MAPTexpression is mediated by long-range interactions withcis-regulatory elements

Abstract

ABSTRACTBackgroundTauopathies are a group of neurodegenerative diseases driven by abnormal aggregates of tau, a microtubule associated protein encoded by theMAPTgene.MAPTexpression is absent in neural progenitor cells (NPCs) and increases during differentiation. This temporally dynamic expression pattern suggests thatMAPTexpression is controlled by transcription factors and cis-regulatory elements specific to differentiated cell types. Given the relevance ofMAPTexpression to neurodegeneration pathogenesis, identification of such elements is relevant to understanding genetic risk factors.MethodsWe performed HiC, chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq+ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in NPCs and neurons differentiated from human iPSC cultures. We nominated candidate cis-regulatory elements (cCREs) forMAPTin human NPCs, differentiated neurons, and pure cultures of inhibitory and excitatory neurons. We then assayed these cCREs using luciferase assays and CRISPR interference (CRISPRi) experiments to measure their effects onMAPTexpression. Finally, we integrated cCRE annotations into an analysis of genetic variation in AD cases and controls.ResultsUsing orthogonal genomics approaches, we nominated 94 cCREs forMAPT, including the identification of cCREs specifically active in differentiated neurons. Eleven regions enhanced reporter gene transcription in luciferase assays. Using CRISPRi, 5 of the 94 regions tested were identified as necessary forMAPTexpression as measured by RT-qPCR and RNA-seq. Rare and predicted damaging genetic variation in both nominated and confirmed CREs was depleted in AD cases relative to controls (OR = 0.40, p = 0.004), consistent with the hypothesis that variants that disruptMAPTenhancer activity, and thereby reduceMAPTexpression, may be protective against neurodegenerative disease.ConclusionsWe identified both proximal and distal regulatory elements forMAPTand confirmed the regulatory function for several regions, including three regions centromeric toMAPTbeyond the well-described H1/H2 haplotype inversion breakpoint. This study provides compelling evidence for pursuing detailed knowledge of CREs for genes of interest to permit better understanding of disease risk.