Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNAi knock down of mSin3a-b and SBTB4 in human colon carcinoma cell line HCT116

ABSTRACT: Efffects of silencing ZBTB4, mSin3a/mSin3b on HCT 116 human colon carcinoma cell lines for 48 hours

ORGANISM(S): Homo sapiens

SUBMITTER: Dave Elzi

PROVIDER: E-MEXP-1509 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Zbtb4 represses transcription of P21CIP1 and controls the cellular response to p53 activation.

Weber Axel A Marquardt Judith J Elzi David D Forster Nicole N Starke Sven S Glaum Andre A Yamada Daisuke D Defossez Pierre-Antoine PA Delrow Jeffrey J Eisenman Robert N RN Christiansen Holger H Eilers Martin M

The EMBO journal 20080501 11

In response to stimuli that activate p53, cells can undergo either apoptosis or cell cycle arrest, depending on the precise pattern of p53 target genes that is activated. We show here that Zbtb4, a transcriptional repressor protein, associates with the Sin3/histone deacetylase co-repressor and represses expression of P21CIP1 as part of a heterodimeric complex with Miz1. In vivo, expression of ZBTB4 is downregulated in advanced stages of multiple human tumours. In cell culture, depletion of ZBTB4 ...[more]

PMID: 18451802

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Project description:Modification of microRNA sequences by the 3' addition of nucleotides to generate so-called “isomiRs” adds to the complexity of miRNA function, with recent reports showing that 3' modifications can influence miRNA stability and efficiency of target repression. Here we show that the 3' modification of miRNAs is a physiological and common post-transcriptional event that shows selectivity for specific miRNAs and is observed across species ranging from C. elegans to human. The modifications result predominantly from adenylation and uridylation, and are seen across tissue types, disease states, and developmental stages. To quantitatively profile 3' nucleotide additions, we developed and validated a novel assay based on NanoString Technologies' nCounter platform. For certain miRNAs, the frequency of modification was altered by processes such as cell differentiation, indicating that 3' modification is a biologically regulated process. To investigate the mechanism of 3' nucleotide additions, we used RNA interference to screen a panel of eight candidate miRNA nucleotidyl transferases for 3' miRNA modification activity in human cells. Multiple enzymes, including PAPD1, PAPD4, PAPD5, ZCCHC6, ZCCHC11, and TUT1, were found to govern 3' nucleotide addition to miRNAs in a miRNA-specific manner. Three of these enzymes–PAPD1, ZCCHC6 and TUT1–have not previously been known to modify miRNAs. Collectively, our results indicate that 3' modification observed in next generation small RNA sequencing data is a biologically relevant process, and identify enzymatic mechanisms that may lead to new approaches for modulating miRNA activity in vivo. Total RNA was isolated from HCT-116 cells 48 hours post transfection with siRNAs targeting a panel of nucleotidyl transferases, and profiled with a version of the NanoString nCounter miRNA expression assay adapted to discriminate miRNA 3' variants. Four biological replicates of cells treated with the negative control siRNA directed against Cyclophilin B were profiled. Two biological replicates of cells treated individually with siRNAs targeting each of eight nucleotidyl transferases were profiled.

Dataset Information

RNAi knock down of mSin3a-b and SBTB4 in human colon carcinoma cell line HCT116

Publications

Zbtb4 represses transcription of P21CIP1 and controls the cellular response to p53 activation.

Similar Datasets

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