Fig. 1

Chromosomal interactions involving TEs can be analyzed using 4Tran-PCR. a Design of 4C-Seq primers to capture interactions from multiple transposon integration sites. The scheme shows how baits are designed within the transposon as well as the potential location of the two primers and the restriction enzyme sites necessary for amplification of a 4Tran-PCR library. The bottom of the scheme displays an interaction identified by Illumina sequencing containing the barcode, the sequence corresponding to the TE bait and the interaction fragment captured with the bait. b Schematic representation of all IAPEz integration events. Each line represents a different integration and the black lines show which part of the consensus sequence (shown under the plot) is retained by each integration. Integration events are sorted by 5′ position on the consensus sequence and by size of integration. Arrows represent the two locations tested for IAPEz baits. c 4Tran data in ES cells for the two IAPEz baits. Boxes represent three integration events detected by bait 1 that are not captured by bait 2. d 4Tran data for four different mouse ERVs on chromosome 3. Regions predicted to form bait-like profiles based on the presence of primers sequences (Predicted) and our algorithm based on bait like profiles (Observed) are shown under each 4Tran signal plot. e The left plot shows the number of annotated integrations in the mm10 genome for each ERV (annotated), the number of predicted integrations and the number of observed bait-like profiles. The plot on the right shows the number of observed and predicted bait-like profiles