MicroRNA rules: Made to be broken
P. Shannon PENDERGRAST, Tom VOLPE
MicroRNA rules: Made to be broken
MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression. For over a decade the deluge of research describing the biogenesis and activity of miRNAs has lead researchers to postulate rules to help make sense of the enormous amount of data produced. These rules are repeated in miRNA research papers and reviews. While these rules have been helpful one must be conscious of their limitations or risk missing future breakthroughs. Here we describe some of the most commonly stated rules, the reasoning behind their formation, their uses, and limitations.
microRNA / post-transcriptional / gene regulation / mRNA / 3' UTR / conservation rule / seed pairing rule / biogenesis rule / mechanism of action rule
[1] |
Alexiou P, Maragkakis M, Papadopoulos G L, Reczko M, Hatzigeorgiou A G (2009). Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics, 25(23): 3049-3055
CrossRef
Pubmed
Google scholar
|
[2] |
Baek D, Villén J, Shin C, Camargo F D, Gygi S P, Bartel D P (2008). The impact of microRNAs on protein output. Nature, 455(7209): 64-71
CrossRef
Pubmed
Google scholar
|
[3] |
Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, Eachus R, Pasquinelli A E (2005). Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation. Cell, 122(4): 553-563
CrossRef
Pubmed
Google scholar
|
[4] |
Bartel D P (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136(2): 215-233
CrossRef
Pubmed
Google scholar
|
[5] |
Bazzini A A, Lee M T, Giraldez A J (2012). Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science, 336(6078): 233-237
CrossRef
Pubmed
Google scholar
|
[6] |
Behm-Ansmant I, Rehwinkel J, Doerks T, Stark A, Bork P, Izaurralde E (2006). mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev, 20(14): 1885-1898
CrossRef
Pubmed
Google scholar
|
[7] |
Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z (2005). Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet, 37(7): 766-770
CrossRef
Pubmed
Google scholar
|
[8] |
Berezikov E, van Tetering G, Verheul M, van de Belt J, van Laake L, Vos J, Verloop R, van de Wetering M, Guryev V, Takada S, van Zonneveld A J, Mano H, Plasterk R, Cuppen E (2006). Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res, 16(10): 1289-1298
CrossRef
Pubmed
Google scholar
|
[9] |
Brennecke J, Stark A, Cohen S M (2005). Not miR-ly muscular: microRNAs and muscle development. Genes Dev, 19(19): 2261-2264
CrossRef
Pubmed
Google scholar
|
[10] |
Carthew R W, Sontheimer E J (2009). Origins and mechanisms of miRNAs and siRNAs. Cell, 136(4): 642-655
CrossRef
Pubmed
Google scholar
|
[11] |
Chi S W, Zang J B, Mele A, Darnell R B (2009). Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature, 460(7254): 479-486
Pubmed
|
[12] |
D'Alessio G, Riordan J F (1997) Ribonucleases: Structures and Functions. Academic Press, New York, NY
|
[13] |
Djuranovic S, Nahvi A, Green R (2012). miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science, 336(6078): 237-240
CrossRef
Pubmed
Google scholar
|
[14] |
Elbashir S M, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature, 411(6836): 494-498
CrossRef
Pubmed
Google scholar
|
[15] |
Elefant N, Altuvia Y, Margalit H (2011). A wide repertoire of miRNA binding sites: prediction and functional implications. Bioinformatics, 27(22): 3093-3101
CrossRef
Pubmed
Google scholar
|
[16] |
Elkayam E, Kuhn C D, Tocilj A, Haase A D, Greene E M, Hannon G J, Joshua-Tor L (2012). The structure of human argonaute-2 in complex with miR-20a. Cell, 150(1): 100-110
CrossRef
Pubmed
Google scholar
|
[17] |
Friedman R C, Farh K K, Burge C B, Bartel D P (2009). Most mammalian mRNAs are conserved targets of microRNAs. Genome Res, 19(1): 92-105
CrossRef
Pubmed
Google scholar
|
[18] |
Giraldez A J, Mishima Y, Rihel J, Grocock R J, Van Dongen S, Inoue K, Enright A J, Schier A F (2006). Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science, 312(5770): 75-79
CrossRef
Pubmed
Google scholar
|
[19] |
Grimson A, Farh K K, Johnston W K, Garrett-Engele P, Lim L P, Bartel D P (2007). MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell, 27(1): 91-105
CrossRef
Pubmed
Google scholar
|
[20] |
Gu S, Jin L, Zhang F, Sarnow P, Kay M A (2009). Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs. Nat Struct Mol Biol, 16(2): 144-150
CrossRef
Pubmed
Google scholar
|
[21] |
Guo H, Ingolia N T, Weissman J S, Bartel D P (2010). Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature, 466(7308): 835-840
CrossRef
Pubmed
Google scholar
|
[22] |
Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr, Jungkamp A C, Munschauer M, Ulrich A, Wardle G S, Dewell S, Zavolan M, Tuschl T (2010). Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141(1): 129-141
CrossRef
Pubmed
Google scholar
|
[23] |
Hendrickson D G, Hogan D J, McCullough H L, Myers J W, Herschlag D, Ferrell J E, Brown P O (2009). Concordant regulation of translation and mRNA abundance for hundreds of targets of a human microRNA. PLoS Biol, 7(11): e1000238
CrossRef
Pubmed
Google scholar
|
[24] |
Jopling C L, Yi M, Lancaster A M, Lemon S M, Sarnow P (2005). Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science, 309(5740): 1577-1581
CrossRef
Pubmed
Google scholar
|
[25] |
Kim V N, Han J, Siomi M C (2009). Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol, 10(2): 126-139
CrossRef
Pubmed
Google scholar
|
[26] |
Krol J, Krzyzosiak W J (2004). Structural aspects of microRNA biogenesis. IUBMB Life, 56(2): 95-100
CrossRef
Pubmed
Google scholar
|
[27] |
Krol J, Loedige I, Filipowicz W (2010). The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet, 11(9): 597-610
Pubmed
|
[28] |
Krützfeldt J, Rajewsky N, Braich R, Rajeev K G, Tuschl T, Manoharan M, Stoffel M (2005). Silencing of microRNAs in vivo with ‘antagomirs’. Nature, 438(7068): 685-689
CrossRef
Pubmed
Google scholar
|
[29] |
Lee R C, Feinbaum R L, Ambros V (1993). The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75(5): 843-854
CrossRef
Pubmed
Google scholar
|
[30] |
Lee S, Vasudevan S (2013). Post-transcriptional stimulation of gene expression by microRNAs. Adv Exp Med Biol, 768: 97-126
CrossRef
Pubmed
Google scholar
|
[31] |
Lewis B P, Shih I H, Jones-Rhoades M W, Bartel D P, Burge C B (2003). Prediction of mammalian microRNA targets. Cell, 115(7): 787-798
CrossRef
Pubmed
Google scholar
|
[32] |
Lim L P, Lau N C, Weinstein E G, Abdelhakim A, Yekta S, Rhoades M W, Burge C B, Bartel D P (2003). The microRNAs of Caenorhabditis elegans. Genes Dev, 17(8): 991-1008
CrossRef
Pubmed
Google scholar
|
[33] |
Llave C, Xie Z, Kasschau K D, Carrington J C (2002). Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science, 297(5589): 2053-2056
CrossRef
Pubmed
Google scholar
|
[34] |
Machlin E S, Sarnow P, Sagan S M (2011). Masking the 5′ terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex. Proc Natl Acad Sci USA, 108(8): 3193-3198
CrossRef
Pubmed
Google scholar
|
[35] |
Mayr C, Bartel D P (2009). Widespread shortening of 3’UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell, 138(4): 673-684
CrossRef
Pubmed
Google scholar
|
[36] |
Mitchell P S, Parkin R K, Kroh E M, Fritz B R, Wyman S K, Pogosova-Agadjanyan E L, Peterson A, Noteboom J, O’Briant K C, Allen A, Lin D W, Urban N, Drescher C W, Knudsen B S, Stirewalt D L, Gentleman R, Vessella R L, Nelson P S, Martin D B, Tewari M (2008). Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA, 105(30): 10513-10518
CrossRef
Pubmed
Google scholar
|
[37] |
Miyoshi K, Miyoshi T, Siomi H (2010). Many ways to generate microRNA-like small RNAs: non-canonical pathways for microRNA production. Mol Genet Genomics, 284(2): 95-103
CrossRef
Pubmed
Google scholar
|
[38] |
Nguyen H T, Frasch M (2006). MicroRNAs in muscle differentiation: lessons from Drosophila and beyond. Curr Opin Genet Dev, 16(5): 533-539
CrossRef
Pubmed
Google scholar
|
[39] |
Olsen P H, Ambros V (1999). The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol, 216(2): 671-680
CrossRef
Pubmed
Google scholar
|
[40] |
Pasquinelli A E, McCoy A, Jiménez E, Saló E, Ruvkun G, Martindale M Q, Baguñà J (2003). Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history evolution? Evol Dev, 5(4): 372-378
CrossRef
Pubmed
Google scholar
|
[41] |
Pasquinelli A E, Reinhart B J, Slack F, Martindale M Q, Kuroda M I, Maller B, Hayward D C, Ball E E, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G (2000). Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature, 408(6808): 86-89
CrossRef
Pubmed
Google scholar
|
[42] |
Rehwinkel J, Behm-Ansmant I, Gatfield D, Izaurralde E (2005). A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing. RNA, 11(11): 1640-1647
CrossRef
Pubmed
Google scholar
|
[43] |
Reinhart B J, Slack F J, Basson M, Pasquinelli A E, Bettinger J C, Rougvie A E, Horvitz H R, Ruvkun G (2000). The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403(6772): 901-906
CrossRef
Pubmed
Google scholar
|
[44] |
Roush S, Slack F J (2008). The let-7 family of microRNAs. Trends Cell Biol, 18(10): 505-516
CrossRef
Pubmed
Google scholar
|
[45] |
Sandberg R, Neilson J R, Sarma A, Sharp P A, Burge C B (2008). Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science, 320(5883): 1643-1647
CrossRef
Pubmed
Google scholar
|
[46] |
Schirle N T, MacRae I J (2012). The crystal structure of human Argonaute2. Science, 336(6084): 1037-1040
CrossRef
Pubmed
Google scholar
|
[47] |
Schnall-Levin M, Rissland O S, Johnston W K, Perrimon N, Bartel D P, Berger B (2011). Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs. Genome Res, 21(9): 1395-1403
CrossRef
Pubmed
Google scholar
|
[48] |
Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N (2008). Widespread changes in protein synthesis induced by microRNAs. Nature, 455(7209): 58-63
CrossRef
Pubmed
Google scholar
|
[49] |
Shin C, Nam J W, Farh K K, Chiang H R, Shkumatava A, Bartel D P (2010). Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell, 38(6): 789-802
CrossRef
Pubmed
Google scholar
|
[50] |
Sokol N S, Ambros V (2005). Mesodermally expressed Drosophila microRNA-1 is regulated by Twist and is required in muscles during larval growth. Genes Dev, 19(19): 2343-2354
CrossRef
Pubmed
Google scholar
|
[51] |
Sun J, Gao B, Zhou M, Wang Z Z, Zhang F, Deng J E, Li X (2013). Comparative genomic analysis reveals evolutionary characteristics and patterns of microRNA clusters in vertebrates. Gene, 512(2): 383-391
CrossRef
Pubmed
Google scholar
|
[52] |
Tsui N B, Ng E K, Lo Y M (2002). Stability of endogenous and added RNA in blood specimens, serum, and plasma. Clin Chem, 48(10): 1647-1653
Pubmed
|
[53] |
Wang Y, Sheng G, Juranek S, Tuschl T, Patel D J (2008). Structure of the guide-strand-containing argonaute silencing complex. Nature, 456(7219): 209-213
CrossRef
Pubmed
Google scholar
|
[54] |
Weber J A, Baxter D H, Zhang S, Huang D Y, Huang K H, Lee M J, Galas D J, Wang K (2010). The microRNA spectrum in 12 body fluids. Clin Chem, 56(11): 1733-1741
CrossRef
Pubmed
Google scholar
|
[55] |
Wen M, Shen Y, Shi S, Tang T (2012). miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. BMC Bioinformatics, 13(1): 140
CrossRef
Pubmed
Google scholar
|
[56] |
Wightman B, Ha I, Ruvkun G (1993). Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell, 75(5): 855-862
CrossRef
Pubmed
Google scholar
|
[57] |
Williamson V, Kim A, Xie B, McMichael G O, Gao Y, Vladimirov V (2013). Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation. Brief Bioinform, 14(1): 36-45
CrossRef
Pubmed
Google scholar
|
[58] |
Wu L, Fan J, Belasco J G (2006). MicroRNAs direct rapid deadenylation of mRNA. Proc Natl Acad Sci USA, 103(11): 4034-4039
CrossRef
Pubmed
Google scholar
|
[59] |
Yang J S, Lai E C (2011). Alternative miRNA biogenesis pathways and the interpretation of core miRNA pathway mutants. Mol Cell, 43(6): 892-903
CrossRef
Pubmed
Google scholar
|
[60] |
Yekta S, Shih I H, Bartel D P (2004). MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304(5670): 594-596
CrossRef
Pubmed
Google scholar
|
[61] |
Zamore P D, Tuschl T, Sharp P A, Bartel D P (2000). RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell, 101(1): 25-33
CrossRef
Pubmed
Google scholar
|
[62] |
Zhang R, Wang Y Q, Su B (2008). Molecular evolution of a primate-specific microRNA family. Mol Biol Evol, 25(7): 1493-1502
CrossRef
Pubmed
Google scholar
|
/
〈 | 〉 |