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

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 hu...

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Autores principales: Hassan, Imtiaz Ul, Rehman, Hafiz Mamoon, Liu, Ziran, Zhou, Liangji, Samma, Muhammad Kaleem, Wang, Chengdong, Rong, Zixin, Qi, Xufeng, Cai, Dongqing, Zhao, Hui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Science Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10236294/
https://www.ncbi.nlm.nih.gov/pubmed/37161653
http://dx.doi.org/10.24272/j.issn.2095-8137.2022.418
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author Hassan, Imtiaz Ul
Rehman, Hafiz Mamoon
Liu, Ziran
Zhou, Liangji
Samma, Muhammad Kaleem
Wang, Chengdong
Rong, Zixin
Qi, Xufeng
Cai, Dongqing
Zhao, Hui
author_facet Hassan, Imtiaz Ul
Rehman, Hafiz Mamoon
Liu, Ziran
Zhou, Liangji
Samma, Muhammad Kaleem
Wang, Chengdong
Rong, Zixin
Qi, Xufeng
Cai, Dongqing
Zhao, Hui
author_sort Hassan, Imtiaz Ul
collection PubMed
description 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.
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spelling pubmed-102362942023-06-03 Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes Hassan, Imtiaz Ul Rehman, Hafiz Mamoon Liu, Ziran Zhou, Liangji Samma, Muhammad Kaleem Wang, Chengdong Rong, Zixin Qi, Xufeng Cai, Dongqing Zhao, Hui Zool Res Article 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. Science Press 2023-05-18 /pmc/articles/PMC10236294/ /pubmed/37161653 http://dx.doi.org/10.24272/j.issn.2095-8137.2022.418 Text en https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Hassan, Imtiaz Ul
Rehman, Hafiz Mamoon
Liu, Ziran
Zhou, Liangji
Samma, Muhammad Kaleem
Wang, Chengdong
Rong, Zixin
Qi, Xufeng
Cai, Dongqing
Zhao, Hui
Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes
title Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes
title_full Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes
title_fullStr Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes
title_full_unstemmed Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes
title_short Genome-wide identification and spatiotemporal expression profiling of zinc finger SWIM domain-containing protein family genes
title_sort genome-wide identification and spatiotemporal expression profiling of zinc finger swim domain-containing protein family genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10236294/
https://www.ncbi.nlm.nih.gov/pubmed/37161653
http://dx.doi.org/10.24272/j.issn.2095-8137.2022.418
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