Journal of Genetics and Genomics最新文献_第4页

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 : 2024-07-13 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":"https://doi.org/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 obtained the ancient genome of a hereditary elite family, Gao Bin (, 503-572 AD), at 0.6473-fold coverage with 475132 single-nucleotide polymorphisms (SNPs) on the 1240k panel. His mitochondrial haplogroup belonged to Z4 and Y-haplogroup to O1a1a2b-F2444*. The genetic profile of Gao Bin was most similar to that of the northern Han Chinese. He could be modelled 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":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":"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

A multi-ancestry GWAS meta-analysis of facial features and its application in predicting archaic human features. 对面部特征及其在预测古人类特征中的应用进行多种姓 GWAS 元分析。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-11 DOI: 10.1016/j.jgg.2024.07.005

Siyuan Du, Jieyi Chen, Jiarui Li, Wei Qian, Sijie Wu, Qianqian Peng, Yu Liu, Ting Pan, Yi Li, Sibte Syed Hadi, Jingze Tan, Ziyu Yuan, Jiucun Wang, Kun Tang, Zhuo Wang, Yanqin Wen, Xinran Dong, Wenhao Zhou, Andrés Ruiz-Linares, Yongyong Shi, Li Jin, Fan Liu, Manfei Zhang, Sijia Wang

{"title":"A multi-ancestry GWAS meta-analysis of facial features and its application in predicting archaic human features.","authors":"Siyuan Du, Jieyi Chen, Jiarui Li, Wei Qian, Sijie Wu, Qianqian Peng, Yu Liu, Ting Pan, Yi Li, Sibte Syed Hadi, Jingze Tan, Ziyu Yuan, Jiucun Wang, Kun Tang, Zhuo Wang, Yanqin Wen, Xinran Dong, Wenhao Zhou, Andrés Ruiz-Linares, Yongyong Shi, Li Jin, Fan Liu, Manfei Zhang, Sijia Wang","doi":"10.1016/j.jgg.2024.07.005","DOIUrl":"10.1016/j.jgg.2024.07.005","url":null,"abstract":"Facial morphology, a complex trait influenced by genetics, holds great significance in evolutionary research. However, due to limited fossil evidence, the facial characteristics of Neanderthals and Denisovans have remained largely unknown. In this study, we conducted a large-scale multi-ethnic meta-analysis of the genome-wide association study (GWAS), including 9674 East Asians and 10,115 Europeans, quantitatively assessing 78 facial traits using 3D facial images. We identified 71 genomic loci associated with facial features, including 21 novel loci. We developed a facial polygenic score (FPS) that enables the prediction of facial features based on genetic information. Interestingly, the distribution of FPSs among populations from diverse continental groups exhibited relevant correlations with observed facial features. Furthermore, we applied the FPS to predict the facial traits of seven Neanderthals and one Denisovan using ancient DNA and aligned predictions with the fossil records. Our results suggested that Neanderthals and Denisovans likely shared similar facial features, such as a wider but shorter nose and a wider endocanthion distance. The decreased mouth width was characterized specifically in Denisovans. The integration of genomic data and facial trait analysis provides valuable insights into the evolutionary history and adaptive changes in human facial morphology.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604560","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

Synchronized lineage tracing of cell membranes and nuclei by dual recombinases and dual fluorescent. 利用双重组酶和双荧光对细胞膜和细胞核进行同步系谱追踪。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-10 DOI: 10.1016/j.jgg.2024.07.006

Xueying Yang, Shun He, Xufeng Li, Zhihou Guo, Haichang Wang, Zhuonan Zhang, Xin Song, Ke Jia, Lingjuan He, Bin Zhou

{"title":"Synchronized lineage tracing of cell membranes and nuclei by dual recombinases and dual fluorescent.","authors":"Xueying Yang, Shun He, Xufeng Li, Zhihou Guo, Haichang Wang, Zhuonan Zhang, Xin Song, Ke Jia, Lingjuan He, Bin Zhou","doi":"10.1016/j.jgg.2024.07.006","DOIUrl":"10.1016/j.jgg.2024.07.006","url":null,"abstract":"Genetic lineage tracing has been widely employed to investigate cell lineages and fate. However, conventional reporting systems often label the entire cytoplasm, making it challenging to discern cell boundaries. Additionally, single Cre-loxP recombination systems have limitations in tracing specific cell populations. This study proposes three reporting systems that utilizing Cre, Dre, and Dre + Cre mediated recombination. These systems incorporate tdTomato expression on the cell membrane and PhiYFP expression within the nucleus, allowing for clear observation of the nucleus and membrane. The efficacy of these systems is successfully demonstrated by labeling cardiomyocytes and hepatocytes. The potential for dynamic visualization of the cell membrane is showcased using intravital imaging microscopy or three-dimensional imaging. Furthermore, by combining this dual recombinase system with the ProTracer system, hepatocyte proliferation is traced with enhanced precision. This reporting system holds significant importance for advancing the understanding of cell fate studies in development, homeostasis, and diseases.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141602196","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

multiMotif: a generalized tool for scanning and visualization of diverse and distant multiple motifs. multiMotif：一种用于扫描和可视化多种远距离多重图案的通用工具。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-09 DOI: 10.1016/j.jgg.2024.07.003

Sainan Luo, Binghan Xiao, Jianing Geng, Songnian Hu

引用次数: 0

Gene therapy and gene editing strategies in inherited blood disorders. 遗传性血液病的基因治疗和基因编辑策略。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-08 DOI: 10.1016/j.jgg.2024.07.004

Xuemei Song, JinLei Liu, Tangcong Chen, Tingfeng Zheng, Xiaolong Wang, Xiang Guo

{"title":"Gene therapy and gene editing strategies in inherited blood disorders.","authors":"Xuemei Song, JinLei Liu, Tangcong Chen, Tingfeng Zheng, Xiaolong Wang, Xiang Guo","doi":"10.1016/j.jgg.2024.07.004","DOIUrl":"https://doi.org/10.1016/j.jgg.2024.07.004","url":null,"abstract":"Gene therapy has shown significant potential in treating various diseases, particularly inherited blood disorders such as hemophilia, sickle cell disease, and thalassemia. Advances in understanding the regulatory network of disease-associated genes have led to the identification of additional therapeutic targets for treatment, especially for β-hemoglobinopathies. Erythroid regulatory factor BCL11A offers the most promising therapeutic target for β-hemoglobinopathies and reduction of its expression using the commercialized gene therapy product Casgevy was approved for use in the UK and USA in 2023. Notably, the emergence of innovative gene editing technologies has further broadened the gene therapy landscape, presenting new possibilities for treatment. Intensive studies indicate that base editing and prime editing, built upon CRISPR technology, enable precise single-base modification in hematopoietic stem cells for addressing inherited blood disorders ex vivo and in vivo. In this review, we present an overview of the current landscape of gene therapies, focusing on clinical research and gene therapy products for inherited blood disorders, evaluation of potential gene targets, and the gene editing tools employed in current gene therapy practices, which provides an insight for the establishment of safer and more effective gene therapy methods for a wider range of diseases in the future.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581548","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

Toll-9 prevents the proliferation of injected oncogenic cells in adult flies. Toll-9 能阻止成蝇体内注入的致癌细胞增殖。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-06 DOI: 10.1016/j.jgg.2024.07.002

Shanming Ji, Jules A Hoffmann

引用次数: 0

Population-scale variability of the human UDP-glycosyltransferase gene family. 人类 UDP-糖基转移酶基因家族的种群规模变异。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-04 DOI: 10.1016/j.jgg.2024.06.018

Daianna González-Padilla, Mahamadou D Camara, Volker M Lauschke, Yitian Zhou

{"title":"Population-scale variability of the human UDP-glycosyltransferase gene family.","authors":"Daianna González-Padilla, Mahamadou D Camara, Volker M Lauschke, Yitian Zhou","doi":"10.1016/j.jgg.2024.06.018","DOIUrl":"10.1016/j.jgg.2024.06.018","url":null,"abstract":"Human UDP-glycosyltransferases (UGTs) are responsible for the glucuronidation of a wide variety of endogenous substrates and commonly prescribed drugs. Different genetic polymorphisms in UGT genes are implicated in interindividual differences in drug response and cancer risk. However, the genetic complexity beyond these variants has not been comprehensively assessed. We here leveraged whole-exome and whole-genome sequencing data from 141,456 unrelated individuals across 7 major human populations to provide a comprehensive profile of genetic variability across the human UGT gene family. Overall, 9666 exonic variants were observed of which 98.9% were rare. To interpret the functional impact of UGT missense variants, we developed a gene family-specific variant effect predictor. This algorithm identified a total of 1208 deleterious variants, most of which were found in African and South Asian populations. Structural analysis corroborated the predicted effects for multiple variations in substrate binding sites. Combined, our analyses provide a systematic overview of UGT variability, which can yield insights into interindividual differences in phase 2 metabolism and facilitate the translation of sequencing data into personalized predictions of UGT substrate disposition.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538953","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

Epigenomic features associated with body temperature stabilize tissues during cold exposure in cold-resistant pigs. 与体温相关的表观基因组特征可稳定耐寒猪在寒冷暴露期间的组织。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-04 DOI: 10.1016/j.jgg.2024.06.017

Yaping Guo, Mingyang Hu, Hao Peng, Yan Zhang, Renzhuo Kuang, Zheyu Han, Daoyuan Wang, Yinlong Liao, Ruixian Ma, Zhixiang Xu, Jiahao Sun, Yu Shen, Changzhi Zhao, Hong Ma, Di Liu, Shuhong Zhao, Yunxia Zhao

{"title":"Epigenomic features associated with body temperature stabilize tissues during cold exposure in cold-resistant pigs.","authors":"Yaping Guo, Mingyang Hu, Hao Peng, Yan Zhang, Renzhuo Kuang, Zheyu Han, Daoyuan Wang, Yinlong Liao, Ruixian Ma, Zhixiang Xu, Jiahao Sun, Yu Shen, Changzhi Zhao, Hong Ma, Di Liu, Shuhong Zhao, Yunxia Zhao","doi":"10.1016/j.jgg.2024.06.017","DOIUrl":"10.1016/j.jgg.2024.06.017","url":null,"abstract":"Cold stress in low-temperature environments can trigger changes in gene expression, but epigenomics regulation of temperature stability in vital tissues, including the fat and diencephalon, is still unclear. Here, we explore the cold-induced changes in epigenomic features in the diencephalon and fat tissues of two cold-resistant Chinese pig breeds, Min and Enshi black (ES) pigs, utilizing H3K27ac CUT&Tag, RNA-seq, and selective signature analysis. Our results show significant alterations in H3K27ac modifications in the diencephalon of Min pigs and the fat of ES pigs after cold exposure. Dramatic changes in H3K27ac modifications in the diencephalon of Min pig are primarily associated with genes involved in energy metabolism and hormone regulation, whereas those in the fat of ES pig are primarily associated with immunity-related genes. Moreover, transcription factors PRDM1 and HSF1, which show evidence of selection, are enriched in genomic regions presenting cold-responsive alterations in H3K27ac modification in the Min pig diencephalon and ES pig fat, respectively. Our results indicate the diversity of epigenomic response mechanisms to cold exposure between Min and ES pigs, providing unique epigenetic resources for studies of low-temperature adaptation in large mammals.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141538950","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 : 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 new 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 new 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":null,"pages":null},"PeriodicalIF":6.6,"publicationDate":"2024-07-03","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

The interplay between extracellular and intracellular auxin signaling in plants. 植物中细胞外和细胞间叶绿素信号的相互作用

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-07-03 DOI: 10.1016/j.jgg.2024.06.019

Wenxin Tang, Yongqiang Yu, Tongda Xu

引用次数: 0