Identification of cis‐regulatory elements associated with MAPT expression in human induced pluripotent stem cell derived neural cells

• DOI: 10.1002/alz.072171
• Publication Date: 2023-12-25T09:32:58Z
• Authors: Brianne B. Rogers; Ashlyn G Anderson; Shelby N. Lauzon; M. Natalie Davis; Rebecca M. Hauser; Sydney C. Roberts; Ivan Rodriguez‐Nunez; Katie Trausch‐Low...; Brian S. Roberts; Erin A. Barinaga; Lindsay F. Rizzardi; Sara J. Cooper; Richard M. Myers; J. Nicholas Cochran

Abstract Background Tau is encoded by MAPT and abnormal aggregates of tau are a hallmark many neurodegenerative diseases. highly expressed in neurons but much more lowly other cell types, including neural precursor cells (NPCs), suggesting that its expression may be controlled neuron‐specific transcription factors cis‐regulatory elements. reduction, even endogenous tau, current therapeutic strategy both model systems humans; therefore, understanding regulation point to new strategies achieve reduction. Additionally, genome sequencing studies continue identify disease‐associated variants non‐coding regions the genome. These likely located regulatory affect target genes whose function contributes neurodegeneration. Therefore, an additional benefit this study high confidence for provide way important associated with disease. Methods Three‐dimensional chromatin conformation capture (Capture‐C), single‐cell multiomics (RNAseq + ATACseq), marks H3K27ac, H3K4me1, DNase hypersensitivity were used candidate enhancers human NPCs, NPCs differentiated neurons, pure inhibitory or excitatory neuron cultures (all lines H1/H1). Approaches included nomination elements signals specific neuronal subtypes. The nominated then assessed using luciferase assays test sufficiency activity as well CRISPR‐dCas9‐KRAB assess effect on expression. Results We identified proximal distal confirmed up four orthogonal approaches (chromatin capture, single multiomics, reporter assay, element inhibition dCas9‐KRAB). Several these neurons. One particularly region was centromeric beyond H2 inversion breakpoint. Conclusions Overall, results indicate elements, Next steps include trans‐regulatory (i.e., factors) control recruitment assessment effects genetic variation MAPT.