miRNA Targeting: Growing beyond the Seed

Lee, 1993, The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14, Cell, 75, 843, 10.1016/0092-8674(93)90529-Y Wightman, 1993, Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans, Cell, 75, 855, 10.1016/0092-8674(93)90530-4 Kozomara, 2018, miRBase: from microRNA sequences to function, Nucleic Acids Res. Bartel, 2018, Metazoan microRNAs, Cell, 173, 20, 10.1016/j.cell.2018.03.006 Liu, 2018, Small but powerful: function of microRNAs in plant development, Plant Cell Rep., 37, 515, 10.1007/s00299-017-2246-5 Paul, 2018, Interplay between miRNAs and human diseases, J. Cell. Physiol., 233, 2007, 10.1002/jcp.25854 Gebert, 2018, Regulation of microRNA function in animals, Nat. Rev. Mol. Cell Biol., 20, 21, 10.1038/s41580-018-0045-7 Elkayam, 2012, The structure of human argonaute-2 in complex with miR-20a, Cell, 150, 100, 10.1016/j.cell.2012.05.017 Nakanishi, 2012, Structure of yeast Argonaute with guide RNA, Nature, 486, 368, 10.1038/nature11211 Schirle, 2012, The crystal structure of human Argonaute2, Science, 336, 1037, 10.1126/science.1221551 Chandradoss, 2015, A dynamic search process underlies microRNA targeting, Cell, 162, 96, 10.1016/j.cell.2015.06.032 Jo, 2015, Human argonaute 2 has diverse reaction pathways on target RNAs, Mol. Cell, 59, 117, 10.1016/j.molcel.2015.04.027 Salomon, 2015, Single-molecule imaging reveals that Argonaute reshapes the binding properties of its nucleic acid guides, Cell, 162, 84, 10.1016/j.cell.2015.06.029 Schirle, 2014, Structural basis for microRNA targeting, Science, 346, 608, 10.1126/science.1258040 Yan, 2018, The sequence features that define efficient and specific hAGO2-dependent miRNA silencing guides, Nucleic Acids Res., 46, 8181, 10.1093/nar/gky546 Helwak, 2013, Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding, Cell, 153, 654, 10.1016/j.cell.2013.03.043 Grosswendt, 2014, Unambiguous identification of miRNA: target site interactions by different types of ligation reactions, Mol. Cell, 54, 1042, 10.1016/j.molcel.2014.03.049 Moore, 2015, MiRNA-target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity, Nat. Commun., 6, 1, 10.1038/ncomms9864 Broughton, 2016, Pairing beyond the seed supports microRNA targeting specificity, Mol. Cell, 64, 320, 10.1016/j.molcel.2016.09.004 Reinhart, 2000, The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans, Nature, 403, 901, 10.1038/35002607 Slack, 2000, The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor, Molecular, 5, 659 Brancati, 2018, An interplay of miRNA abundance and target site architecture determines miRNA activity and specificity, Nucleic Acids Res., 46, 3259, 10.1093/nar/gky201 Chi, 2009, Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps, Nature, 460, 479, 10.1038/nature08170 Hafner, 2010, Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP, Cell, 141, 129, 10.1016/j.cell.2010.03.009 Zisoulis, 2010, Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans, Nat. Struct. Mol. Biol., 17, 173, 10.1038/nsmb.1745 Xue, 2013, Direct conversion of fibroblasts to neurons by reprogramming PTB-regulated microRNA circuits, Cell, 152, 82, 10.1016/j.cell.2012.11.045 Duursma, 2008, miR-148 targets human DNMT3b protein coding region, RNA, 14, 872, 10.1261/rna.972008 Tay, 2008, MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation, Nature, 455, 1124, 10.1038/nature07299 Hausser, 2013, Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation, Genome Res., 23, 604, 10.1101/gr.139758.112 Gu, 2009, Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs, Nat. Struct. Mol. Biol., 16, 144, 10.1038/nsmb.1552 Zhang, 2018, A novel class of microRNA-recognition elements that function only within open reading frames, Nat. Struct. Mol. Biol., 25, 1019, 10.1038/s41594-018-0136-3 Cai, 2015, Oncogenic miR-17/20a forms a positive feed-forward loop with the p53 kinase DAPK3 to promote tumorigenesis, J. Biol. Chem., 290, 19967, 10.1074/jbc.M115.661504 Ameres, 2010, Target RNA-directed trimming and tailing of small silencing RNAs, Science, 328, 1534, 10.1126/science.1187058 Cazalla, 2010, Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA, Science, 328, 1563, 10.1126/science.1187197 Fuchs Wightman, 2018, Target RNAs strike back on microRNAs, Front. Genet., 9, 435, 10.3389/fgene.2018.00435 Baccarini, 2011, Kinetic analysis reveals the fate of a microRNA following target regulation in mammalian cells, Curr. Biol., 21, 369, 10.1016/j.cub.2011.01.067 Libri, 2012, Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target, Proc. Natl. Acad. Sci. U. S. A., 109, 279, 10.1073/pnas.1114204109 Marcinowski, 2012, Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo, PLoS Pathog., 8, 10.1371/journal.ppat.1002510 Lee, 2013, Selective degradation of host microRNAs by an intergenic HCMV noncoding RNA accelerates virus production, Cell Host Microbe, 13, 678, 10.1016/j.chom.2013.05.007 Bitetti, 2018, MicroRNA degradation by a conserved target RNA regulates animal behavior, Nat. Struct. Mol. Biol., 25, 244, 10.1038/s41594-018-0032-x Kleaveland, 2018, A network of noncoding regulatory RNAs acts in the mammalian brain, Cell, 174, 10.1016/j.cell.2018.05.022 Ghini, 2018, Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation, Nat. Commun., 9, 10.1038/s41467-018-05182-9 Ulitsky, 2011, Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution, Cell, 147, 1537, 10.1016/j.cell.2011.11.055