MOTIVATION: Objective assessment of bioimage analysis methods is an essential step towards understanding their robustness and parameter sensitivity, calling for the availability of heterogeneous bioimage datasets accompanied by their reference annotations. Because manual annotations are known to be arduous, highly subjective and barely reproducible, numerous simulators have emerged over past decades, generating synthetic bioimage datasets complemented with inherent reference annotations. However, the installation and configuration of these tools generally constitutes a barrier to their widespread use. RESULTS: We present a modern, modular web-interface, CytoPacq, to facilitate the generation of synthetic benchmark datasets relevant for multi-dimensional cell imaging. CytoPacq poses a user-friendly graphical interface with contextual tooltips and currently allows a comfortable access to various cell simulation systems of fluorescence microscopy, which have already been recognized and used by the scientific community, in a straightforward and self-contained form. AVAILABILITY AND IMPLEMENTATION: CytoPacq is a publicly available online service running at https://cbia.fi.muni.cz/simulator. More information about it as well as examples of generated bioimage datasets are available directly through the web-interface. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

• MeSH
• počítačová simulace MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

The eukaryotic nucleus is a highly complex structure that carries out multiple functions primarily needed for gene expression, and among them, transcription seems to be the most fundamental. Diverse approaches have demonstrated that transcription takes place at discrete sites known as transcription factories, wherein RNA polymerase II (RNAP II) is attached to the factory and immobilized while transcribing DNA. It has been proposed that transcription factories promote chromatin loop formation, creating long-range interactions in which relatively distant genes can be transcribed simultaneously. In this study, we examined long-range interactions between the POU5F1 gene and genes previously identified as being POU5F1 enhancer-interacting, namely, CDYL, TLE2, RARG, and MSX1 (all involved in transcriptional regulation), in human pluripotent stem cells (hPSCs) and their early differentiated counterparts. As a control gene, RUNX1 was used, which is expressed during hematopoietic differentiation and not associated with pluripotency. To reveal how these long-range interactions between POU5F1 and the selected genes change with the onset of differentiation and upon RNAP II inhibition, we performed three-dimensional fluorescence in situ hybridization (3D-FISH) followed by computational simulation analysis. Our analysis showed that the numbers of long-range interactions between specific genes decrease during differentiation, suggesting that the transcription of monitored genes is associated with pluripotency. In addition, we showed that upon inhibition of RNAP II, long-range associations do not disintegrate and remain constant. We also analyzed the distance distributions of these genes in the context of their positions in the nucleus and revealed that they tend to have similar patterns resembling normal distribution. Furthermore, we compared data created in vitro and in silico to assess the biological relevance of our results.

• Publikační typ
• časopisecké články MeSH