A genome-wide map of conserved MicroRNA targets in C. elegans

Sabbi Lall, Dominic Grün, Azra Krek, Kevin Chen, Yi Lu Wang, Colin N. Dewey, Pranidhi Sood, Teresa Colombo, Nicolas Bray, Philip MacMenamin, Huey Ling Kao, Kristin C. Gunsalus, Lior Pachter, Fabio Piano, Nikolaus Rajewsky

Research output: Contribution to journalArticle

Abstract

Background: Metazoan miRNAs regulate protein-coding genes by binding the 3′ UTR of cognate mRNAs. Identifying targets for the 115 known C. elegans miRNAs is essential for understanding their function. Results: By using a new version of PicTar and sequence alignments of three nematodes, we predict that miRNAs regulate at least 10% of C. elegans genes through conserved interactions. We have developed a new experimental pipeline to assay 3′ UTR-mediated posttranscriptional gene regulation via an endogenous reporter expression system amenable to high-throughput cloning, demonstrating the utility of this system using one of the most intensely studied miRNAs, let-7. Our expression analyses uncover several new potential let-7 targets and suggest a new let-7 activity in head muscle and neurons. To explore genome-wide trends in miRNA function, we analyzed functional categories of predicted target genes, finding that one-third of C. elegans miRNAs target gene sets are enriched for specific functional annotations. We have also integrated miRNA target predictions with other functional genomic data from C. elegans. Conclusions: At least 10% of C. elegans genes are predicted miRNA targets, and a number of nematode miRNAs seem to regulate biological processes by targeting functionally related genes. We have also developed and successfully utilized an in vivo system for testing miRNA target predictions in likely endogenous expression domains. The thousands of genome-wide miRNA target predictions for nematodes, humans, and flies are available from the PicTar website and are linked to an accessible graphical network-browsing tool allowing exploration of miRNA target predictions in the context of various functional genomic data resources.

Original languageEnglish (US)
Pages (from-to)460-471
Number of pages12
JournalCurrent Biology
Volume16
Issue number5
DOIs
StatePublished - Mar 7 2006

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MicroRNAs
microRNA
Genes
Genome
genome
genes
prediction
Nematoda
3' untranslated regions
genomics
3' Untranslated Regions
browsing
sequence alignment
molecular cloning
Biological Phenomena
neurons
Sequence Alignment
Cloning
muscles
Gene expression

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Lall, S., Grün, D., Krek, A., Chen, K., Wang, Y. L., Dewey, C. N., ... Rajewsky, N. (2006). A genome-wide map of conserved MicroRNA targets in C. elegans. Current Biology, 16(5), 460-471. https://doi.org/10.1016/j.cub.2006.01.050

A genome-wide map of conserved MicroRNA targets in C. elegans. / Lall, Sabbi; Grün, Dominic; Krek, Azra; Chen, Kevin; Wang, Yi Lu; Dewey, Colin N.; Sood, Pranidhi; Colombo, Teresa; Bray, Nicolas; MacMenamin, Philip; Kao, Huey Ling; Gunsalus, Kristin C.; Pachter, Lior; Piano, Fabio; Rajewsky, Nikolaus.

In: Current Biology, Vol. 16, No. 5, 07.03.2006, p. 460-471.

Research output: Contribution to journalArticle

Lall, S, Grün, D, Krek, A, Chen, K, Wang, YL, Dewey, CN, Sood, P, Colombo, T, Bray, N, MacMenamin, P, Kao, HL, Gunsalus, KC, Pachter, L, Piano, F & Rajewsky, N 2006, 'A genome-wide map of conserved MicroRNA targets in C. elegans', Current Biology, vol. 16, no. 5, pp. 460-471. https://doi.org/10.1016/j.cub.2006.01.050
Lall S, Grün D, Krek A, Chen K, Wang YL, Dewey CN et al. A genome-wide map of conserved MicroRNA targets in C. elegans. Current Biology. 2006 Mar 7;16(5):460-471. https://doi.org/10.1016/j.cub.2006.01.050
Lall, Sabbi ; Grün, Dominic ; Krek, Azra ; Chen, Kevin ; Wang, Yi Lu ; Dewey, Colin N. ; Sood, Pranidhi ; Colombo, Teresa ; Bray, Nicolas ; MacMenamin, Philip ; Kao, Huey Ling ; Gunsalus, Kristin C. ; Pachter, Lior ; Piano, Fabio ; Rajewsky, Nikolaus. / A genome-wide map of conserved MicroRNA targets in C. elegans. In: Current Biology. 2006 ; Vol. 16, No. 5. pp. 460-471.
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