Genomics and Chromatin Dynamics

Engineered Tn5 Variants Enhance CUT&Tag Fidelity for Transcription Factors

This paper improves CUT&Tag for transcription factors by engineering Tn5 variants, enhancing recovery of TF binding sites in mouse cells and revealing distinct chromatin interaction modes.

Pervasive cis-regulatory co-option of a transposable element family reinforces cell identity across the mouse immune system

The paper identifies two rodent-specific transposable element subfamilies that function as cell-type-specific enhancers in the mouse immune system, contributing to cell identity and gene regulation.

Nascent transcription profiling identifies H3K36 methylation as a custodian of the somatic transcriptome

The paper identifies H3K36 methylation as critical for maintaining transcriptome fidelity in metazoans by suppressing aberrant initiation in heterochromatin.

Hepatocyte nuclear factor-1β recruits the nucleosome remodeling and deacetylase complex to activate gene transcription

This study identifies HNF-1β's role in recruiting the NuRD complex to activate gene transcription through chromatin remodeling and acetylation.

Unpacking Chromatin Accessibility with Fiber-seq

This paper introduces Fiber-seq, a method for detecting chromatin accessibility on individual DNA fibers, and provides guidelines for its proper use and analysis.

Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

The paper identifies localized chromatin rewiring in rice's stable 3D genome that coordinates rhythmic transcription across the circadian cycle.

Locus-specific spatial and transcriptional dynamics direct T cell lineage choice in the thymus

The paper investigates how spatial and transcriptional dynamics at Cd4 and Cd8 loci influence T cell lineage choice in the thymus, revealing locus-specific chromatin environments that drive differentiation.

Best Practices for Pre-Processing Large-Scale ATAC-Seq Data: Why Epidemiological Studies Demand Greater Stringency

The paper introduces PIPPA, a pipeline for processing large-scale ATAC-seq data, showing that peak calling performance varies by dataset and recommending parameters for high-confidence chromatin accessibility profiles.

Lineage-specific transcription factor CEBPA accelerates RNA Polymerase I dynamics

This study shows that the myeloid transcription factor CEBPA accelerates RNA Polymerase I dynamics at rDNA repeats by modulating promoter escape, Pol I accumulation, and DNA supercoiling resolution.

NMR-measured Per-residue Electrostatic Potentials Reveal the Importance of Arginine-Lysine Balance on the Conformational Ensemble of Disordered Histone H3 Tails in Nucleosome Core Particles

The paper measures electrostatic potentials of histone H3 tails using NMR and simulations to show how arginine-lysine balance affects their conformational behavior in nucleosome core particles.

Metazoan Orc6 Proteins Evolved Alternative Mechanisms for Association with the ORC Complex: Insights from Drosophila Modeling

The paper investigates differences in Orc6 protein interactions with the ORC complex in Drosophila and humans, proposing that a nuclear localization signal in humans compensates for weaker binding.

Sequence design for three-dimensional genome folding using Akita Semifreddo

This paper introduces Akita Semifreddo, a framework for designing DNA sequences that produce specific 3D genome folding patterns, demonstrating the ability to create boundaries, dots, and flames with controlled strengths.

A molecular framework of chromatin extrusion in plants

This study identifies PDS5A as a key regulator of chromatin loop extrusion and TAD-like domains in Arabidopsis, revealing a promoter- and motif-based mechanism for loop anchoring and transcriptional control.

Region-specific generation and retention of acetylated cohesin shape the genome-wide pattern of sister chromatid cohesion

The paper investigates how ESCO2-mediated acetylation of cohesin is distributed and retained across the genome, revealing region-specific patterns and post-replicative retention mechanisms.

Exploring DNA movement through the application of droplet based high efficient chromatin conformation capture (DropHiChew) and loop velocity

This paper introduces DropHiChew and loop velocity to study DNA movement dynamics, enabling accurate trajectory estimation with shallow sequencing.

Specification of Origins of DNA Replication Within Distinct Chromatin States in Human Cells

The paper maps ORC1 binding sites across the human genome, linking replication licensing to chromatin states, 3D genome organization, and replication timing.

2C-RT Quantifies Genome-Wide DNA Replication Perturbations and Redefines RIF1-CDC7 Regulation of Replication Timing

Sorting S-phase cells by Cyclin A2 rather than DNA content exposes a uniform genome-wide delay after CDC7 inhibition and a broad replication timing advance in RIF1 knockout.

Regulation by partition predicts enhancer target selection in mammalian genomes

The paper introduces SPIE-seq to study enhancer target selection, finding that genomic context and distance-weighted competition, not enhancer identity, determine target choice.

Histone modifications directly modulate transcription factor binding to nucleosomes

The paper investigates how histone modifications affect transcription factor binding to nucleosomes and finds that specific marks influence binding preferences and modes.

Evolution of CTCF underlies the establishment of loop extrusion as a predominant chromatin folding mechanism in vertebrates

The paper investigates the evolution of CTCF's role in chromatin organization across species, finding that vertebrate CTCF enables loop extrusion but requires additional factors for full genome architecture.

Micro-C-TALE: BAC-based targeted high-resolution measurement of 3D chromatin interactions

Micro-C-TALE provides a cost-effective method for high-resolution targeted chromatin interaction mapping with improved sensitivity and resolution compared to existing techniques.

CTCF gradually acquires novel function modalities during bilaterian evolution

This study investigates how CTCF's functional properties evolved across bilaterian species, revealing gradual changes in its ability to regulate chromatin structure and transcription.

Genome-scale mapping of plant transcription factor effector domains reveals conserved regulatory principles across eukaryotes

The paper maps transcription factor effector domains in plants and compares their function across eukaryotes, revealing conserved and lineage-specific regulatory principles.

Evaluation of object detection neural networks to find topologically associated domains in bulk Hi-C data

This study evaluates YOLOv8 and Mask R-CNN for detecting TADs in bulk Hi-C data by converting Hi-C matrices into images and comparing their performance against reference TADs.

Extrachromosomal circular DNA formation follows a 10.5-bp periodicity reflecting the minor groove orientation around nucleosomes

The paper analyzes eccDNA length distributions and breakpoint organization across multiple datasets to show that eccDNA formation is influenced by nucleosome positioning and DNA helix orientation.

Transglutaminase 3 is a Histone Monoaminylation Writer

The paper identifies TG3 as a new histone monoaminylation writer capable of catalyzing H3Q5 histaminylation.

Coffee induces chromatin structural changes associated with histone H4K16 hypoacetylation

This study shows coffee reduces H4K16ac levels and alters chromatin structure, with transcriptional changes in K562 cells.

Elevated polyadenylated histone gene transcription in human cancer

The paper identifies elevated polyadenylated histone gene transcription in human cancers, showing it is prevalent across diverse tumor types and linked to RNAPII stabilization.

Predicting cell-state-specific gene regulation from DNA across species

Bolero predicts cell-state-specific gene regulation from DNA across species by integrating cell-state embeddings and biological variables.

U-Chrom: a unified framework for single-cell and spatial 3D genome data

U-Chrom provides a unified framework for analyzing single-cell and spatial 3D genome data, showing consistent cell-type differences across assays.