Genomics and Chromatin Dynamics

Repeat element-anchored enhancer-promoter interactions (REEPIs) shape the regulatory landscape of hormone-resistant breast cancer

The paper identifies repeat element-anchored enhancer-promoter interactions (REEPIs) in hormone-resistant breast cancer and links them to transcriptional adaptation and regulatory reprogramming.

FetchPA: a guided, end-to-end solution for local ATAC-Seq data processing and analyses

FetchPA provides an end-to-end ATAC-Seq analysis pipeline for users without bioinformatics expertise, enabling local and public data processing and differential accessibility analysis.

PRDM9-mediated meiotic hotspot specification is constrained in humans despite extensive sequence diversity

The paper functionally characterizes human PRDM9 alleles to show that despite sequence diversity, most alleles function similarly, while rare variants show extreme DNA binding effects.

Ryder: Epigenome normalization using a two-tier model and internal reference regions

Ryder normalizes epigenomic bigWig tracks against stable internal reference regions such as invariant CTCF sites, correcting background and signal separately, recovering expected perturbation effects that depth-only normalization obscured.

Molecular Dynamics-Guided All-Atom Reconstruction of Cryo-ET Maps Reveals Mechanisms of Histone Tail-Mediated Chromatin Compaction

This study uses molecular dynamics and cryo-ET to show histone tails drive chromatin compaction through specific interactions, revealing their role in both structural organization and nucleosome communication.

A Scaffolding Element Rewires Local 3D Chromatin Architecture During Differentiation

This study identifies a scaffolding element that drives chromatin rewiring during differentiation by modulating 3D structure and transcription.

Regulation of immune signal integration and memory by inflammation-induced chromosome conformation

This study shows that inflammation-induced changes in 3D genome conformation regulate immune signal integration and transcriptional memory in macrophages.

TransBind2: Improving Transcription Factor-DNA Binding Prediction with Multimodal Data and Bidirectional Cross Attention

TransBind2 improves TF-DNA binding prediction by integrating TF structure, chromatin context, and bidirectional cross-attention, achieving high accuracy across human ChIP-seq data and cross-species predictions.

Benchmarking CUT&RUN analysis using motif enrichment

This study benchmarks CUT&RUN peak callers using motif enrichment, finding that MACS2 outperforms SEACR in most scenarios with optimal preprocessing.

Alterations to the yeast chromatin landscape during hypoxia

This study investigates chromatin changes in yeast under hypoxia, showing reduced H3K9ac and increased H3K4me3 levels, with implications for gene regulation and survival.

Insulators As Dynamic, Tunable Regulators of Enhancer-Promoter Coordination in Living Drosophila Embryos

This study shows insulators dynamically enhance enhancer-promoter coordination in Drosophila embryos through looping and coordination of transcriptional bursts.

Enhancer Tuning by Sequence-Specific Repressors

This study shows that SNAI1 and SNAI2 repressors tune enhancer activity by shifting chromatin states, affecting enhancer function and evolution.

H3K27me3 Drives Constricted Migration Induced 3D Genome Rewiring in Melanoma

This study shows that H3K27me3 modification drives 3D genome changes in melanoma cells after constricted migration, affecting migration efficiency and chromatin compartment switching.

Single-residue variation in the nucleosome core reveals a regulatory hub for phenotypic innovation

The paper maps single-residue effects of H2A and H2A.Z nucleosome-core variations on cellular functions, revealing non-chromatin regulatory roles and stress-related benefits.

pydreg: a fast Python package for identifying active cis-regulatory elements from nascent transcription

pydreg is a Python port of dREG that improves runtime and memory efficiency while maintaining similar performance in identifying active cis-regulatory elements.

Cooperative CTCF-nucleosome oligomerization stabilizes chromatin loop anchors

CTCF dimerization on stacked nucleosomes is resolved by cryo-EM through a ZnF6-7-8 interface. Disrupting it in mouse stem cells weakens CTCF-cohesin loops more than insulation and impairs germline differentiation.

Chromatin structure of the inactive X chromosome revealed by in situ cryo-electron tomography

This study uses cryo-electron tomography to reveal the multiscale compaction and organisation of the inactive X chromosome, showing the role of histone H1 and acetylation in chromatin structure.

Collaborative binding by diverse pioneer transcription factors amplifies Polycomb repression to preserve lineage fidelity

The paper shows that PRDM1 collaborates with pioneer TFs to enhance enhancer repression during human endoderm differentiation, preserving lineage fidelity through hyper-bivalent enhancers.

Massively parallel characterization reveals context-dependent and non-additive regulatory effects of closely spaced variant pairs

The paper uses a massively parallel reporter assay to study the regulatory effects of variant pairs in enhancers, finding non-additive effects and context-dependent interactions.

ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility

This study compares ATAC-seq and MNase-seq in budding yeast, showing they detect distinct chromatin states and functional roles in gene regulation.

AI-Assisted Cryo-ET Workflow for 3D Visualization of Chromatin during Cellular Differentiation

This paper presents an AI-assisted cryo-ET workflow to visualize chromatin compaction during motor neuron differentiation and correlates findings with Hi-C data.

The meiotic synaptonemal complex is assembled from independently regulated gene programmes

The paper shows that SC genes are independently regulated rather than coordinated, with implications for cancer and somatic expression.

A developmentally regulated long-range enhancer-promoter contact mediates human neural development

The paper identifies a developmentally regulated long-range enhancer-promoter contact that is critical for SOX2 expression and neuroectodermal differentiation in human neural development.

Individual mouse mitotic chromosomes exhibit cell type-specific differences in biomechanical properties

The paper shows that mouse metaphase chromosomes from different cell types have distinct biomechanical properties, with ESC-derived chromosomes showing conserved force-dependent responses but differing from those of NSCs and preB cells.

Directionality of Transcriptional Regulatory Elements

This study compares divergent and unidirectional transcriptional regulatory elements, finding that unidirectional elements are younger and less constrained, with some transcription factors modulating their directionality.

Looplook: Integrating multiomics refinement and graph clustering for target assignment and functional inference of chromatin regulatory networks

Looplook integrates 3D chromatin topology with functional genomics to improve CRE-target gene assignment and functional inference in chromatin regulatory networks.

Native in situ architecture of the human inactive X chromosome revealed by correlative light and electron microscopy

The paper uses correlative light and electron microscopy to reveal the ultrastructural organization of the inactive X chromosome in human cells.

Comparing bulk and single-cell methodologies and models to profile gene expression, chromatin accessibility and regulatory links in endothelial cells treated with TNFα

The paper compares bulk and single-cell RNA-seq/ATAC-seq data and models to assess their impact on predicting causal genes from GWAS variants in TNFα-treated endothelial cells.

Determinants of centromeric nucleosome conformation

This study investigates how the N-terminal regions of CENP-A contribute to the open DNA conformation of centromeric nucleosomes compared to canonical H3 nucleosomes.

Overcoming artificial structures in resolution-enhanced Hi-C data by signal decomposition and multi-scale attention

This paper introduces SHARP, a method to enhance Hi-C data resolution while avoiding artificial structures by decomposing signals and using multi-scale attention.