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A human-specific cytotoxic neopeptide generated by the deafness gene Cingulin. 由耳聋基因 Cingulin 生成的人类特异性细胞毒性新肽。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-08-05 DOI: 10.1016/j.jgg.2024.07.017
Yuhang Huang, Linqing Zhang, Yuecen Sun, Qing Liu, Jie Chen, Xiaoyun Qian, Xia Gao, Guang-Jie Zhu, Guoqiang Wan
{"title":"A human-specific cytotoxic neopeptide generated by the deafness gene Cingulin.","authors":"Yuhang Huang, Linqing Zhang, Yuecen Sun, Qing Liu, Jie Chen, Xiaoyun Qian, Xia Gao, Guang-Jie Zhu, Guoqiang Wan","doi":"10.1016/j.jgg.2024.07.017","DOIUrl":"10.1016/j.jgg.2024.07.017","url":null,"abstract":"<p><p>Accumulation of mutant proteins in cells can induce proteinopathies and cause functional damage to organs. Recently, the Cingulin (CGN) protein has been shown to maintain the morphology of cuticular plates of inner ear hair cells and a frameshift mutation in CGN causes autosomal dominant non-syndromic hearing loss. Here, we find that the mutant CGN proteins form insoluble aggregates which accumulate intracellularly and lead to cell death. Expression of the mutant CGN in the inner ear results in severe hair cell death and hearing loss in mice, resembling the auditory phenotype in human patients. Interestingly, a human-specific residue (V1112) in the neopeptide generated by the frameshift mutation is critical for the aggregation and cytotoxicity of the mutant human CGN. Moreover, the expression of heat shock factor 1 (HSF1) decreases the accumulation of insoluble mutant CGN aggregates and rescues cell death. In summary, these findings identify mutant-specific toxic polypeptides as a disease-causing mechanism of the deafness mutation in CGN, which can be targeted by the expression of the cell chaperone response regulator HSF1.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141891031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Engineering the future cereal crops with big biological data: toward intelligence-driven breeding by design. 利用生物大数据设计未来的谷类作物：实现智能驱动的设计育种。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-08-01 Epub Date: 2024-03-24 DOI: 10.1016/j.jgg.2024.03.005
Lei Liu, Jimin Zhan, Jianbing Yan
{"title":"Engineering the future cereal crops with big biological data: toward intelligence-driven breeding by design.","authors":"Lei Liu, Jimin Zhan, Jianbing Yan","doi":"10.1016/j.jgg.2024.03.005","DOIUrl":"10.1016/j.jgg.2024.03.005","url":null,"abstract":"<p><p>How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades, especially under an unpredicted climate change. Crop breeding, initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding, has played a critical role in securing the global food supply. However, regarding the changing environment and ever-increasing human population, can we breed outstanding crop varieties fast enough to achieve high productivity, good quality, and widespread adaptability? This review outlines the recent achievements in understanding cereal crop breeding, including the current knowledge about crop agronomic traits, newly developed techniques, crop big biological data research, and the possibility of integrating them for intelligence-driven breeding by design, which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops. This review focuses on the major cereal crops, including rice, maize, and wheat, to explain how intelligence-driven breeding by design is becoming a reality.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140295401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Corrigendum to "Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis" [Journal of Genetics and Genomics (2024) 51, 749-761]. 根源远距离信号触发拟南芥的 ABA 合成并增强其抗旱性"[《遗传学和基因组学杂志》（2024 年）51，749-761] 更正。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-08-01 DOI: 10.1016/j.jgg.2024.07.012
Qian-Qian Liu, Jin-Qiu Xia, Jie Wu, Yi Han, Gui-Quan Zhang, Ping-Xia Zhao, Cheng-Bin Xiang
{"title":"Corrigendum to \"Root-derived long-distance signals trigger ABA synthesis and enhance drought resistance in Arabidopsis\" [Journal of Genetics and Genomics (2024) 51, 749-761].","authors":"Qian-Qian Liu, Jin-Qiu Xia, Jie Wu, Yi Han, Gui-Quan Zhang, Ping-Xia Zhao, Cheng-Bin Xiang","doi":"10.1016/j.jgg.2024.07.012","DOIUrl":"https://doi.org/10.1016/j.jgg.2024.07.012","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141879855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modern phenomics to empower holistic crop science, agronomy, and breeding research. 利用现代表型组学开展综合作物科学、农艺学和育种研究。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-08-01 Epub Date: 2024-05-10 DOI: 10.1016/j.jgg.2024.04.016
Ni Jiang, Xin-Guang Zhu
{"title":"Modern phenomics to empower holistic crop science, agronomy, and breeding research.","authors":"Ni Jiang, Xin-Guang Zhu","doi":"10.1016/j.jgg.2024.04.016","DOIUrl":"10.1016/j.jgg.2024.04.016","url":null,"abstract":"<p><p>Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales, representing a greater data collection throughput compared with traditional measurements. Most modern crop phenomics use different sensors to collect reflective, emitted, and fluorescence signals, etc., from plant organs at different spatial and temporal resolutions. Such multi-modal, high-dimensional data not only accelerates basic research on crop physiology, genetics, and whole plant systems modeling, but also supports the optimization of field agronomic practices, internal environments of plant factories, and ultimately crop breeding. Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection, management, sharing, and processing, developing capabilities to measure physiological parameters, and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140908971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects. 揭示高粱功能基因组学和分子育种：过去的成就和未来的前景。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-07-23 DOI: 10.1016/j.jgg.2024.07.016
Fangyuan Liu, Wodajo Baye, Kangxu Zhao, Sanyuan Tang, Qi Xie, Peng Xie
{"title":"Unravelling sorghum functional genomics and molecular breeding: past achievements and future prospects.","authors":"Fangyuan Liu, Wodajo Baye, Kangxu Zhao, Sanyuan Tang, Qi Xie, Peng Xie","doi":"10.1016/j.jgg.2024.07.016","DOIUrl":"https://doi.org/10.1016/j.jgg.2024.07.016","url":null,"abstract":"<p><p>Sorghum, renowned for its substantial biomass production and remarkable tolerance to various stresses, possesses extensive gene resources and phenotypic variations. A comprehensive understanding of the genetic basis underlying complex agronomic traits is essential for unlocking the potential of sorghum in addressing food and feed security and utilizing marginal lands. In this context, we provide an overview of the major trends in genomic resource studies focusing on key agronomic traits over the past decade, accompanied by a summary of functional genomic platforms. We also delve into the molecular functions and regulatory networks of impactful genes for important agricultural traits. Lastly, we discuss and synthesize the current challenges and prospects for advancing molecular design breeding by gene-editing and polymerization of the excellent alleles, with the aim of accelerating the development of desired sorghum varieties.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141762721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Toward a universal approach for predicting variant pathogenicity in diverse disease landscapes. 在不同疾病景观中预测变体致病性的通用方法。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-07-22 DOI: 10.1016/j.jgg.2024.07.015
Xiang Chen, Xiaomin Yu
{"title":"Toward a universal approach for predicting variant pathogenicity in diverse disease landscapes.","authors":"Xiang Chen, Xiaomin Yu","doi":"10.1016/j.jgg.2024.07.015","DOIUrl":"10.1016/j.jgg.2024.07.015","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development. 结合单细胞剖析和功能分析，探索假基因在人类早期胚胎发育中的作用。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-07-20 DOI: 10.1016/j.jgg.2024.07.013
Mengyao Sun, Le Chang, Liu He, Li Wang, Zhengyang Jiang, Yanmin Si, Jia Yu, Yanni Ma
{"title":"Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development.","authors":"Mengyao Sun, Le Chang, Liu He, Li Wang, Zhengyang Jiang, Yanmin Si, Jia Yu, Yanni Ma","doi":"10.1016/j.jgg.2024.07.013","DOIUrl":"10.1016/j.jgg.2024.07.013","url":null,"abstract":"<p><p>More and more studies have demonstrated that pseudogenes possess coding ability, and the functions of their transcripts in the development of diseases have been partially revealed. However, the role of pseudogenes in maintenance of normal physiological states and life activities has long been neglected. Here, we identify pseudogenes that are dynamically expressed during human early embryogenesis, showing different expression pattern from that of adult tissues. We explore the expression correlation between pseudogenes and the parent genes, part due to their shared gene regulatory elements or the potential regulation network between them. The essential role of three pseudogenes, PI4KAP1, TMED10P1, and FBXW4P1, in maintaining self-renewal of human embryonic stem cells is demonstrated. We further find that the three pseudogenes might perform their regulatory functions by binding to proteins or microRNAs. The pseudogene-related single-nucleotide polymorphisms are significantly associated with human congenital disease, further illustrating their importance during early embryonic development. Overall, this study is an excavation and exploration of functional pseudogenes during early human embryonic development, suggesting that pseudogenes are not only capable of being specifically activated in pathological states, but also play crucial roles in the maintenance of normal physiological states.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
CCDC181 is required for proper spermiogenesis in mice. 小鼠精子正常生成需要 CCDC181。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-07-15 DOI: 10.1016/j.jgg.2024.07.010
Xirui Zi, Qingchao Li, Yue Lu, Qian Lyu, Heng Guo, Xiaoqian Meng, Jun Zhou, Huijie Zhao
{"title":"CCDC181 is required for proper spermiogenesis in mice.","authors":"Xirui Zi, Qingchao Li, Yue Lu, Qian Lyu, Heng Guo, Xiaoqian Meng, Jun Zhou, Huijie Zhao","doi":"10.1016/j.jgg.2024.07.010","DOIUrl":"https://doi.org/10.1016/j.jgg.2024.07.010","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141635925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
NanoTrans: an integrated computational framework for comprehensive transcriptome analysis with nanopore direct RNA sequencing. NanoTrans：利用纳米孔直接 RNA 测序进行转录组综合分析的集成计算框架。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-07-14 DOI: 10.1016/j.jgg.2024.07.007
Ludong Yang, Xinxin Zhang, Fan Wang, Li Zhang, Jing Li, Jia-Xing Yue
{"title":"NanoTrans: an integrated computational framework for comprehensive transcriptome analysis with nanopore direct RNA sequencing.","authors":"Ludong Yang, Xinxin Zhang, Fan Wang, Li Zhang, Jing Li, Jia-Xing Yue","doi":"10.1016/j.jgg.2024.07.007","DOIUrl":"10.1016/j.jgg.2024.07.007","url":null,"abstract":"<p><p>Nanopore direct RNA sequencing (DRS) provides the direct access to native RNA strands with full-length information, shedding light on rich qualitative and quantitative properties of gene expression profiles. Here with NanoTrans, we present an integrated computational framework that comprehensively covers all major DRS-based application scopes, including isoform clustering and quantification, poly(A) tail length estimation, RNA modification profiling, and fusion gene detection. In addition to its merit in providing such a streamlined one-stop solution, NanoTrans also shines in its workflow-orientated modular design, batch processing capability, all-in-one tabular and graphic report output, as well as automatic installation and configuration supports. Finally, by applying NanoTrans to real DRS datasets of yeast, Arabidopsis, as well as human embryonic kidney and cancer cell lines, we further demonstrate its utility, effectiveness, and efficacy across a wide range of DRS-based application settings.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Ancient genomes illuminate the demographic history of Shandong over the past two millennia. 古代基因组揭示了山东两千年来的人口历史。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-07-13 DOI: 10.1016/j.jgg.2024.07.008
Qu Shen, Zhigang Wu, Jinguo Zan, Xiaomin Yang, Jianxin Guo, Zhi Ji, Baitong Wang, Yilan Liu, Xiaolu Mao, Xinyi Wang, Xinyue Zou, Hongming Zhou, Yanying Peng, Hao Ma, Haifeng He, Tianyou Bai, Mengting Xu, Shaoqing Wen, Li Jin, Qun Zhang, Chuan-Chao Wang
{"title":"Ancient genomes illuminate the demographic history of Shandong over the past two millennia.","authors":"Qu Shen, Zhigang Wu, Jinguo Zan, Xiaomin Yang, Jianxin Guo, Zhi Ji, Baitong Wang, Yilan Liu, Xiaolu Mao, Xinyi Wang, Xinyue Zou, Hongming Zhou, Yanying Peng, Hao Ma, Haifeng He, Tianyou Bai, Mengting Xu, Shaoqing Wen, Li Jin, Qun Zhang, Chuan-Chao Wang","doi":"10.1016/j.jgg.2024.07.008","DOIUrl":"https://doi.org/10.1016/j.jgg.2024.07.008","url":null,"abstract":"<p><p>Shandong province, located in the Lower Yellow River, is one of the birthplaces of ancient Chinese civilization. However, the comprehensive genetic histories of this region have remained largely unknown until now due to a lack of ancient human genomes. Here, we present 21 ancient genomes from Shandong dating from the Warring States period to the Jin-Yuan Dynasties. Unlike the early Neolithic samples from Shandong, the historical samples are most closely related to post-Late Neolithic populations of the Middle Yellow River Basin, suggesting a population turnover in Shandong from the Neolithic Age to the Historical era. In addition, we detect a close genetic affinity between the historical samples in Shandong and present-day Han Chinese, showing long-term genetic stability in Han Chinese at least since the Warring States period.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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