Widespread Regulatory Turnover Across Human Segmental Duplications

Segmental duplications (SDs) are a pervasive feature of eukaryotic genomes, enabling genomic innovation via the duplication of genes and cis-regulatory elements. However, the regulatory mechanisms that govern these regions of the genome after duplication are not well understood. The repetitive nature of SDs pose problems for short-read assays such as ChIP-seq and DNase-seq as they create reads that map to more than one location along the genome. Moreover, the newest Telomere-to-Telomere (T2T) human genome assembly has revealed previously unknown segmental duplications. In this study, we used the Telomere-to-Telomere genome assembly along with the probabilistic allocation of multi-mapped reads by our software Allo to better understand the regulatory mechanisms governing segmental duplications in the human genome. Using 134 transcription factor ChIP-seq datasets in GM12878, we found that transcription factor binding sites within segmental duplications are rarely conserved across paralogous copies. Similarly, chromatin states defined via histone ChIP-seq datasets are also poorly conserved across segmentally duplicated regions. In contrast, paralogous genes within SDs exhibit highly correlated expression patterns. Hi-C analysis revealed that many SD paralogs have higher than expected spatial proximity, suggesting that three-dimensional genome organization may buffer transcriptional divergence following duplication despite the loss of cis-regulatory regions. Together, our results suggest that regulatory regions undergo rapid turnover following segmental duplication, but the regulatory impact may be buffered by spatial proximity within the nucleus. Tissue-specific genes and transcription factors showed greater divergence, highlighting the role of SDs in expanding specialized cellular functions.