16. The evolutionary conserved developmental regulome define high risk regions for long range position effects

Abstract

Balanced chromosomal rearrangements (BCRs) have been used for decades to identify disease loci, an approach which has been facilitated by global paired-end sequencing methods to detect chromosomal breakpoints at near sequence level. BCRs do not only cause disease by gene truncation, but also by removing cis-acting regulatory elements, e.g. tissue-specific enhancers, from specific target genes (long-range position effects – LRPE), and/or by bringing external regulatory elements into contact with a new target gene (enhancer adoption). In this study, we show that the majority of the known LRPE-associated breakpoints occur in Topologically Associating Domains (TADs) overlapping with clusters of evolutionary conserved non-genic elements (CNE), and where the dysregulated target genes frequently are marked by large transposon free promoters. By a genome-wide search we defined 316 TADs (cneTADs) with these conservation features, covering 18% of the genome, with 382 predicted target genes that are highly enriched in developmental genes including homeobox genes and other transcription factors. By systematic whole genome mate-pair sequencing, where we more than double the number of mapped two-way BCRs, and include the first large cohort of healthy BCR carriers, we show that >40% of all affected BCR-carriers, including all published ones, have one or two breakpoints in cneTADs, a significantly increase compared to the frequency in healthy BCR carriers. Our data support not only that cneTADs are candidate high-risk LRPE regions, but also that TAD-boundaries are LRPE-boundaries. Moreover, cneTADs are high-risk regions for enhancer adoption events, and a new extreme variant of this, enhancer swapping, where exchanges between two cneTADs may lead to unpredictable, novel phenotypes. Our concerted action will have the potential to establish a saturated map of genotype-phenotype links for this major part of the human developmental regulome, in addition to provide genotype-phenotype links for thousands of truncated protein-coding and non-coding genes.