Genomics and Chromatin Dynamics

Deciphering context-dependent epigenetic program by network-based prediction of clustered open regulatory elements from single-cell chromatin accessibility

The paper introduces enCORE, a framework to identify clustered open regulatory elements from single-cell ATAC-seq data, revealing regulatory programs and potential therapeutic targets in colorectal cancer.

Hierarchical refinements of cis-regulatory inputs improve scalable gene expression prediction

The paper introduces a two-stage framework for gene expression prediction from cis-regulatory elements, showing improved performance across human cell types and tissues.

MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data

MINTsC identifies multi-way chromatin interactions from scHi-C data, revealing gene regulation by multiple enhancers and reducing multiple-testing burden in molecular QTL studies.

Genome-wide mapping of Bicoid/DNA interactions reveals quantitative constraints on transcriptional regulation

The paper quantifies Bicoid/DNA interactions in Drosophila to model transcriptional regulation and explains the sharp posterior boundary of hunchback gene expression.

Mammalian epigenomic conservation of promoters and enhancers in the heart associates with trait-associated variation and impacts cardiomyocyte phenotypes

The paper identifies epigenomically conserved promoters and enhancers in the heart, links them to cardiovascular trait variation, and shows their impact on cardiomyocyte phenotypes through experimental validation.

Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency

The paper investigates the chromosomal contacts of poised enhancers during the transition from naive to primed human pluripotency, revealing their dynamics and functional significance.

Single-cell mapping of regulatory DNA:Protein interactions

This paper introduces D&D-seq, a single-cell method to map DNA:Protein interactions with high specificity and resolution, and applies it to study TF binding in human cells.

DanioDecima: A DNA sequence-to-function model of zebrafish embryogenesis

DanioDecima improves gene expression prediction in zebrafish by transferring knowledge from human and mouse models, enhancing correlations and generating synthetic promoters with expected lineage-specific motifs.

Rare RNA Polymerase II failure modes mark the cancer-driving genes most affected by epigenetic perturbation

The paper introduces compPASS, a tool to identify Pol2 failure modes in cancer, revealing rare modes linked to gene regulation and therapy response.

Cooperative FOXA1-HNF4A binding emerges from motif spacing and nucleosome architecture

The paper identifies sequence and chromatin features that enable cooperative binding between FOXA1 and HNF4A, showing that motif spacing and nucleosome architecture are key factors.

Molecular Basis of Histone H3 Reading and Writing by Legionella pneumophila SET Domain Lysine Methyltransferases

This study investigates how Legionella pneumophila's SET domain enzymes methylate histone H3K14, revealing structural mechanisms for substrate specificity and nucleosome engagement.

ModCRE-NN: Interpretable Deep Learning Harnesses Structural and Evolutionary Synergy to Predict Transcription Factor Binding Specificity

ModCRE-NN predicts transcription factor DNA-binding motifs by integrating structural and evolutionary data, showing improved performance under low similarity and uncertainty.

Histone lactylation H3K18la and acetylation H3K27ac encode two separable epigenomic features for enhancer regulation

This study identifies H3K18la and H3K27ac as distinct epigenomic features that encode separate aspects of enhancer regulation, with H3K18la associated with lineage-specific factors and p300/CBP dependency, while H3K27ac is linked to BRD4/MED1 and phase separation.

ELOF1 is a core component of the promoter-proximal paused RNA polymerase II complex

This study identifies ELOF1 as a critical factor enhancing promoter-proximal RNA polymerase II pausing, showing its role in counteracting TFIIF effects.

Chromatin architecture sets origin licensing capacity

The paper shows that chromatin architecture limits replication origin licensing capacity in budding yeast by restricting helicase loading through Isw2-dependent nucleosome repositioning.

Atg8 orchestrates stress-responsive chromatin programs across immunity and metabolism

This study identifies Atg8/LC3 as a stress-responsive chromatin cofactor that coordinates immune and metabolic transcription through interactions with NF-κB/Dif in Drosophila.

Transcription initiation profiling defines the regulatory logic of astrocyte gene regulation

This study maps transcription initiation in mouse astrocytes to define how inflammatory signals drive cell-type-specific gene regulation and links enhancer activity to human disease risk.

Accelerated Aging Signatures in 3D Genome Organization and Transcriptome in Schizophrenia

This study identifies accelerated aging patterns in 3D genome organization and transcriptome in schizophrenia using Hi-C data and transcriptomic analysis.

Histone modifications analysis reveals enhancers reprogramming during maternal-to-zygotic transition

This study analyzes histone modifications H3K4me1 and H3K27ac during maternal-to-zygotic transition in mouse embryos, revealing dynamic reprogramming and enhancer type changes.

Lineage-specific retrotransposon co-option reveals a conserved ASH2L isoform as an epigenetic primer of developmental gene promoters

The paper shows that a truncated ASH2L isoform, generated via a lineage-specific retrotransposon, primes developmental gene promoters during pluripotency and is required for later developmental transitions.

Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes

The paper develops STEAM, an evolution-augmented deep learning model, to predict mammalian enhancer landscapes across species using comparative genomics and single-cell data.

Humanization of the rpb9 locus in fission yeast reveals conserved and divergent roles of rpb9 and human POLR2I

This study humanizes the rpb9 gene in fission yeast to examine the functional and structural conservation of POLR2I, revealing both conserved and divergent roles in growth, aging, stress responses, and chemoresistance.

A Non-Canonical Role of SMAD4 in Regulating 3D Genome Architecture to Inhibit Lung Squamous Cell Carcinoma Development

This study identifies SMAD4 as a regulator of 3D genome architecture in lung squamous cell carcinoma, showing its role in inhibiting tumor development by constraining chromatin looping.

Transcription condensates are promoter hubs that enhance transcriptional bursts

This study uses super-resolution microscopy to show that Pol II clusters form promoter hubs with layered chromatin organization, enhancing transcriptional bursts through cohesin loop extrusion.

Large RNA polymerase II condensates are promoter-centric assemblies associated with early stages of transcription at all expressed genes

The paper characterizes large RNA polymerase II condensates, showing they are promoter-centric and involved in early transcription stages across expressed genes.

Benchmarking normalisation methods for differential binding analysis in CUT&RUN

This study benchmarks normalization methods for differential binding analysis in CUT&RUN, finding data-driven normalization to be most robust and highlighting variable performance of spike-in normalization.

Activator-binding domains are required but insufficient for Med15 recruitment to UAS, revealing a critical role for its disordered C-terminus in directing genome targeting

The paper shows that Med15's activator-binding domains are necessary but not sufficient for UAS recruitment, and its disordered C-terminus is critical for directing genome targeting.

Cohesin collisions maintain ordered nucleosome architecture at boundaries and promoters

The paper shows cohesin collisions maintain ordered nucleosome architecture at CTCF sites and promoters, independent of CTCF occupancy or cohesin levels.

Analysis of multi-way chromatin interactions at sub-nucleosome resolution identifies synergistic nano-scale interactions within super-enhancers

The paper introduces mwMCC, a method to detect multi-way chromatin interactions at sub-nucleosome resolution, revealing synergistic nano-scale interactions within super-enhancers and their role in gene regulation.

Disentangling polymer confinement from specific-folding interactions reveals the drivers of E. coli chromosome organization

The paper develops a polymer simulation framework to distinguish specific-folding interactions from polymer compaction in E. coli, revealing SFIs shape chromosome organization and gene expression.