Hi-C

DeDoc2 identifies and characterizes the dynamic hierarchy of TAD-like domains in single cells, showing their variability during the cell cycle and across human brain cortex cells.

The paper introduces RCMC, a method to capture deep 3D genome structure, revealing microcompartments where enhancers and promoters coalesce.

This study introduces a mesoscale model to show how transcription and epigenetic reactions regulate heterochromatin domain sizes, finding that transcription loss increases domain size and compaction.

The paper maps structural variants and neoloops in glioblastoma stem cells to show how they sustain tumor-specific transcriptional programs and identify patient-specific vulnerabilities.

This study identifies MECOM, PAX8, SOX17, and WT1 as master regulators in HGSC, showing their rewired cistromes and tumor-specific inhibition potential.

The paper analyzes gene regulatory programs in the neocortex of rodents and primates using single-cell multiomics, finding rapid evolution of cell type-specific gene expression and TE-driven cCREs.

The paper shows that alleles of monoallelic genes are paired at Sun1-enriched nuclear periphery domains, enriched with T1A3 repeats and bound by Hnrnpd.

The paper identifies autoimmune disease-associated genes and regulatory elements by analyzing chromatin dynamics during CD4+ T cell activation using RNA-seq, ATAC-seq, and HiC.

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper investigates the role of RNAPII in chromatin loop formation and shows that enhancer-promoter contacts are selectively lost upon RNAPII depletion, repressing gene expression.

This study identifies high changing curvature (HCC) regions in Hi-C data that correlate with gene expression and CTCF density, showing cell-to-cell variability.

The paper shows Matrin3 stabilizes chromatin accessibility and loop-domain interactions, and facilitates YY1-mediated enhancer-promoter interactions during differentiation.

This paper introduces a method to extract effective interaction energies from Hi-C data to model chromosome organization, showing that heterochromatin attraction drives compartment formation in conventional and inverted nuclei.

The paper investigates how chromosome pairing affects 3D chromatin organization in Drosophila, showing it reinforces intrachromosomal interactions but not compartmental organization.

The paper develops a workflow to generate 3D chromosome models from Hi-C data and applies it to fungal species, revealing new structural insights.

SCHAF generates spatially resolved single-cell transcriptomes from H&E histology images using vision transformers and adversarial learning, showing good agreement with ground-truth data.

This paper introduces an efficient algorithm to convert Hi-C data into contact energies, revealing chromatin loop anchors and enabling 3D structure prediction.

The paper introduces MultiomicsTracks96, a high-throughput multi-omics workflow for analyzing frozen and FFPE tissues, showing high correlation between data types and improved protein prediction using multi-omics data.

The paper shows that transcribing RNA polymerases act as moving barriers to cohesin, altering chromatin organization near active genes.

The paper analyzes TAD boundaries across species to show evolutionary conservation and functional significance, finding ultraconserved boundaries have stronger insulation and CTCF binding.

The paper identifies cis-regulatory elements (cCREs) controlling MAPT expression and links genetic variation in these elements to Alzheimer's disease risk.

The paper shows Foxa2 enables chromatin conformation changes during FXR ligand activation in mouse livers, increasing long-range interactions and altering TADs and loops.

The paper introduces optimalTAD, an algorithm for identifying TADs by maximizing chromatin mark enrichment differences between TADs and boundaries, showing it works across species and cell types.

The paper introduces HiCFlow to analyze allele-specific chromatin conformation and identifies allele-specific TADs (ASTADs) beyond imprinted gene clusters.

The paper defines a TAD separation landscape to address inconsistencies in TAD identification across methods and identifies Consensus Topological Associating Domains.

This study demonstrates that a novel siRNA modality, conjugated with an accessory oligonucleotide, improves survival and motor function in a mouse model of ALS when delivered locally to the CNS.

This study shows that transcription factors maintain CD8+ T cell naivety by enforcing a distinct chromatin architecture that remodels upon activation.

This paper shows that mutations in SF3B1 and U2AF1 cause transcription elongation defects leading to chromatin changes and identifies targeting the Sin3/HDAC complex as a potential therapy.

The paper compares 3D chromatin organization across species to propose a layer cake model that refines the two compartments model by identifying distinct chromatin layers.

The paper evaluates two functional link methods for identifying enhancer/gene relationships using benchmark data and finds neither performs best, highlighting the need for reliable genome-wide reference data.