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Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells

ABSTRACT: 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.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Bonini Nancy

PROVIDER: E-GEOD-32683 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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

Project description:This SuperSeries is composed of the following subset Series: GSE32683: Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells GSE32684: Small RNA profiling in Drosophila wild-type and nbr[f02257] mutants Refer to individual Series

2011-11-01 | E-GEOD-32564 | biostudies-arrayexpress

Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells

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

Drosophila melanogaster

Project description:Genes affected upon dsRNA knockdown treatment for nbr/CG9247 in Drosophila DL1 cells

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Effect of Nbr on the length of piRNAs and endo-siRNAs in Drosophila

2015-02-02 | GSE50055 | GEO

Small RNA profiling in Drosophila wild-type and nbr[f02257] mutants

2011-11-01 | GSE32684 | GEO

Project description: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

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Effect of Nbr on the length of piRNAs and endo-siRNAs in Drosophila

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

Small RNA profiling in Drosophila wild-type and nbr[f02257] mutants

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

The Exoribonuclease Nibbler Controls 3' End Processing of MicroRNAs in Drosophila

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 3′ end, suggesting a novel biogenesis mechanism involving 3′ end processing. To define the cellular factors responsible, we performed an RNA interference (RNAi) screen and identified a putative 3′→5′ 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 3′ end processing represents a critical step in miRNA maturation that impacts miRNA diversity.

2011-11-17 | GSE31689 | GEO

The Exoribonuclease Nibbler Controls 3' End Processing of MicroRNAs in Drosophila

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

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