ATAC-seq

This paper identifies a SOX9 C-terminal module that recruits cBAF to enhancers, controlling cell state by remodeling chromatin.

The paper uses long-read sequencing to analyze human 5S rDNA arrays, revealing zoned methylation patterns linked to chromatin structure.

The paper investigates how B chromosomes in maize affect chromatin accessibility and gene expression in pollen nuclei using ATAC-seq and RNA-seq.

The paper maps gene expression, chromatin accessibility, and DNA methylation in developing human brain cells to understand regulatory interactions and their role in disease.

This study maps genome-wide chromatin accessibility in A. calliptera embryos across three stages, revealing dynamic changes in regulatory elements and transcription factor activity during early development.

The paper identifies ST18 as a regulator of deep CA3 pyramidal neuron identity, showing its role in restricting a superficial-like program and shaping circuit integration through molecular and electrophysiological changes.

This study identifies factors influencing Sleeping Beauty transposition, showing chromatin context, cargo size, and transcriptional activity affect efficiency and reintegration patterns.

This study shows SMARCA4 mutations in T-ALL lead to chemotherapy resistance by altering chromatin remodeling at AP-1 regulatory regions, reducing stress response genes.

This study shows that during nutrient starvation, chromatin accessibility decreases genome-wide, but RNA abundance increases selectively in stress-adaptive genes, indicating limited predictive power of ATAC-seq for transcript abundance.

The paper optimizes ATAC-see for high-throughput chromatin accessibility imaging in aging and reprogramming, revealing age-related chromatin changes and reprogramming-induced remodeling.

The paper investigates how genomic changes in coleoid cephalopods shape 3D genome architecture and regulatory landscapes, revealing species-specific chromatin loops and their role in neural development.

The paper identifies chromatin-opening transcription factors in mouse embryonic stem cells using CRISPRa screens, revealing autonomous, opportunistic, and hierarchical mechanisms.

This study shows paclitaxel induces cancer cell contraction via GEF-H1 dissociation from microtubules and RhoA/ROCK activation, with tubulin acetylation regulating this process.

This study shows nuclear βactin regulates chromatin accessibility and ECM mechanics to maintain pluripotency and lineage decisions in mESCs.

This study shows that non-cancerous fibroblasts experience reversible nuclear and 3D genomic changes after constricted migration, unlike stable changes in cancer cells.

The paper shows that conserved motif vocabularies constrain genome access in cell type evolution across species.

tATAC-see captures target-specific chromatin states using a visual assay, showing dynamic remodeling in aging models and LAD resistance.

The paper shows that eGATA3 mutations alter transcriptional regulation and lineage identity in luminal breast cancer without losing DNA-binding function.

This study shows mitochondrial translation is sensitive to ATP synthase activity, with matrix GTP availability identified as a key constraint.

This study shows that elevated cholesterol in APOE4 astrocytes causes mitochondrial cristae collapse and ATP synthase dysfunction, linking cholesterol imbalance to mitochondrial disease.

The paper reports an in vitro system of lipid kinases and phosphatases that self-organize into dynamic spatiotemporal patterns on model membranes.

The paper identifies regulatory variation driving lineage divergence in European sea bass by analyzing epigenomic and genomic data from Atlantic and Mediterranean populations.

The paper investigates craniofacial genetic network evolution in syngnathid fishes using multiomics data, finding conserved core networks with localized changes contributing to morphological diversity.

This study shows that inhibiting Notch signaling and forcing cell cycle re-entry in Müller glia promotes their reprogramming into neurons in uninjured mouse retina.

The paper shows BRCA1-A complex restricts replication fork reversal in ATM-deficient cells, leading to hypersensitivity to Topoisomerase I inhibitors and resistance to PARP1 inhibitors.

The paper profiles chromatin accessibility in post-sepsis MDSCs, showing divergent epigenetic trajectories between rapid recovery and chronic critical illness, with MHC class II repression in CCI.

The paper characterizes ~700,000 conserved noncoding elements in the human genome, showing many have cis-regulatory potential and are enriched in TAD centers.

The paper uses ATAC-Seq to study chromatin accessibility in neutrophils stimulated with inflammatory factors, finding stimulus-specific programs linked to sepsis transcriptional states.

This paper identifies lineage-specific chromatin accessibility differences at IFN gene loci in pDCs and epithelial cells, revealing ETS-IRF composite elements as key regulators of divergent interferon responses.

This study identifies age-related epigenetic changes in AT2 cells that promote basal cell metaplasia, contributing to idiopathic pulmonary fibrosis.