Genomics and Chromatin Dynamics

A generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species

HiCFoundation is a Hi-C-based model that integrates chromatin structure with epigenomic regulation across species, improving analysis of 3D genome architecture and single-cell data.

Intrinsic DNA codes govern distinct modes of nucleosome-transcription factor interactions

The paper identifies four nucleosomal DNA classes and shows their association with TF binding, revealing DNA-encoded codes for nucleosome positioning and interaction modes.

RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription

The paper shows that RNA enhances condensate formation by ENL mutants, promoting oncogenic transcription and leukemogenesis in mouse models.

STAG2 Maintains Chromatin Compartmentalization and Represses Regulatory Element Contact to Promote Oncogenic Signaling in Muscle Invasive Bladder Cancer

This study identifies STAG2's role in regulating chromatin architecture and gene expression in muscle invasive bladder cancer, revealing its context-specific activation and repression of genes involved in oncogenic signaling.

Explainable AI identifies H3K18ac as a new marker of active enhancers

The paper develops AI models to predict enhancers in human and mouse cell lines, identifying H3K18ac as a new enhancer marker and annotating enhancers using a combination of epigenetic marks.

Hyper3D-lite: count-preserving representation auditing for long-read multi-contact genome data

Hyper3D-lite audits long-read multi-contact genome data by preserving counts during all-pair projections to avoid overcounting contact evidence.

Sequence-encoded H2A.Z nucleosome dynamics control DNA unwrapping and SUV420H1 recognition

This study shows that H2A.Z's sequence-encoded flexibility in specific regions enhances DNA unwrapping and enables SUV420H1 recognition, revealing a mechanism linking nucleosome dynamics to epigenetic enzyme specificity.

Symmetry and force response of cohesin loop extrusion are determined by diffusion of its motor and anchor domains

This study shows cohesin extrudes DNA loops symmetrically or asymmetrically based on applied force, with loop extrusion controlled by stochastic switching of the motor domain and diffusive motion of the anchor domain.

Pan-cell type continuous chromatin state annotation of all epigenomes from the International Human Epigenome Consortium

The paper introduces a pan-cell type chromatin state annotation that integrates all IHEC epigenomes using the epigenome-ssm method, avoiding cell type-specific annotations.

A Modular Framework for Automated Segmentation and Analysis of AFM Imaging of Chromatin Organization

DNAsight automates AFM image analysis of chromatin organization, revealing protein-specific structural signatures and nucleosome spacing distributions.

Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements

This study compares cis-regulatory elements in immortalized liver cell lines to primary liver tissue using ATAC-seq, finding significant differences in transcription factor binding and gene regulation.

Visualization of the architecture of flexible chromatin and the binding of chromatin regulators

The paper visualizes chromatin structure and chromatin regulator binding using cryo-ET and subtomogram averaging, revealing nucleosome heterogeneity as a key factor in chromatin flexibility.

Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq

This paper introduces TraceBIND, a method to correct Tn5 bias in ATAC-seq data, improving TF footprint detection and revealing age-related regulatory changes in scATAC-seq.

Translocation-driven chr19-der(14) interaction is associated with disease-specific transcriptional programs in mantle cell lymphoma

This study identifies interchromosomal interactions between chr19 and the CCND1 locus in MCL, linking spatial genome reorganization to disease-specific transcriptional programs.

Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics

This paper identifies Ab-trapping as a staining artifact in antibody-based techniques, showing it results from high epitope abundance, high Ab affinity, and low diffusion rates, and suggests mitigation strategies.

Uncoupling the TFIIH Core and Kinase Modules Leads To Misregulated RNA Polymerase II CTD Serine 5 Phosphorylation

This study uncouples the TFIIH kinase and core modules by splitting Tfb3, revealing that module coupling is necessary for localized CTD Serine 5 phosphorylation during transcription.

BRD4, Mediator, and Pol II form heterogeneous condensates with distinct transcriptional and acetylation-dependent states

The paper quantifies transcriptional condensate states using chemical perturbations and finds BRD4-only condensates that are acetylation-dependent and distinct from canonical transcriptionally engaged condensates.

Epigenetic conditioning improves sequence-based modeling of gene regulation across cell types and alleles

This paper introduces MethylSeqNet, a model that improves sequence-based gene regulation predictions by conditioning on CpG methylation, showing benefits for cell-type-specific regulation and allele-specific phenomena.

Heterochromatin organization and liquid-liquid phase separation: it is not about if but about when

The paper investigates how heterochromatin proteins form barrier compartments in cells, showing differences between proteins, cell types, and compartments, and proposes a model based on protein accumulation and competition.

CREP: Cis-Regulatory Element Predictor Based on Fine-Tuned Enformer

CREP predicts cis-regulatory element identity from DNA sequence using a fine-tuned Enformer model trained on cell-type-specific annotations.

Development of a Staining-based Electrophoretic Mobility Shift Assay for Analyzing Pbx1, DNA and HoxA9 Interactions

This paper develops a label-free, staining-based EMSA to study Pbx1 and HoxA9 DNA interactions, showing high sensitivity and quantitative results comparable to labeled methods.

Learning quality scores for chromatin accessibility bigWig tracks using Machine Learning

The paper develops a machine learning framework to assess quality of chromatin accessibility bigWig tracks using biologically relevant features and internal controls.

KDM: embedding DNA/RNA motifs and sequences in a shared k-mer space for unified discovery, analysis and binding prediction

KDM provides a unified framework for motif discovery, analysis, and binding prediction by embedding DNA/RNA sequences and motifs in a shared k-mer space using the Hellinger transformation and Bhattacharyya coefficient.

An enhancer-centric approach applied to human immune system epigenomes revealed the association of macrophage enhancers with cardiovascular disease

The paper identifies associations between macrophage enhancers and cardiovascular disease variants using epigenomic data from immune cells.

A latent interaction landscape inferred from Micro-C encodes chromatin regulatory identity and conformational diversity beyond contact frequency

This paper introduces a latent interaction landscape from Micro-C data that captures chromatin regulatory identity and structural diversity beyond contact frequency.

Structural Dynamics of RNA Polymerase II During Nucleotide Addition Cycle

This study presents 43 cryo-EM structures of RNAPII elongation complex during the nucleotide addition cycle, revealing structural dynamics and transition intermediates.

Single-molecule nucleosome spacing coordinates chromatin fiber interactions

The paper introduces LASSI, a method to measure nucleosome spacing in chromatin interactions, revealing fiber homotypy as a structural pattern influenced by genomic features and cohesin dynamics.

CLASH (Chromatin Loop Across-sample Score Harmonizer) quantifies the relative contributions of genetic variation, methylation, and CTCF occupancy on chromatin loop strength across individuals

The paper introduces CLASH, a method to quantify how genetic variation, methylation, and CTCF occupancy affect chromatin loop strength across individuals.

Multidomain Coupling Governs FoxP1 Assembly and Nuclear Compartmentalization

This study investigates FoxP1 assembly and nuclear organization, revealing that its leucine-zipper and Forkhead domains antagonistically regulate complex formation and DNA binding.

Integrated flexible DNA methylation-chromatin segmentation modeling enhances epigenomic state annotation

ESMM improves epigenomic state annotation by integrating DNA methylation and chromatin marks, enhancing the detection of heterochromatic regions and regulatory element boundaries.