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Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes.
BMC Genomics. 2020 Jul 08; 21(1):471.BG

Abstract

BACKGROUND

Zebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types such as the oocyte.

RESULTS

We performed single-cell RNA-seq of the zebrafish oocyte and compared it with two studies that have performed single-cell RNA-seq of the human oocyte. We carried out a comparative analysis of genes expressed in the oocyte and genes highly expressed in the oocyte across the three studies. Overall, we found high consistency between the human studies and high concordance in expression for the orthologous genes in the two organisms. According to the Ensembl database, about 60% of the human protein coding genes are orthologous to the zebrafish genes. Our results showed that a higher percentage of the genes that are highly expressed in both organisms show orthology compared to the lower expressed genes. Systems biology analysis of the genes highly expressed in the three studies showed significant overlap of the enriched pathways and GO terms. Moreover, orthologous genes that are commonly overexpressed in both organisms were involved in biological mechanisms that are functionally essential to the oocyte.

CONCLUSIONS

Orthologous genes are concurrently highly expressed in the oocytes of the two organisms and these genes belong to similar functional categories. Our results provide evidence that zebrafish could serve as a valid model organism to study the oocyte with direct implications in human.

Authors+Show Affiliations

Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.LARCEL, Andalusian Laboratory of Cell Reprogramming (LARCel), Andalusian Center for Nanomedicine and Biotechnology-BIONAND, 29590, Málaga, Spain. Department of Cell Biology, Genetics and Physiology, University of Málaga and; Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, (CIBER-BBNE), 29071, Málaga, Spain.Department of Anatomy, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand.Department of Electrical and Computer Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA. hotu2@unl.edu.Departments of Animal Science and Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, 48824, USA. cibelli@msu.edu.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32640983

Citation

Can, Handan, et al. "Comparative Analysis of Single-cell Transcriptomics in Human and Zebrafish Oocytes." BMC Genomics, vol. 21, no. 1, 2020, p. 471.
Can H, Chanumolu SK, Gonzalez-Muñoz E, et al. Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes. BMC Genomics. 2020;21(1):471.
Can, H., Chanumolu, S. K., Gonzalez-Muñoz, E., Prukudom, S., Otu, H. H., & Cibelli, J. B. (2020). Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes. BMC Genomics, 21(1), 471. https://doi.org/10.1186/s12864-020-06860-z
Can H, et al. Comparative Analysis of Single-cell Transcriptomics in Human and Zebrafish Oocytes. BMC Genomics. 2020 Jul 8;21(1):471. PubMed PMID: 32640983.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes. AU - Can,Handan, AU - Chanumolu,Sree K, AU - Gonzalez-Muñoz,Elena, AU - Prukudom,Sukumal, AU - Otu,Hasan H, AU - Cibelli,Jose B, Y1 - 2020/07/08/ PY - 2020/03/30/received PY - 2020/06/22/accepted PY - 2020/7/10/entrez PY - 2020/7/10/pubmed PY - 2020/7/10/medline KW - Oocyte KW - Orthology KW - RNA-seq KW - Transcriptome KW - Zebrafish SP - 471 EP - 471 JF - BMC genomics JO - BMC Genomics VL - 21 IS - 1 N2 - BACKGROUND: Zebrafish is a popular model organism, which is widely used in developmental biology research. Despite its general use, the direct comparison of the zebrafish and human oocyte transcriptomes has not been well studied. It is significant to see if the similarity observed between the two organisms at the gene sequence level is also observed at the expression level in key cell types such as the oocyte. RESULTS: We performed single-cell RNA-seq of the zebrafish oocyte and compared it with two studies that have performed single-cell RNA-seq of the human oocyte. We carried out a comparative analysis of genes expressed in the oocyte and genes highly expressed in the oocyte across the three studies. Overall, we found high consistency between the human studies and high concordance in expression for the orthologous genes in the two organisms. According to the Ensembl database, about 60% of the human protein coding genes are orthologous to the zebrafish genes. Our results showed that a higher percentage of the genes that are highly expressed in both organisms show orthology compared to the lower expressed genes. Systems biology analysis of the genes highly expressed in the three studies showed significant overlap of the enriched pathways and GO terms. Moreover, orthologous genes that are commonly overexpressed in both organisms were involved in biological mechanisms that are functionally essential to the oocyte. CONCLUSIONS: Orthologous genes are concurrently highly expressed in the oocytes of the two organisms and these genes belong to similar functional categories. Our results provide evidence that zebrafish could serve as a valid model organism to study the oocyte with direct implications in human. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/32640983/Comparative_analysis_of_single-cell_transcriptomics_in_human_and_Zebrafish_oocytes L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-06860-z DB - PRIME DP - Unbound Medicine ER -
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