Joseph R. Nery
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View article: Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer’s Disease
Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer’s Disease Open
Alzheimer’s disease (AD) is the most common neurodegenerative disorder, yet the molecular mechanisms underlying its region– and cell-type-specific pathogenesis remain poorly defined. Here, we generated a large-scale, single-cell multi-omic…
View article: Drought recovery in plants triggers a cell-state-specific immune activation
Drought recovery in plants triggers a cell-state-specific immune activation Open
All organisms experience stress as an inevitable part of life, from single-celled microorganisms to complex multicellular beings. The ability to recover from stress is a fundamental trait that determines the overall resilience of an organi…
View article: A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle
A single-cell, spatial transcriptomic atlas of the Arabidopsis life cycle Open
View article: Maternal Immune Activation Disrupts Epigenomic and Functional Maturation of Cortical Excitatory Neurons
Maternal Immune Activation Disrupts Epigenomic and Functional Maturation of Cortical Excitatory Neurons Open
Summary Elevated levels of maternal pro-inflammatory cytokines during gestation can disrupt offspring neural development, increasing the risk of neurodevelopmental disorders. We studied the effects of Poly(I:C)-induced maternal immune acti…
View article: DNA Methylation Dynamics of Dose-dependent Acute Exercise, Training Adaptation, and Detraining
DNA Methylation Dynamics of Dose-dependent Acute Exercise, Training Adaptation, and Detraining Open
Exercise and diet are direct physical contributors to human health, wellness, resilience, and performance 1–5 . Endurance and resistance training are known to improve healthspan through various biological processes such as mitochondrial fu…
View article: Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain
Cell-type-specific transposable element demethylation and TAD remodeling in the aging mouse brain Open
Aging is a major risk factor for neurodegenerative diseases, yet underlying epigenetic mechanisms remain unclear. Here, we generated a comprehensive single-nucleus cell atlas of brain aging across multiple brain regions, comprising 132,551…
View article: Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation
Human Body Single-Cell Atlas of 3D Genome Organization and DNA Methylation Open
Higher-order chromatin structure and DNA methylation are critical for gene regulation, but how these vary across the human body remains unclear. We performed multi-omic profiling of 3D genome structure and DNA methylation for 86,689 single…
View article: Stress drives plasticity in leaf maturation transcriptional dynamics
Stress drives plasticity in leaf maturation transcriptional dynamics Open
Leaf development is dynamic, adapting to environmental stress to optimize resource use. For example, in response to drought, Arabidopsis restricts leaf growth to enhance water use efficiency. While this plastic response is well described a…
View article: A rare PRIMER cell state in plant immunity
A rare PRIMER cell state in plant immunity Open
View article: Cell-Type-Specific Transposable Element Demethylation and TAD Remodeling in the Aging Mouse Brain
Cell-Type-Specific Transposable Element Demethylation and TAD Remodeling in the Aging Mouse Brain Open
View article: Exaptation of ancestral cell-identity networks enables C4 photosynthesis
Exaptation of ancestral cell-identity networks enables C4 photosynthesis Open
C 4 photosynthesis is used by the most productive plants on the planet, and compared with the ancestral C 3 pathway, it confers a 50% increase in efficiency 1 . In more than 60 C 4 lineages, CO 2 fixation is compartmentalized between tissu…
View article: Author response: Arabidopsis transcriptome responses to low water potential using high-throughput plate assays
Author response: Arabidopsis transcriptome responses to low water potential using high-throughput plate assays Open
View article: Arabidopsis transcriptome responses to low water potential using high-throughput plate assays
Arabidopsis transcriptome responses to low water potential using high-throughput plate assays Open
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana . Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol, and sal…
View article: Reviewer #2 (Public Review): Arabidopsis transcriptome responses to low water potential using high throughput plate assays
Reviewer #2 (Public Review): Arabidopsis transcriptome responses to low water potential using high throughput plate assays Open
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol and salt …
View article: Reviewer #3 (Public Review): Arabidopsis transcriptome responses to low water potential using high throughput plate assays
Reviewer #3 (Public Review): Arabidopsis transcriptome responses to low water potential using high throughput plate assays Open
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol and salt …
View article: Author response: Arabidopsis transcriptome responses to low water potential using high throughput plate assays
Author response: Arabidopsis transcriptome responses to low water potential using high throughput plate assays Open
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol and salt …
View article: Arabidopsis transcriptome responses to low water potential using high throughput plate assays
Arabidopsis transcriptome responses to low water potential using high throughput plate assays Open
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol and salt …
View article: Cell-type-specific effects of age and sex on human cortical neurons
Cell-type-specific effects of age and sex on human cortical neurons Open
Altered transcriptional and epigenetic regulation of brain cell types may contribute to cognitive changes with advanced age. Using single-nucleus multi-omic DNA methylation and transcriptome sequencing (snmCT-seq) in frontal cortex from yo…
View article: Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex
Author Correction: Conserved and divergent gene regulatory programs of the mammalian neocortex Open
In the version of the article initially published, in Figs.2c andd and5e, numbers in labels had been rounded.These have been corrected to exact numbers.In Fig. 2c andd, the labels now read "Mammal level 3 (16,068)", "Human biased ↑ (10,743…
View article: Brain-wide correspondence of neuronal epigenomics and distant projections
Brain-wide correspondence of neuronal epigenomics and distant projections Open
Single-cell analyses parse the brain’s billions of neurons into thousands of ‘cell-type’ clusters residing in different brain structures 1 . Many cell types mediate their functions through targeted long-distance projections allowing intera…
View article: Conserved and divergent gene regulatory programs of the mammalian neocortex
Conserved and divergent gene regulatory programs of the mammalian neocortex Open
View article: Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain Open
Cytosine DNA methylation is essential in brain development and is implicated in various neurological disorders. Understanding DNA methylation diversity across the entire brain in a spatial context is fundamental for a complete molecular at…
View article: Cell type-specific effects of age and sex on human cortical neurons
Cell type-specific effects of age and sex on human cortical neurons Open
Summary Excitatory and inhibitory neurons establish specialized identities early in life through cell type-specific patterns of epigenetic regulation and gene expression. Although cell types are largely stable throughout the lifespan, alte…
View article: Single nuclei sequencing reveals C<sub>4</sub>photosynthesis is based on rewiring of ancestral cell identity networks
Single nuclei sequencing reveals C<sub>4</sub>photosynthesis is based on rewiring of ancestral cell identity networks Open
Summary In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesi…
View article: Epigenome erosion in Alzheimer’s disease brain cells and induced neurons
Epigenome erosion in Alzheimer’s disease brain cells and induced neurons Open
Late-onset Alzheimer’s disease (LOAD) is typically sporadic, correlated only to advanced age, and has no clear genetic risk factors. The sporadic nature of LOAD presents a challenge to understanding its pathogenesis and mechanisms. Here, w…
View article: Single-cell DNA methylation and 3D genome architecture in the human brain
Single-cell DNA methylation and 3D genome architecture in the human brain Open
Delineating the gene-regulatory programs underlying complex cell types is fundamental for understanding brain function in health and disease. Here, we comprehensively examined human brain cell epigenomes by probing DNA methylation and chro…
View article: Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome
Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome Open
The epigenomic landscape of human immune cells is dynamically shaped by both genetic factors and environmental exposures. However, the relative contributions of these elements are still not fully understood. In this study, we employed sing…
View article: Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes
Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes Open
Single-cell sequencing could help to solve the fundamental challenge of linking millions of cell-type-specific enhancers with their target genes. However, this task is confounded by patterns of gene co-expression in much the same way that …
View article: Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections
Brain-wide Correspondence Between Neuronal Epigenomics and Long-Distance Projections Open
Single-cell genetic and epigenetic analyses parse the brain’s billions of neurons into thousands of “cell-type” clusters, each residing in different brain structures. Many of these cell types mediate their unique functions by virtue of tar…
View article: Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain
Single-cell DNA Methylome and 3D Multi-omic Atlas of the Adult Mouse Brain Open
Cytosine DNA methylation is essential in brain development and has been implicated in various neurological disorders. A comprehensive understanding of DNA methylation diversity across the entire brain in the context of the brain’s 3D spati…