Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs (original) (raw)
References
Moore, M. J. From birth to death: the complex lives of eukaryotic mRNAs. Science309, 1514–1518 (2005) ArticleADSCAS Google Scholar
Martin, K. C. & Ephrussi, A. mRNA localization: gene expression in the spatial dimension. Cell136, 719–730 (2009) ArticleCAS Google Scholar
Ahringer, J. & Kimble, J. Control of the sperm-oocyte switch in Caenorhabditis elegans hermaphrodites by the fem-3 3′ untranslated region. Nature349, 346–348 (1991) ArticleADSCAS Google Scholar
Wightman, B., Burglin, T. R., Gatto, J., Arasu, P. & Ruvkun, G. Negative regulatory sequences in the lin-14 3′-untranslated region are necessary to generate a temporal switch during Caenorhabditis elegans development. Genes Dev.5, 1813–1824 (1991) ArticleCAS Google Scholar
Merritt, C., Rasoloson, D., Ko, D. & Seydoux, G. 3′ UTRs are the primary regulators of gene expression in the C. elegans germline. Curr. Biol.18, 1476–1482 (2008) ArticleCAS Google Scholar
Mangone, M., Macmenamin, P., Zegar, C., Piano, F. & Gunsalus, K. C. UTRome.org: a platform for 3′UTR biology in C. elegans . Nucleic Acids Res.36, D57–D62 (2008) ArticleCAS Google Scholar
Nam, D. K. et al. Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc. Natl Acad. Sci. USA99, 6152–6156 (2002) ArticleADSCAS Google Scholar
Hillier, L. W. et al. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans . Genome Res.19, 657–666 (2009) ArticleCAS Google Scholar
Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res.35, D61–D65 (2007) ArticleCAS Google Scholar
Nunes, N. M., Li, W., Tian, B. & Furger, A. A functional human poly(A) site requires only a potent DSE and an A-rich upstream sequence. EMBO J.29, 1523–1536 (2010) ArticleCAS Google Scholar
Evans, D. et al. A complex containing CstF-64 and the SL2 snRNP connects mRNA 3′ end formation and _trans_-splicing in C. elegans operons. Genes Dev.15, 2562–2571 (2001) ArticleCAS Google Scholar
Prescott, E. M. & Proudfoot, N. J. Transcriptional collision between convergent genes in budding yeast. Proc. Natl Acad. Sci. USA99, 8796–8801 (2002) ArticleADSCAS Google Scholar
Batista, P. J. et al. PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans . Mol. Cell31, 67–78 (2008) ArticleCAS Google Scholar
Chiang, H. R. et al. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes. Genes Dev.24, 992–1009 (2010) ArticleCAS Google Scholar
Ruby, J. G., Jan, C. H. & Bartel, D. P. Intronic microRNA precursors that bypass Drosha processing. Nature448, 83–86 (2007) ArticleADSCAS Google Scholar
Friedman, R. C., Farh, K. K., Burge, C. B. & Bartel, D. P. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res.19, 92–105 (2009) ArticleCAS Google Scholar
Zisoulis, D. G. et al. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans . Nature Struct. Mol. Biol.17, 173–179 (2010) ArticleCAS Google Scholar
Clark, A. M. et al. The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans . Nucleic Acids Res.38, 3780–3793 (2010) ArticleADSCAS Google Scholar
Lall, S. et al. A genome-wide map of conserved microRNA targets in C. elegans . Curr. Biol.16, 460–471 (2006) ArticleCAS Google Scholar
Reinhart, B. J. et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans . Nature403, 901–906 (2000) ArticleADSCAS Google Scholar
Abrahante, J. E. et al. The _Caenorhabditis elegans hunchback_-like gene lin-57/hbl-1 controls developmental time and is regulated by microRNAs. Dev. Cell4, 625–637 (2003) ArticleCAS Google Scholar
Tian, B., Hu, J., Zhang, H. & Lutz, C. S. A large-scale analysis of mRNA polyadenylation of human and mouse genes. Nucleic Acids Res.33, 201–212 (2005) ArticleCAS Google Scholar
Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature456, 470–476 (2008) ArticleADSCAS Google Scholar
Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. & Burge, C. B. Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science320, 1643–1647 (2008) ArticleADSCAS Google Scholar
Ji, Z., Lee, J. Y., Pan, Z., Jiang, B. & Tian, B. Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl Acad. Sci. USA106, 7028–7033 (2009) ArticleADSCAS Google Scholar
Mayr, C. & Bartel, D. P. Widespread shortening of 3′UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell138, 673–684 (2009) ArticleCAS Google Scholar
Lau, N. C., Lim, L. P., Weinstein, E. G. & Bartel, D. P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans . Science294, 858–862 (2001) ArticleADSCAS Google Scholar
Mandel, C. R., Bai, Y. & Tong, L. Protein factors in pre-mRNA 3'-end processing. Cell Mol. Life Sci.65, 1099–1122 (2008) ArticleCAS Google Scholar
Guo, H., Ingolia, N. T., Weissman, J. S. & Bartel, D. P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature466, 835–840 (2010) ArticleADSCAS Google Scholar
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol.10, R25 (2009) Article Google Scholar
Maglott, D., Ostell, J., Pruitt, K. D. & Tatusova, T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res.35, D26–D31 (2007) ArticleCAS Google Scholar
The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science282, 2012–2018 (1998)