Extended Data Fig. 6: AGO2HA is enriched at young LINE and ERV retrotransposons.
From: AGO2 silences mobile transposons in the nucleus of quiescent cells
(a) Example genome browser view showing enrichment of AGO2HA over the consensus sequence of young LINE-1 elements (blue) or young ERV elements (green). For each bin, enrichment was calculated as the log2 value of the ratio between the reads per million (RPM) of AGO2HA samples (HARPM) and those of the wild-type samples (WTRPM). As a result, regions where AGO2HA is enriched are represented by positive values, and those where AGO2HA is depleted are represented by negative values. (b) Example genome browser view over a young L1 element for the indicated ChIP-seq data. Individual biological replicates are shown in light blue (Ago2HA/HA samples) or light grey (Ago2+/+ samples). Tracks with replicate data merged are show in dark blue or dark grey. Notice the enrichment of ChIP-seq reads in Ago2HA/HA samples over the LINE-1 element compared to control Ago2+/+ samples when all reads (uniquely mapping as well as multimapping) are considered. In contrast, because of its repetitive nature, reads mapping uniquely to this element are mostly absent. Notice also how paired-end sequencing (PE seq) which increases the length of the reads compared to single-read (SR) allows the identification of a peak for uniquely mapping reads at the border between the L1 element and the uniquely mappable region of the genome in the Ago2HA/HA but not the Ago2+/+ ChIP confirming that enrichment is not an artefact of multimapping reads. A detailed view of this peak as well as the underlying reads is show in (c).
