Genomics and Chromatin Dynamics

TFBindFormer: A Cross-Attention Transformer for Transcription Factor-DNA Binding Prediction

TFBindFormer improves TF-DNA binding prediction by integrating DNA and TF protein features using cross-attention, outperforming DNA-only models.

Evolutionary conditioning enables guided generation of functionally diverse enhancers

This paper introduces EnhancAR, a deep learning model that generates functionally diverse enhancers using evolutionary homologs instead of cell type labels.

The Zelda Interactome Reveals Diverse Co-factors Essential for Pioneer Factor-Mediated Zygotic Genome Activation

The paper identifies the Zld interactome in Drosophila embryos, revealing co-factors essential for ZGA, including dCBP, Fsh, and Smr, and shows RNAPII associates with Zld-bound enhancers.

TAD boundaries and gene activity are uncoupled

The paper investigates the relationship between TAD boundaries and gene activity using single-cell imaging, finding they are largely uncoupled.

CTCF-mediated cis-regulatory chromatin insulation enforces a central B-cell tolerance checkpoint

This study identifies a CTCF-binding insulator element that regulates receptor editing and B-cell tolerance by controlling chromatin loop extrusion and Ig{lambda} development.

Hi-C Calibration by Chemically Induced Chromosomal Interactions

This study uses a chemical method to create controlled chromosomal interactions in yeast to assess Hi-C's quantitative properties, finding it sensitive, unbiased, and linear.

SPEAR: Predicting Gene Expression from Single-Cell Chromatin Accessibility

SPEAR predicts gene expression from chromatin accessibility in single-cell multiome data, showing that transformer models achieve the highest correlation across two biological systems.

BRD4 recruitment desilences transcription without erasure or depletion of repressive chromatin

This study shows that BRD4 recruitment can desilence transcription within repressive chromatin without removing H3K9me3 or HP1, challenging conventional models of chromatin regulation.

CENP-B binds hairpin motifs in chromosome arms influencing gene expression

This study identifies a non-centromeric role for CENP-B in binding hairpin motifs in chromosome arms, leading to dysregulated gene expression upon depletion.

Altered chromatin accessibility and nucleosome positioning landscape upon HDAC and LSD1 inhibition in cancer cell

The paper investigates how HDAC and LSD1 inhibition alters chromatin accessibility and nucleosome positioning in cancer cells, revealing a JunB-mediated mechanism that highlights therapeutic vulnerabilities.

An information content principle explains regulatory patterns of gene expression across human tissues

The paper identifies an information content principle that links regulatory demands, expression specificity, and gene age across human tissues.

H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility

This study investigates how H2A.Z affects Sox2 and Oct4 binding to nucleosomes by altering DNA and histone H3 tail dynamics.

Ubiquitylated H2A.Z is associated with diverse types of silenced chromatin including methylated CpG islands and homopurine/homopyrimidine sequences

This study identifies H2A.Z ubiquitylation as a marker of repressive chromatin by associating it with silenced regions like methylated CpG islands and homopurine/homopyrimidine sequences.

A Joint Promoterome-Proteome Atlas Highlights the Molecular Diversity of Human Skeletal Muscles

The paper creates a promoterome and proteome atlas of human skeletal muscles, revealing molecular diversity and identifying key transcription factors and genetic variants associated with muscle traits.

Cleavage of histone H2A during embryonic stem cell differentiation destabilizes nucleosomes to counteract gene activation

The paper shows that cleavage of histone H2A by Cathepsin L during ESC differentiation reduces nucleosome stability and counteracts gene activation.

Structure and function of IWS1 in transcription elongation

This study identifies IWS1 as a modular scaffold that organizes the transcription elongation complex through its disordered region, revealing its role in recruitment and stimulation of elongation.

Deep-Plant: a supervised foundation model for plant regulatory genomics

This paper introduces a supervised foundation model for plant regulatory genomics that predicts chromatin state from genomic sequence, showing improved speed, accuracy, and interpretability over DNA language models.

Socially regulated genes are spatially hyperconnected to enhancers in the ant brain

The paper identifies socially regulated genes in ants that show increased 3D chromatin contacts with enhancers, suggesting pre-existing connectivity supports brain plasticity during caste transition.

Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells

This study shows that linker histone H1 acts as a liquid-like glue in chromatin domains, enabling dynamic interactions that support DNA transactions in human cells.

The transcription factor LSL-1 interacts with the chromatin factors HIM-17, XND-1 and BRA-2 to promote the germline-specific transcriptional repertoire and to safeguard germ cell fate in C. elegans

The paper identifies LSL-1's interaction with chromatin factors to maintain germline transcriptional programs and cell fate in C. elegans.

DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci

DNA O-MAP identifies molecular neighborhoods around specific genomic loci using programmable probes and proteomics.

Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions

The paper uses MPRAs to assess context-dependent regulatory activity in type 2 diabetes-linked noncoding regions across different promoters and cell types.

Distinct principles of genome compartmentalization in Drosophila and humans revealed by osmotic stress

This study compares genome compartmentalization in Drosophila and humans under osmotic stress, revealing distinct organizational principles involving LLPS and architectural proteins.

CellLoop: Identifying single-cell 3D genome chromatin loops

CellLoop identifies single-cell chromatin loops using a density-based framework, improving accuracy in mouse brain and embryogenesis data.

Organ-specific and conserved regulatory logic orchestrates gene expression in the embryonic mesothelium

The paper identifies regulatory elements and transcription factors governing gene expression in the embryonic mesothelium across three organs, revealing conserved and organ-specific mechanisms.

CREsted: modeling genomic and synthetic cell type-specific enhancers across tissues and species

CREsted is a software package for modeling and designing cell type-specific enhancers using deep learning, validated across tissues and species.

Correcting Preprocessing Bias in Sparse Chromatin Contact Data Enables Physically Interpretable Reconstruction of Genome Architecture

The paper identifies preprocessing bias in chromatin contact data and introduces a framework to correct it, enabling physically interpretable genome architecture reconstruction.

YY1-concentration-dependent formation of mechanically distinct DNA condensates through different interaction mechanisms

This study investigates how YY1 forms mechanically distinct DNA condensates through different interaction mechanisms, showing concentration-dependent assembly and domain-specific contributions.

Exonic enhancers are a widespread class of dual-function regulatory elements

The paper identifies exonic enhancers as dual-function regulatory elements that influence gene expression and are associated with disease and evolution.

Histone Modification Metapeaks are Epigenetic Landmarks Predictive of Cell State

The paper identifies histone modification metapeaks across diverse cell and tissue types and shows they can predict cell state using machine learning.