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 251 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. Overall design: Two human (WTC11 and HS1) and two chimpanzee (C3649 and Pt2a) induced pluripotent cell lines (iPSCs) were cultured in Matrigel-coated plates with mTeSR media (WTC11 and C3649 were cultured in StemFlex) in an undifferentiated state. Cells were propagated at a 1:3 ratio by treatment with 200 U/mL collagenase IV (or PBS-EDTA) and mechanical dissection. WTC11 and C3649 iPSCs were differentiated to neural progenitor cells (NPCs) and validated as previously described (24). Briefly, 2-2.5×105 cells per cm² were seeded on Matrigel-coated wells in StemFlex containing 2 µM Thiazovivin. The following day (Day 0), medium was replaced with E6 containing 500 nM LDN193189 (Selleckchem), 10 µM SB431542 (Selleckchem), and 5 µM XAV-939 (Selleckchem). Starting on Day 3, medium was replaced with E6 containing 500 nM LDN193189 and 10 µM SB431542 every 48 hrs. Starting on Day 12, medium was replaced with Neurobasal containing 2 mM GlutaMAX, 60 µg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A every 48 hours. Around Day 16, cells were washed with PBS, dissociated with Accutase, pelleted and resuspended in Neurobasal containing 2 mM GlutaMAX, 60 µg per ml L-Ascorbic acid 2-phosphate, N2, and B27 without Vitamin A, 10 ng per ml fibroblast growth factor 2, and 10 ng per ml epidermal growth factor, and seeded on poly-L-ornithine-, fibronectin-, and laminin-coated wells. Cells were collected for HiC at passage 5-7. To differentiate HS1 and Pt2a iPSCs into NPCs, cells were split with EDTA at 1:5 ratios in culture dishes coated with matrigel and culture in N2B27 medium (comprised of DMEM/F12 medium (Invitrogen) supplemented with 1% MEM-nonessential amino acids (Invitrogen), 1 mM L-glutamine, 1% penicillin-streptomycin, 50 ng/mL bFGF (FGF-2) (Millipore), 1x N2 supplement, and 1 x B27 supplement without Vitamin A (Invitrogen)) supplemented with 100 ng/ml mouse recombinant Noggin (R&D systems). Cells at passages 1-3 were split by collagenase into small clumps, and continuously cultured in N2B27 medium with Noggin. After passage 3, cells were plated at the density of 5×105 cells/cm² after disassociation by TrypLE express (Invitrogen) into single-cell suspension, and cultured in N2B27 medium supplemented with 20 ng/mL bFGF and EGF. Cells were maintained and collected at passage 18-20. Our use of two differentiation protocols reflects rapid progress in stem cell research during the course of this study. Cells from the same populations were validated and used in a previous study (24). We verified that the chromatin interactions in the resulting Hi-C data did not show a batch effect across protocols. Hi-C was performed using the Arima Hi-C kit (Arima Genomics) according to the manufacturer's instructions. 10 million cells were used. The sequencing library was prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences) according to the manufacturer's protocol. Two independent biological replicates were prepared for each cell line. In total eight libraries were pooled and sequenced with paired-end 150-bp reads using two lanes of a NovaSeq6000 S2 (Illumina) at the Chan Zuckerberg Biohub.