microRNAs and siRNAs Determinants of targeting by endogenous and exogenous

Vertebrate mRNAs are frequently targeted for post-transcriptional repression by microRNAs (miRNAs) through mechanisms involving pairing of 39 UTR seed matches to bases at the 59 end of miRNAs. Through analysis of expression array data following miRNA or siRNA overexpression or inhibition, we found that mRNA fold change increases multiplicatively (i.e., log-additively) with seed match count and that a single 8 mer seed match mediates down-regulation comparable to two 7 mer seed matches. We identified several targeting determinants that enhance seed match-associated mRNA repression, including the presence of adenosine opposite miRNA base 1 and of adenosine or uridine opposite miRNA base 9, independent of complementarity to the siRNA/miRNA. Increased sequence conservation in the ;50 bases 59 and 39 of the seed match and increased AU content 39 of the seed match were each independently associated with increased mRNA down-regulation. All of these determinants are enriched in the vicinity of conserved miRNA seed matches, supporting their activity in endogenous miRNA targeting. Together, our results enable improved siRNA off-target prediction, allow integrated ranking of conserved and nonconserved miRNA targets, and show that targeting by endogenous and exogenous miRNAs/siRNAs involves similar or identical determinants.

[1]  Donald C. Chang,et al.  The MicroRNA. , 2018, Methods in molecular biology.

[2]  Uwe Ohler,et al.  Spatial preferences of microRNA targets in 3' untranslated regions , 2007, BMC Genomics.

[3]  Anton J. Enright,et al.  Requirement of bic/microRNA-155 for Normal Immune Function , 2007, Science.

[4]  Ola Snøve,et al.  Distance constraints between microRNA target sites dictate efficacy and cooperativity , 2007, Nucleic acids research.

[5]  J. Steitz,et al.  AU-Rich-Element-Mediated Upregulation of Translation by FXR1 and Argonaute 2 , 2007, Cell.

[6]  Zissimos Mourelatos,et al.  An mRNA m 7 G Cap Binding-like Motif withinHumanAgo2RepressesTranslation , 2007 .

[7]  Mihaela Zavolan,et al.  Inference of miRNA targets using evolutionary conservation and pathway analysis , 2007, BMC Bioinformatics.

[8]  Mihaela Zavolan,et al.  Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells , 2006, Nucleic acids research.

[9]  J. Schelter,et al.  Designing siRNA That Distinguish between Genes That Differ by a Single Nucleotide , 2006, PLoS genetics.

[10]  L. Lim,et al.  Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. , 2006, RNA.

[11]  W. Filipowicz,et al.  Relief of microRNA-Mediated Translational Repression in Human Cells Subjected to Stress , 2006, Cell.

[12]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[13]  Anton J. Enright,et al.  Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs , 2006, Science.

[14]  Ligang Wu,et al.  MicroRNAs direct rapid deadenylation of mRNA. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[15]  G. Hannon,et al.  Control of translation and mRNA degradation by miRNAs and siRNAs. , 2006, Genes & development.

[16]  L. Paillard,et al.  AU-rich elements and associated factors: are there unifying principles? , 2006, Nucleic acids research.

[17]  R. Russell,et al.  Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution , 2005, Cell.

[18]  Isabelle Behm-Ansmant,et al.  A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. , 2005, RNA.

[19]  W. Filipowicz,et al.  Inhibition of Translational Initiation by Let-7 MicroRNA in Human Cells , 2005, Science.

[20]  Phillip D. Zamore,et al.  Ribo-gnome: The Big World of Small RNAs , 2005, Science.

[21]  A. Pasquinelli,et al.  Regulation by let-7 and lin-4 miRNAs Results in Target mRNA Degradation , 2005, Cell.

[22]  Michael T. McManus,et al.  The RNaseIII enzyme Dicer is required for morphogenesis but not patterning of the vertebrate limb. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  K. Rajewsky,et al.  Aberrant T cell differentiation in the absence of Dicer , 2005, The Journal of experimental medicine.

[24]  W. Filipowicz,et al.  Post-transcriptional gene silencing by siRNAs and miRNAs. , 2005, Current opinion in structural biology.

[25]  Kristin C. Gunsalus,et al.  microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets , 2005, PLoS Comput. Biol..

[26]  V. Kim.  MicroRNA biogenesis: coordinated cropping and dicing , 2005, Nature Reviews Molecular Cell Biology.

[27]  Thomas Tuschl,et al.  Structural basis for 5′-end-specific recognition of guide RNA by the A. fulgidus Piwi protein , 2005, Nature.

[28]  D. Barford,et al.  Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex , 2005, Nature.

[29]  Y. Li,et al.  Incorporating structure to predict microRNA targets. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[30]  J. Castle,et al.  Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs , 2005, Nature.

[31]  R. Russell,et al.  Principles of MicroRNA–Target Recognition , 2005, PLoS biology.

[32]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[33]  Hans Lassmann,et al.  The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution , 2005 .

[34]  Anton J. Enright,et al.  Human MicroRNA Targets , 2004, PLoS biology.

[35]  C. Perou,et al.  A custom microarray platform for analysis of microRNA gene expression , 2004, Nature Methods.

[36]  P. Green,et al.  Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[37]  V. Ambros.  The functions of animal microRNAs , 2004, Nature.

[38]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[39]  D. Bartel,et al.  MicroRNA-Directed Cleavage of HOXB8 mRNA , 2004, Science.

[40]  John G Doench,et al.  Specificity of microRNA target selection in translational repression. , 2004, Genes & development.

[41]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[42]  Eun-Young Choi,et al.  The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. , 2004, Genes & development.

[43]  C. Burge,et al.  Prediction of Mammalian MicroRNA Targets , 2003, Cell.

[44]  Edwin Cuppen,et al.  The microRNA-producing enzyme Dicer1 is essential for zebrafish development , 2003, Nature Genetics.

[45]  S. Elledge,et al.  Dicer is essential for mouse development , 2003, Nature Genetics.

[46]  B. Cullen,et al.  MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  B. Li,et al.  Expression profiling reveals off-target gene regulation by RNAi , 2003, Nature Biotechnology.

[48]  Phillip A Sharp,et al.  siRNAs can function as miRNAs , 2003 .

[49]  C. Llave,et al.  Cleavage of Scarecrow-like mRNA Targets Directed by a Class of Arabidopsis miRNA , 2002, Science.

[50]  G. Hutvagner,et al.  A microRNA in a Multiple-Turnover RNAi Enzyme Complex , 2002, Science.

[51]  Eric J Wagner,et al.  Both natural and designed micro RNAs can inhibit the expression of cognate mRNAs when expressed in human cells. , 2002, Molecular cell.

[52]  Andrew P McMahon,et al.  Efficient recombination in diverse tissues by a tamoxifen-inducible form of Cre: a tool for temporally regulated gene activation/inactivation in the mouse. , 2002, Developmental biology.

[53]  Philippe Soriano.  Generalized lacZ expression with the ROSA26 Cre reporter strain , 1999, Nature Genetics.

[54]  A. McMahon,et al.  Modification of gene activity in mouse embryos in utero by a tamoxifen-inducible form of Cre recombinase , 1998, Current Biology.

[55]  G. Ruvkun,et al.  Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans , 1993, Cell.

[56]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[57]  C. Stewart,et al.  Derivation of embryonic stem cell lines. , 1993, Methods in enzymology.