Genomics and Chromatin Dynamics

The paper models transcript isoform expression levels using epigenomic data from 324 human samples, showing that a universal model outperforms tissue-specific models.

This study shows that DNA flexibility descriptors improve TF binding prediction across multiple TF families and experimental platforms.

The paper identifies ~2,000 cis-regulatory elements (CREs) across 27 dsDNA viruses using reporter assays and machine learning, revealing their regulatory features and associated transcription factors.

The paper identifies a gene regulatory element that modulates MYH6 expression and influences cardiomyocyte response to stress.

This study shows SETD2 methyltransferase activity is crucial for correct transcription initiation and termination, with distinct effects on gene classes in RCC.

This study evaluates DNA foundation models for predicting TFBSs in plants, finding HyenaDNA outperforms other methods in accuracy and efficiency.

This study identifies RIF1's role in restoring H3K9me3 post-replication by facilitating SUV39H1, HP1, and PP1 recruitment and restraining Aurora kinase activity.

This study identifies conserved chromatin states in Arabidopsis thaliana and Marchantia polymorpha, showing their association with transcription factor binding and function across land plant evolution.

The paper tests regulatory potential of conserved enhancers in thylacine and wolf to assess functional convergence over 160 million years of evolution, finding limited evidence of convergent divergence.

The paper expands the DNA motif lexicon of transcriptional regulatory code by identifying composite elements and using a deep learning model to predict their activity and impact of variants.

This study shows SMCHD1 directly compacts DNA in a flexible, ATP-independent manner, forming clusters that may contribute to gene silencing and genome organization.

The paper investigates how BRD4-NUT condensates physically constrain chromatin movement in human cells through liquid-like dynamics and nucleosome crosslinking.

The paper shows Notch signaling forms transcription hubs that regulate gene expression by correlating hub dynamics with transcription profiles.

This study shows H3K4me3 is a post-transcriptional histone mark, not a cause but a consequence of transcriptional activation, with delayed deposition relative to RNA synthesis.

This study identifies the role of H3K9 methyltransferases in maintaining centromere compartmentalization by regulating CENP-A and heterochromatin distribution.

The paper compares transcriptomes and chromatin accessibility in MEP, ERY, and MEG cells to reveal divergence in gene regulation during differentiation.

This study identifies IBD1 as a bridge between histone acetylation and H2A.Z deposition, showing its role in maintaining transcriptional homeostasis by preventing hyperactivation.

The paper introduces a high-resolution single-molecule chromatin accessibility mapping method to quantify transcription factor occupancy and co-accessibility in human cell lines.

The paper identifies TFIID and SAGA complex subunits in C. albicans and shows that TAF12 paralogs form heterodimers through cotranslational assembly, ensuring specificity and stability of histone-like complexes.

This study identifies ZNF512B as a neuronal-expressed protein that interacts with the NuRD complex to regulate neural-specific gene expression programs.

The paper identifies ELOA-dependent mechanisms regulating transcription maturation and links them to cellular senescence and aging through RNA processing defects and growth arrest.

This study shows that R-loops maintain promoter architecture and balanced lineage allocation during differentiation by influencing H2A.Z occupancy and chromatin structure in mouse embryonic stem cells.

Hicberg reconstructs contact signals from repeated elements in genomes by statistically reassigning reads from Hi-C data, revealing new insights into their impact on chromosome architecture.

The paper shows that poised enhancers are susceptible to non-coding variants causing gene activation and disease, using the ZRS and autism-associated variants as examples.

This study shows that near-critical chromatin dynamics in Drosophila embryos best explain experimental data on long-range contacts and structural organization.

The paper introduces DeepCompARE, an in silico ablation framework to analyze TF cooperativity, finding most TF motifs are independent with defined synergy and redundancy effects.

This study shows Satb1 interacts with cohesin and CTCF to regulate chromatin organization and gene expression during T cell development.

This paper shows that a conserved disordered region of a splicing factor promotes histone H2B ubiquitination by stabilizing a ubiquitin ligase complex.

Epilogos provides an information-theoretic framework for visualizing and analyzing multi-tissue chromatin state maps, enabling navigation, prioritization, and comparison of genomic regions.

The paper uses super-resolution microscopy to show that estrogen receptor activity regulates distinct chromatin structures marked by H3K27ac, revealing dynamic epigenetic states and their implications for transcriptional activity and cancer resistance.