Stefan Schoenfelder

Familial medullary thyroid carcinoma secondary to an SLC30A9 intragenic deletion and translation reinitiation

The paper identifies an SLC30A9 deletion causing familial medullary thyroid carcinoma through translation reinitiation and shows its oncogenic effects.

Signatures of digital Polycomb regulation in functional iPSC heterogeneity between individuals

The paper identifies Polycomb-regulated gene expression and chromatin state differences in iPSCs that correlate with differentiation efficiency.

Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells

The paper identifies non-canonical enhancers in human pluripotent stem cells that lack typical enhancer features but regulate gene expression and cell fate.

The KRAB-Zinc Finger protein ZKSCAN3 represses enhancers via embedded retrotransposons

This study shows ZKSCAN3 represses enhancers by targeting retrotransposons without forming heterochromatin, linking it to neurodevelopmental processes and schizophrenia.

Epigenetic restoration of differentiation competency via reversal of epiblast regionalisation

This study identifies histone modification fluctuations as a cause of PSC differentiation bias and presents a chemical chromatin restoration method to reverse it, restoring epiblast-like differentiation potential.

Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks

The paper identifies epigenetically primed enhancers in early embryonic development and shows their role in regulating developmental gene networks across species.

Rewiring of chromatin loops in adipogenesis reveals targets for obesity and diabetes intervention

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

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.

Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification

The paper investigates how DNA methylation dynamics during pluripotency exit influence enhancer priming and hematopoietic gene activation in mouse cells.

High-resolution promoter interaction analysis implicates genes involved in the activation of Type 3 Innate Lymphoid Cells in autoimmune disease risk

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.

Transcription-driven cohesin repositioning rewires chromatin loops in cellular senescence

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

Cohesin-dependent and independent mechanisms support chromosomal contacts between promoters and enhancers

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.

Network analysis of promoter interactions reveals the hierarchical differences in genome organisation between human pluripotent states

The paper analyzes promoter interactions in human pluripotent states to reveal hierarchical differences in genome organization using a network-graph approach.

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

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

CTCF, WAPL and PDS5 proteins control the formation of TADs and loops by cohesin

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

Heterogeneous chromatin mobility derived from chromatin states is a determinant of genome organisation in S. cerevisiae

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

CHiCAGO: Robust Detection of DNA Looping Interactions in Capture Hi-C data

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, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data

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