Tim Lohoff
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View article: A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space
A spatiotemporal atlas of mouse gastrulation and early organogenesis to explore axial patterning and project in vitro models onto in vivo space Open
During gastrulation, mouse epiblast cells form the three germ layers that establish the body plan and initiate organogenesis. While single-cell atlases have advanced our understanding of lineage diversification, spatial aspects of differen…
View article: Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks
Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks Open
Background Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enhancers adopt a primed chromatin state pr…
View article: Eomes directs the formation of spatially and functionally diverse extraembryonic hematovascular tissues
Eomes directs the formation of spatially and functionally diverse extraembryonic hematovascular tissues Open
During mouse gastrulation, extraembryonic mesoderm (ExEM) contributes to the extraembryonic yolk sac (YS) and allantois, both of which are essential for successful gestation. Although the genetic networks coordinating intra-embryonic mesod…
View article: A new resource of clonal pluripotent human stem cell lines exhibiting inter- and intra-embryo consistency and variability
A new resource of clonal pluripotent human stem cell lines exhibiting inter- and intra-embryo consistency and variability Open
Human naive pluripotent stem cells can generate all somatic tissues and extra-embryonic components of the blastocyst. We derived multiple clonal naive pluripotent stem cell lines from individual embryos by physical separation of inner cell…
View article: A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project<i>In Vitro</i>Models onto<i>In Vivo</i>Space
A Spatiotemporal Atlas of Mouse Gastrulation and Early Organogenesis to Explore Axial Patterning and Project<i>In Vitro</i>Models onto<i>In Vivo</i>Space Open
SUMMARY At the onset of murine gastrulation, pluripotent epiblast cells migrate through the primitive streak, generating mesodermal and endodermal precursors, while the ectoderm arises from the remaining epiblast. Together, these germ laye…
View article: Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks
Epigenetic priming of embryonic enhancer elements coordinates developmental gene networks Open
Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enhancers adopt a primed chromatin state prior to thei…
View article: Eomes directs the formation of spatially and functionally diverse extra-embryonic hematovascular tissues
Eomes directs the formation of spatially and functionally diverse extra-embryonic hematovascular tissues Open
Summary During mouse gastrulation, extraembryonic mesoderm (ExEM) contributes to the extraembryonic yolk sac (YS) and allantois, both of which are essential for successful gestation. Although the genetic networks coordinating intra-embryon…
View article: Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification
Dynamic DNA methylation turnover at the exit of pluripotency epigenetically primes gene regulatory elements for hematopoietic lineage specification Open
Epigenetic mechanisms govern developmental cell fate decisions, but how DNA methylation coordinates with chromatin structure and three-dimensional DNA folding to enact cell-type specific gene expression programmes remains poorly understood…
View article: Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis
Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis Open
Background Perturbation of DNA methyltransferases (DNMTs) and of the active DNA demethylation pathway via ten-eleven translocation (TET) methylcytosine dioxygenases results in severe developmental defects and embryonic lethality. Dynamic c…
View article: Decoding gene regulation in the mouse embryo using single-cell multi-omics
Decoding gene regulation in the mouse embryo using single-cell multi-omics Open
Following gastrulation, the three primary germ layers develop into the major organs in a process known as organogenesis. Single-cell RNA sequencing has enabled the profiling of the gene expression dynamics of these cell fate decisions, yet…
View article: Supervised spatial inference of dissociated single-cell data with SageNet
Supervised spatial inference of dissociated single-cell data with SageNet Open
Spatially-resolved transcriptomics uncovers patterns of gene expression at supercellular, cellular, or subcellular resolution, providing insights into spatially variable cellular functions, diffusible morphogens, and cell-cell interactions…
View article: Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis Open
View article: Multi-omics characterisation of mouse gastrulation and organogenesis at single-cell resolution
Multi-omics characterisation of mouse gastrulation and organogenesis at single-cell resolution Open
Soon after implantation, the mammalian embryo needs to instruct the specification of the epiblast precursors required for the formation of the foetal tissues. At the exit from pluripotency, global epigenetic and transcriptional remodelling…
View article: Metabolic control of DNA methylation in naive pluripotent cells
Metabolic control of DNA methylation in naive pluripotent cells Open
View article: Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis
Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis Open
Transcriptional and epigenetic profiling of single-cells has advanced our knowledge of the molecular bases of gastrulation and early organogenesis. However, current approaches rely on dissociating cells from tissues, thereby losing the cru…
View article: Multi-omics profiling of mouse gastrulation at single-cell resolution
Multi-omics profiling of mouse gastrulation at single-cell resolution Open
View article: Distinct Molecular Trajectories Converge to Induce Naive Pluripotency
Distinct Molecular Trajectories Converge to Induce Naive Pluripotency Open
View article: Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency
Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency Open
View article: Inactivation of Cancer Mutations Utilizing CRISPR/Cas9
Inactivation of Cancer Mutations Utilizing CRISPR/Cas9 Open
Although whole-genome sequencing has uncovered a large number of mutations that drive tumorigenesis, functional ratification for most mutations remains sparse. Here, we present an approach to test functional relevance of tumor mutations em…
View article: The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading
The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading Open
Circadian control of gene expression is well characterized at the transcriptional level, but little is known about diel or circadian control of translation. Genome-wide translation state profiling of mRNAs in Arabidopsis thaliana seedlings…