Biology subjects

Zeller, P.

Publications and source records attributed to Zeller, P..

7 recordsLinked to original sources

bioRxiv2024

Single-cell multi-omic analysis reveals principles of transcription-chromatin interaction during embryogenesis

Establishing a cell-type-specific chromatin landscape is crucial for the maintenance of cell identity during embryonic development. However, our knowledge of how this landscape is set during vertebrate embryogenesis has been limited, due to the lack of methods to jointly detect chromatin modifications and gene expression in the same cell. Here we present a multimodal measurement of full-length transcriptome and histone modifications in individual cells during early embryonic development in zebrafish. We show that before the formation of germ layers, the chromatin and transcription states of cells are uncoupled, and become progressively connected during gastrulation and somitogenesis. Silencing of developmental genes is achieved by local spreading of repressive chromatin together with cell-type specific demethylation. Combining transcription factor (TF) expression and chromatin states within an interpretable machine learning model, we classify TFs as lineage-specific activators and repressors and identify a subset of TFs that are epigenetically regulated. Altogether, our data resolves the dynamic relationship between chromatin and transcription during early vertebrate development and clarifies how these two layers interact to establish cell identity.

genomics↗

bioRxiv2024

T-ChIC: multi-omic detection of histone modifications and full-length transcriptomes in the same single cell

Epigenetic mechanisms, including histone modifications, are key regulators of transcription and influence cellular differentiation. To uncover the interplay between histone modifications and transcription, we developed T-ChIC (Transcriptome + Chromatin ImmunoCleavage), which detects full-length transcripts and histone modifications in the same single cell. We applied T-ChIC to gastruloids, an in vitro model containing cell types derived from all three germ layers. During gastruloid development we observed a switch in transcription start site usage from multiple regions marked by H3K4me3 to one marked start site per gene. H3K27me3 coverage transitions from global marking of non-transcribed regions towards localised marking of repressive regions. Upon lineage commitment, bivalent regions are sequentially resolved towards a germ layer-specific state, where endoderm retains a high abundance of H3K27me3 while ectoderm displays a widespread loss. Together, we propose a model for a cell-intrinsic epigenetic timer, which ensures sequential perceptiveness of pluripotent cells to transcriptional activation of germ layer-specific genes.

genomics↗

bioRxiv2024

Stem cell culture conditions affect in vitro differentiation potential and efficiency of mouse gastruloid development

By aggregating low numbers of mouse embryonic stem cells (mESCs) followed by exposure to Wnt activation, structures termed gastruloids are produced that display an anteroposterior organisation of cell types derived from all three germ layers. Since current gastruloid protocols display considerable heterogeneity between experiments in terms of morphology, elongation efficiency, and cell type composition, we investigated whether an optimised mESC pluripotency state would provide more consistent results. By growing mESCs in different intervals of ESLIF and 2i medium the pluripotency state of cells was modulated, and mESC culture as well as the resulting gastruloids were analysed. Microscopy analysis showed a pre-culture-specific effect on gastruloid formation, in terms of efficiency, elongation index and reproducibility. RNA-seq analysis of the mESC start population confirmed that short-term pulses of 2i and ESLIF modulate the pluripotency state, and result in different cellular states. With multiple epigenetic regulators among the top differentially expressed genes we further analysed genome-wide DNA methylation and H3K27me3 distributions. We observed the same divergence between conditions, most dominantly displayed in the promoter regions of developmental regulators. Lastly, when we investigated the cell type composition of gastruloids grown from these different pre-cultures, we observed that mESCs subjected to 2i-ESLIF preceding aggregation generated gastruloids more consistently, including more complex mesodermal contributions as compared to the ESLIF-only control. This indicates that optimisation of the mESCs pluripotency state allows the modulation of cell differentiation during gastruloid formation.

developmental biology↗

bioRxiv2023

Time-resolved and multifactorial profiling in single cells resolves the order of heterochromatin formation events during X-chromosome inactivation

The regulation of gene expression is governed at multiple levels of chromatin organization. However, how coordination is achieved remains relatively unexplored. Here we present Dam&ChIC, a method that enables time-resolved and multifactorial chromatin profiling at high resolution in single cells. Analysis of genome-lamina interactions in haploid cells reveals highly dynamic spatial repositioning of small domains during interphase and partial inheritance over mitosis. Dam&ChIC applied to study random X-inactivation uncovers that spreading of H3K27me3 on the inactive X chromosome (Xi) overlaps with remarkable genome-lamina detachment. We find that genome-lamina detachment precedes H3K27me3 accumulation on the Xi and occurs upon mitotic exit. Domains that retain genome-lamina interactions are marked by high pre-existing H3K9me3 levels. These findings imply an important role for genome-lamina interactions in regulating H3K27me3 accumulation on the Xi. We anticipate that Dam&ChIC will be instrumental in unraveling the interconnectivity and order of chromatin events underlying cell-state changes in single cells.

genomics↗

bioRxiv2023

An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying translocation RCC.

Translocation renal cell carcinoma (tRCC) is a rare, aggressive type of kidney cancer primarily occurring in children. They are genetically defined by translocations involving MiT/TFE gene family members, TFE3 or, in rare cases, TFEB. The biology underlying tRCC development remains poorly understood, partly due to the lack of representative experimental models. Here, we utilized human kidney organoids, or tubuloids, to engineer a tRCC model by expression of one of the most common MiT/TFE fusions, SFPQ-TFE3. Fusion expressing tubuloids adopt a tRCC-like phenotype and gene expression signature in vitro and grow as clear cell RCC upon xenotransplantation in mice. Genome-wide binding analysis reveals that SFPQ-TFE3 reprograms gene expression signatures by aberrant, gain-of-function genome-wide DNA binding. Combining these analyses with single-cell mRNA readouts reveals an epithelium-to-mesenchymal differentiation trajectory underlying tRCC transformation, potentially caused by deregulated Wnt signaling. Our study demonstrates that SFPQ-TFE3 expression is sufficient to transform kidney epithelial cells into tRCC and defines the trajectories underlying malignant transformation, thereby facilitating the development of new therapeutic interventions.

cancer biology↗

bioRxiv2021

Hierarchical chromatin regulation during blood formation uncovered by single cell sortChIC

Post-translational histone modifications modulate chromatin packing to regulate gene expression. How chromatin states, at euchromatic and heterochromatic regions, underlie cell fate decisions in single cells is relatively unexplored. We develop sort assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in hematopoietic stem and progenitor cells (HSPCs), and mature blood cells in the mouse bone marrow. During differentiation, HSPCs acquire distinct active chromatin states that depend on the specific cell fate, mediated by cell type-specifying transcription factors. By contrast, most regions that gain or lose repressive marks during differentiation do so independent of cell fate. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin-repressed states. This suggests hierarchical chromatin regulation during hematopoiesis: heterochromatin dynamics define differentiation trajectories and lineages, while euchromatin dynamics establish cell types within lineages.

genomics↗

bioRxiv2021

Deconvolving multiplexed histone modifications in single cells

Recent advances have enabled mapping of histone modifications in single cells1-12, but current methods are constrained to profile only one histone modification per cell. Here we present an integrated experimental and computational framework, scChIX (single-cell chromatin immunocleavage and unmixing), to map multiple histone modifications in single cells. scChIX multiplexes two histone modification profiles together in single cells, then computationally deconvolves the signal using training data from respective histone modification profiles. We first validate this method using purified blood cells and show that although the two repressive marks, H3K27me3 and H3K9me3, are generally mutually exclusive, the transitions between the two regions can vary between cell types. Next we apply scChIX to a heterogenous cell population from mouse bone marrow to generate linked maps of active (H3K4me1) and repressive (H3K27me3) chromatin landscapes in single cells, where coordinates in the active modification map correspond to coordinates in the repressive map. Linked analysis reveals that immunoglobulin genes in the Igkv region are in a repressed chromatin state in pro-B cells, but become activated in B cells. Overall, scChIX unlocks systematic interrogation of the interplay between histone modifications in single cells.

genomics↗