EOFAD-causing mutations in psen1 orchestrate dedifferentiation through remodeling of the chromatin landscape in hiPSC-derived neurons [ChIP-Seq]

In this work, we used an integrative, multi-omics approach and systems-level analysis to generate a mechanistic disease model for EOFAD in an hiPSC-derived neuron model system. Overall design: hiPSC-derived neurons were generated from patient-specific Non-Demented Control, PSEN1M146L, PSEN1H163R, PSEN1A246E, and PSEN1A431E fibroblasts and subjected to RNA-Seq, ATAC-Seq, and histone methylation ChiP-Seq. For H3K4Me3 and H3K27Me3 ChIP-Seq experiments, NDC, PSEN1M146L, and PSEN1A246E (n = 1) hiPSC-derived neurons were processed using the Active Motif ChIP-IT High Sensitivity kit. 500 ng of purified, sonicated chromatin was incubated with 5 µL of H3K4Me3 or H3K27Me3 Rabbit polyclonal antibody overnight at 4C. After de-crosslinking, ChIP DNA was purified using the Qiagen MinElute PCR Purification Kit; libraries for H3K4Me3, H3K27Me3, and 1% Input were generated using Illumina TruSeq LT adaptors. Sequencing was performed on an Illumina HiSeq4000 generating Single-Read, 75bp reads with an average of 20 million reads per sample.