PMC

Flow diagram for microRNA prediction algorithm.

Gene ontology (GO) terms grouping of the mRNA targets.

High level flow diagram of mRNA target prediction algorithm.

Sampling of predicted mRNA targets. ("mfe" is the minimal free energy of the duplex, as calculated by RNAhybrid.)

RNA folding structure as calculated by the program mfold for miR-72. Text output of putative miR-72 for Ciona intestinalis, Ciona savignyi and C.elegans.

RNA folding structure as calculated by the program mfold for let-7. Text output of putative let-7 for Ciona intestinalis, Ciona savignyi and C.elegans.

ClustalX alignments of the miRNA predictions. The first two columns contain the alignments for the miRNAs that we attempted to validate. The third column contains the alignments for the five miRNAs that we did not attempt to validate.

PAGE Northern blot validation of miRNA predictions. PAGE Northern blot analyses using adult C. intestinalis total RNA were performed to determine the indicated miRNAs. Ethidium bromide staining of the 5S rRNA is shown as a control for RNA loading and quality. Anti-sense (AS) probes were tested for let-7 and miR-72.

Venn diagram summarizing the distribution of the predicted C. intestinalis miRNAs into the C. elegans vs. H. sapiens families. Family counts for C. elegans, and for the intersection of C. elegans with H. sapiens were based on conserved 6-mer seeds [22]. The family count for H. sapiens was extracted from the miFam.dat microRNA family data file available from the miRNA database [6].