Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells and small RNA profiling in Drosophila wild-type and nbr[f02257] mutants
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Bonini Nancy
PROVIDER: E-GEOD-32564 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:nbr/CG9247 gene function regulates the length of the 3'end of miRNAs. Such 3'end heterogeneity of miRNAs may impact miRNA target gene silencing. To address this, we performed microarray analysis for genes altered upon nbr knockdown in Drosophila DL1 cells. This approach revealed a subset of genes upregulated upon nbr knockdown. Five independent replicates of DL1 cells treated with control (dsRNA to renilla) or nbr (dsRNA RNA to nbr/CG9247) were collected 5 days after dsRNA bathing. Total RNA from from each replicate was extracted using TRIzol reagent (Invitrogen). A portion of total RNA for each replicate was used to confirm the effect of nbr knockdown on one of the nbr-dependent miRNAs, miR-34, by small RNA northern.
2011-11-01 | E-GEOD-32683 | biostudies-arrayexpress
Project description:nbr/CG9247 gene regulates 3'end heterogeneity of a subset of miRNAs. It is not clear how broad this effect is on small RNA population. To address this, we compared small RNA population in wild-type and tmr[f02257] mutants. This approach identified more miRNAs whose 3'end heterogeneity was affected in nbr[f02257] mutants. 2-3 day old control (w homogeneous strain Bloomington stock center 5905) and nbr[f02257] null mutant flies were collected. nbr[f02257] line was in the homogenous (Bloomington stock center stock 5905) background through a minimum of 5 backcrosses. Total RNA from whole flies was extracted using TRIzol reagent (Invitrogen). 40ug of total RNA from each genotype was used for small RNA library preparation with Small RNA Sample Prep kit (v1.5) (Illumina).
2011-11-01 | E-GEOD-32684 | biostudies-arrayexpress
Project description:nbr/CG9247 gene function regulates the length of the 3'end of miRNAs. Such 3'end heterogeneity of miRNAs may impact miRNA target gene silencing. To address this, we performed microarray analysis for genes altered upon nbr knockdown in Drosophila DL1 cells. This approach revealed a subset of genes upregulated upon nbr knockdown.
2011-11-01 | GSE32683 | GEO
Project description:nbr/CG9247 gene regulates the length of a subset of miRNAs. It is not clear whether Nbr affects the length of other classes of small RNAs, such as piRNAs and endo-siRNAs. To address this, we compared small RNA population in wild-type, Df(2L)BSC312/+, nbr null (nbrf02257/Df(2L)BSC312), (nbr null; pCaSper-nbr (WT)), and (nbr null; pCaSper-nbr (D435A,E437A)). This approach revealed that, in addition to miRNAs, piRNAs and endo-siRNAs were also affected in their length in nbr null and nbr null; pCaSper-nbr (D435A,E437A). 4-7d ovaries were dissected in PBS, and 40ug total RNA was prepared from wild-type, Df(2L)BSC312/+, nbr null (nbrf02257/Df(2L)BSC312), (nbr null; pCaSper-nbr (WT)), and (nbr null; pCaSper-nbr (D435A,E437A)), using Trizol Reagent (#15596-018, Life Technologies, Carlsbad, CA) following the manufacturer's protocol. The small RNAs between ~16 to ~29 nt in size were purified from 15% TBE-urea gel (#EC6885BOX, Life Technologies, Carlsbad, CA). Small RNA libraries were prepared using Illumina's TruSeq small RNA sample preparation kit (#RS-200-0012, Illumina, Inc. San Diego, CA), following the manufacturer's protocol The libraries were sequenced on HiSeq2000 platform (Illumina).
2015-02-02 | E-GEOD-50055 | biostudies-arrayexpress
Project description:Spinocerebellar ataxia type 3 (SCA3) is one of the polyglutamine (polyQ) diseases, which are caused by a CAG repeat expansion within the coding region of the associated genes. The CAG repeat specifies glutamine, and the expanded polyQ domain with mutation confers dominant toxicity on the protein. Traditionally, studies have focused on protein toxicity in polyQ disease mechanisms. Recent findings, however, demonstrate that the CAG repeat RNA, which encodes the toxic polyQ protein, also contributes to the disease in Drosophila. To provide insight into the nature of the RNA toxicity, we extracted brain-enriched RNA from flies expressing a toxic CAG repeat mRNA (CAG100) and a non-toxic interrupted CAA/G mRNA repeat (CAA/G105) for microarray analysis. This approach identified a set of genes that are differentially expressed specifically in CAG100 flies. Four independent replicates of flies expressing CAG0, CAG100, or CAA/G105 by elav-GAL4 were collected at 3 days. The transgenes are DsRed with either (CAG0) no CAG repeat in the 3'UTR, (CAG100) a CAG repeat of 100 CAGs in the 3'UTR, or (CAA/G105) an interrupted CAA CAG repeat in the 3'UTR (ref: Li et al., Nature 453:1107) The transgenes were adjusted to match in mRNA expression such that CAG0 flies had one copy of the transgene, CAG100 flies had 5 copies, and CAA/G105 had two copies. Fly brain tissue (about 20 brains per sample, dissected from head capsule, eyes, lamina and outer medulla removed) was dissected in cold phosphate buffered saline (PBS) and stored in Trizol reagent (Invitrogen Corporation, Carlsbad, CA) at -80Ë?C. Total brain RNA was extracted and purified using TRIzol reagent (Invitrogen) and the RNeasy Mini system (Qiagen), and treated with RNase-free DNase I (Qiagen). To define genes whose expression is altered in response to a toxic CAG repeat RNA, we compared CAG100 flies with age-matched flies expressing CAG0. To exclude transcriptional changes in response to a non-toxic trinucleotide repeat, a second gene list was generated by comparing CAA/G105 flies with age-matched CAG0 flies.
2011-11-22 | E-GEOD-31875 | biostudies-arrayexpress
Project description:nbr/CG9247 gene regulates the length of a subset of miRNAs. It is not clear whether Nbr affects the length of other classes of small RNAs, such as piRNAs and endo-siRNAs. To address this, we compared small RNA population in wild-type, Df(2L)BSC312/+, nbr null (nbrf02257/Df(2L)BSC312), (nbr null; pCaSper-nbr (WT)), and (nbr null; pCaSper-nbr (D435A,E437A)). This approach revealed that, in addition to miRNAs, piRNAs and endo-siRNAs were also affected in their length in nbr null and nbr null; pCaSper-nbr (D435A,E437A).
2015-02-02 | GSE50055 | GEO
Project description:nbr/CG9247 gene regulates 3'end heterogeneity of a subset of miRNAs. It is not clear how broad this effect is on small RNA population. To address this, we compared small RNA population in wild-type and tmr[f02257] mutants. This approach identified more miRNAs whose 3'end heterogeneity was affected in nbr[f02257] mutants.
2011-11-01 | GSE32684 | GEO
Project description:RNAseq transcriptional profiling of Drosophila brains from wildtype, and period loss-of-function animals with time points taken over two days. 2 days of brain collection, time points at ZT0, ZT6, ZT12, and ZT18; wildtype and per0 flies. 10-12 brains per time point.
2012-01-01 | E-GEOD-29972 | biostudies-arrayexpress
Project description:Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells
| PRJNA154375 | ENA
Project description:MicroRNAs (miRNAs) are endogenous noncoding small RNAs with important roles in many biological pathways; their generation and activity are under precise regulation. Emerging evidence suggests that miRNA pathways are precisely modulated with controls at the level of transcription, processing, and stability, with miRNA deregulation linked with diseases and neurodegenerative disorders. In the Drosophila miRNA biogenesis pathway, long primary miRNA transcripts undergo sequential cleavage to release the embedded miRNAs. Mature miRNAs are then loaded into Argonaute1 (Ago1) within the RNA-induced silencing complex (RISC). Intriguingly, we found that Drosophila miR-34 displays multiple isoforms that differ at the 3M-bM-^@M-2 end, suggesting a novel biogenesis mechanism involving 3M-bM-^@M-2 end processing. To define the cellular factors responsible, we performed an RNA interference (RNAi) screen and identified a putative 3M-bM-^@M-2M-bM-^FM-^R5M-bM-^@M-2 exoribonuclease CG9247/nibbler essential for the generation of the smaller isoforms of miR-34. Nibbler (Nbr) interacts with Ago1 and processes miR-34 within RISC. Deep sequencing analysis revealed a larger set of multi-isoform miRNAs that are controlled by nibbler. These findings suggest that Nbr-mediated 3M-bM-^@M-2 end processing represents a critical step in miRNA maturation that impacts miRNA diversity. Total RNA was isolated using mirVana (Ambion) and size-fractionated by PAGE into 18-30nt. These were independently processed and sequenced using the Illumina GAII platform. In total, four libraries were analyzed.
2011-11-17 | E-GEOD-31689 | biostudies-arrayexpress