Hi-C

A Super-Loop Extrusion Mechanism Shapes the 3D Mitotic Chromosome Folding

The paper proposes a three-layer loop-extrusion model to explain mitotic chromosome folding, showing it can reproduce structural features observed in Hi-C maps and microscopy.

Understanding the physical processes behind DNA-DNA proximity ligation assays

This study uses numerical experiments and theoretical modeling to investigate the physical processes in DNA-DNA proximity ligation assays and their impact on experimental outcomes.

Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans

This study investigates cohesin's role in organizing 3D DNA contacts around active enhancers in C. elegans, revealing cohesin-dependent 'fountains' and differences in processivity compared to mammals.

Tri-omic mapping revealed concerted dynamics of 3D epigenome and transcriptome in brain cells

The paper introduces a tri-omic method to study 3D epigenome and transcriptome dynamics in brain cells across mouse lifespan, revealing distinct genomic mechanisms in neurons and non-neuronal cells.

Trichostatin A Treatment Has Little Impact on Nuclear compartments in Cells Depleted of H3K9me, H3K27me3, and uH2A

The paper investigates the effect of Trichostatin A on nuclear compartments in cells lacking H3K9me, H3K27me3, and uH2A, finding minimal impact on compartment structure despite increased H3K27ac levels.

Trans-homologous interactions identified in Hi-C data are associated with embryonic development

The paper identifies trans-homologous chromatin interactions in Drosophila Hi-C data and links them to regulatory regions and developmental processes.

Unveiling multi-scale architectural features in single-cell Hi-C data using scCAFE

scCAFE is a deep learning model that detects multi-scale chromatin architectural features in single-cell Hi-C data, outperforming existing methods and enabling cell-type annotation from 3D genome features.

Polymer Model Integrates Super-Resolution Imaging and Epigenomic Sequencing to Elucidate the Role of Epigenetic Reactions in Shaping 4D Chromatin Organization

The paper develops a polymer model integrating super-resolution imaging and epigenomic sequencing to show how epigenetic reactions shape 4D chromatin organization and influence gene expression and metastatic potential.

Embryonic stem cells do not have a globally disrupted higher-order chromatin fibre structure

This study shows that embryonic stem cells (ESCs) have a chromatin structure similar to differentiated cells, challenging the idea that their pluripotency is driven by a globally open chromatin conformation.

Membrane-associated σ factors disrupt rRNA operon clustering in E. coli

The paper shows that membrane-associated σ factors disrupt rRNA operon clustering in E. coli by interacting with core-RNAP and competing with σD.

Hidden origami in Trypanosoma cruzi nuclei highlights its nonrandom 3D genomic organization

This study reveals the nonrandom 3D genomic organization of Trypanosoma cruzi nuclei through Hi-C data analysis, showing repetitive DNA and noncoding RNA influence chromatin structure and gene regulation.

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing

The paper presents diploid genome assemblies for two human fibroblast cell lines, enabling clone-specific variant calling, improved read mapping, and accurate phasing.

StACKER, A TOOL FOR SYSTEMS LEVEL ANALYSIS OF BASE STACKING IN NUCLEOTIDE-RICH STRUCTURES

The paper introduces StACKER, a Python tool for analyzing base stacking in nucleic acid structures, and applies it to ribosome simulations to reveal conformational changes linked to translation phenotypes.

On the path to reference genomes for all biodiversity: lessons learned and laboratory protocols created in the Sanger Tree of Life core laboratory over the first 2000 species

Across 4883 species, standardised high-molecular-weight DNA extraction passed 96% of chordate and 91% of plant species, while fungi failed at 34.2%; ultra-low-input PacBio libraries rescue many low-yield samples.

Rules of engagement for condensins and cohesins guide mitotic chromosome formation

In DT40 cells, condensins displace extrusive cohesin, bypass cohesive cohesin and stall against each other while extruding ~1-3 kb/sec, yielding irregular helical chromatids of consecutive loops.

Predicting 3D Chromatin Interactions Using Transformer-Enhanced Deep Learning Models

This study uses a Transformer-based model to predict 3D chromatin interactions from DNA sequences, improving accuracy over convolutional models by capturing long-range genomic interactions.

Chromatin Structures from Integrated AI and Polymer Physics Model

The paper develops a framework combining polymer physics and machine learning to estimate chromatin structures from Hi-C data with high accuracy.

Deciphering Pre-existing and Induced 3D Genome Architecture Changes involved in Constricted Melanoma Migration

The paper identifies 3D genome architecture changes in melanoma cells before and after constricted migration, linking them to migration ability and cell fate changes.

Learning the dynamic organization of a replicating bacterial chromosome from time-course Hi-C data

The paper develops a 4D Maximum Entropy model to analyze time-course Hi-C data and reveals dynamic chromosome organization in Caulobacter crescentus during replication.

Nuc3DMap delineates finer nucleosome-based three-dimensional chromatin architecture

Nuc3DMap integrates MNase-seq, Hi-C, and Micro-C data to delineate finer nucleosome-based 3D chromatin architecture and identifies distinct subtypes of chromatin features.

Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis

The paper integrates single-cell transcriptomics and epigenomics to show how neural stem cells shift lineage bias and epigenetic states during mouse corticogenesis.

Chromatin as a Coevolutionary Graph: Modeling the Interplay of Replication with Chromatin Dynamics

The paper introduces RepliSage, a framework that dynamically integrates replication timing, loop extrusion, and compartmentalization to simulate chromatin architecture during the cell cycle.

Nuclear actin-dependent Meg3 expression suppresses metabolic genes by affecting the chromatin architecture at sites of elevated H3K27 acetylation levels

This study shows that β-actin depletion increases Meg3 expression, which alters chromatin architecture and represses metabolic genes through promoter-enhancer interaction disruption.

Neur-Ally: A deep learning model for regulatory variant prediction based on genomic and epigenomic features in brain and its validation in certain neurological disorders

Neur-Ally predicts regulatory non-coding SNPs in brain tissues and validates their effect in neurological disorders using deep learning and epigenomic data.

TRUHiC: A TRansformer-embedded U-2 Net to enhance Hi-C data for 3D chromatin structure characterization

TRUHiC enhances low-resolution Hi-C data using deep generative modeling to improve 3D chromatin structure characterization across cell lines and species.

Charm is a flexible pipeline to simulate chromosomal rearrangements on Hi-C-like data.

Charm simulates Hi-C-like data with chromosomal rearrangements to benchmark SV detection tools and provides a dataset for future benchmarking.

Chromosome-level genome assembly of a doubled haploid brook trout (Salvelinus fontinalis)

The paper presents a chromosome-level genome assembly for brook trout using Hi-C and long-read sequencing, achieving high contiguity and annotation coverage.

Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes

This study uses nanoscale DNA tracing to show that mitotic chromosomes form through self-organization via large, overlapping loops driven by Condensins.

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration

The paper creates a single-cell multiome atlas of RPE and choroid tissues to identify pathogenic variants and mechanisms in AMD using HiChIP, Activity-by-Contact, and STARR-seq.

Comparing chromatin contact maps at scale: methods and insights

This study introduces novel methods for comparing chromatin contact maps and evaluates their performance using Hi-C data and in silico maps, highlighting the need for biologically informed approaches.