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Quantitative and Automated High-throughput Genome-wide RNAi Screens in C. elegans
Published on: February 27, 2012
A genome-wide map of conserved microRNA targets in C. elegans
Sabbi Lall1, Dominic Grün, Azra Krek
1Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA.
Current Biology : CB
|February 7, 2006
Summary
MicroRNAs (miRNAs) regulate gene expression in C. elegans, with predictions suggesting they target at least 10% of genes. New methods identify conserved miRNA targets and their roles in biological processes.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Metazoan microRNAs (miRNAs) post-transcriptionally regulate gene expression by binding to the 3' untranslated region (UTR) of messenger RNAs (mRNAs).
- Understanding the function of the 115 known C. elegans miRNAs requires accurate identification of their target genes.
Purpose of the Study:
- To predict conserved miRNA targets in C. elegans using an updated PicTar algorithm and cross-species sequence alignments.
- To develop and validate an experimental pipeline for assaying miRNA-mediated 3' UTR regulation in an endogenous reporter system.
- To explore genome-wide trends in miRNA target gene functions and integrate predictions with other functional genomic data.
Main Methods:
- Utilized a new version of the PicTar algorithm combined with sequence alignments of three nematode species to predict miRNA targets.
- Developed a high-throughput experimental pipeline using an endogenous reporter expression system to validate 3' UTR-mediated gene regulation.
- Analyzed functional categories of predicted miRNA targets and integrated predictions with existing C. elegans functional genomic data.
Main Results:
- Predicted that miRNAs regulate at least 10% of C. elegans genes through conserved interactions.
- Demonstrated the utility of the new experimental pipeline using the let-7 miRNA, identifying new targets and potential roles in head muscle and neurons.
- Found that target gene sets for one-third of C. elegans miRNAs are enriched for specific functional annotations.
Conclusions:
- At least 10% of C. elegans genes are predicted to be miRNA targets, with evidence suggesting miRNAs regulate biological processes by targeting functionally related genes.
- Successfully developed and applied an in vivo system for testing miRNA target predictions within endogenous expression domains.
- Genome-wide miRNA target predictions for nematodes, humans, and flies are publicly available via the PicTar website with a network-browsing tool for exploring functional genomic contexts.
