Wolf Reik

The paper identifies a non-catalytic repressor function of TET1 and an activating role of macroH2A.2 in bivalent chromatin during neuroectoderm differentiation.

The paper identifies average polycomb CpG methylation as a hallmark of cellular aging using single-cell whole-genome methylation data, showing cell-to-cell variability and accelerated aging in faster proliferating cells.

This paper introduces scDynaBar, a method using CRISPR barcoding to track temporal cellular events at single-cell resolution, showing the transient nature of the 2C-like state in mESCs.

This paper introduces a physics-based model explaining how cells maintain histone methylation patterns after division, validated by simulations and experimental data.

The paper uses human pluripotent stem cells to study the epiblast development transition, revealing a transcriptional clock mechanism that governs timing and directionality through gene regulatory networks.

The paper shows that DNA methylation ageing is reflected in correlations between genomic loci, with a preference for 500 bp apart sites, and links this to PRC2-dependent H3K27me3 dilution.

This study creates a spatiotemporal atlas of mouse gastrulation and early organogenesis using spatial transcriptomics and scRNA-seq, revealing gene expression dynamics and mesodermal fate decisions.

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

The paper identifies Eomes's role in directing the formation of distinct extra-embryonic hematovascular tissues in mice, revealing functional and mechanistic diversity in their development.

The paper shows that DNA translesion synthesis is essential for primordial germ cell development and DNA demethylation in mammals, linking DDR to fertility.

This study shows that maternal SMARCA5 is essential for major ZGA in mouse embryos by regulating promoter and distal regulatory region accessibility and nucleosome positioning.

The paper examines DNA methylation patterns in neurons derived from mouse ES-cells and cultured primary neurons, finding similarities and differences in mCH deposition compared to in vivo conditions.

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

The paper uses single-cell RNA-sequencing to study heterogeneity in mouse gastruloids over time, revealing distinct mesodermal and neural differentiation trajectories and their implications for perturbation studies.

A mouse embryo multiome atlas (E7.5 to E8.75) and an unsupervised transcription factor binding predictor; a Brachyury knockout supports its network predictions in neuromesodermal progenitors.

This paper introduces a method to rejuvenate human fibroblasts by transient reprogramming to the maturation phase of iPSCs, followed by recovery of fibroblast identity, resulting in significant rejuvenation of transcriptome, epigenome, and functional markers.

GwEEP quantifies DNA modifying enzyme efficiencies using HPoxBS data, revealing dynamic changes in methylation and hydroxylation during cellular reprogramming and development.

This study shows Dppa2/4 are not required for zygotic genome activation but are important for offspring survival, as maternal depletion leads to reduced litter size and increased preweaning lethality.

The paper examines how MEK and GSK3 inhibition affects the methylome and transcriptome of mouse embryonic stem cells, revealing distinct epigenetic and transcriptional changes.

This paper identifies 8-cell like cells (8CLCs) in human naive stem cells that model zygotic genome activation, expressing ZGA markers and transposable elements, and can be manipulated to enhance ZGA-like transcription.

The paper shows that H3K4me1 retention in enhancers supports germline competence by maintaining enhancer accessibility and responsiveness during in vitro differentiation.

This paper uses spatial transcriptomics to study mouse organogenesis, revealing spatial gene expression patterns and cell fate decisions not captured by single-cell RNA sequencing.

The paper uses single-cell bisulfite sequencing to analyze DNA methylation in spermatozoa from lean and obese humans, revealing distinct epigenetic patterns that may affect intergenerational health outcomes.

The paper shows that histone modifications form cell-type-specific chromosomal patterns that remain stable through the cell cycle, helping maintain gene expression identity.

This paper develops a framework to infer spatio-temporal processes in the nucleus from single-cell methylome data, showing feedback between DNA methylation and chromatin condensates during pluripotency exit.

This study identifies molecular differences between extraocular and limb muscle stem cells, showing that EOM MuSCs reprogram their transcriptome and epigenome after transplantation, with some genes resisting engraftment.

The paper shows DNA methylation prevents HIF binding, affecting hypoxia responses and tumour immunotolerance.

The paper uses CRISPR-activation and single-cell RNA-seq to identify 44 epigenetic regulators that induce a zygotic genome activation-like state in mouse embryonic stem cells.

This study identifies Dppa2/4 as epigenetic factors that establish bivalency at developmental promoters, enabling lineage commitment by maintaining poised RNA polymerase and preventing DNA methylation.

This study shows that ageing increases transcriptional heterogeneity and DNA methylation drift in muscle stem cells, disrupting transcriptional networks and stem cell function.