The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease
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Abstract
Abstract Much is still unknown about the neurobiology of Alzheimer’s disease (AD). To better understand AD, we generated 636 ATAC-seq libraries from cases and controls to construct detailed genomewide chromatin accessibility maps of neurons and non-neurons from two AD-affected brain regions, the entorhinal cortex and superior temporal gyrus. By analyzing a total of 19.6 billion read pairs, we expanded the known repertoire of regulatory sequences in the human brain. Multi-omic data integration associated global patterns of chromatin accessibility with gene expression and identified cell-specific enhancer-promoter interactions. Using inter-individual variation in chromatin accessibility, we define cis -regulatory domains capturing the 3D structure of the genome. Multifaceted analyses uncovered disease associated perturbations impacting chromatin accessibility, transcription factor regulatory networks and the 3D genome, and implicated transcriptional dysregulation in AD. Overall, we applied a systematic approach to understand the role of the 3D genome in AD and to illuminate novel disease biology that can advance diagnosis and therapy.
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Chromatin accessibility has been shown to be disrupted in the AD brain.
“Chromatin accessibility has also been shown to be disrupted in the AD brain”
From Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration (2023) · cites this paper as [45]
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A mathematical model clarifies the ABC Score formula used in enhancer-gene predictionPreprint
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- Authors
- Bendl, J., Hauberg, M. E., Girdhar, K., Im, E., Vicari, J. M., Rahman, S., Fernando, M. B., Townsley, K. G., Dong, P., Misir, R., Kleopoulos, S. P., Reach, S. M., Apontes, P., Zeng, B., Zhang, W., Voloudakis, G., Brennand, K. J., Nixon, R. A., Haroutunian, V., Hoffman, G. E., Fullard, J. F., & Roussos, P.
- Affiliations
- Icahn School of Medicine at Mount Sinai (US)
- Aarhus University (DK)
- Nathan Kline Institute for Psychiatric Research (US)
- Yale University (US)
- James J. Peters VA Medical Center (US)
- Corresponding author
- Roussos, Panos
- ORCID
- Bendl, Jaroslav
- Hauberg, Mads E.
- Girdhar, Kiran
- Im, Eunju
- Vicari, James M.
- Rahman, Samir
- Fernando, Michael B.
- Townsley, Kayla G.
- Dong, Pengfei
- Kleopoulos, Steven P.
- Reach, Sarah M.
- Apontes, Pasha
- Voloudakis, Georgios
- Brennand, Kristen J.
- Nixon, Ralph A.
- Haroutunian, Vahram
- Hoffman, Gabriel E.
- Fullard, John F.
- Roussos, Panos
- Venue
- Nature Neuroscience
- Published
- 2022-09-28
- Volume
- 25
- Issue
- 10
- Pages
- 1366-1378
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC9581463
- OpenAlex
- W4297498024
- Cited by
- 65
- References
- 117
- Citations by year
- 2026: 13 · 2025: 18 · 2024: 12 · 2023: 15 · 2022: 5 · 2021: 2
- FWCI
- 4.08
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Nature Neuroscience (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Alzheimer’s Association (AARF-21-722200, AARF-21-722582)
- Brain and Behavior Research Foundation (Young Investigator Grant 29683, Young Investigator Grant 26313)
- U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (R01-MH121074, R01-MH106056, R01-MH109897)
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (R01-AG067025, R01-AG065582, R01-AG050986)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
- Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
- Keywords
- Alzheimer's disease, chromatin accessibility, open chromatin regions, 3D genome organization, enhancer-promoter interactions, transcriptional regulatory networks, USF2, lysosomal genes, superior temporal gyrus, entorhinal cortex, postmortem brain, interindividual variability
- MeSH terms
- Alzheimer Disease, Chromatin, Humans, Promoter Regions, Genetic, Transcription Factors
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