MicroRNAs and Other Tiny Endogenous RNAs in C. elegans

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MicroRNAs and Other Tiny Endogenous RNAs in C. elegans Victor Ambros, Rosalind C. Lee, Ann Lavanway, Peter T. Williams, David Jewell Current Biology Volume 13, Issue 10, Pages 807-818 (May 2003) DOI: 10.1016/S0960-9822(03)00287-2

Figure 1 Secondary-Structure Prediction of Putative miRNA and tncRNA Precursors (A) MicroRNA candidates identified by comparative genomic analysis of C. elegans and C. briggsae sequences. C. elegans/C. briggsae genomic sequence alignments [47] were obtained from Wormbase and processed computationally as described in the Experimental Procedures. A total of 6985 C. elegans/C. briggsae aligned sequence pairs were scored via a secondary-structure model based on the hairpin precursors of published miRNAs. The score range from 6.5 to 10 contained 31 miRNAs that had been previously published or identified as cDNA sequences in this study. Six additional novel miRNA sequences were confirmed by Northern blot from among the 288 best-scoring candidates. (B) Examples of miRNA candidates predicted computationally based on C. elegans/C. briggsae sequence and structural alignment. (C and D) Predicted putative foldback structures for two tncRNAs. These structures do not meet minimal criteria for annotation as miRNAs [36], based on excessive bulges (C) and fewer than 16 base pairs involving the small RNA (D). Current Biology 2003 13, 807-818DOI: (10.1016/S0960-9822(03)00287-2)

Figure 2 Families of Similar MicroRNAs The threshold for inclusion was 80% sequence identity. The only families shown are those that include members from C. elegans[8, 9], insects [10, 45], and/or vertebrates [10–12]. Identical nucleotides are shaded yellow; conservation of purines or pyrimidines is indicated by blue shading. Sequences were aligned with ClustalW [48] and adjusted by hand. Current Biology 2003 13, 807-818DOI: (10.1016/S0960-9822(03)00287-2)

Figure 3 Examples of Developmental Patterns of Expression of Worm MicroRNAs Detected by Northern Blot Hybridization Panels (A), (B), and (D–F) show the ∼22 nt (mature miRNA) size range, and panels (C) and (G) also include the ∼65 nt (miRNA precursor) range. In panels (A)–(C), the lanes contain total RNA samples from (left to right): lane 1, embryos; lane 2, L1 larvae; lane 3, L2 larvae; lane 4, L3 larvae; lane 5, L4 larvae; and lane 6, adults. In panels (D)–(G), the lanes contain total RNA samples from (left to right): lane 1, embryos; lane 2, L1 larvae held in developmental arrest for 24 hours by starvation; lane 3, L1 larvae 12 hours after feeding; lane 4, L1 larvae 18 hours after feeding. Current Biology 2003 13, 807-818DOI: (10.1016/S0960-9822(03)00287-2)

Figure 4 Examples of Developmental Patterns of Expression of Worm tncRNAs Detected by Northern Blot Hybridization The lanes contain total RNA samples from (left to right): lane 1, embryos; lane 2, L1 larvae; lane 3, L2 larvae; lane 4, L3 larvae; lane 5, L4 larvae; and lane 6, adults. We did not test whether the two species in panel (C) represent isoforms of tncR17 or whether one of them is a cross-hybridizing RNA from another locus. Current Biology 2003 13, 807-818DOI: (10.1016/S0960-9822(03)00287-2)