Hi-C

Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

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

Active Transcription and Epigenetic Reactions Synergistically RegulateMeso-Scale Genomic Organization

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.

Extreme structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs

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.

Rewiring of master transcription factor cistromes during high-grade serous ovarian cancer development

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

Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex

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.

Allele pairing at Sun1-enriched domains at the nuclear periphery via T1A3 tandem DNA repeats

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

Chromatin conformation dynamics during CD4+ T cell activation implicates autoimmune disease-associated genes and regulatory elements

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.

The ENCODE Uniform Analysis Pipelines

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.

Enhancer-promoter contact formation requires RNAPII and antagonizes loop extrusion

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.

High changing curvature regions detect chromatin enrichment in single cell data

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.

Matrin3 mediates differentiation through stabilizing chromatin accessibility and chromatin loop-domain interactions, and YY1 mediated enhancer-promoter interactions

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

A method for extracting effective interactions from Hi-C data with applications to interphase chromosomes and inverted nuclei

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.

Somatic chromosome pairing has a determinant impact on 3D 1 chromatin organization

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

Visual integration of omics data to improve 3D models of fungal chromosomes

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

Inference of single cell profiles from histology stains with the Single-Cell omics from Histology Analysis Framework (SCHAF)

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.

Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction

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

MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes

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.

Transcription shapes 3D chromatin organization by interacting with loop extrusion

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

TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

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

MAPT expression is mediated by long-range interactions with cis-regulatory elements

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

Pioneer factor Foxa2 mediates chromatin conformation changes in ligand-dependent activation of nuclear receptor FXR

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

optimalTAD: annotation of topologically associating domains based on chromatin marks enrichment

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.

Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

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

Defining the separation landscape of topological domains for decoding consensus domain organization of 3D genome

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

Local administration of a novel siRNA modality into the CNS extends survival and improves motor function in the SOD1G93A mouse model for ALS

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.

Active maintenance of CD8+ T cell naivety through regulation of global genome architecture

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

Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape

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.

A layer cake model for plant and metazoan chromatin

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.

Enhancer/gene relationships: need for more reliable genome-wide reference sets

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.

Foxp3 Orchestrates Reorganization of Chromatin Architecture to Establish Regulatory T Cell Identity

The paper shows Foxp3 is essential for establishing Treg-specific 3D chromatin architecture during differentiation, though not dependent on a specific dimer formation.