Genomics and Chromatin Dynamics

Distal super-enhancer drives aberrant CXCL13 expression in Cancer cells driving growth and p53 dysregulation via CXCR5-CXCL13 axis

This study identifies a distal super-enhancer near CCNG2 that drives aberrant CXCL13 expression in cancer cells, leading to growth promotion and p53 dysregulation via the CXCR5-CXCL13 axis.

Machine learning-assisted Repli-Histo labeling reveals distinct transcription-dependent constraints on chromatin motion in living cells

The paper uses machine learning to classify chromatin classes and shows how different transcription systems affect nucleosome motion in distinct chromatin regions.

Visualizing the Epigenetic Landscape of Aging and Cellular Reprogramming: Optimized ATAC-see for Cells and Tissues

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

PDS5A and TOP2B cooperate for chromatin recruitment via CTCF

This study identifies a functional interaction between PDS5A and TOP2B at CTCF-bound chromatin sites, showing their cooperative recruitment and impact on gene expression and chromatin structure in gliomas.

Multivariate Mutual Information based Feature Selection for Predicting Histone Post-Translational Modifications in Epigenetic Datasets

This paper introduces multivariate mutual information (MMI) for selecting histone PTM features to predict epigenetic data, showing improved accuracy over traditional methods.

Multi-omics analysis reveals chromatin and transcriptomic remodeling in hippocampal CA1 following adolescent social isolation

Two weeks of post-weaning isolation in male mice altered expression of 106 CA1 genes, enriched for myelination, while chromatin accessibility shifted only at nominal significance and tracked expression weakly.

STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data

This paper introduces STRIDE, a sequencing depth-insensitive metric for comparing sparse single-cell Hi-C data, enabling robust analysis of 3D genome organization.

XChrom: a cross-cell chromatin accessibility prediction model integrating genomic sequence and cellular context

XChrom predicts chromatin accessibility across cells and genomic regions using genomic sequence and cell identity, outperforming existing methods and enabling cross-species analysis.

Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin accessibility profiles

The paper maps cell type-specific genetic effects on nucleosome-free regions and nucleosome occupancy using snATAC-seq data from human muscle biopsies, showing causal relationships between these elements and GWAS traits.

Dynamics of TFIIH and Spt4/5 during the transition from transcription initiation to elongation

The paper uses single-molecule fluorescence microscopy to show that TFIIH dissociates from RNA polymerase II before Spt4/5 binds, indicating Spt4/5 does not actively displace TFIIH.

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

The paper identifies two rodent-specific transposable element subfamilies that function as cell-type-specific enhancers in the mouse immune system, contributing to cell identity and gene regulation.

Unpacking Chromatin Accessibility with Fiber-seq

This paper introduces Fiber-seq, a method for detecting chromatin accessibility on individual DNA fibers, and provides guidelines for its proper use and analysis.

Metazoan Orc6 Proteins Evolved Alternative Mechanisms for Association with the ORC Complex: Insights from Drosophila Modeling

The paper investigates differences in Orc6 protein interactions with the ORC complex in Drosophila and humans, proposing that a nuclear localization signal in humans compensates for weaker binding.

Sequence design for three-dimensional genome folding using Akita Semifreddo

This paper introduces Akita Semifreddo, a framework for designing DNA sequences that produce specific 3D genome folding patterns, demonstrating the ability to create boundaries, dots, and flames with controlled strengths.

A molecular framework of chromatin extrusion in plants

This study identifies PDS5A as a key regulator of chromatin loop extrusion and TAD-like domains in Arabidopsis, revealing a promoter- and motif-based mechanism for loop anchoring and transcriptional control.

Region-specific generation and retention of acetylated cohesin shape the genome-wide pattern of sister chromatid cohesion

The paper investigates how ESCO2-mediated acetylation of cohesin is distributed and retained across the genome, revealing region-specific patterns and post-replicative retention mechanisms.

Exploring DNA movement through the application of droplet based high efficient chromatin conformation capture (DropHiChew) and loop velocity

This paper introduces DropHiChew and loop velocity to study DNA movement dynamics, enabling accurate trajectory estimation with shallow sequencing.

Integrative analysis reveals extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors

The paper identifies extensive interactions among C2H2 zinc finger proteins at chromatin loop anchors using ChIP-seq, interactome data, and chromatin interaction maps.

Enhancer binding kinetics explain transcription factor hub formation

The paper uses live-imaging and computational modeling to show that Dorsal hub formation in Drosophila embryos depends on TF-DNA binding kinetics, not enhancer sequence or higher-order regulatory structures.

MacroH2A-Mediated Gene Repression through Nucleosome Compaction and Remodeling Inhibition

This study investigates how MacroH2A (mH2A) contributes to gene repression by stabilizing nucleosome dynamics and inhibiting chromatin remodelers.

tangermeme: A toolkit for understanding cis-regulatory logic using deep learning models

tangermeme provides tools to interpret deep learning models for cis-regulatory analysis, extracting human-readable insights from genomic predictions.

The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguard metabolic and cellular homeostasis

This study identifies RBBP5 as an essential epigenetic regulator of the 12h oscillator and proteostasis, linking it to metabolic and cellular homeostasis in mammals.

Average local nucleosome motion remains nearly constant during interphase in living human cells

The paper measures local nucleosome motion in living human cells during interphase and finds it remains nearly constant, with changes observed under specific perturbations.

Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase

This study uses Hi-C in mouse embryonic stem cells to show A/B compartment strength increases during S-phase, challenging previous views on cell-cycle dynamics.

Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation

This study introduces OpenCGChromatin, a model that simulates chromatin structure and phase separation, revealing how linker-DNA length and histone modifications affect chromatin organization.

Genome-wide discovery of cis-regulatory elements in a large genome

The paper develops resources to identify cis-regulatory elements in the Parhyale hawaiensis genome using ATAC-seq and sequence conservation analysis.

Active field theory approach to explain size control of transcriptional condensates

The paper uses microscopy and field theory to show transcriptional condensates exhibit size control through non-equilibrium dynamics.

Fetal signatures in the 3D genome of iPSC-derived neurons and their implications for disease modeling

This study compares chromatin architecture in iPSC-derived neurons to fetal and mature neurons, finding iPSC-derived neurons resemble fetal neurons and have distinct chromatin features.

METANet: A supervised ensemble learning framework for reconstructing direct and functional tissue-specific transcription factor networks

METANet predicts direct, functional TF targets across human tissues by integrating motif, cis-regulatory, and expression features, outperforming existing methods.

Inferring binding specificities of human transcription factors with the wisdom of crowds

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.