Journal of Genetics and Genomics

Interplay of RNA-binding proteins controls germ cell development in zebrafish

De-Li Shi

2024, 51(9): 889-899. doi: 10.1016/j.jgg.2024.06.020

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The specification of germ cells in zebrafish mostly relies on an inherited mechanism by which localized maternal determinants, called germ plasm, confer germline fate in the early embryo. Extensive studies have partially allowed the identification of key regulators governing germ plasm formation and subsequent germ cell development. RNA-binding proteins, acting in concert with other germ plasm components, play essential roles in the organization of the germ plasm and the specification, migration, maintenance, and differentiation of primordial germ cells. The loss of their functions impairs germ cell formation and causes sterility or sexual conversion. Evidence is emerging that they instruct germline development through differential regulation of mRNA fates in somatic and germ cells. However, the challenge remains to decipher the complex interplay of maternal germ plasm components in germ plasm compartmentalization and germ cell specification. Because failure to control the developmental outcome of germ cells disrupts the formation of gametes, it is important to gain a complete picture of regulatory mechanisms operating in the germ cell lineage. This review sheds light on the contributions of RNA-binding proteins to germ cell development in zebrafish and highlights intriguing questions that remain open for future investigation.

A role for Retinoblastoma 1 in hindbrain morphogenesis by regulating GBX family

Shuang Zhao, Chen Wang, Haiping Luo, Feifei Li, Qiang Wang, Jin Xu, Zhibin Huang, Wei Liu, Wenqing Zhang

2024, 51(9): 900-910. doi: 10.1016/j.jgg.2024.03.008

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The hindbrain, which develops from the anterior end of the neural tube expansion, can differentiate into the metencephalon and myelencephalon, with varying sizes and functions. The midbrain-hindbrain boundary (MHB) and hindbrain myelencephalon/ventral midline (HMVM) are known to be the source of the progenitors for the anterior hindbrain and myelencephalon, respectively. However, the molecular networks regulating hindbrain morphogenesis in these structures remain unclear. In this study, we show that retinoblastoma 1 (rb1) is highly expressed at the MHB and HMVM in zebrafish. Knocking out rb1 in mice and zebrafish results in an enlarged hindbrain due to hindbrain neuronal hyperproliferation. Further study reveals that Rb1 controls the hindbrain morphogenesis by suppressing the expression of Gbx1/Gbx2, essential transcription factors for hindbrain development, through its binding to E2f3/Hdac1, respectively. Interestingly, we find that Gbx1 and Gbx2 are expressed in different types of hindbrain neurons, suggesting distinct roles in hindbrain morphogenesis. In summary, our study clarifies the specific role of RB1 in hindbrain neural cell proliferation and morphogenesis by regulating the E2f3-Gbx1 axis and the Hdac1-Gbx2 axis. These findings provide a research paradigm for exploring the differential proliferation of neurons in various brain regions.

microRNA-2184 orchestrates Mauthner-cell axon regeneration in zebrafish via syt3 modulation

Xinghan Chen, Yueru Shen, Zheng Song, Xinliang Wang, Huaitong Yao, Yuan Cai, Zi-Ang Zhao, Bing Hu

2024, 51(9): 911-921. doi: 10.1016/j.jgg.2024.03.016

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MicroRNAs (miRNAs) play a significant role in axon regeneration following spinal cord injury. However, the functions of numerous miRNAs in axon regeneration within the central nervous system (CNS) remain largely unexplored. Here, we elucidate the positive role of microRNA-2184 (miR-2184) in axon regeneration within zebrafish Mauthner cells (M-cells). The upregulation of miR-2184 in a single M-cell can facilitate axon regeneration, while the specific sponge-induced silencing of miR-2184 leads to impeded regeneration. We show that syt3, a downstream target of miR-2184, negatively regulates axon regeneration, and the regeneration suppression modulated by syt3 depends on its binding to Ca²⁺. Furthermore, pharmacological stimulation of the cAMP/PKA pathway suggests that changes in the readily releasable pool may affect axon regeneration. Our data indicate that miR-2184 promotes axon regeneration of M-cells within the CNS by modulating the downstream target syt3, providing valuable insights into potential therapeutic strategies.

A zebrafish tufm mutant model for the COXPD4 syndrome of aberrant mitochondrial function

Ting Li, Tursunjan Aziz, Guangyuan Li, Lin Zhang, Jihua Yao, Shunji Jia

2024, 51(9): 922-933. doi: 10.1016/j.jgg.2024.05.009

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Mitochondrial dysfunction is a critical factor leading to a wide range of clinically heterogeneous and often severe disorders due to its central role in generating cellular energy. Mutations in the TUFM gene are known to cause combined oxidative phosphorylation deficiency 4 (COXPD4), a rare mitochondrial disorder characterized by a comprehensive quantitative deficiency in mitochondrial respiratory chain (MRC) complexes. The development of a reliable animal model for COXPD4 is crucial for elucidating the roles and mechanisms of TUFM in disease pathogenesis and benefiting its medical management. In this study, we construct a zebrafish tufm^-/- mutant that closely resembles the COXPD4 syndrome, exhibiting compromised mitochondrial protein translation, dysfunctional mitochondria with oxidative phosphorylation defects, and significant metabolic suppression of the tricarboxylic acid cycle. Leveraging this COXPD4 zebrafish model, we comprehensively validate the clinical relevance of TUFM mutations and identify probucol as a promising therapeutic approach for managing COXPD4. Our data offer valuable insights for understanding mitochondrial diseases and developing effective treatments.

ccdc141 is required for left-right axis development by regulating cilia formation in the Kupffer's vesicle of zebrafish

Pengcheng Wang, Wenxiang Shi, Sijie Liu, Yunjing Shi, Xuechao Jiang, Fen Li, Sun Chen, Kun Sun, Rang Xu

2024, 51(9): 934-946. doi: 10.1016/j.jgg.2024.07.014

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Laterality is a crucial physiological process intricately linked to the cilium-centrosome complex during embryo development. Defects in the process can result in severe organ mispositioning. Coiled-coil domain containing 141 (CCDC141) has been previously known as a centrosome-related gene, but its role in left-right (LR) asymmetry has not been characterized. In this study, we utilize the zebrafish model and human exome analysis to elucidate the function of ccdc141 in laterality defects. The knockdown of ccdc141 in zebrafish disrupts early LR signaling pathways, cilia function, and Kupffer's vesicle formation. Unlike ccdc141-knockdown embryos exhibiting aberrant LR patterns, ccdc141-null mutants show no apparent abnormality, suggesting a genetic compensation response effect. In parallel, we observe a marked reduction in α-tubulin acetylation levels in the ccdc141 crispants. The treatment with histone deacetylase (HDAC) inhibitors, particularly the HDAC6 inhibitor, rescues the ccdc141 crispant phenotypes. Furthermore, exome analysis of 70 patients with laterality defects reveals an increased burden of CCDC141 mutations, with in-vivo studies verifying the pathogenicity of the patient mutation CCDC141-R123G. Our findings highlight the critical role of ccdc141 in ciliogenesis and demonstrate that CCDC141 mutations lead to abnormal LR patterns, identifying it as a candidate gene for laterality defects.

Achieving single-cell-resolution lineage tracing in zebrafish by continuous barcoding mutations during embryogenesis

Zhan Liu, Hui Zeng, Huimin Xiang, Shanjun Deng, Xionglei He

2024, 51(9): 947-956. doi: 10.1016/j.jgg.2024.04.004

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Unraveling the lineage relationships of all descendants from a zygote is fundamental to advancing our understanding of developmental and stem cell biology. However, existing cell barcoding technologies in zebrafish lack the resolution to capture the majority of cell divisions during embryogenesis. A recently developed method, a substitution mutation-aided lineage-tracing system (SMALT), successfully reconstructed high-resolution cell phylogenetic trees for Drosophila melanogaster. Here, we implement the SMALT system in zebrafish, recording a median of 14 substitution mutations on a one-kilobase-pair barcoding sequence for one-day post-fertilization embryos. Leveraging this system, we reconstruct four cell lineage trees for zebrafish fin cells, encompassing both original and regenerated fin. Each tree consists of hundreds of internal nodes with a median bootstrap support of 99%. Analysis of the obtained cell lineage trees reveals that regenerated fin cells mainly originate from cells in the same part of the fins. Through multiple times sampling germ cells from the same individual, we show the stability of the germ cell pool and the early separation of germ cell and somatic cell progenitors. Our system offers the potential for reconstructing high-quality cell phylogenies across diverse tissues, providing valuable insights into development and disease in zebrafish.

Establishment and transcriptome analysis of single blastomere-derived cell lines from zebrafish

Jia Xu, Siqi Liu, Yirui Ai, Yunbin Zhang, Shifeng Li, Yiping Li

2024, 51(9): 957-969. doi: 10.1016/j.jgg.2024.07.018

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Maintaining chromosome euploidy in zebrafish embryonic cells is challenging because of the degradation of genomic integrity during cell passaging. In this study, we report the derivation of zebrafish cell lines from single blastomeres. These cell lines have a stable chromosome status attributed to BMP4 and exhibit continuous proliferation in vitro. Twenty zebrafish cell lines are successfully established from single blastomeres. Single-cell transcriptome sequencing analysis confirms the fidelity of gene expression profiles throughout long-term culturing of at least 45 passages. The long-term cultured cells are specialized into epithelial cells, exhibiting similar expression patterns validated by integrative transcriptomic analysis. Overall, this work provides a protocol for establishing zebrafish cell lines from single blastomeres, which can serve as valuable tools for in vitro investigations of epithelial cell dynamics in terms of life-death balance and cell fate determination during normal homeostasis.

Assessing the efficacy and safety of gemcitabine-induced thrombocytopenia/neutropenia and thrombocytopenia interventions in zebrafish

Jialong Deng, Ziyuan Zhou, Wangjun Liao, Qing Lin, Yiyue Zhang

2024, 51(9): 970-973. doi: 10.1016/j.jgg.2024.06.009

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Permissive role of CTCF-Hoxb7a-Cdkn2a/b axis in the emergence of hematopoietic stem and progenitor cells during zebrafish embryogenesis

Wenjuan Zhang, Xiaofen Liu, Wenzhi Xue, Lei Gao, Dantong Li, Changbin Jing, Jian Zhao, Weijun Pan

2024, 51(9): 974-977. doi: 10.1016/j.jgg.2024.06.001

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PDGFRB mutation causes intracranial aneurysm

Junyu Liu, Chunling Wang, Enyu Huang, Luming Wang, Chengchao Wu, Weixi Jiang, Mei Wu, Xiuru Zhang, Junxia Yan, Yeqi Wang, Jingjing Zhang

2024, 51(9): 978-981. doi: 10.1016/j.jgg.2024.07.011

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2024 Vol. 51, No. 9