Journal of Genetics and Genomics最新文献_第9页

Annotation and assessment of functional variants in livestock through epigenomic data. 通过表观基因组数据对家畜功能变异的注释和评估。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-04 DOI: 10.1016/j.jgg.2025.03.013

Ruixian Ma, Renzhuo Kuang, Jingcheng Zhang, Jiahao Sun, Yueyuan Xu, Xinbo Zhou, Zheyu Han, Mingyang Hu, Daoyuan Wang, Yuhua Fu, Yong Zhang, Xinyun Li, Mengjin Zhu, Shuhong Zhao, Tao Xiang, Mengwei Shi, Yunxia Zhao

{"title":"Annotation and assessment of functional variants in livestock through epigenomic data.","authors":"Ruixian Ma, Renzhuo Kuang, Jingcheng Zhang, Jiahao Sun, Yueyuan Xu, Xinbo Zhou, Zheyu Han, Mingyang Hu, Daoyuan Wang, Yuhua Fu, Yong Zhang, Xinyun Li, Mengjin Zhu, Shuhong Zhao, Tao Xiang, Mengwei Shi, Yunxia Zhao","doi":"10.1016/j.jgg.2025.03.013","DOIUrl":"10.1016/j.jgg.2025.03.013","url":null,"abstract":"Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding. However, the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods. In this study, we gather 1030 raw epigenomic datasets from 10 animal species and systematically annotate 7 types of key regulatory regions, creating a comprehensive functional annotation map of animal genomic variants. Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits, underscoring the utility of these annotations in functional variant discovery. Using our functional annotations, we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories, with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs. Incorporating these variants into genomic prediction models can improve estimated breeding value (EBV) accuracy, demonstrating their practical utility in breeding programs. To facilitate the use of our results, we develop the Integrated Functional Mutation (IFmut: http://www.ifmutants.com:8212) platform, enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently. Our study provides a robust framework for functional genomic annotations in farm animals, enhancing variant function assessment and breeding precision.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143797157","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

Local trafficking and long-distance transport of small RNAs in plants. 植物小rna的局部转运和远距离转运。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-03 DOI: 10.1016/j.jgg.2025.03.011

Yi Zhao, Binglian Zheng

{"title":"Local trafficking and long-distance transport of small RNAs in plants.","authors":"Yi Zhao, Binglian Zheng","doi":"10.1016/j.jgg.2025.03.011","DOIUrl":"10.1016/j.jgg.2025.03.011","url":null,"abstract":"Canonical small RNAs in plants, including microRNAs and small interfering RNAs, are key triggers of RNA interference and regulate nearly every major biological process in plants. To establish systemic silencing, small RNAs undergo both short-distance intracellular trafficking or intercellular communication and long-distance transport from one organ to another, even across parasites or pathogens. This enables the delivery of effector molecules throughout the plant, promoting the spread of gene silencing. Biologically, the spatiotemporal regulation of small RNAs results in gradient distributions within cells or along the direction of organogenesis. Furthermore, the spreading capacity of small RNAs, generated in somatic or nurse cells, can guide target gene silencing in germlines in plants. In this review, we summarize recent advances in understanding the regulation and the functional roles of local trafficking and long-distance transport of plant small RNAs in developmental polarity, the maintenance of cell identity, and with a particular focus, the mechanisms of small RNA movement and delivery between companion cells and gametes in plants. Additionally, we discuss the methods and challenges of monitoring small RNA transport in vivo through live imaging, as well as the potential applications of small RNA transport and delivery in the development of RNA-based pesticides.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789348","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

Forensic investigative genetic genealogy: expanding pedigree tracing and genetic inquiry in the genomic era. 法医调查遗传系谱学：在基因组时代扩大血统追踪和遗传调查。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-01 Epub Date: 2024-07-03 DOI: 10.1016/j.jgg.2024.06.016

Mengge Wang, Hongyu Chen, Lintao Luo, Yuguo Huang, Shuhan Duan, Huijun Yuan, Renkuan Tang, Chao Liu, Guanglin He

{"title":"Forensic investigative genetic genealogy: expanding pedigree tracing and genetic inquiry in the genomic era.","authors":"Mengge Wang, Hongyu Chen, Lintao Luo, Yuguo Huang, Shuhan Duan, Huijun Yuan, Renkuan Tang, Chao Liu, Guanglin He","doi":"10.1016/j.jgg.2024.06.016","DOIUrl":"10.1016/j.jgg.2024.06.016","url":null,"abstract":"Genetic genealogy provides crucial insights into the complex biological relationships within contemporary and ancient human populations by analyzing shared alleles and chromosomal segments that are identical by descent to understand kinship, migration patterns, and population dynamics. Within forensic science, forensic investigative genetic genealogy (FIGG) has gained prominence by leveraging next-generation sequencing technologies and population-specific genomic resources, opening useful investigative avenues. In this review, we synthesize current knowledge, underscore recent advancements, and discuss the growing role of FIGG in forensic genomics. FIGG has been pivotal in revitalizing dormant inquiries and offering genetic leads in numerous cold cases. Its effectiveness relies on the extensive single-nucleotide polymorphism profiles contributed by individuals from diverse populations to specialized genomic databases. Advances in computational genomics and the growth of human genomic databases have spurred a profound shift in the application of genetic genealogy across forensics, anthropology, and ancient DNA studies. As the field progresses, FIGG is evolving from a nascent practice into a more sophisticated and specialized discipline, shaping the future of forensic investigations.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"460-472"},"PeriodicalIF":6.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538951","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

Genomic characterization reveals distinct mutational landscape of acral melanoma in East Asian. 基因组特征揭示了东亚肢端黑色素瘤不同的突变景观。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-01 Epub Date: 2025-01-09 DOI: 10.1016/j.jgg.2024.12.018

Fenghao Zhang, Xiaowen Wu, Tao Jiao, Haizhen Du, Qian Guo, Chuanliang Cui, Zhihong Chi, Xinan Sheng, Dezhi Jiang, Yuhong Zhang, Jiayan Wu, Yan Kong, Lu Si

{"title":"Genomic characterization reveals distinct mutational landscape of acral melanoma in East Asian.","authors":"Fenghao Zhang, Xiaowen Wu, Tao Jiao, Haizhen Du, Qian Guo, Chuanliang Cui, Zhihong Chi, Xinan Sheng, Dezhi Jiang, Yuhong Zhang, Jiayan Wu, Yan Kong, Lu Si","doi":"10.1016/j.jgg.2024.12.018","DOIUrl":"10.1016/j.jgg.2024.12.018","url":null,"abstract":"Acral melanoma, the most common melanoma subtype in East Asia, is associated with a poor prognosis. This study aims to comprehensively analyze the genomic characteristics of acral melanoma in East Asians. We conduct whole-genome sequencing of 55 acral melanoma tumors and perform data mining with relevant clinical data. Our findings reveal a unique mutational profile in East Asian acral melanoma, characterized by fewer point mutations and structural variations, a higher prevalence of NRAS mutations, and a lower frequency of BRAF mutations compared to patients of European descent. Notably, we identify previously underestimated ultraviolet radiation signatures and their significant association with BRAF and NRAS mutations. Structural rearrangement signatures indicate distinct mutational processes in BRAF-driven versus NRAS-driven tumors. We also find that homologous recombination deficiency with MAPK pathway mutations correlated with poor prognosis. The structural variations and amplifications in EP300, TERT, RAC1, and LZTR1 point to potential therapeutic targets tailored to East Asian populations. The high prevalence of whole-genome duplication events in BRAF/NRAS-mutated tumors suggests a synergistic carcinogenic effect that warrants further investigation. In summary, our study provides important insights into the genetic underpinnings of acral melanoma in East Asians, creating opportunities for targeted therapies.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"525-538"},"PeriodicalIF":6.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142973388","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

A rare KLHDC4 variant Glu510Lys is associated with genetic susceptibility and promotes tumor metastasis in nasopharyngeal carcinoma. 一种罕见的KLHDC4变异Glu510Lys与鼻咽癌的遗传易感性相关，并促进肿瘤转移。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-01 Epub Date: 2024-12-18 DOI: 10.1016/j.jgg.2024.12.008

Xi-Xi Cheng, Guo-Wang Lin, Ya-Qing Zhou, Yi-Qi Li, Shuai He, Yang Liu, Yan-Ni Zeng, Yun-Miao Guo, Shu-Qiang Liu, Wan Peng, Pan-Pan Wei, Chun-Ling Luo, Jin-Xin Bei

{"title":"A rare KLHDC4 variant Glu510Lys is associated with genetic susceptibility and promotes tumor metastasis in nasopharyngeal carcinoma.","authors":"Xi-Xi Cheng, Guo-Wang Lin, Ya-Qing Zhou, Yi-Qi Li, Shuai He, Yang Liu, Yan-Ni Zeng, Yun-Miao Guo, Shu-Qiang Liu, Wan Peng, Pan-Pan Wei, Chun-Ling Luo, Jin-Xin Bei","doi":"10.1016/j.jgg.2024.12.008","DOIUrl":"10.1016/j.jgg.2024.12.008","url":null,"abstract":"Various genetic association studies have identified numerous single nucleotide polymorphisms (SNPs) associated with nasopharyngeal carcinoma (NPC) risk. However, these studies have predominantly focused on common variants, leaving the contribution of rare variants to the \"missing heritability\" largely unexplored. Here, we integrate genotyping data from 3925 NPC cases and 15,048 healthy controls to identify a rare SNP, rs141121474, resulting in a Glu510Lys mutation in KLHDC4 gene linked to increased NPC risk. Subsequent analyses reveal that KLHDC4 is highly expressed in NPC and correlates with poorer prognosis. Functional characterizations demonstrate that KLHDC4 acts as an oncogene in NPC cells, enhancing their migratory and metastatic capabilities, with these effects being further augmented by the Glu510Lys mutation. Mechanistically, the Glu510Lys mutant exhibits increased interaction with Vimentin compared to the wild-type KLHDC4 (KLHDC4-WT), leading to elevated Vimentin protein stability and modulation of the epithelial-mesenchymal transition process, thereby promoting tumor metastasis. Moreover, Vimentin knockdown significantly mitigates the oncogenic effects induced by overexpression of both KLHDC4-WT and the Glu510Lys variant. Collectively, our findings highlight the critical role of the rare KLHDC4 variant rs141121474 in NPC progression and propose its potential as a diagnostic and therapeutic target for NPC patients.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"559-569"},"PeriodicalIF":6.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873453","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

Genome-wide DNA methylation profile and predictive biomarkers in premature ovarian insufficiency. 卵巢早衰的全基因组 DNA 甲基化图谱和预测性生物标志物

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-01 Epub Date: 2024-10-18 DOI: 10.1016/j.jgg.2024.10.004

Xinmiao He, Xinyue Chang, Shuning Zhuang, Jianing Liu, Yuteng Wang, Yingying Qin, Ting Guo

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 : 2025-04-01 Epub Date: 2024-07-14 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

引用次数: 0

Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties. 中国南北朝时期世袭精英的古代基因组分析。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-01 Epub Date: 2024-07-14 DOI: 10.1016/j.jgg.2024.07.009

Yao Yu, Xiaomin Yang, Daiyun Liu, Panxin Du, Hailiang Meng, Zixiao Huang, Jianxue Xiong, Yi Ding, Xiaoying Ren, Edward Allen, Hui Wang, Sheng Han, Li Jin, Chuan-Chao Wang, Shaoqing Wen

{"title":"Ancient genomic analysis of a Chinese hereditary elite from the Northern and Southern Dynasties.","authors":"Yao Yu, Xiaomin Yang, Daiyun Liu, Panxin Du, Hailiang Meng, Zixiao Huang, Jianxue Xiong, Yi Ding, Xiaoying Ren, Edward Allen, Hui Wang, Sheng Han, Li Jin, Chuan-Chao Wang, Shaoqing Wen","doi":"10.1016/j.jgg.2024.07.009","DOIUrl":"10.1016/j.jgg.2024.07.009","url":null,"abstract":"China's Northern and Southern Dynasties period (3rd-6th centuries AD) marked a significant era of ethnic integration in northern China. However, previous ancient DNA studies have primarily focused on northern ethnic groups, with limited research on the genetic formation of the hereditary elite family, especially considering their abundant archaeological record and clear material identity. In this study, we obtain the ancient genome of a hereditary elite family, Gao Bin (, 503 AD-572 AD), at 0.6473-fold coverage with 475,132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belongs to Z4 and Y-haplogroup to O1a1a2b-F2444∗. The genetic profile of Gao Bin is most similar to that of the northern Han Chinese. He can be modeled as deriving all his ancestry from Late Neolithic to Iron Age Yellow River farmers without influence from Northeast Asia, Korea, or the Mongolian Plateau. Our study sheds light on the genetic formation of hereditary elite families in the context of the Southern and Northern Dynasties ethnic integration.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"473-482"},"PeriodicalIF":6.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621831","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 DNA reveals genetic exchange in the Hehuang valley in the context of demic diffusion during the Han dynasty. 古代DNA揭示了汉代学术传播背景下河黄流域的基因交换。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-01 Epub Date: 2024-12-03 DOI: 10.1016/j.jgg.2024.11.013

Langyun Wang, Yutong Wang, Bing Sun, Daxuan Zhang, Guanjin Liang, Pengcheng Ma, Hao Zhang, Chunxiang Li, Xiaojun Hu, Quanchao Zhang, Yinqiu Cui

引用次数: 0

Expression quantitative trait loci (eQTL): from population genetics to precision medicine. 表达数量性状位点（eQTL）：从群体遗传学到精准医学。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-04-01 Epub Date: 2025-02-20 DOI: 10.1016/j.jgg.2025.02.003

Zhi Qi Wong, Lian Deng, Alvin Cengnata, Thuhairah Abdul Rahman, Aletza Mohd Ismail, Renee Lay Hong Lim, Shuhua Xu, Boon-Peng Hoh

{"title":"Expression quantitative trait loci (eQTL): from population genetics to precision medicine.","authors":"Zhi Qi Wong, Lian Deng, Alvin Cengnata, Thuhairah Abdul Rahman, Aletza Mohd Ismail, Renee Lay Hong Lim, Shuhua Xu, Boon-Peng Hoh","doi":"10.1016/j.jgg.2025.02.003","DOIUrl":"10.1016/j.jgg.2025.02.003","url":null,"abstract":"Evidence has shown that differential transcriptomic profiles among human populations from diverse ancestries, supporting the role of genetic architecture in regulating gene expression alongside environmental stimuli. Genetic variants that regulate gene expression, known as expression quantitative trait loci (eQTL), are primarily shaped by human migration history and evolutionary forces, likewise, regulation of gene expression in principle could have been influenced by these events. Therefore, a comprehensive understanding of how human evolution impacts eQTL offers important insights into how phenotypic diversity is shaped. Recent studies, however, suggest that eQTL is enriched in genes that are selectively constrained. Whether eQTL is minimally affected by selective pressures remains an open question and requires comprehensive investigations. In addition, such studies are primarily dominated by the major populations of European ancestry, leaving many marginalized populations underrepresented. These observations indicate there exists a fundamental knowledge gap in the role of genomics variation on phenotypic diversity, which potentially hinders precision medicine. This article aims to revisit the abundance of eQTL across diverse populations and provide an overview of their impact from the population and evolutionary genetics perspective, subsequently discuss their influence on phenomics, as well as challenges and opportunities in the applications to precision medicine.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"449-459"},"PeriodicalIF":6.6,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476897","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