Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Poly(A) specific ribonuclease (PARN)-dependent trimming of H ACA box RNAs

ABSTRACT: Microarray comprising probe sets for miRNAs and other small RNAs was used to determine which and how many small RNAs are potential substrates of poly(A) specific ribonuclease (PARN) in U2OS cells . Hybridization probes were generated by oligo(dT) priming.

ORGANISM(S): Homo sapiens

SUBMITTER: Heike Berndt

PROVIDER: E-MEXP-3344 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming.

Berndt Heike H Harnisch Christiane C Rammelt Christiane C Stöhr Nadine N Zirkel Anne A Dohm Juliane C JC Himmelbauer Heinz H Tavanez Joao-Paulo JP Hüttelmaier Stefan S Wahle Elmar E

RNA (New York, N.Y.) 20120322 5

Small nucleolar and small Cajal body RNAs (snoRNAs and scaRNAs) of the H/ACA box and C/D box type are generated by exonucleolytic shortening of longer precursors. Removal of the last few nucleotides at the 3' end is known to be a distinct step. We report that, in human cells, knock-down of the poly(A) specific ribonuclease (PARN), previously implicated only in mRNA metabolism, causes the accumulation of oligoadenylated processing intermediates of H/ACA box but not C/D box RNAs. In agreement with ...[more]

PMID: 22442037

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Project description:We sought to determine the effect of TbPARN-1 overexpression on global mRNA steady-state levels in T. brucei. The mRNA expression profile of tet-induced TbPARN-1 OvEx procyclic cells was compared to the mRNA profile of control cells (expressing tet-induced TAP tag alone) by microarray analysis. Since overexpression of TbPARN-1 showed increased deadenylation activity in cytoplasmic extracts, overexpressing PARN-1 in vivo should result in more rapid deadenylation and decay of mRNAs targeted by PARN-1. Thus, mRNAs with lower steady state levels in PARN-1 OvEx cells can be considered likely targets for PARN-1-dependent deadenylation. Three different clones of the PARN-1 OvEx and Control cell lines were used for analysis. Each experiment was run in duplicate, with the dye-labeling reversed between duplicates. The T. brucei version 3 microarray chip (PFGRC) was used for this experiment. Each gene on the microarray was represented in duplicate, so for each experiment, mRNA levels were obtained from both points and averaged. As a control between arrays, we used a control probe set obtained from PFGRC. "The probe set consists of Cy3 and Cy5 end labeled 40-mer probes that are complementary to a set of 500 Arabidopsis thaliana 70-mer targets on PFGRC DNA microarrays. The UMSS is supplied as a ready to use mix of the Cy3 and Cy5 labeled oligonucleotides. A small aliquot is spiked into Cy-dye labeled nucleic acid samples just prior to hybridization on PFGRC microarrays. The UMSS produces a set of reference fluorescent signal intensities and ratios that are generated independent of the user-specific experimental samples. Since PFGRC intentionally targeted a heavy representation of Cy3 and Cy5 signals in the mid-range of detection, the Cy3 and Cy5 signal intensities and ratios generated by the UMSS should be highly reproducible. These signals serve as a reference point to judge the success of microarray experiments, and troubleshoot potential problems."

Dataset Information

Poly(A) specific ribonuclease (PARN)-dependent trimming of H ACA box RNAs

Publications

Maturation of mammalian H/ACA box snoRNAs: PAPD5-dependent adenylation and PARN-dependent trimming.

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