ATAC-seq

Brain cell type nuclei enrichment without fixative for nanoCUT&Tag and other omics approaches

The paper introduces a workflow for cell-type-specific epigenomic profiling of brain cells using nanoCUT&Tag and FANS, applicable to unfixed human and mouse brain tissue.

Assessing molecular gene by treatment interactions using a population of neural progenitors exposed to valproic acid and lithium

The paper exposes human neural progenitors to valproic acid and lithium, identifying gene by treatment interactions linked to psychiatric disorder risk and folate metabolism.

Monocyte Lineage Expansion Drives Transcriptomic Individuality in Genetically Identical Armadillo Quadruplets

The paper shows transcriptomic individuality in genetically identical armadillo quadruplets is driven by monocyte lineage expansion and stable gene expression differences.

Specialized high-capacity mitochondria fuel cell invasion

The paper identifies specialized high-capacity mitochondria in C. elegans anchor cells that generate elevated ATP to fuel basement membrane invasion.

OmicGlaze: Spatial Multi-Omic Mapping of Traumatic Brain Injury

OmicGlaze provides a spatial multi-omic framework to analyze TBI, identifying gene regulatory networks and region-specific biological changes.

A conserved enhancer cluster regulates efnb2 expression in the vertebrate dorsal retina

The paper identifies a conserved enhancer cluster regulating efnb2 expression in the dorsal retina and links it to human retinal thickness variation.

Myeloid Gi signaling acts as a weight-independent immunometabolic switch controlling systemic insulin sensitivity

This paper identifies myeloid Gi signaling as a weight-independent immunometabolic switch that regulates systemic insulin sensitivity through opposing cytokine programs.

Identifying Inheritance Patterns of Allelic Imbalance, using Integrative Modeling and Bayesian Inference

The paper develops a Bayesian method to infer inheritance patterns of allelic imbalance across trios, improving ASE estimation and linking it to chromatin state and causal variants.

Beat-locked ATP microdomains in the sinoatrial node map a calcium-timed energetic hierarchy and regional pacemaker roles

The paper tracks beat-resolved ATP dynamics in mouse sinoatrial node myocytes, revealing distinct ATP-gain and -dip modes linked to regional pacemaker roles and energy supply.

Modeling gene regulatory perturbations via deep learning from high-throughput reporter assays

The paper introduces BlueSTARR, a predictive modeling framework trained on whole-genome STARR-seq data to assess variant effects on regulatory functions, revealing purifying selection against loss-of-function and gain-of-function variants.

Foxp3 and BATF cooperatively direct cis-regulatory programs and gene expression for functional differentiation of Treg cells

The paper identifies cooperative roles of Foxp3 and BATF in directing cis-regulatory programs and gene expression for Treg cell differentiation.

Beyond chromatin accessibility: bulk ATAC-seq as an integrative assay to portray genomes and epigenomes

This study evaluates bulk ATAC-seq's ability to detect genomic variants, CNVs, and telomere repeats, showing its potential as an integrative tool for cancer research.

Identification of Parkinson's disease-associated regulatory variants in human dopaminergic neurons reveals modulators of SCARB2 and BAG3 expression

The paper identifies Parkinson's disease-associated regulatory variants in human dopaminergic neurons and shows they modulate SCARB2 and BAG3 expression.

Bi-allelic ATG12 variants impair autophagy and cause a neurodevelopmental disorder

The paper identifies bi-allelic ATG12 variants causing a neurodevelopmental disorder by impairing autophagy, with clinical and functional evidence from patient cells, yeast, and zebrafish models.

Trait-specific chromatin architectures channel pleiotropic genes toward sexually dimorphic development in horned beetles

The paper investigates how chromatin architecture and gene regulation contribute to trait-specific sexual dimorphism in horned beetles by analyzing gene expression and chromatin accessibility across multiple traits.

Single-cell spatial multi-omics molecular pathology enabled by SuperFocus

SuperFocus integrates histopathology with single-cell spatial multi-omics data from spot-based measurements, improving accuracy by 28-73% over existing methods.

Stress-responsive enhancer RNAs couple chromatin reprogramming to post-transcriptional control of senescence

The paper identifies senescence-associated enhancer RNAs (SAeRs) and shows their functional role in linking chromatin reprogramming to post-transcriptional regulation of senescence.

Gene regulatory network determinants of rapid recall in human memory CD4+ T cells

This study identifies gene regulatory networks in human memory CD4+ T cells that drive rapid recall, linking specific transcription factors to immune-mediated disease risk.

Multi-omic identification of key transcriptional regulatory programs during endurance exercise training in rats

The paper identifies tissue-specific transcriptional regulatory programs in rats undergoing endurance exercise training by integrating chromatin accessibility, DNA methylation, and gene expression data.

HDI-STARR-seq Identifies Functional Growth Hormone-regulated Sex-Biased Hepatocyte Enhancers Linked to Liver Metabolism and Disease

The paper identifies GH-regulated sex-biased hepatocyte enhancers linked to liver metabolism and disease using HDI-STARR-seq and chromatin accessibility data.

Inflammatory signaling differentially changes chromatin accessibility and gene expression of the PD- associated kinase LRRK2 between human and mice

The paper shows that inflammatory signaling affects LRRK2 regulation differently in human and mouse models, highlighting species-specific regulatory mechanisms.

KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival

This study identifies KLF5-bound enhancers in pancreatic cancer that regulate cell survival, showing their subtype-independent role in maintaining tumor viability.

A dual role for CTCF in development

This study shows CTCF has dual roles in early mammalian development: promoting morphogenesis through promoter binding early on and enabling correct development via looping later.

In vivo multiomic Perturb-seq with enhanced nuclear gRNA capture

This paper develops an in vivo multiomic Perturb-seq platform to improve gRNA recovery and applies it to study neurodevelopmental disorder risk genes in the cortex.

Co-regulatory changes in Homo sapiens prefrontal cortex shape RNA-chromatin interactions

The paper maps RNA-chromatin interactions in human prefrontal cortex, revealing co-regulatory changes linked to brain evolution and disease pathways.

Vascular smooth muscle cell atherosclerosis trajectories characterized at single cell resolution identify causal transcriptomic and epigenomic mechanisms of disease risk

The paper characterizes atherosclerosis trajectories in vascular smooth muscle cells using single-cell data and identifies causal transcriptomic and epigenomic mechanisms of CAD risk.

Single-cell chromatin profiling reveals dynamic regulatory logic and enhancer elements in brain and retina development

The paper creates a single-cell chromatin accessibility atlas of zebrafish brain and retina development, identifies chromatin states, and validates enhancer elements involved in gene regulation.

Circulating miR-10b-5p drives Kawasaki vasculitis through endothelial reprogramming and nominates CXCL8 as an early diagnostic biomarker

This study identifies miR-10b-5p as a driver of Kawasaki disease vasculitis through endothelial reprogramming and shows CXCL8 as an early diagnostic biomarker.

A deep-time landscape of plant cis-regulatory sequence evolution

Conservatory, an orthogroup-centric conserved noncoding sequence finder, catalogs 2.3 million unique CNSs across 314 plant genomes and reveals regulatory elements older than angiosperms and seed plants.

3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis

The paper defines a 3D chromatin compartment blueprint that programs histone-to-protamine exchange during spermiogenesis using ATAC-seq, CUT&Tag, and Hi-C.