Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNAi knock down of miR-30a-3p in human HepG2 cells to identify the target transcripts against miR-30a-3p in vivo

ABSTRACT: Human miR-30a-3p was knocked-down in HepG2 using siRNA duplex against the miRNA precursor, and compared to control cells on GeneChip to identify the target transcripts against miR-30a-3p in vivo.

ORGANISM(S): Homo sapiens

SUBMITTER: Mika Nakamoto

PROVIDER: E-MEXP-456 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Physiological identification of human transcripts translationally regulated by a specific microRNA.

Nakamoto Mika M Jin Peng P O'Donnell William T WT Warren Stephen T ST

Human molecular genetics 20051020 24

One mechanism by which endogenous microRNAs (miRNAs) function is to suppress translation of target mRNAs. Computational identification of target mRNAs is hampered by the partial complementarity between miRNAs and their targets and the lack of in vivo approaches to identify targets. Here, we identify mRNAs that are regulated by specific endogenous miRNA by detecting shifts in individual mRNA abundance in polyribosome profiles following miRNA knockdown via siRNA. We have identified human genes who ...[more]

PMID: 16239240

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Project description:Background: The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear. Results: We report the first genome-wide identification and characterization of TR4 in vivo binding. Using chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), we identified TR4 binding sites in 4 different human cell types and found that the majority of target genes were shared among different cells. TR4 target genes are involved in fundamental biological processes such as RNA metabolism and protein translation. In addition, we found that a subset of TR4 target genes exerts cell-type specific functions. Analysis of the TR4 binding sites revealed that less than 30% of the peaks from any of the cell types contained the DR1 motif previously derived from in vitro studies, suggesting that TR4 may be recruited to the genome via interaction with other proteins. A bioinformatics analysis of the TR4 binding sites predicted a cis regulatory module involving TR4 and ETS transcription factors. To test this prediction, we performed ChIP-seq for the ETS factor ELK4 and found that 30% of TR4 binding sites were also bound by ELK4. Motif analysis of the sites bound by both factors revealed a lack of the DR1 element, suggesting that TR4 binding at a subset of sites is facilitated through the ETS transcription factor ELK4. Further studies will be required to investigate the functional interdependence of these two factors. Conclusions: Our data suggest that TR4 plays a pivotal role in fundamental biological processes across different cell types. In addition, the identification of cell type specific TR4 binding sites enables future studies of the pathways underlying TR4 action and its possible role in metabolic diseases. This is one part of the study that involved the examination of HepG2 gene expression. Biological triplicate Illumina Sentrex bead arrays.

Dataset Information

RNAi knock down of miR-30a-3p in human HepG2 cells to identify the target transcripts against miR-30a-3p in vivo

Publications

Physiological identification of human transcripts translationally regulated by a specific microRNA.

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