Genomics and Chromatin Dynamics

Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome

The paper develops DNABERT-Enhancer, a genomic language model for enhancer prediction, achieving high accuracy and identifying allele-specific activity and candidate SNPs.

HiCPotts: An R/Bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of biases.

HiCPotts is an R/Bioconductor package that identifies significant chromatin interactions in Hi-C data while modeling biases using a zero-inflated Negative Binomial distribution.

Promiscuous RNA binding by WDR5 remodels the KMT2A (MLL1) histone methyltransferase complex to an inactive state

The paper shows WDR5 binds RNA non-specifically, displacing it from the MLL1 complex and inhibiting its catalytic activity.

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

TCOF1 dosage is limiting for transitional human neural crest cells; its enhancers buffer promoter output against MYC fluctuations rather than amplifying it, a pattern seen across 14 dosage-sensitive promoters.

A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation

The paper introduces a model-based framework to compare promoter-proximal pausing dynamics across biological contexts, revealing kinetic and distributional variations in pausing.

Formation of an RNA-mediated nuclear compartment

The paper identifies RNA as the molecular glue forming a stable chromatin compartment associated with nuclear speckles, independent of speckles themselves.

Hi-Cformer enables multi-scale chromatin contact map modeling for single-cell Hi-C data analysis

Hi-Cformer models multi-scale chromatin contact maps from single-cell Hi-C data, improving cell type separation and imputation of 3D genome features.

Sequence-to-function deep learning decodes human cis-regulatory evolution

This study uses sequence-to-function deep learning to identify lineage-specific cis-regulatory elements in human evolution, finding they are shorter, less conserved, and enriched in neurodevelopmental pathways.

HP6/Umbrea, a rapidly evolving Drosophila HP1-family paralog, is a candidate HP1a-recruited plasticizer of heterochromatin

This paper investigates HP6/Umbrea's role as a plasticizer of HP1a condensates, showing it enhances permeability to transcriptional machinery without altering phase separation properties.

Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

tATAC-see captures target-specific chromatin states using a visual assay, showing dynamic remodeling in aging models and LAD resistance.

The human RNA-DNA interactome is cell type-specific and dynamic

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

Epromoter 3D interaction-associated regulation in T-acute Lymphoblastic Leukemia

This study identifies Epromoters involved in 3D promoter-promoter interactions that regulate gene expression and are critical for T-ALL cell survival.

J-domain proteins bridge the PKL and ATRX complex to transcription factors to fine-tune gene expression via H3.3 deposition

The paper identifies J-domain proteins as mediators of PKL recruitment to gene promoters, enabling H3.3 deposition and influencing gene expression through interactions with transcription factors and ATRX.

Biological Features Underlying Factor-Specific Predictability of Cross-Species Regulatory Occupancy

The paper identifies biological features that influence cross-species predictability of regulatory occupancy and provides a framework to estimate predictability probabilities.

DPF3a couples H3K36me2-dependent chromatin remodeling to genome architecture during myogenesis

This study identifies DPF3a as a chromatin remodeler that regulates myogenesis through three-dimensional genome organization rather than local chromatin accessibility.

Irregular nucleosome positioning governs a crystalline to liquid-like phase transition and tunes chromatin accessibility

The paper shows that nucleosome positioning determines chromatin's physical state, with irregular positioning enabling accessibility for transcription while maintaining genome protection.

Integrative spatial profiling of 3D genome organization and gene expression in tissue

This paper introduces Spatial Hi-C-RNA, a spatial multi-omics technology that co-maps chromatin conformation and transcriptome in tissue, revealing spatially coherent domains and new insights into gene regulation.

Improved spike-in normalization clarifies the relationship between active histone modifications and transcription

The paper introduces a novel dual-spike-in normalization method for ChIP-seq, demonstrating its ability to clarify the relationship between RNA polymerase II activity and histone modifications.

CpG islands act as topological sinks for transcription-induced DNA supercoiling

The paper shows CpG islands act as topological sinks for transcription-induced DNA supercoiling by focusing torsional stress and promoting DNA melting.

Chromatin compartments define distinct modes of action and biological roles of the pioneer Pax7

The paper shows PAX7 acts in two chromatin compartments, with distinct mechanisms and biological outcomes during pituitary development.

Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs

The paper maps and interprets low-affinity transcription factor motifs in mESCs, showing they enhance chromatin accessibility and regulatory potential through cooperative interactions.

Addressing technical variations in ATAC-seq data and improving motif accessibility analyses

The paper introduces three R/bioconductor packages to address technical variations in ATAC-seq data and improve motif accessibility analysis.

Predictive design of tissue-specific mammalian enhancers that function in vivo in the mouse embryo

The paper designs tissue-specific enhancers for mouse embryos using deep learning models trained on chromatin accessibility data and validated enhancers.

GATA3-extension mutants rewire lineage identity in luminal breast cancer

The paper shows that eGATA3 mutations alter transcriptional regulation and lineage identity in luminal breast cancer without losing DNA-binding function.

Trust-Aware Sequence-to-Function Modelling in Regulatory Genomics

The paper introduces RegTrust-XAI, a trust-aware framework for sequence-to-function models in regulatory genomics, showing how reliability, explanation validity, and sequence novelty are distinct properties.

Histone modification crosstalk between host and pathogen

This study shows how bacterial effector RomA is regulated by host histone modifications, revealing a new layer of host-pathogen interaction through epigenetic crosstalk.

Actin-related ACTL8 localizes to the nucleus and modulates locus-specific transcription through chromatin regulation

This study identifies ACTL8 as a nuclear actin-related protein that modulates transcription through interaction with KDM5B, affecting migration pathways in cancer cells.

Cohesin acts as a transcriptional gatekeeper by restraining pause-release to promote processive elongation

This study shows cohesin regulates multiple transcription steps, with loss leading to reduced induction but minimal steady-state expression changes.

RapidMACS: MACS3-identical peak calling, 50x faster

RapidMACS provides a faster narrow peak caller for ATAC-seq and related data, achieving 3.5 to 51x speed improvements over MACS3 while producing identical output.

Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3

This study shows that SUMOylation loss in Drosophila disrupts PRC1 condensates, causing 3D genome rewiring and gene misregulation without affecting H3K27me3 levels.