Genomics and Chromatin Dynamics

This study maps chromatin folding pathways and rates using a coarse-grained model, showing that linker DNA length and nucleosome condensate affect stability and structure.

This study reveals the 3D genome architecture of Zymoseptoria tritici, showing how chromatin structure and function are interconnected through nuclear organization and gene regulation.

The paper shows FoxP3 forms head-to-head dimers and stabilizes multimerization on microsatellites in Tregs, revealing a dual DNA-binding mode.

Chrom-Sig de-noises 1-dimensional genomic coverage tracks using signal processing to separate signal from noise, validated across multiple datasets.

This study develops a single-molecule platform to analyze mammalian transcription elongation dynamics and identifies kinetic regulation by elongation factors.

This study shows that CTCF-ZF1 RNA interactions are essential for maintaining cell-type-specific chromatin loops during differentiation, with disruption leading to gene dysregulation and loop loss.

This study shows that SMC5/6-mediated plasmid silencing requires SIMC1-SLF2, while SLF1/2 is dispensable, and that LT antagonizes this repression similar to viral proteins.

The paper shows that Brd4 acts as a mitotic bookmark to coordinate transcription and replication timing in Drosophila embryos, preventing collisions between replication forks and transcripts.

This study links in vitro transcription factor affinities to in vivo single-molecule chromatin states using thermodynamic models and experimental data for KLF1.

The paper investigates how heterochromatin boundaries maintain centromere position, size, and number through specific histone modifications and methyltransferases.

This study examines how the G34R and G33R mutations in histone H3.3 affect nucleosome structure and dynamics using NMR and molecular dynamics simulations.

This study shows that short activation domains, not just DNA-binding domains, significantly influence chromatin association of transcription factors in living cells.

The paper develops machine learning models to analyze the human initiator region, identifying key features of core promoters and their functional relationships.

This study quantifies chromosomal structural dynamics during embryogenesis, revealing allele-symmetric and asymmetric patterns in higher-order structures and geometrical compaction.

This study uses molecular dynamics simulations to show how H2A and H2B ubiquitination opposingly affect nucleosome stability and assembly kinetics through structural changes.

This study reconstitutes gene-scale chromatin arrays with controlled histone modifications to show acetylation increases structural fluctuations and reduces nucleosome contact frequency.

ChromPolymerDB reconstructs single-cell 3D chromatin structures from bulk Hi-C data and provides a database for analyzing chromatin conformation across 50 human cell types.

The paper introduces DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW, a benchmark suite for long-range DNA prediction tasks, and evaluates five methods on five genomics tasks.

GAT-HiC predicts 3D chromosome structure from Hi-C data using graph attention networks, showing generalization across different datasets and outperforming existing methods.

The paper identifies NMNAT2 regulatory elements and associated genes using 4C-seq and bioinformatics in human cells, showing correlations with mRNA levels in single-nuclei RNA-seq datasets.

The paper shows that recruiting transcription factors to non-regulatory genomic sites can create enhancers or repressors, influencing gene expression at a distance with nonlinear dependence on site distance.

The paper tracks TAD anchors in human cells to quantify cohesin-mediated loop extrusion dynamics and shows consistent extrusion rates across diverse genomic regions.

This study transplants E. coli chromosomes into artificial cells and shows transcription-dependent swelling and condensin-mediated compaction.

The paper identifies hangover's role in regulating gene expression by inhibiting NSL-mediated H4K16 acetylation at transcriptional start sites in Drosophila.

The paper identifies ThPOK/ZBTB7B as a master regulator that restricts breast cancer cells to a luminal non-migratory phenotype by suppressing metastatic pathways.

The paper develops a general AI model that integrates diverse genomic modalities and knowledge, showing strong performance across cell types and tissues.

This study identifies 3D genome compartment changes associated with epithelial-mesenchymal transition and organotropism in breast cancer metastasis.

The paper investigates how the nuclear to cytoplasmic ratio influences H3.3 incorporation during zygotic genome activation in Drosophila by analyzing cell cycle state and chaperone binding.

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.