ArticleNature neuroscience2022
The three-dimensional landscape of cortical chromatin accessibility in Alzheimer's disease.
Article in Nature neuroscience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.Communications biology · 2023Pooled it
- Spatially resolved mapping of histones reveals selective neuronal response in Rett syndrome.The FEBS journal · 2026Article
- Efficient differential expression analysis of large-scale single-cell transcriptomics data using Dreamlet.Nature communications · 2026Article
- Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays.Molecular systems biology · 2026Article
- miR155, triplicated in Down syndrome, regulates the development of neural stem cells and GABAergic interneurons in Alzheimer's disease mouse and human iPSC models.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Article
- Single-cell multiomics connects 3D genome and transcriptome alterations in Alzheimer's disease.Science (New York, N.Y.) · 2026Article
- SECmeres outperform extracellular vesicles as potential blood RNA biomarkers for Alzheimer's disease.Nature communications · 2026Article
- Cellular Senescence of Patient-derived Fibroblasts Reveals the Mid-old Stage as a Critical Window for Transcriptomic Signatures Linked to Alzheimer's Disease Biomarkers and Classification.Clinical psychopharmacology and neuroscience : the official scientific journal of the Korean College of Neuropsychopharmacology · 2026Article
- Sex Differences in Brain Cell Type-Specific Chromatin Accessibility in Schizophrenia.Biological psychiatry · 2026Article
- The neuronal chromatin landscape in brains from individuals with schizophrenia is linked to early fetal development.Nature neuroscience · 2025Article
- Age-related microbiome metabolites alter RNA splicing and chromatin accessibility in the brain.bioRxiv : the preprint server for biology · 2025Article
- Multiscale proteomic modeling reveals protein networks driving Alzheimer's disease pathogenesis.Cell · 2025Article
- An ATAC-seq protocol for neuroscience research.Anatomical science international · 2025Article
- Article
- A Transcriptomic Roadmap of Parkinson's Disease Progression at Single Cell Resolution.medRxiv : the preprint server for health sciences · 2025Article
- Chromatin accessibility provides a window into the genetic etiology of human brain disease.Trends in genetics : TIG · 2025Review
- Alzheimer's Disease Prediction Using Fisher Mantis Optimization and Hybrid Deep Learning Models.Diagnostics (Basel, Switzerland) · 2025Article
- Population-scale cross-disorder atlas of the human prefrontal cortex at single-cell resolution.Scientific data · 2025Article
- Alzheimer's Prediction Methods with Harris Hawks Optimization (HHO) and Deep Learning-Based Approach Using an MLP-LSTM Hybrid Network.Diagnostics (Basel, Switzerland) · 2025Article
- Comparison of the amyloid plaque proteome in Down syndrome, early-onset Alzheimer's disease, and late-onset Alzheimer's disease.Acta neuropathologica · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors.
Funding
Abstract
To characterize the dysregulation of chromatin accessibility in Alzheimer's disease (AD), we generated 636 ATAC-seq libraries from neuronal and nonneuronal nuclei isolated from the superior temporal gyrus and entorhinal cortex of 153 AD cases and 56 controls. By analyzing a total of ~20 billion read pairs, we expanded the repertoire of known open chromatin regions (OCRs) in the human brain and identified cell-type-specific enhancer-promoter interactions. We show that interindividual variability in OCRs can be leveraged to identify cis-regulatory domains (CRDs) that capture the three-dimensional structure of the genome (3D genome). We identified AD-associated effects on chromatin accessibility, the 3D genome and transcription factor (TF) regulatory networks. For one of the most AD-perturbed TFs, USF2, we validated its regulatory effect on lysosomal genes. Overall, we applied a systematic approach to understanding the role of the 3D genome in AD. We provide all data as an online resource for widespread community-based analysis.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.