Genomics and Chromatin Dynamics

Polyphosphate as a Novel Regulator of Super-Enhancer Complexes: Disruption of Phase Separation and Gene Expression

This paper shows polyP regulates gene expression by modifying super-enhancer complex components, disrupting phase separation and impairing transcription factor function.

Kaiso reads methylated CpGs at nucleosome entry/exit and displaces the H3 tail

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: Context-aware boundary learning for TAD calling from Hi-C contact maps

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

Systematic Regional Bias is Widespread in ChIP-seq

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

Effects of Lamina-Chromatin Attachment on Super Long-Range Chromatin Interactions

This study uses 3D polymer models to show that LAD-lamin interactions influence chromatin organization and induce super long-range chromatin contacts in mouse cells.

Temporal chromatin and transcriptome dynamics driven by JUND and progesterone receptor binding in the pregnant mouse myometrium

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.

The +1 nucleosome functions in Pol II transcription initiation and the transition to elongation

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.

VIDEO - Visual Integration of Drosophila Enhancer Organization: A tool for integrating and visualizing chromatin accessibility, in vivo transcription factor binding and motif occurrence in tissue-specific differentially expressed genes

VIDEO is a web-based tool that integrates and visualizes chromatin accessibility, TF binding, and motif occurrence in tissue-specific genes to explore gene regulation in Drosophila.

A Fractal-Dimension Framework for Quantifying Self-Similarity in Chromatin Folding

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.

Cohesin bridging as a physical principle of enhancer-promoter communication

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.

Apical Localization of RNA Polymerases Modulates Transcription Dynamics and Supercoiling Domains Revealed by Cryo-ET

The paper uses cryo-ET to show RNAP localization at DNA supercoiling apices influences transcription dynamics and supercoiling domains.

A radial map of the budding yeast genome reveals novel organizational principles

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.

Acetyl-CoA Synthetase 1 Regulates Global Histone Propionylation and Metabolic Stress Responses

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.

Enhancer Placement Impacts Transcriptional Dynamics in Drosophila Embryos

This study shows that enhancer-promoter configurations in Drosophila embryos affect transcriptional dynamics, with downstream enhancer positioning reducing mRNA output by 70%.

CpG island density predicts CBP/p300 dependency across 3D chromatin clusters

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

Loop extrusion dynamics and cooperative activation independently regulate enhancer-driven transcription

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

H1.3 depletion in AML cells prompts H1.2 redistribution, chromatin remodeling and cell cycle defects

Modular control of CpG islands by chromatin-opening transcription factors specifies transcription start sites

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.

BandHiC: a memory-efficient and user-friendly Python package for organizing and analyzing Hi-C matrices down to sub-kilobase resolution

BandHiC reduces memory usage for Hi-C matrices by 99% using a banded storage strategy while enabling efficient analysis of ultra-high-resolution data.

In vivo measurement and prediction of cell-type-resolved non-coding variant effects in human immunity

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.

Nucleosome remodeling by a CHD enzyme promotes H3K9 methylation establishment and spreading via remodeler-writer feedback

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

Structural basis for site-specific histone H3 acetylation-dependent regulation of RNAPII transcription through nucleosomes

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

UniversalEPI: robust prediction of cell type-specific and differential chromatin interactions from DNA sequence and chromatin accessibility

UniversalEPI predicts cell type-specific and differential chromatin interactions using DNA sequence and ATAC-seq data, showing robust performance across cell types and conditions.

Cohesin extrudes chromatin loop unidirectionally through two modes of mechanisms in human cells

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.

H3K9me3 as a gatekeeper of lineage-specific enhancers in embryonic progenitor cells

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

IGS38, a lncRNA from the human rDNA intergenic spacer, regulates rRNA transcription by altering rDNA chromatin organisation and activating the transcription machinery

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

Toward a probabilistic definition of chromatin accessible regions at the single-cell level

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.

H2A.Z levels control the timing of major events at the maternal-zygotic transition

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.

Impact of histone N-terminal domains and linker DNA on H2A.Z deposition by yeast SWR1C

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.

Bipartite DNA binding domain of transcription factor BCL11B binds clustered short DNA sequence motifs

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