Extended Data Fig. 6: Off-target ChIP-seq DNA binding analyses.
From: Transposon-encoded nucleases use guide RNAs to promote their selfish spread
a, ChIP-seq experiments reveal recruitment of dIscB to the target site (blue triangle) with a targeting ωRNA. Genome-wide representation of ChIP-seq data for dIscB reshown from Fig. 4b, with addition of a second replicate. Representative off-target sites for dIscB identified by MACS3 are highlighted (OT1-4) and analyzed in the right panel. The middle panel highlights analysis of off-target binding events using MEME-ChIP, as shown in Fig. 4b. Motifs shared by off-target peaks reveal conserved TAM sequences and little conservation of the adjacent seed sequence. The sequence of the 5′ end of the corresponding ωRNA is shown below each motif. n indicates the number of peaks contributing to the motif and their percentage of total peaks called by MACS3; E, E-value significance of the motif generated from the MEME-ChIP analysis. DNA sequences corresponding to the on-target and off-target sites are shown on the right, with TAM (yellow) and mismatches (orange) highlighted. b, ChIP-seq experiments reveal recruitment of dTnpB2 to the target site (blue triangle) with a targeting ωRNA. Data shown as in a. Similar to dIscB, dTnpB2 shows limited seed sequence requirements. c, ChIP-seq experiments reveal recruitment of dCas9 to the target site (blue triangle) with a targeting ωRNA. Data shown as in a. Analysis of off-target sites reveal a short (3–4 nt) seed sequence adjacent to the PAM motif. d, ChIP-seq experiments reveal recruitment of dCas12a to the target site (blue triangle) with a targeting ωRNA. Data shown as in a. Analysis of off-target sites reveals a short (5–7 nt) seed sequence adjacent to the PAM motif.
