Mapping cis-and trans-regulatory target genes of human-specific deletions

摘要: Deletion of functional sequence is predicted to represent a fundamental mechanism of molecular evolution 1, 2. Comparative genetic studies of primates 2, 3 have identified thousands of human-specific deletions (hDels), and the cis-regulatory potential of short (≤ 31 base pairs) hDels has been assessed using reporter assays 4. However, how structural variant-sized (≥ 50 base pairs) hDels influence molecular and cellular processes in their native genomic contexts remains unexplored. Here, we design genome-scale libraries of single-guide RNAs targeting 7.2 megabases of sequence in 6,358 hDels and present a systematic CRISPR interference (CRISPRi) screening approach to identify hDels that modify cellular proliferation in chimpanzee pluripotent stem cells. By intersecting hDels with chromatin state features and performing single-cell CRISPRi (Perturb-seq) to identify their cis-and trans-regulatory target …