Journal of Genetics and Genomics

Mitotic inheritance of DNA methylation: more than just copy and paste

Xuan Ming, Bing Zhu, Yingfeng Li

2021, 48(1): 1-13. doi: 10.1016/j.jgg.2021.01.006

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Abstract:
Decades of investigation on DNA methylation have led to deeper insights into its metabolic mechanisms and biological functions. This understanding was fueled by the recent development of genome editing tools and our improved capacity for analyzing the global DNA methylome in mammalian cells. This review focuses on the maintenance of DNA methylation patterns during mitotic cell division. We discuss the latest discoveries of the mechanisms for the inheritance of DNA methylation as a stable epigenetic memory. We also highlight recent evidence showing the rapid turnover of DNA methylation as a dynamic gene regulatory mechanism. A body of work has shown that altered DNA methylomes are common features in aging and disease. We discuss the potential links between methylation maintenance mechanisms and disease-associated methylation changes.

Conditional gene expression in invertebrate animal models

Brecht Driesschaert, Lucas Mergan, Liesbet Temmerman

2021, 48(1): 14-31. doi: 10.1016/j.jgg.2021.01.005

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Abstract:
A mechanistic understanding of biology requires appreciating spatiotemporal aspects of gene expression and its functional implications. Conditional expression allows for (ir)reversible switching of genes on or off, with the potential of spatial and/or temporal control. This provides a valuable complement to the more often used constitutive gene (in)activation through mutagenesis, providing tools to answer a wider array of research questions across biological disciplines. Spatial and/or temporal control are granted primarily by (combinations of) specific promoters, temperature regimens, compound addition, or illumination. The use of such genetic tool kits is particularly widespread in invertebrate animal models because they can be applied to study biological processes in short time frames and on large scales, using organisms amenable to easy genetic manipulation. Recent years witnessed an exciting expansion and optimization of such tools, of which we provide a comprehensive overview and discussion regarding their use in invertebrates. The mechanism, applicability, benefits, and drawbacks of each of the systems, as well as further developments to be expected in the foreseeable future, are highlighted.

The oral microbiome of pregnant women facilitates gestational diabetes discrimination

Xiaoqing Li, Jiayong Zheng, Xiuling Ma, Bing Zhang, Jinyang Zhang, Wenhuan Wang, Congcong Sun, Yeping Wang, Jianqiong Zheng, Haiying Chen, Jiejing Tao, Hai Wang, Fengyi Zhang, Jinfeng Wang, Hongping Zhang

2021, 48(1): 32-39. doi: 10.1016/j.jgg.2020.11.006

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Abstract:
The oral microbiota plays an important role in the development of various diseases, whereas its association with gestational diabetes mellitus (GDM) remains largely unclear. The aim of this study is to identify biomarkers from the oral microbiota of GDM patients by analyzing the microbiome of the saliva and dental plaque samples of 111 pregnant women. We find that the microbiota of both types of oral samples in GDM patients exhibits differences and significantly varies from that of patients with periodontitis or dental caries. Using bacterial biomarkers from the oral microbiota, GDM classification models based on support vector machine and random forest algorithms are constructed. The area under curve (AUC) value of the classification model constructed by combination of Lautropia and Neisseria in dental plaque and Streptococcus in saliva reaches 0.83, and the value achieves a maximum value of 0.89 by adding clinical features. These findings suggest that certain bacteria in either saliva or dental plaque can effectively distinguish women with GDM from healthy pregnant women, which provides evidence of oral microbiome as an informative source for developing noninvasive biomarkers of GDM.

Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene

Paul D. Hartley, Richard L. Tillett, David P. AuCoin, Joel R. Sevinsky, Yanji Xu, Andrew Gorzalski, Mark Pandori, Erin Buttery, Holly Hansen, Michael A. Picker, Cyprian C. Rossetto, Subhash C. Verma

2021, 48(1): 40-51. doi: 10.1016/j.jgg.2021.01.004

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Abstract:
Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the variants of SARS-CoV-2 circulating in the state of Nevada, specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform, which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads, without the need of culture-based amplification. High genome coverage allowed the identification of single and multi-nucleotide variants in SARS-CoV-2 in the community and their phylogenetic relationships with other variants present during the same period of the outbreak. We report the occurrence of a novel mutation at 323aa (314aa of orf1b) of nsp12 (RNA-dependent RNA polymerase) changed to phenylalanine (F) from proline (P), in the first reported isolate of SARS-CoV-2, Wuhan-Hu-1. This 323F variant was present at a very high frequency in Northern Nevada. Structural modeling determined this mutation in the interface domain, which is important for the association of accessory proteins required for the polymerase. In conclusion, we report the introduction of specific SARS-CoV-2 variants at very high frequency in distinct geographic locations, which is important for understanding the evolution and circulation of SARS-CoV-2 variants of public health importance, while it circulates in humans.

Crumbs proteins stabilize the cone mosaics of photoreceptors and improve vision in zebrafish

Qinlong Hao, Mingjie Zheng, Kechao Weng, Yumei Hao, Yao Zhou, Yuchen Lin, Feng Gao, Ziqi Kou, Shoji Kawamura, Ke Yao, Pinglong Xu, Jinghai Chen, Jian Zou

2021, 48(1): 52-62. doi: 10.1016/j.jgg.2020.12.002

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Abstract:
Although the unique organization of vertebrate cone mosaics was first described long ago, both their underlying molecular basis and physiological significance are largely unknown. Here, we demonstrate that Crumbs proteins, the key regulators of epithelial apical polarity, establish the planar cellular polarity of photoreceptors in zebrafish. Via heterophilic Crb2a-Crb2b interactions, the apicobasal polarity protein Crb2b restricts the asymmetric planar distribution of Crb2a in photoreceptors. The planar polarized Crumbs proteins thus balance intercellular adhesions and tension between photoreceptors, thereby stabilizing the geometric organization of cone mosaics. Notably, loss of Crb2b in zebrafish induces a nearsightedness-like phenotype in zebrafish accompanied by an elongated eye axis and impairs zebrafish visual perception for predation. These data reveal a detailed mechanism for cone mosaic homeostasis via previously undiscovered apical-planar polarity coordination and propose a pathogenic mechanism for nearsightedness.

Cyclin A2/cyclin-dependent kinase 1-dependent phosphorylation of Top2a is required for S phase entry during retinal development in zebrafish

Miaomiao Jin, Jingyu Li, Ruikun Hu, Baijie Xu, Guanliang Huang, Weilai Huang, Bo Chen, Jie He, Ying Cao

2021, 48(1): 63-74. doi: 10.1016/j.jgg.2021.01.001

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Cyclin-dependent kinase 1 (CDK1) plays an essential role in cell cycle regulation. However, as mouse Cdk1 embryos die early, the role of CDK1 in regulating the cell cycle and embryo development remains unclear. Here, we showed that zebrafish cdk1 embryos exhibit severe microphthalmia accompanied by multiple defects in S phase entry, M phase progression, and cell differentiation but not in interkinetic nuclear migration. We identified Top2a as a potential downstream target and cyclin A2 and cyclin B1 as partners of Cdk1 in cell cycle regulation via an in silico analysis. While depletion of either cyclin A2 or Top2a led to the decreased S phase entry in zebrafish retinal cells, the depletion of cyclin B1 led to M phase arrest. Moreover, phosphorylation of Top2a at serine 1213 (S1213) was nearly abolished in both cdk1 and ccna2 mutants, but not in ccnb1 mutants. Furthermore, overexpression of TOP2A^S1213D, the phosphomimetic form of human TOP2A, rescued S phase entry and alleviated the microphthalmia defects in both cdk1 and ccna2 embryos. Taken together, our data suggest that Cdk1 interacts with cyclin A2 to regulate S phase entry partially through Top2a phosphorylation and interacts with cyclin B1 to regulate M phase progression.

Identifying a melanogenesis-related candidate gene by a high-quality genome assembly and population diversity analysis in Hypsizygus marmoreus

Gang Wang, Lianfu Chen, Weiqi Tang, Yuanyuan Wang, Qing Zhang, Hongbo Wang, Xuan Zhou, Haofeng Wu, Lin Guo, Meijie Dou, Lei Liu, Baiyu Wang, Jingxian Lin, Baogui Xie, Zhengchao Wang, ZhongJian Liu, Ray Ming, Jisen Zhang

2021, 48(1): 75-87. doi: 10.1016/j.jgg.2021.01.002

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Abstract:
Hypsizygus marmoreus is one of the most important edible fungi in Basidiomycete division and includes white and gray strains. However, very limited knowledge is known about the genomic structures and the genetic basis for the white/gray diversity of this mushroom. Here, we report the near-complete high-quality H. marmoreus genome at the chromosomal level. Comparative genomics analysis indicates that chromosome structures were relatively conserved, and variations in collinearity and chromosome number were mainly attributed by chromosome split/fusion events inAragicales, whereas the fungi genome experienced many genomic chromosome fracture, fusion, and genomic replication events after the split of Aragicales from Basidiomycetes. Resequencing of 57 strains allows us to classify the population into four major groups and associate genetic variations with morphological features, indicating that white strains were not originated independently. We further generated genetic populations and identified a cytochrome P450 as the candidate causal gene for the melanogenesis in H. marmoreus based on bulked segregant analysis (BSA) and comparative transcriptome analysis. The high-quality H. marmoreus genome and diversity data compiled in this study provide new knowledge and resources for the molecular breeding of H. marmoreus as well as the evolution of Basidiomycete.

MIT1, encoding a 15-cis-ζ-carotene isomerase, regulates tiller number and stature in rice

Lihua Liu, Mengmeng Ren, Peng Peng, Yan Chun, Lu Li, Jinfeng Zhao, Jingjing Fang, Lixiang Peng, Jijun Yan, Jinfang Chu, Yiqin Wang, Shoujiang Yuan, Xueyong Li

2021, 48(1): 88-91. doi: 10.1016/j.jgg.2020.11.008

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Improving the Cpf1-mediated base editing system by combining dCas9/dead sgRNA with human APOBEC3A variants

Meng Lian, Fangbing Chen, Xingyun Huang, Xiaozhu Zhao, Shixue Gou, Nan Li, Qin Jin, Hui Shi, Yanhui Liang, Jingke Xie, Weikai Ge, Zhenpeng Zhuang, Jiaowei Wang, Yinghua Ye, Yi Yang, Kepin Wang, Liangxue Lai, Han Wu

2021, 48(1): 92-95. doi: 10.1016/j.jgg.2020.07.010

Abstract (130) HTML PDF (16)

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2021 Vol. 48, No. 1