Journal of Genetics and Genomics

Coordinating gibberellin and brassinosteroid signaling beyond Green Revolution

Hongning Tong, Chengcai Chu

2023, 50(7): 459-461. doi: 10.1016/j.jgg.2023.04.009

Abstract (264) PDF (60)

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The power of “controllers”: Transposon-mediated duplicated genes evolve towards neofunctionalization

Huijing Ma, Mengxia Wang, Yong E. Zhang, Shengjun Tan

2023, 50(7): 462-472. doi: 10.1016/j.jgg.2023.04.003

Abstract (339) PDF (29)

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Since the discovery of the first transposon by Dr. Barbara McClintock, the prevalence and diversity of transposable elements (TEs) have been gradually recognized. As fundamental genetic components, TEs drive organismal evolution not only by contributing functional sequences (e.g., regulatory elements or “controllers” as phrased by Dr. McClintock) but also by shuffling genomic sequences. In the latter respect, TE-mediated gene duplications have contributed to the origination of new genes and attracted extensive interest. In response to the development of this field, we herein attempt to provide an overview of TE-mediated duplication by focusing on common rules emerging across duplications generated by different TE types. Specifically, despite the huge divergence of transposition machinery across TEs, we identify three common features of various TE-mediated duplication mechanisms, including end bypass, template switching, and recurrent transposition. These three features lead to one common functional outcome, namely, TE-mediated duplicates tend to be subjected to exon shuffling and neofunctionalization. Therefore, the intrinsic properties of the mutational mechanism constrain the evolutionary trajectories of these duplicates. We finally discuss the future of this field including an in-depth characterization of both the duplication mechanisms and functions of TE-mediated duplicates.

Nitric oxide-mediated S-nitrosylation of IAA17 protein in intrinsically disordered region represses auxin signaling

Hongwei Jing, Xiaolu Yang, Ryan J. Emenecker, Jian Feng, Jian Zhang, Marcelo Rodrigues Alves de Figueiredo, Patarasuda Chaisupa, R. Clay Wright, Alex S. Holehouse, Lucia C. Strader, Jianru Zuo

2023, 50(7): 473-485. doi: 10.1016/j.jgg.2023.05.001

Abstract (216) PDF (40)

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The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development. Auxin signaling is activated through the phytohormone-induced proteasomal degradation of the Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) family of transcriptional repressors. Notably, many auxin-modulated physiological processes are also regulated by nitric oxide (NO) that executes its biological effects predominantly through protein S-nitrosylation at specific cysteine residues. However, little is known about the molecular mechanisms in regulating the interactive NO and auxin networks. Here, we show that NO represses auxin signaling by inhibiting IAA17 protein degradation. NO induces the S-nitrosylation of Cys-70 located in the intrinsically disordered region of IAA17, which inhibits the TIR1-IAA17 interaction and consequently the proteasomal degradation of IAA17. The accumulation of a higher level of IAA17 attenuates auxin response. Moreover, an IAA17^C70W nitrosomimetic mutation renders the accumulation of a higher level of the mutated protein, thereby causing partial resistance to auxin and defective lateral root development. Taken together, these results suggest that S-nitrosylation of IAA17 at Cys-70 inhibits its interaction with TIR1, thereby negatively regulating auxin signaling. This study provides unique molecular insights into the redox-based auxin signaling in regulating plant growth and development.

O-GlcNAcylation regulates phagocytosis by promoting Ezrin localization at the cell cortex

Song Yang, Hanyu Liu, Hua Ni, Lingyu Jiang, Mulin Yang, Quan Chen, Jun Zhou, Fan Yu

2023, 50(7): 486-496. doi: 10.1016/j.jgg.2023.02.003

Abstract (202) PDF (19)

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O-GlcNAcylation is a post-translational modification that serves as a cellular nutrient sensor and participates in multiple physiological and pathological processes. However, it remains uncertain whether O-GlcNAcylation is involved in the regulation of phagocytosis. Here, we demonstrate a rapid increase in protein O-GlcNAcylation in response to phagocytotic stimuli. Knockout of the O-GlcNAc transferase or pharmacological inhibition of O-GlcNAcylation dramatically blocks phagocytosis, resulting in the disruption of retinal structure and function. Mechanistic studies reveal that the O-GlcNAc transferase interacts with Ezrin, a membrane-cytoskeleton linker protein, to catalyze its O-GlcNAcylation. Our data further show that Ezrin O-GlcNAcylation promotes its localization to the cell cortex, thereby stimulating the membrane-cytoskeleton interaction needed for efficient phagocytosis. These findings identify a previously unrecognized role for protein O-GlcNAcylation in phagocytosis with important implications in both health and diseases.

Phosphorylation of ATF2 promotes odontoblastic differentiation via intrinsic HAT activity

Huanyan Zuo, Yao Xiao, Jiahao Han, Yuxiu Lin, Cheng Tian, Shu Zhang, Guohua Yuan, Huan Liu, Zhi Chen

2023, 50(7): 497-510. doi: 10.1016/j.jgg.2023.02.005

Abstract (194) PDF (13)

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Mouse dental papilla cells (mDPCs) are cranial neural crest-derived dental mesenchymal cells that give rise to dentin-secreting odontoblasts after the bell stage during odontogenesis. The odontoblastic differentiation of mDPCs is spatiotemporally regulated by transcription factors (TFs). Our previous work reveals that chromatin accessibility was correlated with the occupation of the basic leucine zipper TF family during odontoblastic differentiation. However, the detailed mechanism by which TFs regulate the initiation of odontoblastic differentiation remains elusive. Here, we report that phosphorylation of ATF2 (p-ATF2) is particularly increased during odontoblastic differentiation in vivo and in vitro. ATAC-seq and p-ATF2 CUT&Tag experiments further demonstrate a high correlation between p-ATF2 localization and increased chromatin accessibility of regions near mineralization-related genes. Knockdown of Atf2 inhibits the odontoblastic differentiation of mDPCs, while overexpression of p-ATF2 promotes odontoblastic differentiation. ATAC-seq after overexpression of p-ATF2 reveals that p-ATF2 increases the chromatin accessibility of regions adjacent to genes associated with matrix mineralization. Furthermore, we find that p-ATF2 physically interacts with and promotes H2BK12 acetylation. Taken together, our findings reveal a mechanism that p-ATF2 promotes odontoblastic differentiation at initiation via remodeling chromatin accessibility and emphasize the role of the phosphoswitch model of TFs in cell fate transitions.

Point mutations of homologs as an adaptive solution to the gene loss

Guosheng Ma, Xiaojing Zhao, Xinyi Shentu, Liye Zhang

2023, 50(7): 511-518. doi: 10.1016/j.jgg.2023.02.012

Abstract (185) PDF (10)

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Gene loss is common and influences genome evolution trajectories. Multiple adaptive strategies to compensate for gene loss have been observed, including copy number gain of paralogous genes and mutations in genes of the same pathway. By using the Ubl-specific protease 2 (ULP2) eviction model, we identify compensatory mutations in the homologous gene ULP1 by laboratory evolution and find that these mutations are capable of rescuing defects caused by the loss of ULP2. Furthermore, bioinformatics analysis of genomes of yeast gene knockout library and natural yeast isolate datasets suggests that point mutations of a homologous gene might be an additional mechanism to compensate for gene loss.

Delta.EPI: a probabilistic voting-based enhancer-promoter interaction prediction platform

Yuyang Zhang, Haoyu Wang, Jing Liu, Junlin Li, Qing Zhang, Bixia Tang, Zhihua Zhang

2023, 50(7): 519-527. doi: 10.1016/j.jgg.2023.02.006

Abstract (204) PDF (3)

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Enhancer promoter interaction (EPI) involves most of gene transcriptional regulation in the high eukaryotes. Predicting the EPIs from given genomic loci or DNA sequences is not a trivial task. The benchmarking work so far for EPI predictors is more or less empirical and lacks quantitative model-based comparisons, posing challenges for molecular biologists to obtain reliable EPI predictions. Here, we present an EPI prediction platform, namely Delta.EPI. Based on a statistic model of the data integration, Delta.EPI is capable of comprehensively assessing the predictions from four state-of-the-art EPI predictors. Equipped with a user-friendly interface and visualization platform, Delta.EPI presents the sorted results with the confidence of EPI relevance, which may guide the molecular biologists who lack the pre-knowledge of the algorithms of EPI prediction. Last, we showcase the utility of Delta.EPI with a case study. Delta.EPI provides a powerful tool to fuel the gene regulation and 3D genome studies by ease-to-access EPI predictions. Delta.EPI can be freely accessed at https://ngdc.cncb.ac.cn/deltaEPI/.

Heterotrimeric G protein γ subunit DEP1 synergistically regulates grain quality and yield by modulating the TTP (TON1-TRM-PP2A) complex in rice

Yunzhe Wu, Ying Zhao, Jianping Yu, Chenchen Wu, Qi Wang, Xueying Liu, Xiuhua Gao, Kun Wu, Xiangdong Fu, Qian Liu

2023, 50(7): 528-531. doi: 10.1016/j.jgg.2023.02.009

Abstract (466) PDF (102)

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Haplotype-resolved and chromosome-level genome assembly of Colorado potato beetle

Ziqi Ye, Ruirui Lu, Chao Li, Doudou Yang, Zhuozhen Zeng, Weichao Lin, Jie Cheng, Zhongmin Yang, Li Wang, Yulin Gao, Sanwen Huang, Xingtan Zhang, Suhua Li

2023, 50(7): 532-535. doi: 10.1016/j.jgg.2023.04.005

Abstract (396) PDF (96)

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Genetic causes of macrozoospermia and proposal for an optimized genetic diagnosis strategy based on sperm parameters

Alicia Coudert, Caroline Cazin, Amir Amiri-Yekta, Selima Fourati Ben Mustapha, Raoudha Zouari, Julien Bessonat, Abdelali Zoghmar, Antoine Clergeau, Catherine Metzler-Guillemain, Chema Triki, Hervé Lejeune, Nathalie Sermondade, Eva Pipiras, Nadia Prisant, Isabelle Cedrin, Isabelle Koscinski, Leila Keskes, Florence Lestrade, Laetitia Hesters, Nathalie Rives, Béatrice Dorphin, Agnes Guichet, Catherine Patrat, Emmanuel Dulioust, Aurélie Feraille, François Robert, Sophie Brouillet, Frédéric Morel, Aurore Perrin, Nathalie Rougier, Eric Bieth, Arthur Sorlin, Jean-Pierre Siffroi, Mariem Ben Khelifa, Florence Boiterelle, Sylvianne Hennebicq, Veronique Satre, Christophe Arnoult, Charles Coutton, Anne-Laure Barbotin, Nicolas Thierry-Mieg, Zine-Eddine Kherraf, Pierre F. Ray

2023, 50(7): 536-540. doi: 10.1016/j.jgg.2023.04.007

Abstract (289) PDF (15)

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2023 Vol. 50, No. 7