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Rogers BB, Anderson AG, Lauzon SN, Davis MN, Hauser RM, Roberts SC, Rodriguez-Nunez I, Trausch-Lowther K, Barinaga EA, Hall PI, Knuesel MT, Taylor JW, Mackiewicz M, Roberts BS, Cooper SJ, Rizzardi LF, Myers RM, Cochran JN. Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements. Am J Hum Genet 2024; 111:259-279. [PMID: 38232730 PMCID: PMC10870142 DOI: 10.1016/j.ajhg.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Tauopathies are a group of neurodegenerative diseases defined by abnormal aggregates of tau, a microtubule-associated protein encoded by MAPT. MAPT expression is near absent in neural progenitor cells (NPCs) and increases during differentiation. This temporally dynamic expression pattern suggests that MAPT expression could be controlled by transcription factors and cis-regulatory elements specific to differentiated cell types. Given the relevance of MAPT expression to neurodegeneration pathogenesis, identification of such elements is relevant to understanding disease risk and pathogenesis. Here, we performed chromatin conformation assays (HiC & Capture-C), single-nucleus multiomics (RNA-seq+ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27ac and CTCF in NPCs and differentiated neurons to nominate candidate cis-regulatory elements (cCREs). We assayed these cCREs using luciferase assays and CRISPR interference (CRISPRi) experiments to measure their effects on MAPT expression. Finally, we integrated cCRE annotations into an analysis of genetic variation in neurodegeneration-affected individuals and control subjects. We identified both proximal and distal regulatory elements for MAPT and confirmed the regulatory function for several regions, including three regions centromeric to MAPT beyond the H1/H2 haplotype inversion breakpoint. We also found that rare and predicted damaging genetic variation in nominated CREs was nominally depleted in dementia-affected individuals relative to control subjects, consistent with the hypothesis that variants that disrupt MAPT enhancer activity, and thereby reduced MAPT expression, may be protective against neurodegenerative disease. Overall, this study provides compelling evidence for pursuing detailed knowledge of CREs for genes of interest to permit better understanding of disease risk.
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Affiliation(s)
- Brianne B Rogers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Shelby N Lauzon
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - M Natalie Davis
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Rebecca M Hauser
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sydney C Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Erin A Barinaga
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Paige I Hall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Jared W Taylor
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Brian S Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
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