Human MicroRNA Targets
Bino John1 , Anton J. Enright1 2 , Alexei Aravin3 , Thomas Tuschl3 , Chris Sander1 , Debora S. Marks4*
1 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America, 2 Wellcome Trust Sanger Institute, Cambridge, United Kingdom, 3 Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, United States of America, 4 Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
MicroRNAs (miRNAs) interact with target mRNAs at specific sites to induce cleavage of the message or inhibit translation. The specific function of most mammalian miRNAs is unknown. We have predicted target sites on the 3¢ untranslated regions of human gene transcripts for all currently known 218 mammalian miRNAs to facilitate focused experiments. We report about 2,000 human genes with miRNA target sites conserved in mammals and about 250 human genes conserved as targets between mammals and fish. The prediction algorithm optimizes sequence complementarity using position-specific rules and relies on strict requirements of interspecies conservation. Experimental support for the validity of the method comes from known targets and from strong enrichment of predicted targets in mRNAs associated with the fragile X mental retardation protein in mammals. This is consistent with the hypothesis that miRNAs act as sequence-specific adaptors in the interaction of ribonuclear particles with translationally regulated messages. Overrepresented groups of targets include mRNAs coding for transcription factors, components of the miRNA machinery, and other proteins involved in translational regulation, as well as components of the ubiquitin machinery, representing novel feedback loops in gene regulation. Detailed information about target genes, target processes, and open-source software for target prediction (miRanda) is available at microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes.
Received May 18, 2004; Accepted August 20, 2004; Published October 5, 2004
DOI: 10.1371/journal.pbio.0020363
Copyright: © 2004 John et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abbreviations: AGO, Argonaute; APP, amyloid precursor protein; CPE, cytoplasmic polyadenylation element; CPEB, cytoplasmic polyadenylation binding protein; FMRP, fragile X mental retardation protein; GO, Gene Ontology; miRNA, microRNA; nt, nucleotide; PSD95, postsynaptic density protein 95; RISC, RNA-induced silencing complex; RNP, ribonuclear particle; siRNA, small interfering RNA; UTR, untranslated region
Academic Editor: James C. Carrington, Oregon State University
*To whom correspondence should be addressed. E-mail: mirnatargets@cbio.mskcc.org
Citation: John B, Enright AJ, Aravin A, Tuschl T, Sander C, et al. (2004) Human MicroRNA Targets. PLoS Biol 2(11): e363.
plosbiology.org
...Principles of Regulation by miRNAs
Although the predicted targets are subject to error (see estimate of false positives) and the prediction rules in need of improvement, several general principles of gene regulation by miRNAs are emerging. (1) Except in cases where a highly complementary match causes cleavage of the target message, miRNAs appear to act cooperatively, requiring two or more target sites per message, for either one or several different miRNAs. (2) Most miRNAs are involved in the translational regulation of several target genes, which in some cases are grouped into functional categories. (3) miRNAs carried in the context of RNPs appear to be sequence-specific adaptors guiding RNPs to particular target sequences. miRNA regulation of cellular messages may therefore range from a switch-like behavior (e.g., cleavage of mRNA message) to a subtle modulation of protein dosage in a cell through low-level translational repression (Bartel and Chen 2004).
These aspects of miRNA regulation complicate the design of experiments aiming at testing target predictions, or, more generally, at discovering biologically meaningful targets. Straightforward experiments that test one target site for one miRNA on one UTR will not be able to disentangle the effects of multiplicity or cooperativity. Tests for multiple sites on one UTR for one miRNA capture aspects of cooperativity (Doench and Sharp 2004), but still do not capture signal integration by diverse miRNAs. The most complicated situation is one in which multiple miRNAs affect multiple genes in combinatorial fashion, with fine-tuning depending on the state of the cell. We look forward to the results of ingenious experiments designed to deal with the complexity of miRNA regulation... |
