Genomics and Chromatin Dynamics

ArChIPelago combines multiple PWMs using classic machine learning to improve TFBS prediction, outperforming individual PWMs and other models across species.

This study shows Kaiso binds methylated nucleosomes with position-specific affinity and displaces the H3 tail, suggesting a general mechanism for chromatin remodeling by DNA-binding factors.

ContextTAD improves TAD calling from Hi-C contact maps by learning context-aware boundary evidence, achieving strong performance across multiple evaluation settings.

The paper identifies systematic regional bias in ChIP-seq data across multiple experiments and proposes metrics to improve data integration.

The paper identifies JUND and progesterone receptor binding dynamics in the pregnant mouse myometrium, linking chromatin accessibility changes to gene expression during pregnancy, labor, and postpartum.

This study investigates the role of the +1 nucleosome in transcription initiation and the transition to elongation using in vitro experiments and cryo-EM structures.

This paper introduces a fractal-dimension framework to quantify self-similarity in chromatin folding using Hi-C data, revealing fractal-like organization and scale-dependent patterns in chromatin structure.

This study proposes that cohesin bridging, not spatial proximity, mediates enhancer-promoter communication and develops a model to validate this mechanism through engineered cell systems.

The paper uses GPSeq to map the budding yeast genome's radial organization, revealing that centromeres and telomeres constrain chromatin positioning, and GC-content organizes chromatin in their absence.

The paper identifies histone propionylation as a response to glucose starvation and shows that Acs1 generates propionyl-CoA for this modification, linking metabolism to chromatin regulation.

The paper identifies two classes of Pol2-mediated chromatin clusters and shows CpG island density predicts CBP/p300 dependency.

The paper shows that loop extrusion and enhancer cooperativity independently affect enhancer-driven transcription through synthetic gene activation experiments.

The paper shows chromatin-opening transcription factors determine transcription start sites by binding near the initiation site, with loss of these factors redirecting initiation to secondary sites.

The paper measures and predicts non-coding variant effects in human immune cells using single-cell ATAC-seq and whole-genome sequencing, revealing regulatory mechanisms and applications in systemic lupus erythematosus.

This study shows that the CHD remodeler Mit1 initiates heterochromatin formation and H3K9 methylation independently of Clr4, revealing a remodeler-writer feedback mechanism.

The paper investigates how specific acetylation sites on histone H3 affect RNAPII transcription through nucleosomes using cryo-EM structures.

The paper investigates cohesin-mediated chromatin loop extrusion in human cells, revealing two dynamic modes of extrusion and showing that CTCF depletion increases extrusion activity.

The paper shows H3K9me3 represses lineage-specific enhancers in progenitor cells, restricting transcription factor access to prevent inappropriate activation during development.

This paper identifies IGS38, a lncRNA that enhances rRNA transcription by altering chromatin structure and promoting RNA polymerase I promoter escape.

The paper introduces a probabilistic framework to define chromatin accessibility in single-cell snATAC-seq data, avoiding arbitrary thresholds and providing a dynamic understanding of accessible regions.

This study shows that H2A.Z levels act as a timer for the maternal-zygotic transition in Drosophila and zebrafish, influencing developmental timing through both nuclear and non-nuclear mechanisms.

This study investigates the factors influencing SWR1C-mediated H2A.Z deposition in yeast, finding that histone tails and acetylation are less critical than linker DNA.

This paper investigates the DNA-binding properties of BCL11B's bipartite zinc finger domain and its mutations linked to neurodevelopmental disorders.

The paper develops a polymer micelle model to explain how enhancer-promoter conformation and micelle stability influence transcriptional bursting kinetics.

The paper shows CTCF forms dynamic DNA bridges that stabilize chromatin loops independently of cohesin, challenging the loop extrusion model.

The paper shows a Tcra enhancer can regulate a distal gene in a different TAD during T-cell development, challenging the idea that TAD boundaries block enhancer-promoter interactions.

This study maps chromatin changes at repetitive DNA during aging and cancer using epigenomic data from hematopoietic cells and malignancies.

This study shows light intensity affects higher-order DNA structure in Synechocystis sp. PCC 6803, revealing a light-dependent adaptation in chromosome organization.

The paper shows that single transcription factors dominantly activate essential genes through regulatory dominance rather than cooperation in murine stem cells.

The paper investigates how human transcription factors bind specific DNA sites in yeast, finding that disordered regions influence binding selectivity beyond DNA motifs.