Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes

Imtiaz Ul Hassan; Hafiz Mamoon Rehman; Ziran Liu; Liangji Zhou; Muhammad Kaleem Samma; Chengdong Wang; Zixin Rong; Xufeng Qi; Dongqing Cai; Hui Zhao

doi:10.24272/j.issn.2095-8137.2022.418

Volume 44 Issue 3

May 2023

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Article Navigation > Zoological Research > 2023 > 44(3): 663-674

Imtiaz Ul Hassan, Hafiz Mamoon Rehman, Ziran Liu, Liangji Zhou, Muhammad Kaleem Samma, Chengdong Wang, Zixin Rong, Xufeng Qi, Dongqing Cai, Hui Zhao. Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes. Zoological Research, 2023, 44(3): 663-674. doi: 10.24272/j.issn.2095-8137.2022.418

Citation:

Imtiaz Ul Hassan, Hafiz Mamoon Rehman, Ziran Liu, Liangji Zhou, Muhammad Kaleem Samma, Chengdong Wang, Zixin Rong, Xufeng Qi, Dongqing Cai, Hui Zhao. Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes. Zoological Research, 2023, 44(3): 663-674. doi: 10.24272/j.issn.2095-8137.2022.418

Citation:

Imtiaz Ul Hassan, Hafiz Mamoon Rehman, Ziran Liu, Liangji Zhou, Muhammad Kaleem Samma, Chengdong Wang, Zixin Rong, Xufeng Qi, Dongqing Cai, Hui Zhao. Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes. Zoological Research, 2023, 44(3): 663-674. doi: 10.24272/j.issn.2095-8137.2022.418

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Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes

doi: 10.24272/j.issn.2095-8137.2022.418

1.
Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
2.
Centre for Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
3.
Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong 266034, China
4.
Key Laboratory of Regenerative Medicine of Ministry of Education, Department of Developmental & Regenerative Biology, Jinan University, Guangzhou 511436, China
6.
Department of Biology and Chemistry, City University of Hong Kong, Hong Kong SAR, China
6.
Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), KTH Royal Institute of Technology, 10691 Stockholm, Sweden
7.
Kunming Institute of Zoology - The Chinese University of Hong Kong (KIZ-CUHK) Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China
8.
Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Hong Kong SAR, China

Supplementary data to this article can be found online.
The authors declare that they have no competing interests.
I.U.H. performed the experiments, analyzed the data, prepared the figures, and wrote the manuscript. H.M.R. conducted bioinformatics analysis. Z.L. and L.Z. provided valuable suggestions. M.K.S. and C.W. revised the manuscript, Z.R., X.Q., and D.C. provided analytical tools. H.Z. conceived, designed, and supervised this study, wrote the manuscript, and approved the final draft. All authors read and approved the final version of the manuscript.

Funds: This work was supported by the National Key R&D Program of China, Synthetic Biology Research (2019YFA0904500), and Research Grants Council of Hong Kong (14119120, 14112618, and CRF C5033-19E to H.Z.). Additional support was provided by the Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, Chinese University of Hong Kong

More Information

Corresponding author: E-mail: zhaohui@cuhk.edu.hk
Received Date: 2022-12-27
Accepted Date: 2023-05-05

Published Online: 2023-05-09

Publish Date: 2023-05-18

Abstract

Abstract

The biological function of the novel zinc-finger SWIM domain-containing protein family (ZSWIM) during embryonic development remains elusive. Here, we conducted a genome-wide analysis to explore the evolutionary processes of the ZSWIM gene family members in mice, Xenopus tropicalis, zebrafish, and humans. We identified nine putative ZSWIM genes in the human and mouse genome, eight in the Xenopus genome, and five in the zebrafish genome. Based on multiple sequence alignment, three members, ZSWIM5, ZSWIM6, and ZSWIM8, demonstrated the highest homology across all four species. Using available RNA sequencing (RNA-seq) data, ZSWIM genes were found to be widely expressed across different tissues, with distinct tissue-specific properties. To identify the functions of the ZSWIM protein family during embryogenesis, we examined temporal and spatial expression patterns of zswim family genes in Xenopus embryos. Quantitative real-time polymerase chain reaction (qRT-PCR) revealed that each member had a distinct expression profile. Whole-mount in situ hybridization showed that both zswim1 and zswim3 were maternally expressed genes; zswim5 and zswim6 were expressed throughout embryogenesis and displayed dynamic expression in the brain, eyes, somite, and bronchial arch at the late tailbud stages; zswim7 was detected in the eye area; zswim8 showed a dynamic expression pattern during the tailbud stages, with expression detected in the brain, eyes, and somite; zswim9 was faintly expressed throughout embryonic development. This study provides a foundation for future research to delineate the functions of ZSWIM gene members.
- ZSWIM gene family,
- Xenopus,
- Gene expression,
- Phylogenetic analysis,
- Bioinformatics

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References(36)

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