Roles of the Developmental Regulator unc-62/Homothorax in Limiting Longevity in Caenorhabditis elegans
Figure 4
Identification of direct and regulated targets of UNC-62 in adults by ChIP–seq and RNA–seq.
(A) An example of UNC-62 ChIP-seq read density at a significantly enriched binding site is shown. Top tracks show read density in ChIP-seq experiments for UNC-62 in young adults (green) and L3 larvae (blue) as well as non-immunoprecipitated input control (grey). Boxes underneath the read density tracks indicate significant binding sites (q-value≤10−5). Bottom tracks indicate genes (with coding exons in thick blue boxes). (B) Examples of unc-62 RNAi 3′-end enriched RNA-seq data is shown. We performed three independent experiments in which we fed worms either unc-62 RNAi or control bacteria, isolated mRNA and generated RNA-seq libraries, and sequenced these libraries on the Illumina HiSeq platform. For the ilys-5 (left) and vit-2 (right) genomic regions, reads map to annotated exon regions on the proper strand, and are enriched at the 3′ end of the transcript. Read densities are displayed for control (black) and unc-62 RNAi (blue), scaled as reads per million uniquely mapping reads. (C) Rank Products-based analysis (based on [27]; see Methods and Figure S5) to identify genes reproducibly altered across all three biological replicates identified 67 genes significantly increased and 115 genes significantly decreased upon unc-62 RNAi at a 10% false positive rate.