Abstract
MicroRNAs (miRNAs) are ∼22 nucleotide single-stranded RNA molecules that originate from hairpin precursors and regulate gene expression at the posttranscriptional level by basepairing with target messenger RNA and blocking its translation or inducing its degradation. miRNAs play important roles in a variety of biological processes, including development, proliferation, differentiation, cell fate determination, apoptosis, signal transduction, host–viral interactions, and tumorigenesis. Methodological advances in miRNA studies allowed identification of biological roles for many miRNAs, and establishing the spatiotemporal expression patterns of miRNAs is one of the approaches to elucidate their biological functions. Expression pattern analysis of miRNAs helps to identify potential genetic interactors that exhibit similar expression patterns and this, combined with further supporting experiments, helps to identify the genetic pathways in which the specific miRNAs are involved. In this chapter, we describe a detailed protocol for the analysis of miRNA expression patterns in Caenorhabditis elegans.
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References
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Schratt GM, Tuebing F, Nigh EA, Kane CG, Sabatini ME, Kiebler M, Greenberg ME (2006) A brain-specific microRNA regulates dendritic spine development. Nature 439:283–289
Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318:1931–1934
Martinez NJ, Ow MC, Reece-Hoyes JS, Barrasa MI, Ambros VR, Walhout AJ (2008) Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res 18:2005–2015
Kato M, Slack FJ (2008) MicroRNAs: small molecules with big roles—C. elegans to human cancer. Biol Cell 100:71–81
Miska EA, Alvarez-Saavedra E, Abbott AL, Lau NC, Hellman AB et al (2007) Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet 3:e215
Brenner JL, Jasiewicz KL, Fahley AF, Kemp BJ, Abbott AL (2010) Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans. Curr Biol 20:1321–1325
Aboobaker AA, Tomancak P, Patel N, Rubin GM, Lai EC (2005) Drosophila microRNAs exhibit diverse spatial expression patterns during embryonic development. Proc Natl Acad Sci USA 102:18017–18022
Wienholds E, Kloosterman WP, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz HR, Kauppinen S, Plasterk RH (2005) MicroRNA expression in zebrafish embryonic development. Science 309:310–311
Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294:858–862
Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862–864
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M et al (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401–1414
Ruby JG, Stark A, Johnston WK, Kellis M, Bartel DP, Lai EC (2007) Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. Genome Res 17:1850–1864
Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A et al (2007) High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol 5:e237
Reece-Hoyes JS, Shingles J, Dupuy D, Grove CA, Walhout AJ, Vidal M, Hope IA (2007) Insight into transcription factor gene duplication from Caenorhabditis elegans promoterome-driven expression patterns. BMC Genomics 8:27
Boulin T, Etchberger JF, Hobert O (2006) Reporter gene fusions. In: WormBook (ed) The C. elegans Research Community. doi:10.1895/wormbook.1.106.1, http://www.wormbook.org
Xiong H, Qian J, He T, Li F (2009) Independent transcription of miR-281 in the intron of ODA in Drosophila melanogaster. Biochem Biophys Res Commun 378:883–889
Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE (2008) Chromatin structure analyses identify miRNA promoters. Genes Dev 22:3172–3183
Corcoran DL, Pandit KV, Gordon B, Bhattacharjee A, Kaminski N, Benos PV (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One 4:e5279
Wang X, Xuan Z, Zhao X, Li Y, Zhang MQ (2009) High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res 19:266–275
Isik M, Korswagen HC, Berezikov E (2010) Expression patterns of intronic microRNAs in Caenorhabditis elegans. Silenc 1:5
Evans TC (2006) Transformation and microinjection. In: WormBook (ed) The C. elegans Research Community, WormBook. doi:10.1895/wormbook.1.108.1, http://www.wormbook.org
Bio-Rad (1997) Bio-Rad Biolistic® PDS-1000/He Particle Delivery System Instruction Manual, Hercules, CA
Etchberger JF, Hobert O (2008) Vector-free DNA constructs improve transgene expression in C. elegans. Nat Methods 5:3
Sivamani E, DeLong RK, Qu R (2009) Protamine-mediated DNA coating remarkably improves bombardment transformation efficiency in plant cells. Plant Cell Rep 28:213–221
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Isik, M., Berezikov, E. (2013). Expression Pattern Analysis of MicroRNAs in Caenorhabditis elegans . In: Ying, SY. (eds) MicroRNA Protocols. Methods in Molecular Biology, vol 936. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-083-0_11
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DOI: https://doi.org/10.1007/978-1-62703-083-0_11
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