References
- Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136, 215-233 https://doi.org/10.1016/j.cell.2009.01.002
- Grimson A, Farh KK-H, Johnston WK, Garrett-Engele P, Lim LP and Bartel DP (2007) MicroRNA Targeting Specificity in Mammals: Determinants beyond Seed Pairing. Molecular Cell 27, 91-105 https://doi.org/10.1016/j.molcel.2007.06.017
- Baek D, Villen J, Shin C, Camargo FD, Gygi SP and Bartel DP (2008) The impact of microRNAs on protein output. Nature 455, 64-71 https://doi.org/10.1038/nature07242
- Shin C, Nam J-W, Farh KK-H, Chiang HR, Shkumatava A and Bartel DP (2010) Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing. Mol Cell 38, 789-802 https://doi.org/10.1016/j.molcel.2010.06.005
- Garcia DM, Baek D, Shin C, Bell GW, Grimson A and Bartel DP (2011) Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 18, 1139-1146 https://doi.org/10.1038/nsmb.2115
- Agarwal V, Bell GW, Nam J-W and Bartel DP (2015) Predicting effective microRNA target sites in mammalian mRNAs. eLife 4, e05005
- Bagga S, Bracht J, Hunter S et al (2005) Regulation by let-7 and lin-4 miRNAs Results in Target mRNA Degradation. Cell 122, 553-563 https://doi.org/10.1016/j.cell.2005.07.031
- Lim LP, Lau NC, Garrett-Engele P et al (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433, 769-773 https://doi.org/10.1038/nature03315
- Lee RC, Feinbaum RL and Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75, 843-854 https://doi.org/10.1016/0092-8674(93)90529-Y
- Guo H, Ingolia NT, Weissman JS and Bartel DP (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466, 835-840 https://doi.org/10.1038/nature09267
- Eichhorn SW, Guo H, McGeary SE et al (2014) mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell 56, 104-115 https://doi.org/10.1016/j.molcel.2014.08.028
- Djuranovic S, Nahvi A and Green R (2012) miRNAmediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237-240 https://doi.org/10.1126/science.1215691
- Bazzini AA, Lee MT and Giraldez AJ (2012) Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336, 233-237 https://doi.org/10.1126/science.1215704
- Subtelny AO, Eichhorn SW, Chen GR, Sive H and Bartel DP (2014) Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508, 66-71 https://doi.org/10.1038/nature13007
- Liu Q, Huang J, Zhou N et al (2013) LncRNA loc285194 is a p53-regulated tumor suppressor. Nucleic Acids Res 41, 4976-4987 https://doi.org/10.1093/nar/gkt182
- Cesana M, Cacchiarelli D, Legnini I et al (2011) A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA. Cell 147, 358-369 https://doi.org/10.1016/j.cell.2011.09.028
- Faghihi MA, Zhang M, Huang J et al (2010) Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 11, R56 https://doi.org/10.1186/gb-2010-11-5-r56
- Dey BK, Pfeifer K and Dutta A (2014) The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR-675-5p to promote skeletal muscle differentiation and regeneration. Genes Dev 28, 491-501 https://doi.org/10.1101/gad.234419.113
- Quinn JJ and Chang HY (2016) Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet 17, 47-62 https://doi.org/10.1038/nrg.2015.10
- Denzler R, McGeary Sean E, Title Alexandra C, Agarwal V, Bartel David P and Stoffel M (2016) Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression. Mol Cell 64, 565-579 https://doi.org/10.1016/j.molcel.2016.09.027
- Denzler R, Agarwal V, Stefano J, Bartel David P and Stoffel M (2014) Assessing the ceRNA Hypothesis with Quantitative Measurements of miRNA and Target Abundance. Mol Cell 54, 766-776 https://doi.org/10.1016/j.molcel.2014.03.045
- Leucci E, Patella F, Waage J et al (2013) microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus. Sci Rep 3, 2535 https://doi.org/10.1038/srep02535
- Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ and Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465, 1033-1038 https://doi.org/10.1038/nature09144
- Yoon JH, Abdelmohsen K, Srikantan S et al (2012) LincRNA-p21 suppresses target mRNA translation. Mol Cell 47, 648-655 https://doi.org/10.1016/j.molcel.2012.06.027
- Hansen TB, Jensen TI, Clausen BH et al (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495, 384-388 https://doi.org/10.1038/nature11993
- Franco-Zorrilla JM, Valli A, Todesco M et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39, 1033-1037 https://doi.org/10.1038/ng2079
- Nam JW and Bartel DP (2012) Long non-coding RNAs in C. elegans. Genome Res 22, 2529-2540 https://doi.org/10.1101/gr.140475.112
- Ulitsky I and Bartel David P (2013) lincRNAs: Genomics, Evolution, and Mechanisms. Cell 154, 26-46 https://doi.org/10.1016/j.cell.2013.06.020
- Bazzini AA, Johnstone TG, Christiano R et al (2014) Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J 33, 981-993 https://doi.org/10.1002/embj.201488411
- Calviello L, Mukherjee N, Wyler E et al (2016) Detecting actively translated open reading frames in ribosome profiling data. Nat Methods 13, 165-170 https://doi.org/10.1038/nmeth.3688
- Ruiz-Orera J, Messeguer X, Subirana JA and Alba MM (2014) Long non-coding RNAs as a source of new peptides. Elife 3, e03523
- Smith JE, Alvarez-Dominguez JR, Kline N et al (2014) Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae. Cell Rep 7, 1858-1866 https://doi.org/10.1016/j.celrep.2014.05.023
- Andrews SJ and Rothnagel JA (2014) Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 15, 193-204 https://doi.org/10.1038/nrg3520
- Hezroni H, Koppstein D, Schwartz MG, Avrutin A, Bartel DP and Ulitsky I (2015) Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species. Cell Rep 11, 1110-1122 https://doi.org/10.1016/j.celrep.2015.04.023
- Pauli A, Valen E, Lin MF et al (2012) Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res 22, 577-591 https://doi.org/10.1101/gr.133009.111
- Ulitsky I, Shkumatava A, Jan CH, Sive H and Bartel DP (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147, 1537-1550 https://doi.org/10.1016/j.cell.2011.11.055
- Nepal C, Hadzhiev Y, Previti C et al (2013) Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res 23, 1938-1950 https://doi.org/10.1101/gr.153692.112
- Jan CH, Friedman RC, Ruby JG and Bartel DP (2011) Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature 469, 97-101 https://doi.org/10.1038/nature09616
- Kong L, Zhang Y, Ye ZQ et al (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35, W345-349 https://doi.org/10.1093/nar/gkm391
- Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22, 1775-1789 https://doi.org/10.1101/gr.132159.111
- Clark MB, Johnston RL, Inostroza-Ponta M et al (2012) Genome-wide analysis of long noncoding RNA stability. Genome Res 22, 885-898 https://doi.org/10.1101/gr.131037.111
- Li B and Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 https://doi.org/10.1186/1471-2105-12-323
- Colgan DF and Manley JL (1997) Mechanism and regulation of mRNA polyadenylation. Genes Dev 11, 2755-2766 https://doi.org/10.1101/gad.11.21.2755
- Wang Z and Kiledjian M (2000) The Poly(A)-Binding Protein and an mRNA Stability Protein Jointly Regulate an Endoribonuclease Activity. Mol Cell Biol 20, 6334-6341 https://doi.org/10.1128/MCB.20.17.6334-6341.2000
- Clark MB, Johnston RL, Inostroza-Ponta M et al (2012) Genome-wide analysis of long noncoding RNA stability. Genome Res 22, 885-898 https://doi.org/10.1101/gr.131037.111