As embryos develop, stem cells differentiate into distinct cell lineages with diverse transcriptional profiles. Transcription factors regulate gene expression for cell type specification and maintenance of cellular functions.1 Understanding transcriptomes in different cell populations at different developmental stages is required to map cell fates.
With the recent advancement of single-cell RNA sequencing (scRNA-seq) we can study the transcriptomics driving cell differentiation, providing invaluable insights into the developmental dynamics of different cell types. Many novel biomedical discoveries have been made thanks to this powerful tool and, with the ability to identify the transcriptomic signatures of rare, uncharacterized cells, scRNA-seq will revolutionize disease research. However, the transcriptomic signatures of different cell lineages during development have barely been described.2
Zebrafish as a Model Organism
The zebrafish (Danio rerio) has become an important model for studying transcriptomic development in vertebrates. The signaling pathways determining zebrafish development are conserved in higher vertebrates, making zebrafish analysis attractive for studying developmental transcriptomes.2
Zebrafish analysis has revealed astonishing conservation of genes transcribed within the intestines of zebrafish and humans, along with cross-species-conserved regulatory regions.1 Zebrafish analysis is deciphering the transcriptional mechanisms behind the specification of cells from the endoderm and will provide novel, fundamental insights into the specific molecular and cellular signatures of digestive system development.
Zebrafish Analysis 30 Hours Post-fertilization
Recent zebrafish analysis of embryonic trunks 30 hours post-fertilization (PF) documented 27 cell groups with unique transcriptional signatures. Only a single cluster #17 corresponded to endodermal lineages and the main genes in this cell population were claudin c and aldolase-b, which are expressed in the intestines and liver. They thought this cluster likely encompassed different liver and intestinal progenitors and went on to identify four subclusters. Two of these subclusters incorporated liver and/or intestine enriched, top marker genes and a significant genetic overlap was observed these subclusters.2
Here, zebrafish analysis revealed unique information on the cell lineages in zebrafish embryonic trunks, which will be fundamental for interpretation of the transcriptional process and signaling pathways that control cell differentiation/establishment in the intestine and liver.2 These results will be useful for studying the genetics of digestive system diseases.
Zebrafish analysis 5 days post-fertilization
Previously, zebrafish analysis to identify feature genes that mark specific cell types in the liver and intestines of embryos 5 days PF, that have begun food intake, hadn’t been conducted. Zebrafish analysis of 5-day old embryos described distinctive transcriptomes for liver and intestines, and identified a variety of feature genes that marked the intestinal bulb, mid-intestine and hindgut, as well as hepatocytes. This zebrafish analysis also resulted in the identification of 135 intestine- and 97 liver-enriched transcription factor genes.1
Further zebrafish analysis revealed the digestive system is well established to achieve its physiological role 5 days PF. As well as sharing many house-keeping genes that promote cellular function, zebrafish analysis revealed the liver bud and intestine share some common pan-endodermal transcription factors, fundamental for cell specification during development.1 This zebrafish analysis identified key cellular and molecular resources for understanding cell specification during early development of the intestine and liver.
Zebrafish analysis of microbiota
Embryonic development also involves microbial associations, however, the response of different cells to these microbes had not been properly explored. Zebrafish analysis assessing transcriptional responses to microbes revealed cell-type-specific responses to microbiota. Intestinal gene co-clusters formed in relation to their common cellular responses to microbiota involved in tissue growth and cell regeneration. Microbes involved in fatty acid metabolism were found to drive enrichment genes for lipid metabolism, displaying the importance of microbiota signaling in facilitating intestine development.3
Krüppel-like factor 9 and enlarged livers
Zebrafish analysis has also provided important insights into how ubiquitously expressed transcription factors like Krüppel-like factor 9 (Klf9) affect the transcriptome. Klf9−/− mutation was revealed by zebrafish analysis to increase liver, intestine and pancreatic mRNA. First to report the role of Klf9 in liver development, this zebrafish analysis found Klf9−/− mutants with overrepresentation of liver mRNA develop enlarged livers.4
Zebrafish analysis is decoding the differential transcriptomes involved in the differentiation and specialization of intestine and liver cells. Enhancing our understanding of the transcriptome of intestine and liver cells using zebrafish experiments provides crucial insights into cell specification of developmental pathways. To learn more about zebrafish analysis and how this could excel your transcriptomic research, contact IDEA Bio-Medical for information on our Athena Zebrafish Image Software.
References and further reading:
Gao, Y., Jin, Q., Gao, C., Chen, Y., Sun, Z., Guo, G. and Peng, J. 2022. Unraveling differential transcriptomes and cell types in zebrafish larvae intestine and liver. Cells. 11(20), p.3290.
Metikala, S., Casie Chetty, S. and Sumanas, S. 2021. Single-cell transcriptome analysis of the zebrafish embryonic trunk. PLoS One. 16(7), p.e0254024.
Massaquoi, M.S., Kong, G.L., Chilin-Fuentes, D., Ngo, J.S., Horve, P.F., Melancon, E., Hamilton, M.K., Eisen, J.S. and Guillemin, K. 2023. Cell-type-specific responses to the microbiota across all tissues of the larval zebrafish. Cell Reports. 42(2).
Drepanos, L., Gans, I.M., Grendler, J., Guitar, S., Fuqua, J.H., Maki, N.J., Tilden, A.R., Graber, J.H. and Coffman, J.A. 2023. Loss of Krüppel-like factor 9 deregulates both physiological gene expression and development. Scientific Reports. 13(1), p.12239.