The microRNAs of Caenorhabditis elegans.

By Lee P. Lim, N. Lau, E. Weinstein, A. Abdelhakim, Soraya Yekta, M. W. Rhoades, C. Burge, David P. Bartel. Genes & Development, 2003

1,392 citations recorded by the source corpus.

MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to identify miRNA genes conserved in more than one genome. Applying this program, known as MiRscan, together with molecular identification and validation methods, we have identified most of the miRNA genes in the nematode Caenorhabditis elegans. The total number of validated miRNA genes stands at 88, with no more than 35 genes remaining to be detected or validated. These 88 miRNA genes represent 48 gene families; 46 of these families (comprising 86 of the 88 genes) are conserved in Caenorhabditis briggsae, and 22 families are conserved in humans. More than a third of the worm miRNAs, including newly identified members of the lin-4 and let-7 gene families, are differentially expressed during larval development, suggesting a role for these miRNAs in mediating larval developmental transitions. Most are present at very high steady-state levels-more than 1000 molecules per cell, with some exceeding 50,000 molecules per cell. Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species.

Subfields: Aging, Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7d22c92020ba83e6d48c3f67f51f9a8380a360e2

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Citations in the corpus

Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs (2005, background): “The 5′ region, and particularly seed positions 2–8, is the most conserved region of metazoan miRNA”
Functional diversity of miRNA in plants (2007, background): “For example, loss of function of miR14 increased sensitivity of fly to different stresses [49], and nutrient stress may induce expression of miRNA234 [50].”
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. (2005, background): “MicroRNA genes are abundant, encompassing ∼1% of the genes of worms, flies, and humans (Lai et al. 2003; Lim et al. 2003a,b).”
Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs (2004, background): “MiRNAs are among the more abundant gene-regulatory molecules in the animal cell, constituting almost 1% of the predicted genes in humans, worms and flie”
Evolution of microRNA diversity and regulation in animals (2011, background): “According to mutational profiles of mature miRNAs, positions 2 to 7 represent a particularly conserved regio”
Human MicroRNA Targets (2004, background): “Estimates in worm show that there are approximately 1,000 molecules of miRNA per cell, with some cells exceeding 50,000 molecules (Lim et al. 2003b).”
Molecular evolution of a microRNA cluster. (2004, methodology): “In Figure 3 and in the work by Lim et al.(20) the C.”
Human embryonic stem cells express a unique set of microRNAs. (2004, background): “…so far (Aravin et al., 2003; Dostie et al., 2003; Grad et al., 2003; Lagos-Quintana et al., 2001, 2002, 2003; Lai et al., 2003; Lau et al., 2001; Lee and Ambros, 2001; Lee et al., 1993; Lim et al., 2003b; Llave et al., 2002a; Mourelatos et al., 2002; Park et al., 2002; Reinhart et al., 2000, 2002).”
Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. (2004, background): “Next, we examined the possibility to use high-stringency hybridization and washing conditions that would allow improved specificity in microRNA detection by northern blots, especially when detecting highly homologous miRNAs, e.g. members of the let-7 microRNA family ( 34 ).”
Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing (2010, background): “A Class of miRNA Target Site The most highly conserved region of metazoan miRNAs is the 50 region containing the seed (Lewis et al., 2003; Lim et al., 2003), which is the region most important for recognizing most targets.”
MicroRNA biogenesis: coordinated cropping and dicing (2005, background): “Considering that the affinity of exportin-5 to pre-miRNA is much higher than to tRNA, and that miRNAs are as abundant as 50,000 copies per cel”