Peter Fraser

This study shows p53 rapidly changes 3D chromatin structure to regulate gene transcription, identifying 340 new direct target genes.

The paper identifies chromatin loop rewiring in adipogenesis and discovers novel regulators and gene-trait associations relevant to obesity and diabetes.

The paper maps promoter interactions in human ILC3s using PCHi-C and links GWAS risk variants to target genes, identifying new autoimmune disease risk genes.

This study examines how 3D chromatin organization in mouse liver changes throughout the circadian cycle, revealing dynamic domain assignments and promoter-specific chromatin contacts.

This study shows that oncogenic HRAS-induced senescence in human fibroblasts involves enhancer-promoter rewiring and dynamic cohesin binding, particularly at SASP genes.

The paper investigates chromosomal contacts between promoters and enhancers using Capture Hi-C, showing that cohesin depletion affects long-range contacts but not shorter-range ones.

The paper identifies an intergenic non-coding RNA promoter that regulates histone modifications and gene expression in the human β-globin chromatin domain during development.

The paper links diabetes-associated enhancers with their target genes using 3D chromatin architecture in human pancreatic islets, revealing genetic variants that impact insulin secretion heritability.

The paper identifies how variation in PU.1 binding and chromatin looping at neutrophil enhancers influences autoimmune disease susceptibility and cell count differences.

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

The paper identifies DNA methylation oscillations as a marker for enhancer classification, showing high predictive power compared to other methods.

This study investigates how TPO signaling rapidly remodels the epigenome in HSPCs by altering cis-regulatory activity and chromatin architecture.

This study demonstrates that CTCF, WAPL, and PDS5 proteins regulate TADs and loops by controlling cohesin's interaction with chromatin.

The paper introduces Proximity RNA-seq to study nuclear transcriptome organization, revealing bipartite compartments with distinct RNA density and transcription elongation rates.

The paper shows that differential mobility of chromatin segments, influenced by protein occupancy, drives 3D genome organisation in yeast.

The paper identifies autoimmune disease candidate genes by integrating promoter capture Hi-C data with genetic associations in activated CD4+ T cells.

This study uses single-cell Hi-C to analyze chromosomal organization dynamics across the cell cycle, revealing distinct cell cycle-dependent changes in chromosomal compartments, TADs, and loops.

CHiCAGO detects DNA looping interactions in Capture Hi-C data by addressing statistical challenges with a background model and normalization algorithms, showing enrichment for regulatory features and disease SNPs.

GOTHiC introduces a simple probabilistic model to correct biases and identify significant interactions in Hi-C data, outperforming existing methods.