Figure 1.

Workflow for identification of pseudogene-derived esiRNA–target interactions. Using a systematic computational procedure of homologous sequence alignment between a collection of transcribed pseudogenes and known functional sRNAs, we identified pseudogene-derived esiRNAs and verified these by reference to available Illumina-Solexa reads, and subsequently by reference to regulated protein-coding target genes (see ‘Materials and Methods’ section).