Inter-chromosomal contacts of the 16p11.2 locus connect with gene expression changes of Pcdh genes in autism spectrum disorder

Differentiation experiment of mouse embryonic stem cells (ESCs) to neuronal precursor (NPC) and immature dopaminergic neurons (NEU) commited to ventral midbrain lineage. Controls and mutant cell lines harboring heterozygous deletion (del) or duplication-deletion (dupdel) of 7qF3 locus which is synteny conserved with human 16p11.2 locus. Mice harbouring CNVs in this locus display behavioural phenotypes and distinct changes in brain architecture resembling ASD-like traits. Mouse models are described in Guy Horev et al., 2011 (doi: 10.1073/pnas.1114042108). Samples with same numeric identifier were differentiated in parallel. RNA-seq and Hi-C on controls and mutant cell lines harboring heterozygous deletion (del) or duplication-deletion (dupdel) of 7qF3 locus. Cell types include embronic stem cells, neuronal progenitor cells, dopaminergic neurons.