Biology subjects

Buecker, C.

Publications and source records attributed to Buecker, C..

7 recordsLinked to original sources

bioRxiv2025

In vitro approaches to study centriole and cilium function in early mouse embryogenesis

Although centrioles and primary cilia play an essential role in early mammalian development, their specific function during the interval between their initial formation and the subsequent arrest of embryogenesis in embryos deficient in centrioles or cilia remains largely unexplored. Here, we demonstrate that different 3D in vitro model systems recapitulate early centriole and cilium formation in mouse development. Centrioles and cilia are dispensable in 3D in vitro mouse rosettes, a model system that mimics key events of implantation, including polarization and lumenogenesis. In gastruloids, a model system that recapitulates developmental processes up to 8.5 days after fertilization, centriole loss results in early disassembly. In contrast, cells devoid of cilia continue to form elongated, differentiated and polarized gastruloids, with minor differences at 96 h. Finally, we show that in a mutant affecting the centriolar distal appendages, cilia are absent from 2D cultures but are capable of forming in 3D rosettes and gastruloids, highlighting the importance of multifactorial 3D environment setups in developmental studies. SummaryThis study presents the first in vitro analysis of centriole and cilium formation during early mouse embryonic development, using 3D models to mimic implantation, tissue patterning, and axis elongation, offering a controlled platform for investigating their roles in embryogenesis.

developmental biology↗

bioRxiv2024

Unveiling Gene Perturbation Effects through Gene Regulatory Networks Inference from single-cell transcriptomic data

1Physiological and pathological processes are governed by a network of genes called gene regulatory networks (GRNs). By reconstructing GRNs, we can accurately model how cells behave in their natural state and predict how genetic changes will affect them. Transcriptomic data of single cells are now available for a wide range of cellular processes in multiple species. Thus, a method building predictive GRNs from single-cell RNA sequencing (scRNA-seq) data, without any additional prior knowledge, could have a great impact on our understanding of biological processes and the genes playing a key role in them. To this aim, we developed IGNITE (Inference of Gene Networks using Inverse kinetic Theory and Experiments), an unsupervised machine learning framework designed to infer directed, weighted, and signed GRNs directly from unperturbed single-cell RNA sequencing data. IGNITE uses the GRNs to generate gene expression data upon single and multiple genetic perturbations. IGNITE is based on the inverse problem for a kinetic Ising model, a model from statistical physics that has been successfully applied to biological networks. We tested IGNITE on murine pluripotent stem cells (PSCs) transitioning from the naive to formative states. Using as input only scRNA-seq data of unperturbed PSCs, IGNITE simulated single and triple gene knockouts. Comparison with experimental data revealed high accuracy, up to 74%, outperforming currently available methods. In sum, IGNITE identifies predictive GRNs from scRNA-seq data without additional prior knowledge and faithfully simulates single and multiple gene perturbations. Applications of IGNITE range from studying cell differentiation to identifying genes specifically active under pathological conditions.

systems biology↗

bioRxiv2023

Enhancer cooperativity can compensate for loss of activity over large genomic distances

Enhancers are short DNA sequences that activate their target promoter from a distance; however, increasing the genomic distance between the enhancer and the promoter decreases expression levels. Many genes are controlled by combinations of multiple enhancers, yet the interaction and cooperation of individual enhancer elements is not well understood. Here, we developed a novel synthetic platform that allows building complex regulatory landscapes from the bottom up. We tested the system by integrating individual enhancers at different distances and revealed that the strength of an enhancer determines how strongly it is affected by increased genomic distance. Furthermore, synergy between two enhancer elements depends on the distance at which the two elements are integrated: introducing a weak enhancer between a strong enhancer and the promoter strongly increases reporter gene expression, allowing enhancers to activate from increased genomic distances.

molecular biology↗

bioRxiv2023

The asynchrony in the exit from naive pluripotency cannot be explained by differences in the cell cycle phase

Development is characterized by consecutive cell state transitions that build on each other and ultimately lead to the generation of the numerous different cell types found in the organism. During each of these transitions, cells change their gene expression profiles and take on new identities. Cell state transitions have to be tightly coordinated with proliferation to ensure simultaneous growth and differentiation. The exit from naive pluripotency is an ideal model system for studying the temporal coordination of proliferation and differentiation. Individual cells initiate differentiation earlier compared to others, thereby leading to an asynchronous exit from naive pluripotency. One of the major differences among the cells of the starting population of mouse embryonic stem cells (mESCs) is the cell cycle status, and could therefore be an underlying cause of the differences in the onset of the exit from naive pluripotency. However, through comprehensive analysis including single cell RNA sequencing (scRNA-seq), cell cycle synchronization, and perturbation experiments, we demonstrate here that the cell cycle phase at the initiation of differentiation does not influence the timing of the exit from naive pluripotency.

developmental biology↗

bioRxiv2021

Stem cell specific interferon stimulated gene expression is regulated by the formative pluripotency network through IRF1

Stem cells intrinsically express a subset of genes which are normally associated with interferon stimulation, and thus the innate immunity response. Expression of these interferon stimulated genes (ISG) in stem cells is independent of external stimuli such as viral infection. Here we show that the interferon regulatory factor 1, Irf1, is directly controlled by the murine formative pluripotency gene regulatory network and therefore upregulated in the transition from naive to formative pluripotency. IRF1 in turn binds to regulatory regions of a conserved set of ISGs and is required for their faithful expression in formative pluripotent cells. IRF1 also binds to an enhancer of the formative pluripotency transcription factor Oct6 and is partially required for upregulation of Oct6. IRF1 therefore acts as a link between the formative pluripotency network and the regulation of innate immunity genes in formative pluripotency.

developmental biology↗

bioRxiv2020

NMD is required for timely cell fate transitions by fine-tuning gene expression and controlling translation

Cell fate transitions depend on balanced rewiring of transcription and translation programmes to mediate ordered developmental progression. Here we identify a feedback loop between nonsense-mediated mRNA decay (NMD) and translation initiation. We show that NMD controls the translation initiation factor Eif4a2 and its premature termination codon encoding isoform (Eif4a2PTC). NMD deficiency leads to translation of a specific truncated Eif4a2 protein, which elicits increased translation rates and is causative for significant delays in mouse embryonic stem cell (ESC) differentiation. Our results show identical mRNA targets for Smg5, Smg6 and Smg7, but illustrate a clear hierarchy between KOs in amplitude of target deregulation and differentiation phenotype (Smg5 > Smg6 > Smg7). This hierarchy highlights heterodimer independent functions for Smg5 and Smg7. Together, our findings expose an intricate link between mRNA stability and translation initiation control, that must be maintained for normal dynamics of cell state transitions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

bioRxiv2020

Detailed temporal dissection of an enhancer cluster reveals two distinct roles for individual elements

Many genes are regulated by multiple enhancers that often simultaneously activate their target gene. Yet, how individual enhancers collaborate to activate transcription is not well understood. Here, we dissect the functions and interdependencies of five enhancer elements that form a previously identified enhancer cluster and activate the Fgf5 locus during exit from naive murine pluripotency. Four elements are located downstream of the Fgf5 gene and form a super-enhancer. Each of these elements contributes to Fgf5 induction at a distinct time point of differentiation. The fifth element is located in the first intron of the Fgf5 gene and contributes to Fgf5 expression at every time point by amplifying overall Fgf5 expression levels. This amplifier element strongly accumulates paused RNA Polymerase II but does not give rise to a mature Fgf5 mRNA. By transplanting the amplifier to a different genomic position, we demonstrate that it enriches for high levels of paused RNA Polymerase II autonomously. Based on our data, we propose a model for a mechanism by which RNA Polymerase II accumulation at a novel type of enhancer element, the amplifier, contributes to enhancer collaboration.

molecular biology↗