GSE204778
CRISPR modeling reveals transcriptional and functional changes associated with structural variant disruption to MEF2C and 5q14.3 topological organization in neuronal lineages
Chromosome 5q14.3 harbored an unusual but genome-wide significant excess of noncoding BCA breakpoints that did not directly disrupt MEF2C. This distribution of breakpoints in proximity but not directly disruptive to MEF2C was further supported by microdeletions in NDD cases reported in DECIPHER34. In considering the landscape of de novo SVs across the 5q14.3 locus in NDD cases, the primary unifying thread appears to be distal boundary disruption. Taken together, these data provide compelling clinical genetic and statistical genomics evidence suggesting that both direct disruption of MEF2C and alterations to this gene's encompassing 3D regulatory architecture may result in comparable molecular mechanisms in NDD cases. Motivated by these findings, we have performed a systematic molecular dissection of the 5q14.3 locus to quantify the transcriptomic and electrophysiological effects of MEF2C LoF in human neural derivatives. Through the generation of an allelic series of CRISPR-engineered human induced pluripotent stem cell (hiPSC)-derived neural stem cells (NSCs) and glutamatergic neurons (iNs), we interrogated the impact of enhancer, TAD boundary, and loop boundary deletion on local genome organization, local expression effects on MEF2C, and global transcriptional signatures. Our analyses reveal that direct MEF2C alteration results in both transcriptional and functional changes to the synapse. Moreover, we find that disruption of the distal boundary of the MEF2C-containing loop is insufficient to produce indirect MEF2C haploinsufficiency. By contrast, disruption of the proximal boundary of the same 3D structure results in haploinsufficiency of MEF2C that is comparable to direct gene disruption. Overall, these data suggest that the effects of direct and indirect MEF2C disruption contribute to cell type-specific alterations on neuronal functions that converge on synaptic deficits in neurodevelopment. Overall design: RNASeq based transcriptomics analyses of NSC and iNs and 4C data for regional contacts