Exact breakpoints of the In(1)w m4 rearrangement

Abstract

In(1)w ^m4 has been known for decades as a classic example of a position effect variegation-causing rearrangement and has been mentioned in hundreds of publications. Nevertheless, its euchromatic breakpoint has not been localized with base-pair resolution. We performed nanopore sequencing of DNA from In(1)w ^m4 homozygous flies and determined the exact position of euchromatic (chrX:2767875) and heterochromatic breakpoints of the rearrangement. The heterochromatic breakpoint is located in an unlinked part of the genome in the region, enriched in TEs (transposable elements) fragments. A set of unique piRNAs could be detected in the region.

Figure 1. In(1)w ^m4 inversion scheme

A. EuBP – euchromatin breakpoint, HetBP – heterochromatin breakpoint, c – centromere. The positions of the h28 heterochromatin block and the rDNA cluster are marked. Red triangles denote the position of the white gene. B. Mapping of long reads to the R6.22 Drosophila genome. The image is a collage of UCSC Genome Browser screenshots. The upper part is a close-up view of the euchromatic breakpoint and sequence reads. The lower part is an overview of the 200 kb genomic region containing the breakpoint. The white gene is outlined. The arrow shows the distance between the white TSS and the breakpoint. C. Heterochromatic breakpoint of In(1)w ^m4 inversion. The breakpoint in heterochromatin (HetBP) is in an R1 element in a region saturated with different types of mobile elements. The distribution of unique piRNAs in the region is shown below the TEs map (green – forward strand, red – reverse strand).