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

  • bioRxiv. 2024 Dec 1:2023.12.27.573461. doi: 10.1101/2023.12.27.573461.
Tyler Fair  1  2  3 ,  Bryan J Pavlovic  1  3 ,  Dani Swope  1  3 ,  Octavio E Castillo  4 ,  Nathan K Schaefer  1  3 ,  Alex A Pollen  1  3
Affiliations
  • 1. Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
  • 2. Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA.
  • 3. Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
  • 4. Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
PMID: 38234800 DOI: 10.1101/2023.12.27.573461
Abstract

Deletion of functional sequence is predicted to represent a fundamental mechanism of molecular evolution1,2. Comparative genetic studies of primates2,3 have identified thousands of human-specific deletions (hDels), and the cis-regulatory potential of short (≤31 base pairs) hDels has been assessed using reporter assays4. 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 genes, we discovered 20 hDels controlling gene expression. We highlight two hDels, hDel_2247 and hDel_585, with tissue-specific activity in the brain. Our findings reveal a molecular and cellular role for sequences lost in the human lineage and establish a framework for functionally interrogating human-specific genetic variants.

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