Fig. 4: Non-reference MEIs captured by nanopore Cas9 enrichment approach.
From: Cas9 targeted enrichment of mobile elements using nanopore sequencing
a Number of non-reference L1Hs captured by nanopore Cas9 enrichment at different on-target read coverages for different supporting read cutoffs. The dotted-gray line with italic number represents the theoretical number of MEIs that the guide RNA binds when allowing a ≤ 3 bp mismatch or gap in the PacBio-MEI set. b, c Number of non-reference AluYb, AluYa, SVA_F, and SVA_E, respectively, captured by nanopore Cas9 enrichment at different on-target read coverages. Axis labels and theoretic guide number as in a. d An example of non-reference L1Hs specifically captured by nanopore sequencing at chrX:121,709,076. The tracks from top to bottom are as follows: reference coordinates with a red triangle represent the insertion site, gene track, RepeatMasker track (blue bars) with reference element annotation, PacBio contigs assembly for two haplotypes, four nanopore local-assembled contigs by CANU from different classifications of nanopore reads based on insertion signals (contig1, signal on 3′ end; contig2, signal on 5′ end; contig3, signal in the middle of the read; and contig4, no signal). e Recurrence (dot) plots for nanopore contigs versus the reference region chrX:121,708,576-121,7089,576 sequence. Left panel shows the most 3′ end of contig1 and the most 5′ end of contig2 versus the reference sequence. Yellow bar represents the non-reference L1Hs sequence contained in the contig. The red bar represents one side of the target site duplication motif for the non-reference L1Hs contained in the contig. The upper part of this panel demonstrates sequences at the end of two contigs regarding the cleavage site when aligning to the guide RNA sequence. Blue bars in the middle panel represent the RepeatMasker track with reference L1 information annotated, and the red triangle represents the insertion site in the reference L1 region. The right panel shows contig3 versus the reference sequence. Details of this non-reference L1Hs are detailed in the panel, including length, strand, empty site, and endonuclease (EN) cleavage site sequence.
