Supporting data for: Three-dimensional genome re-wiring in loci with Human Accelerated Regions

Human Accelerated Regions (HARs) are conserved genomic loci that evolved at an accelerated rate in the human lineage and may underlie human-specific traits. We generated HARs and chimpanzee accelerated regions with an automated pipeline and an alignment of 241 mammalian genomes. Combining deep-learning with chromatin capture experiments in human and chimpanzee neural progenitor cells, we discovered a significant enrichment of HARs in topologically associating domains (TADs) containing human-specific genomic variants that change three-dimensional (3D) genome organization. Differential gene expression between humans and chimpanzees at these loci suggests rewiring of regulatory interactions between HARs and neurodevelopmental genes. Thus, comparative genomics together with models of 3D genome folding revealed enhancer hijacking as an explanation for the rapid evolution of HARs., Lentivirus-based massively parallel reporter assay (lentiMPRA) library design and synthesis
Tiles of 270bp in length were generated from all 312 zooHARs. Multiple tiles were generated with a sliding window of 20bp if the zooHAR was longer than 270bp. In total, 549 oligos were designed to cover all zooHARs. We also included 143 oligos centered on active chromatin marks as positive controls. This oligo pool was synthesized by Twist Bioscience.
Primary cortical cell culture for lentiMPRA
De-identified tissue samples were collected with consent in strict observance of legal and institutional ethical regulations. Protocols were approved by the Human Gamete, Embryo, and Stem Cell Research Committee (institutional review board) at the University of California, San Francisco. Gestational week 18 cortical tissue was dissociated into a single-cell suspension using papain (LK003150, Worthington Biochemical) and plated on 15cm dishes coated with poly-O-lysine, laminin, and fibronectin. DMEM culture...,