Genomics and Chromatin Dynamics

Flexible use of conserved motif vocabularies constrains genome access in cell type evolution

The paper shows that conserved motif vocabularies constrain genome access in cell type evolution across species.

Transcription-Coupled Chromatin Reinforcement Maintains the Mature Cardiomyocyte State

This study shows that RNF20 maintains chromatin accessibility in adult cardiomyocytes, preventing stress-responsive enhancer activation and preserving cell state integrity.

GenoME: a MoE-based generative model for individualized, multimodal prediction and perturbation of genomic profiles

GenoME predicts genomic profiles and perturbations using ATAC-seq and DNA sequence, generalizing to new cell types and identifying enhancer-promoter connections.

Motif-based model of transcription predicts effects of sequence variants in AR enhancers and reveals distinct functions for AR-associated transcription factors

The paper develops a motif-based model to predict sequence variant effects in AR enhancers and identifies functional classes of transcription factors, validated against mutagenesis data and GWAS risk alleles.

Structural basis for P-TEFb association with BRD4

This study identifies the structural basis of BRD4 interaction with P-TEFb and shows how BRD4 and AFF4 regulate P-TEFb activity through distinct mechanisms.

Functional dissection of Drosophila Myc cis-regulatory modules (Myc-CRMs) reveals developmentally active DNA-protein interactions

The paper identifies and characterizes Myc cis-regulatory modules in Drosophila using experimental assays and proteomic approaches, revealing their roles in developmental gene expression.

Mitotic chromosomes are mechanically connected by chromatin-based interchromosome linkers

The paper demonstrates that mitotic chromosomes are mechanically connected by DNA-based interchromosome linkers, identified through micropipette manipulation and enzymatic treatments.

KMT2A modulates the epigenetic landscape of rDNA by facilitating the recruitment of histone lysine acetyltransferase PCAF to the rDNA locus.

This study shows KMT2A facilitates PCAF recruitment to rDNA, enhancing H3 acetylation and RNA Pol I transcription, with loss of KMT2A disrupting the pre-initiation complex at the rDNA promoter.

Conformational asymmetry of replicated human chromosomes

The paper reveals a genome-wide asymmetry in sister chromatid alignment due to replication fork asymmetry, maintained by cohesive cohesins.

Multiscale Physical Effects of CpG Methylation on DNA Mechanics, Nucleosome Wrapping, and Chromatin Condensates

This study quantifies how CpG methylation affects chromatin mechanics, nucleosome wrapping, and condensate properties across multiple scales.

Differential analysis of image-based chromatin tracing data with Dory

Dory identifies differential spatial patterns in chromatin tracing data by analyzing structural differences between groups, linking changes to gene regulation.

HiC-LEGO: Biologically Guided High-Resolution 3D Genome Reconstruction Preserves Chromatin Organization at Kilobase Resolution

HiC-LEGO reconstructs high-resolution 3D genomes from Hi-C data, preserving chromatin organization and regulatory interactions at kilobase resolution.

Dynamical Regimes in Rejuvenation

This study identifies three temporal regimes in rejuvenation, showing that an intermediary regime enables successful rejuvenation through epigenetic plasticity and chromatin memory.

Multiscale spatial analysis implicates chromosomal metaloops in gene patterning across the Drosophila brain

The paper identifies chromosomal metaloops in Drosophila brains and shows their role in organizing gene expression patterns through metadomains.

SOX2 can associate with chromatin directly by binding to DNA or indirectly via association with other chromatin-bound proteins

This study shows SOX2 can regulate gene expression both directly via DNA binding and indirectly through interactions with other chromatin proteins.

Hi-cGAN: Prediction of Hi-C interaction matrices with conditional generative adversarial networks

Hi-cGAN predicts Hi-C interaction matrices using conditional generative adversarial networks, achieving better performance than existing methods at certain resolutions.

KAT3 Shuttling Between Neuronal Identity and Activity-Dependent Plasticity Programs Drives Large-Scale Chromatin Remodeling

The paper shows that KAT3 cofactors move between neuronal identity and activity-dependent plasticity programs, causing chromatin remodeling in hippocampal neurons.

Histone H3K9 methylation and Heterochromatin Protein 1 do not limit DNA accessibility in living S. pombe cells

The paper shows that chromatin in living S. pombe cells is generally accessible, challenging the idea that heterochromatin represses DNA access.

Promoter architecture and developmental-expression divergence in the Daphnia pulex complex

This study examines regulatory divergence in the Daphnia pulex complex by analyzing promoter architecture and gene expression across developmental stages.

Leveraging human-trained neural networks for cross-species chromatin regulation annotations

The paper uses human-trained neural networks to predict chromatin annotations in non-human species, showing varying accuracy across species and genomic features.

Improved short nascent strand sequencing (iSNS-seq) enhances DNA replication origin detection and reduces non-origin biases

The paper improves the SNS-seq protocol to better detect DNA replication origins and reduce non-origin biases in yeast.

X-inactivation escapee domains are CTCF-cohesin independent chromatin compartments

The paper investigates the role of CTCF and cohesin in X-inactivation escapee domains and finds that these domains are self-sustaining chromatin compartments independent of CTCF and cohesin.

Genome-wide chromatin recording resolves dynamic cell state changes

This paper introduces LagTag, a method to recover both earlier and endpoint chromatin states in mammalian cells, and applies it to study dynamic chromatin transitions during stem cell differentiation.

HP1 binding creates a local barrier against transcription activation and persists during chromatin decondensation

The paper investigates how HP1 binding represses transcription at chromocenters and persists during decondensation, using a 1D lattice model to explain chromatin state transitions.

Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow

The paper introduces standardized formats and tools for processing MPRA data to improve reproducibility and integration across studies.

High-throughput functional characterization of enhancers in totipotent-like cells

The paper functionally characterizes enhancers in totipotent-like cells using reporter assays and integrates with epigenomic and transcriptomic data to show their role in ZGA gene transcription.

EnhancerDetector: Enhancer Discovery from Human to Fly via Interpretable Deep Learning

EnhancerDetector identifies enhancers across species using interpretable deep learning, showing strong performance and generalizability with experimental validation.

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes

The paper develops a computational method to predict structural variant impacts on genome folding and identifies ASD-associated variants disrupting neuronal regulatory interactions.

Cohesin prevents local mixing of condensed euchromatic domains in living human cells

This study shows cohesin maintains condensed euchromatic domains in human cells by preventing local mixing, which is crucial for transcriptional insulation.

A self-supervised DNA foundation model with collapse-resistant multimodal fusion

This paper introduces a self-supervised DNA foundation model that integrates DNA sequence and chromatin accessibility data to improve regulatory activity prediction and peak detection.