Widespread context dependency of microRNA-mediated regulation

Genome Research

Volumn 24, Issue 6, 2014, Pages 906-919

  Erhard, Florian ^a   Haas, Jürgen ^a,b   Lieber, Diana ^a,c   Malterer, Georg ^c   Jaskiewicz, Lukasz ^d   Zavolan, Mihaela ^d   Dol̈ken, Lars ^e   Zimmer, Ralf ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c UNIVERSITY HOSPITAL ULM   (Germany)

^d UNIVERSITY OF BASEL   (Switzerland)

^e UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; TRANSCRIPTION FACTOR; VIRUS RNA;

ARTICLE; GENE CONTROL; GENE EXPRESSION; GENE TARGETING; HUMAN HERPESVIRUS 8; NONHUMAN; PRIORITY JOURNAL; RNA SEQUENCE; RNA STABILITY; RNA TRANSCRIPTION; CONSERVED SEQUENCE; GENE REGULATORY NETWORK; GENE SILENCING; GENETICS; HUMAN; HUMAN GENOME; METABOLISM; NUCLEOTIDE MOTIF; TUMOR CELL LINE;

CELL LINE, TUMOR; CONSERVED SEQUENCE; GENE REGULATORY NETWORKS; GENE SILENCING; GENOME, HUMAN; HUMANS; MICRORNAS; NUCLEOTIDE MOTIFS; RNA, MESSENGER;

EID: 84901856551     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.166702.113     Document Type: Article

References (51)

1. Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
2. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, et al. 2012. The mRNA-bound proteome and its global occupancy profile on proteincoding transcripts. Mol Cell 46: 674-690.
3. Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
4. Bartel DP. 2009. MicroRNAs: target recognition and regulatory functions. Cell 136: 215-233.
5. Ben-Moshe NB, Avraham R, Kedmi M, Zeisel A, Yitzhaky A, Yarden Y, Domany E. 2012. Context-specific microRNA analysis: identification of functional microRNAs and their mRNA targets. Nucleic Acids Res 40: 10614-10627.
6. Bhattacharyya SN, Habermacher R, Martine U, Closs EI, Filipowicz W. 2006. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125: 1111-1124. (Pubitemid 43866197)
7. Boutet SC, Cheung TH, Quach NL, Liu L, Prescott SL, Edalati A, Iori K, Rando TA. 2012. Alternative polyadenylationmediates microRNA regulation of muscle stem cell function. Cell Stem Cell 10: 327-336.
8. Brennecke J, Stark A, Russell RB, Cohen SM. 2005. Principles of microRNA-target recognition. PLoS Biol 3: e85.
9. Carroll AP, Tooney PA, Cairns MJ. 2013. Context-specific microRNA function in developmental complexity. J Mol Cell Biol 5: 73-84.
10. Cox J, Mann M. 2008. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26: 1367-1372.
11. Cullen BR. 2011. Viruses and microRNAs: RISCy interactions with serious consequences. Genes Dev 25: 1881-1894.
12. Djuranovic S, Nahvi A, Green R. 2011. A parsimonious model for gene regulation by miRNAs. Science 331: 550-553.
13. Dölken L, Ruzsics Z, Rädle B, Friedel CC, Zimmer R, Mages J, Hoffmann R, Dickinson P, Forster T, Ghazal P, et al. 2008. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14: 1959-1972.
14. Dölken L, Malterer G, Erhard F, Kothe S, Friedel CC, Suffert G, Marcinowski L, Motsch N, Barth S, Beitzinger M, et al. 2010. Systematic analysis of viral and cellular microRNA targets in cells latently infected with human g-herpesviruses by RISC immunoprecipitation assay. Cell Host Microbe 7: 324-334.
15. The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
16. Erhard F, Dölken L, Jaskiewicz L, Zimmer R. 2013a. PARma: identification of microRNA target sites in AGO-PAR-CLIP data. Genome Biol 14: R79.
17. Erhard F, Dölken L, Zimmer R. 2013b. RIP-chip enrichment analysis. Bioinformatics 29: 77-83.
18. Eulalio A, Huntzinger E, Izaurralde E. 2008. Getting to the root of miRNA-mediated gene silencing. Cell 132: 9-14.
19. Friedman RC, Farh KK, Burge CB, Bartel DP. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
20. Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, et al. 2011. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host Microbe 10: 515-526.
21. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell 27: 91-105. (Pubitemid 46991392)
22. Guo H, Ingolia NT, Weissman JS, Bartel DP. 2010. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840.
23. Haecker I, Gay LA, Yang Y, Hu J, Morse AM, McIntyre LM, Renne R. 2012. Ago HITS-CLIP expands understanding of Kaposi's sarcoma-associated herpesvirus miRNA function in primary effusion lymphomas. PLoS Pathog 8: e1002884.
24. Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, et al. 2010. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141: 129-141.
25. He L, Hannon GJ. 2004. MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5: 522-531. (Pubitemid 38868508)
26. Hobert O. 2008. Gene regulation by transcription factors and microRNAs. Science 319: 1785-1786. (Pubitemid 351451553)
27. Jacobsen A, Wen J, Marks DS, Krogh A. 2010. Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res 20: 1010-1019.
28. Jaskiewicz L, Bilen B, Hausser J, Zavolan M. 2012. Argonaute CLIP - a method to identify in vivo targets of miRNAs. Methods 58: 106-112.
29. Kedde M, Strasser MJ, Boldajipour B, Oude Vrielink JA, Slanchev K, le Sage C, Nagel R, Voorhoeve PM, van Duijse J, Ørom UA, et al. 2007. RNA-binding protein Dnd1 inhibits microRNA access to target mRNA. Cell 131: 1273-1286.
30. Kedde M, van Kouwenhove M, ZwartW, Oude Vrielink JA, Elkon R, Agami R. 2010. A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility. Nat Cell Biol 12: 1014-1020.
31. Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E. 2007. The role of site accessibility in microRNA target recognition. Nat Genet 39: 1278-1284. (Pubitemid 47482690)
32. Kim HH, Kuwano Y, Srikantan S, Lee EK, Martindale JL, Gorospe M. 2009. HuR recruits let-7/RISC to repress c-Myc expression. GenesDev 23: 1743-1748.
33. Kincaid RP, Sullivan CS. 2012. Virus-encoded microRNAs: an overview and a look to the future. PLoS Pathog 8: e1003018.
34. Kishore S, Jaskiewicz L, Burger L, Hausser J, Khorshid M, Zavolan M. 2011. A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nat Methods 8: 559-564.
35. Kozak M. 2008. Faulty old ideas about translational regulation paved the way for current confusion about how microRNAs function. Gene 423: 108-115.
36. Meijer HA, Kong YW, Lu WT, Wilczynska A, Spriggs RV, Robinson SW, Godfrey JD, Willis AE, Bushell M. 2013. Translational repression and eIF4A2 activity are critical for microRNA-mediated gene regulation. Science 340: 82-85.
37. Mishima Y, Fukao A, Kishimoto T, Sakamoto H, Fujiwara T, Inoue K. 2012. Translational inhibition by deadenylation-independent mechanisms is central to microRNA-mediated silencing in zebrafish. Proc Natl Acad Sci 109: 1104-1109.
38. Mukherji S, Ebert MS, Zheng GX, Tsang JS, Sharp PA, van Oudenaarden A. 2011.MicroRNAs can generate thresholds in target gene expression. Nat Genet 43: 854-859.
39. Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. 2012. Circuitry and dynamics of human transcription factor regulatory networks. Cell 150: 1274-1286.
40. Pasquinelli AE. 2012. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet 13: 271-282.
41. Riley KJ, Rabinowitz GS, Yario TA, Luna JM, Darnell RB, Steitz JA. 2012. EBV and human microRNAs co-target oncogenic and apoptotic viral and human genes during latency. EMBO J 31: 2207-2221.
42. Ritchie W, Flamant S, Rasko JE. 2009. Predicting microRNA targets and functions: traps for the unwary. Nat Methods 6: 397-398.
43. Robinson MD, McCarthy DJ, Smyth GK. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
44. Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. 2008. Proliferating cells express mRNAs with shortened 39 untranslated regions and fewer microRNA target sites. Science 320: 1643-1647. (Pubitemid 351931255)
45. Sethupathy P, Megraw M, Hatzigeorgiou AG. 2006. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat Methods 3: 881-886. (Pubitemid 44614721)
46. Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Kang D, Hafner M, Nusbaum JD, Feederle R, Delecluse HJ, Luftig MA, et al. 2012. The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathog 8: e1002484.
47. Thomas M, Lieberman J, Lal A. 2010. Desperately seeking microRNA targets. Nat Struct Mol Biol 17: 1169-1174.
48. Vens C, Rosso MN, Danchin EG. 2011. Identifying discriminative classification-based motifs in biological sequences. Bioinformatics 27: 1231-1238.
49. Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, et al. 2012a. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res 22: 1680-1688.
50. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, et al. 2012b. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res 22: 1798-1812.
51. Yáñez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A. 2012. Uncovering cis-regulatory sequence requirements for context specific transcription factor binding. Genome Res 22: 2018-2030.