Genomics and Chromatin Dynamics

This study investigates the role of ORC2 in epigenetic regulation and chromosome structure through a multi-omics analysis of a human cell line with ORC mutations.

StripePy is a tool for detecting architectural stripes in Hi-C data, outperforming existing methods on benchmark datasets.

This study shows that CBP, a histone acetyltransferase, has both catalytic and non-catalytic roles in zygotic genome activation, independent of its acetylation function.

The paper shows that Ldb1 (Chip) is a cofactor of Zelda that bridges to CBP to regulate gene expression during zygotic genome activation in Drosophila.

The paper shows that specific DNA replication origins are still used and excess MCM2-7 is loaded in ORC-deficient human cancer cells.

This study identifies MYC and MAX binding near transcriptional end sites (TESs) and shows their role in regulating gene expression, read-through transcription, and intragenic contacts.

The paper introduces TAC-C, a method combining ATAC-seq and Hi-C to study chromatin interactions in crops, revealing SPL-mediated photosynthesis regulation and chromatin loop structures.

The paper determines the crystal structures of Clr4 bound to ubiquitinated and unmodified H3 peptides, revealing how H3K14 ubiquitination synergistically enhances Clr4 catalytic activity through conformational changes and multivalent interactions.

The paper investigates how nucleosome remodelers affect transcription at cis-regulatory elements in murine ES cells, identifying novel roles and mechanisms of action for different remodelers.

BIT identifies transcriptional regulators using a Bayesian hierarchical model, improving accuracy and interpretability by integrating epigenomic data with TR ChIP-seq libraries.

The paper investigates how a disordered linker in the Polyhomeotic protein influences phase separation and oligomerization in Drosophila and human cells through in vitro reconstitution and molecular dynamics simulations.

The paper identifies functionally conserved regulatory elements across distantly related vertebrates despite sequence divergence using a synteny-based method.

TFBSFootprinter predicts transcription factor binding sites across 124 vertebrate species using multiomic data, outperforming existing tools in accuracy.

This study uses HaloTag in C. elegans to track intestinal histone turnover and shows protein stability changes during starvation.

deepTFBS improves TFBS prediction within and across species using deep multi-task and transfer learning, outperforming existing methods in Arabidopsis and wheat.

This paper introduces MaxComp, an unsupervised method to predict single-cell chromatin compartments from 3D chromosome structures, showing that compartment annotations can be derived from geometric considerations alone.

The paper identifies a single HZA enhancer that controls two head-to-head genes in C. elegans under metal stress, demonstrating enhancer function in regulating multiple genes.

The paper quantifies proteins directly interacting with DNA in human cells and identifies key transcription factors and DNA damage proteins in response to treatments.

The paper investigates chromatin structure in immature and mature mouse retina cells, finding that short DNA linkers disrupt the two-start zigzag folding, leading to less compact chromatin in immature cells.

The paper uses single-molecule analysis to show how variant PRC1 complexes interact with chromatin and perform ubiquitylation, revealing subtype-specific activity differences.

This study identifies ALFIN-LIKE proteins as recruiters of SWR1 to direct H2A.Z deposition at H3K4me3-marked gene bodies in Arabidopsis.

The paper investigates how pH dynamics regulate transcription factor DNA binding selectivity, finding pH-dependent binding affinities and activity for FOX family transcription factors.

The paper evaluates computational methods for predicting cell type-specific enhancers in the mouse cortex using in vivo validation data and finds that open chromatin and sequence models improve prediction accuracy.

The paper investigates how cell cycle regulation controls transcriptional pausing of Drosophila replication-dependent histone genes, showing that Cyclin E/Cdk2 activation drives full-length transcript production during S phase.

The paper develops a high-resolution mathematical model to map replication timing profiles across cell lines, revealing correlations between replication dynamics, transcription, and chromatin structure.

This study identifies how histone modifications regulate gene expression in memory and exhausted CD8 T cells, revealing distinct epigenetic programs between these cell types.

The paper introduces a low-cost, flexible method for quantitative chromatin sequencing and enables cross-species epigenomic comparisons.

This study uses simulations to show that binder valency drives chromatin collapse while monomer valency determines reswelling, with two distinct mechanisms identified.

CREATE identifies cell-type-specific cis-regulatory elements using a deep learning model that integrates genomic sequences, chromatin accessibility, and chromatin interactions.