

ABSTRACT: Four libraries were analyzed to assess the level and effects of inducing the ectopic expression of a luciferase targeting miRNA in mouse embryonic fibroblasts (MEFs). Here, we find low level, leaky expression in the absence of ROSA-rtTA and doxycyclin. When expression is effectively induced, the Luciferase miRNA is expressed as the 8th most abundant species in the cells. Keyword(s): Epigenetics 4 libraries were analyzed

ORGANISM(S): Mus musculus

SUBMITTER: Colin Malone

PROVIDER: E-GEOD-19476 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A rapid and scalable system for studying gene function in mice using conditional RNA interference.

Premsrirut Prem K PK Dow Lukas E LE Kim Sang Yong SY Camiolo Matthew M Malone Colin D CD Miething Cornelius C Scuoppo Claudio C Zuber Johannes J Dickins Ross A RA Kogan Scott C SC Shroyer Kenneth R KR Sordella Raffaella R Hannon Gregory J GJ Lowe Scott W SW

Cell 20110401 1

RNA interference is a powerful tool for studying gene function, however, the reproducible generation of RNAi transgenic mice remains a significant limitation. By combining optimized fluorescence-coupled miR30-based shRNAs with high efficiency ES cell targeting, we developed a fast, scalable pipeline for the production of shRNA transgenic mice. Using this system, we generated eight tet-regulated shRNA transgenic lines targeting Firefly and Renilla luciferases, Oct4 and tumor suppressors p53, p16( ...[more]

PMID: 21458673

Similar Datasets

A rapid and scalable system for studying gene function in mice using conditional RNA interference

Project description:Four libraries were analyzed to assess the level and effects of inducing the ectopic expression of a luciferase targeting miRNA in mouse embryonic fibroblasts (MEFs). Here, we find low level, leaky expression in the absence of ROSA-rtTA and doxycyclin. When expression is effectively induced, the Luciferase miRNA is expressed as the 8th most abundant species in the cells. Keyword(s): Epigenetics

2010-12-01 | GSE19476 | GEO

piRNA production requires heterochromatin formation in Drosophila

Project description:Here, we analyzed two small RNA libraries derived from ovarian tissue mutant for either the Drosophila SETDB1 gene, or the Bam gene. Here we show that deposition of histone 3 lysine 9 by the methyltransferase dSETDB1 (egg) is required for piRNA cluster transcription. In the absence of dSETDB1, cluster precursor transcription collapses in germline and somatic gonadal cells and TEs are activated, resulting in germline loss and a block in germline stem cell differentiation. We propose that heterochromatin protects the germline by activating the piRNA pathway. Keyword : Epigenetics 2 libraries were analyzed, with 1 being a developmental control (Bam Mutant).

2011-08-15 | E-GEOD-30086 | biostudies-arrayexpress

Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila.

Project description:Here, we analyzed small RNA libraries derived from ovarian tissues heterozygous or mutant for the Tudor gene, Vreteno. In the absence of vret, Piwi-bound piRNAs are lost without changes in piRNA precursor transcript production, supporting a role for Vret in primary piRNA biogenesis. In the germline, piRNAs can engage in an Aub/Argonaute 3 (AGO3)-dependent amplification in the absence of Vret, suggesting that Vret function can distinguish between primary piRNAs loaded into Piwi/Aub complexes and piRNAs engaged in the amplification cycle. We propose that Vret acts at an early step in primary piRNA processing where it plays an essential role in transposon regulation. Keyword : Epigenetics 2 libraries were analyzed, with 1 being a control (heterozygote).

2011-08-15 | E-GEOD-30088 | biostudies-arrayexpress

An epigenetic role for maternally inherited piRNAs in transposon silencing

Project description: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. In both P- and I-element-mediated hybrid-dysgenesis models, daughters show a markedly different content of piRNAs targeting each element, depending upon its parent of origin. Such differences persist from fertilization through adulthood. This indicates that maternally deposited piRNAs are crucial for mounting an effective silencing response and that a lack of maternal piRNA inheritance underlies hybrid dysgenesis. Mappers table contains all of the sequences in our libraries that map to the drosophila genome (release 5) Nonmappers table contains all of the sequences in our libraries that do not map to the drosophila genome(release 5) 15 small RNA libraries were generated from total RNA of Drosophila melanogaster ovarian and embryo tissues and analyzed for this study

2008-11-28 | E-GEOD-13081 | biostudies-arrayexpress

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

Project description: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 20 libraries were analyzed, with 9 being control samples (heterozygotes).

2009-04-29 | E-GEOD-15186 | biostudies-arrayexpress

Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform

Project description:Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are ~22-23-nt, ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha/Pasha and Dcr-1/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of ~24-28-nt associate with Piwi-family proteins and can arise from single-stranded precursors. piRNAs function in transposon silencing and are mainly restricted to gonadal tissues. Endo-siRNAs are found in both germline and somatic tissues. These ~21-nt RNAs are produced by a distinct Dicer, Dcr-2, and do not depend on Drosha/Pasha complexes. They predominantly bind to AGO2 and target both mobile elements and protein-coding genes. Surprisingly, a subset of endo-siRNAs strongly depend for their production on the dsRNA-binding protein Loquacious (Loqs), thought generally to be a partner for Dcr-1 and a co-factor for miRNA biogenesis. Endo-siRNA production depends on a specific Loqs isoform, Loqs-PD, which is distinct from the one, Loqs-PB, required for the production of microRNAs. Paralleling their roles in the biogenesis of distinct small RNA classes, Loqs-PD and Loqs-PB bind to different Dicer proteins, with Dcr-1/Loqs-PB complexes and Dcr-2/Loqs-PD complexes driving microRNA and endo-siRNA biogenesis, respectively. Small RNA profiling by high throughput sequencing Total RNA was isolated using Trizol reagent (Invitrogen) and size-fractionated by PAGE into 19-24nt. These were independently processed and sequenced using the Illumina GAII platform. In total, six libraries were analyzed.

2009-07-30 | E-GEOD-17171 | biostudies-arrayexpress

The exon junction complex controls transposable element activity by ensuring faithful splicing of the piwi transcript

Project description:The exon junction complex (EJC) is a highly conserved ribonucleoprotein complex which binds RNAs during splicing and remains associated with them following export to the cytoplasm. While the role of this complex in mRNA localization, translation and degradation has been well characterized, its mechanism of action in splicing a subset of Drosophila and human transcripts remains to be elucidated. Here, we describe a novel function for the EJC and its splicing subunit RnpS1 in preventing transposon accumulation in both Drosophila germline and surrounding somatic follicle cells. This function is mediated specifically through the control of piwi transcript splicing, where in the absence of RnpS1 the fourth intron of piwi is retained. Within this intron the polypyrimidine tract is disrupted by a transposon-adjacent A/T-rich sequence that confers dependence on RnpS1. Finally, we demonstrate that RnpS1-dependent removal of this intron requires splicing of the flanking introns, suggesting a model in which the EJC facilitates the splicing of weak introns following its initial deposition at adjacent exon junctions. These data demonstrate a novel role for the EJC in regulating piwi intron excision and provide a mechanism for its function during splicing. Small-RNA libraries from two control samples and four knockdowns in germline or somatic tissues of the Drosophila melanogaster ovary.

2014-08-14 | E-GEOD-59327 | biostudies-arrayexpress

The tudor domain protein Kumo is required to assemble the nuage and to generate germline piRNAs in Drosophila

Project description:We are submitting two small RNA libraries derived from ovarian tissue of mutant and heterozygous for the Kumo/Qin gene, required for the piRNA production in germline cells. In absence of Kumo/Qin, piRNA production is reduced and transposons are derepressed. Analysis of piRNA production in Kumo/Qin mutants

2011-12-31 | E-GEOD-34728 | biostudies-arrayexpress

DNA Topoisomerase 1a Promotes RNA-directed DNA Methylation and Histone Lysine 9 Dimethylation at Transposable Elements in Arabidopsis [RNA-Seq]

Project description:RNA-directed DNA methylation (RdDM) is a transcriptional silencing mechanism mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1a (TOP1a) was able to de-repress LUCL by reducing its DNA methylation and H3K9 dimethylation (H3K9me2) levels. Further studies with Arabidopsis top1a mutants showed that TOP1a promotes RdDM by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at transposable elements (TEs). 5 small RNA libraries were sequenced

2014-07-08 | E-GEOD-50719 | biostudies-arrayexpress

Small RNA SBS signatures identified from maize using Illumina's SBS technology

Project description:Most endogenous siRNAs in Arabidopsis are dependent on RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) for their biogenesis. Recent work has demonstrated that the maize MEDIATOR OF PARAMUTATION1 (mop1) gene is a predicted ortholog of the Arabidopsis RDR2 gene. The mop1 gene is required for establishment of paramutation and maintenance of transcriptional silencing of transposons and transgenes, suggesting the potential involvement of small RNAs. We analyzed small RNAs in wildtype maize and in the isogenic mop1-1 loss-of-function mutant using Illumina’s sequencing-by-synthesis (SBS) technology, which allowed us to characterize the complement of maize small RNAs to considerable depth. Similar to rdr2 in Arabidopsis, in mop1-1, the 24 nt (nucleotide) endogenous heterochromatic short-interfering siRNAs were dramatically reduced resulting in an enrichment of miRNAs and trans-acting siRNAs (ta-siRNAs). In contrast to the Arabidopsis rdr2 mutant, the mop1-1 plants retained a highly abundant heterochromatic ~22 nt class of small RNAs. These data suggest that maize, unlike Arabidopsis, has a second mechanism for heterochromatic siRNA production. The enrichment of miRNAs and loss of 24 nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced. This library was derived from maize variety K55 wild-type and mop1 mutant. Immature ears were harvested from plants grown outdoors in Tuscon, AZ. The material was harvested from plants 68 days after germination, with the floral tissue including young tassels 2-3 cm long. Total RNA was isolated using a standard TRIZOL-based method and the small RNA libraries were generated as described by Lu et al. (Methods 2007, 43:110), followed by sequencing with Illumina's SBS method. The adapter sequences were removed, and the abundance of each distinct small RNA was determined. Raw data are unavailable from Illumina

2008-09-30 | E-GEOD-12173 | biostudies-arrayexpress

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