Genomics and Chromatin Dynamics

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.

An H4K20me3-CTCF switch at stable TAD boundaries enforces reversible cell state transitions

The paper identifies an H4K20me3-CTCF switch at TAD boundaries that regulates reversible cell state transitions between proliferation and quiescence.

3D Reconstruction of Dinoflagellate Chromosomes from Hi-C Data Challenges the Cholesteric Liquid Crystal Hypothesis

This study uses Hi-C data to challenge the Cholesteric Liquid Crystal model of dinoflagellate chromosomes by showing no evidence of cholesteric discs and demonstrating transcription occurs throughout chromosomes.

Induction of hysteretic chromatin states by CRISPRa reveals locus-specific encoding of transcriptional memory

The paper uses CRISPRa to show that transcriptional memory can be induced in MSCs through locus-specific activation, linked to H3K27me3 loss and increased transcription factor reacquisition.

Single-Nucleus Multi-Omic Atlas Maps Regulatory Architecture and Non-Coding Variant Effects across Adult Human Tissues

The paper constructs a single-nucleus multi-omic atlas of adult human tissues, identifying regulatory elements and variant effects across 21 tissues.

Gene-family-dependent thermodynamic effects of oncogenic mutations on nucleosome-DNA binding stability: a comparative molecular dynamics study across 22 cancer hotspots

This study uses molecular dynamics simulations to analyze thermodynamic effects of 22 cancer hotspot mutations on nucleosome-DNA binding stability across 10 oncogene families, revealing gene-family-dependent trends.

Structural basis of nucleosome remodeling by archaeal RNA polymerase during transcription elongation

This study reveals how archaeal RNA polymerase remodels nucleosomes during transcription elongation by redirecting DNA and displacing histones, using cryo-EM structures of a Pyrococcus furiosus complex.

Reconstitution of +1 nucleosome transcription reveals coordinated functions of SAGA, Mediator, and TFIIH

This study reconstitutes transcription through the +1 nucleosome using purified yeast factors and finds that SAGA, Mediator, and TFIIH coordinate to overcome nucleosome barriers and regulate transcription initiation.

Nucleosome-scale p53-hormone receptor grammar distributed by Alu elements

The paper identifies p53-hormone receptor regulatory grammars distributed by Alu elements in mammary and muscle cells, with implications for breast cancer and muscle aging.

Highly inducible transcription is impaired in cells lacking Cyclin T1 (CycT1) of the positive transcription factor b (P-TEFb).

This study shows that CycT1 is critical for inducible gene expression and its loss reduces JQ1-dependent gene expression, with implications for pancreatic adenocarcinoma.

Hi-C data from the filamentous fungus Podospora anserina and associated 3D models to visualize the spatial organization of its chromosomes

The paper presents Hi-C data and 3D models for Podospora anserina to study its chromosomal spatial organization and aid multi-omics integration.

Ancient and Animal-Specific Regulatory Modes of EWS::FLI1 Revealed by a Minimal Yeast Model.

This paper shows EWS::FLI1 can activate GGAASat sequences into enhancers in yeast, suggesting this function is ancient, while broader transcriptome changes require animal-specific factors.

Nucleosome Core Allostery Governs Chromatin Recognition and Cell Fate

This study identifies nucleosome core allostery as a mechanism that amplifies minimal variations in nucleosomes to influence chromatin accessibility and cell fate.

Scaling of structural variability of ecDNA polymer condensates with copy number boosts and stabilises oncogene regulatory contacts

The paper develops a polymer physics model of ecDNA condensates showing that structural variability scales with copy number, stabilizing oncogene regulatory contacts.

Innate immune stress pathway activation underlies heterochromatin dysfunction pathology

The paper identifies activation of the innate immune stress pathway as a mechanism linking heterochromatin dysfunction to pathological phenotypes in C. elegans and human cells.

Discrepancies between ChIP-seq and CUT&Tag histone mark profiles are explained by GC content and chromatin accessibility

FACT-(H3-H4) complex stimulates Pol activity to coordinate DNA synthesis with nucleosome assembly

The paper identifies the role of FACT-(H3-H4) complex in stimulating Pol activity to coordinate DNA synthesis with nucleosome assembly during replication.

Controlling for DNA dosage with Whole Genome Sequencing improves ATAC-seq peak calling

This paper improves ATAC-seq peak calling by integrating whole-genome sequencing data to control for DNA dosage biases, enhancing peak accuracy and relevance to gene regulation.

Euchromatin forms condensed domains with short active regions on the surface

The paper develops a simulation framework to infer nucleosome-resolution chromatin structures from RCMC data, revealing euchromatin as condensed domains with accessible promoter/enhancer regions.

CardioChrom Reconstructs the Human Cardiac Virtual Epigenome from Single-Nucleus Transcriptomes

CardioChrom reconstructs chromatin accessibility and histone modifications from single-nucleus RNA data in human heart failure, improving prediction accuracy and identifying regulatory changes in endothelial cells.

EPIC: An open community challenge for sequence-based prediction of transcription initiation in five non-model metazoans

EPIC challenges teams to predict transcription initiation from DNA sequence in non-model metazoans, aiming to assess generalizability beyond human and model species.

ATACofthesnake: A scalable framework for analyzing multifactorial and time course chromatin accessibility data

The paper introduces ATACofthesnake, a scalable framework for analyzing multifactorial and time course chromatin accessibility data, providing a structured workflow to handle such data reproducibly.

A comprehensive Arabidopsis transcription factor binding atlas reveals pervasive positional and syntactic organization of their DNA binding

This study creates a comprehensive Arabidopsis TF binding atlas, revealing family-specific binding patterns and the importance of DNA sequence syntax in TF-DNA interactions.

Stress triggers global histone synthesis in the liver

The paper measures histone synthesis rates in vivo and finds that stress induces a surge in hepatocyte nucleosome production uncoupled from DNA replication.

Transcription factors read a second regulatory code in chromatin

This study maps how 269 human transcription factors recognize DNA sequences on nucleosomes, revealing a second regulatory code in chromatin that influences gene regulation.

Massively parallel assessment of gene regulatory activity at human cortical structure associated variants

The paper assesses regulatory activity of cortical structure-associated variants using MPRA in human neural progenitor cells, identifying 918 variants with regulatory potential and showing condition-dependent effects.

FourC: identifying significant and differential contacts in 1D chromatin conformation data

FourC identifies significant and differential contacts in 4C-seq data using a Bayesian model and Gaussian processes to address duplication and model spatial patterns.

AI discovery of sequence rules for RNA polymerase II pausing revises the pause-release model of gene activation

The paper uses AI to discover sequence rules for RNA polymerase II pausing, challenging the pause-release model of gene activation by showing pausing is not required for certain activation responses.

FFPE-CUTAC: A Single Assay, Multiple Layers

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.