Assigning insertions to genomic elements

We assigned each transposon insertion to one of the following genomic elements according to their coordinates in the reference genome in decreasing priority: protein-coding gene promoters, protein-coding gene exons, protein-coding gene introns, lncRNA promoters, lncRNA exons, lncRNA introns, small noncoding RNA promoters, small noncoding RNA exons, and intergenic regions. Promoters were defined as regions ±500 bp of TSSs. Transposon insertions in protein-coding gene exons were further assigned to CDSs, 5′-UTRs, and 3′-UTRs in decreasing priority. To determine whether insertion sites were enriched in key epigenetic marks, we divided insertions into five groups: protein-coding gene promoters, protein-coding gene exons, protein-coding gene introns, promoters and gene bodies of noncoding RNAs, and intergenic regions. Furthermore, throughout our study, we used the replication origins defined by Spradling et al. using ChIP-seq data of ORC proteins in fly cell lines (26).