Genomics and Chromatin Dynamics

FFPE-CUTAC is a new assay for analyzing FFPE tissues that provides regulatory and copy-number profiles, showing robustness over time and compatibility with RNA-seq.

This study investigates how linker histone H1.0 binds to nucleosomes and DNA, revealing multiple pathways facilitated by histone chaperones like Nap1.

The paper develops a theory linking chromatin architecture to epigenetic memory stability and predicts compartment fusion over cell generations.

scStripe detects and quantifies chromatin stripes in single-cell Hi-C data, resolving cell-type-specific regulatory features and capturing genome-wide variation.

The paper identifies brain region-specific enhancers linked to neurological disease risk and shows their role in cellular pathology using enhancer activity data and GWAS integration.

The paper identifies AR as the factor driving active enhancer resetting after transcriptional activation, which prevents transcriptional hyperactivation in ER-positive breast cancer.

This study visualizes human INO80's activity on DNA, showing it rapidly moves nucleosomes between chromatin barriers through directional reversal and boundary confinement.

This study shows that H3.3K27M mutation disrupts lamina-associated domain organization, leading to activation of neuronal gene programs in DIPG.

This study investigates the role of H2A.Z-H2B.V nucleosomes in transcription initiation in Trypanosoma brucei, revealing their unique structural and functional properties.

The paper uses Hi-D to track chromatin motion in live human cells and finds that DNA content doubling, not cohesin, reduces chromatin mobility during the cell cycle.

This study shows that condensin I regulates meiotic chromosome structure and recombination by controlling chromatin loops and synaptonemal complex organization in mammals.

inteRelate compares genomic features by analyzing their overlap with a common feature, testing heterogeneity and identifying differing overlap rates across biological contexts.

The paper develops Nanopore-HiChIP to map enhancer hubs and shows they buffer allelic regulatory variation through kinetic compensation, preserving balanced transcriptional output.

The paper analyzes transcription initiation sites in Paramecium species to understand gene expression and sequence architecture.

This study shows that SMCHD1's weak DNA binding is essential for its chromatin retention and function, revealing how DNA binding affects its localization and gene repression.

MIMoSA compares transcription factor binding motifs independently of their representation, showing comparable performance to PWM-based tools on benchmark datasets.

The paper identifies a 3D enhancer hub at 12q24.31 that regulates HCAR2 and explains shared genetic mechanisms in schizophrenia and multiple sclerosis.

The paper develops ARES to analyze TF binding data and finds that motif readers, not canonical TFs, determine regulatory outcomes.

The paper uses deep learning to analyze Alu elements' impact on genome folding, identifying sequence and genomic context features that influence chromatin interactions and boundary formation.

This study identifies DNA elements that mediate vIRF3 and IRF4 cooperation in activating super-enhancers, revealing their role in oncogenesis.

The paper uses RIC-seq and integrates multi-omics data to classify transcription factors into two clusters based on RNA-RNA spatial interactions and their genomic and clinical features.

The paper shows Mi-2 and E93 coordinate cell cycle exit with terminal differentiation by decommissioning enhancers at key genes in Drosophila.

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

This study investigates how EWSR1::FLI1 binds to nucleosomes and DNA motifs, revealing its pioneer factor properties and preference for GGAA repeats.

DiffDomain-Spectrum identifies reorganized TADs from sparse aggregated scHi-C maps by analyzing eigenvalue spectra and comparing to a null model, showing higher sensitivity than existing methods.

The paper shows ecDNA localizes to the nuclear periphery in cancer, resisting silencing and enhancing transcriptional output through interactions with the nuclear lamina.

Epi-PoreC profiles chromatin conformation, DNA methylation, and chromatin accessibility simultaneously using nanopore sequencing on single DNA molecules.

The paper shows that cohesin enables the developmental loss of Polycomb interactions by facilitating other regulatory contacts during cell type transitions.

The paper maps major histone modifications in a reef-building coral to understand chromatin regulation of gene expression and identifies distinct epigenetic states.