Genomics and Chromatin Dynamics

This study develops coarse-grained models to show how nucleosome spacing and ATP-dependent remodeling influence chromatin condensate structure, dynamics, and organization.

This study identifies Rpl3l as a muscle-specific ribosomal protein that regulates chromatin insulation in atrial cardiomyocytes, linking genome structure to cardiac rhythm stability.

The paper develops network-based metrics to visualize interchromosomal interactions at sub-megabase resolution, revealing shared interaction hotspots across chromosomes.

The paper investigates how MYC and RNA polymerase II binding near transcriptional end sites (TESs) regulates gene expression and read-through transcription in human and murine cells.

The paper tests enhancer-promoter compatibility using improved assays, finding that promoter responsiveness, not enhancer rank order, determines activation sensitivity.

This paper shows that overexpressing Eaf1, a NuA4 subunit, rescues growth defects in yeast with H3K36M mutations by acetylating histone H4 tails.

CREPAS is a Nextflow pipeline for analyzing nascent chromatin sequencing data, improving scalability, reproducibility, and compatibility across multiple chromatin assays.

The paper develops a framework to correct cohesin positioning measurements in ChIP-seq by accounting for antibody background, revealing its impact on cohesin positioning estimates.

The paper uses ATAC-seq data and TF footprinting tools to identify novel cis-regulatory elements in Drosophila embryos, finding that many TF binding sites lie outside known enhancers.

The paper introduces effect size-based methods to rank transcription factor binding motifs, showing they outperform p-value rankings under heterogeneous sample sizes.

This paper maps the free-energy landscapes of chromatin structures and shows how linker DNA geometry and sequence modulate their topologies, influencing phase separation and structural polymorphism.

This study investigates how NUP98-HOXA9 drives aberrant chromatin looping in AML by interacting with CTCF and cohesin, revealing a non-canonical mechanism involving phase separation and loop extrusion.

The paper investigates the relationship between chromatin accessibility and transcription during Arabidopsis embryo development, finding that their coupling is regulated rather than fixed.

The paper introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

This study identifies H3K37me1 as a histone modification that regulates DNA replication origin selection by limiting MCM2-7 association with transcribed chromatin.

This paper creates a multimodal single-cell atlas of the human basal ganglia, revealing epigenomic and 3D genome features across cell types and linking them to disease-associated genetic risk.

This study uses live-cell imaging to show that enhancer-promoter interactions drive gene activation through transient contacts of ~25-42 nanometers.

The paper introduces Domino, a deep learning framework that models sequence-to-function relationships to uncover the context-specific grammar of Drosophila chromatin insulation.

The paper predicts transcription factor binding across 43 human cell types using ATAC-seq data and a new platform, revealing promiscuous occupancy and chromatin contacts.

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

This study uses cryo-electron tomography to reveal the dynamic chromatin architecture of archaea, showing variable hypernucleosome structures and growth-phase-dependent organization.

This paper introduces an annotation-based gene-peak linkage method that improves gene expression prediction from chromatin accessibility in human kidney multi-omics data.

The paper characterizes ~700,000 conserved noncoding elements in the human genome, showing many have cis-regulatory potential and are enriched in TAD centers.

This study shows that CAF-1 is necessary for proper structure and function of facultative heterochromatin in Neurospora crassa, working with PRC2 to silence transcription.

This study identifies STAG2's role in regulating chromatin architecture and gene expression in muscle invasive bladder cancer, revealing its context-specific activation and repression of genes involved in oncogenic signaling.

The paper develops AI models to predict enhancers in human and mouse cell lines, identifying H3K18ac as a new enhancer marker and annotating enhancers using a combination of epigenetic marks.

Hyper3D-lite audits long-read multi-contact genome data by preserving counts during all-pair projections to avoid overcounting contact evidence.

This study shows that H2A.Z's sequence-encoded flexibility in specific regions enhances DNA unwrapping and enables SUV420H1 recognition, revealing a mechanism linking nucleosome dynamics to epigenetic enzyme specificity.

This study shows cohesin extrudes DNA loops symmetrically or asymmetrically based on applied force, with loop extrusion controlled by stochastic switching of the motor domain and diffusive motion of the anchor domain.

This study compares cis-regulatory elements in immortalized liver cell lines to primary liver tissue using ATAC-seq, finding significant differences in transcription factor binding and gene regulation.