Journal of Genetics and Genomics最新文献_第5页

Pan-genome analyses add ∼1000 genes to the "complete" genome assembly of chicken. 泛基因组分析为鸡的 "完整 "基因组组装增加了 1000 个基因。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1016/j.jgg.2024.10.009

Jilong Ren, Wenyan Kou, Yuan Xu, Meixuan Lu, Mian Gong, Xinmiao Zhang, Zhenyu Liu, Hengkuan Li, Qimeng Yang, Ali Mujtaba Shah, Feng Zhu, Zhuocheng Hou, Naiyi Xu, Yu Jiang, Fei Wang

引用次数: 0

SpaGRA: Graph augmentation facilitates domain identification for spatially resolved transcriptomics. SpaGRA：图增强技术有助于空间解析转录组学的领域识别。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-10-02 DOI: 10.1016/j.jgg.2024.09.015

Xue Sun, Wei Zhang, Wenrui Li, Na Yu, Daoliang Zhang, Qi Zou, Qiongye Dong, Xianglin Zhang, Zhiping Liu, Zhiyuan Yuan, Rui Gao

{"title":"SpaGRA: Graph augmentation facilitates domain identification for spatially resolved transcriptomics.","authors":"Xue Sun, Wei Zhang, Wenrui Li, Na Yu, Daoliang Zhang, Qi Zou, Qiongye Dong, Xianglin Zhang, Zhiping Liu, Zhiyuan Yuan, Rui Gao","doi":"10.1016/j.jgg.2024.09.015","DOIUrl":"10.1016/j.jgg.2024.09.015","url":null,"abstract":"Recent advances in spatially resolved transcriptomics (SRT) have provided new opportunities for characterizing spatial structures of various tissues. Graph-based geometric deep learning has gained widespread adoption for spatial domain identification tasks. Currently, most methods define adjacency relation between cells or spots by their spatial distance in SRT data, which overlooks key biological interactions like gene expression similarities, and leads to inaccuracies in spatial domain identification. To tackle this challenge, we propose a novel method, SpaGRA (https://github.com/sunxue-yy/SpaGRA), for automatic multi-relationship construction based on graph augmentation. SpaGRA uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks (GATs). This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive learning. Additionally, SpaGRA uses these multi-view relationships to construct negative samples, addressing sampling bias posed by random selection. Experimental results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different protocols. Using SpaGRA, we analyze the functional regions in the mouse hypothalamus, identify key genes related to heart development in mouse embryos, and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD data. Overall, SpaGRA can effectively characterize spatial structures across diverse SRT datasets.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"93-104"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373599","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 : 2025-01-01 Epub Date: 2024-07-03 DOI: 10.1016/j.jgg.2024.06.019

Wenxin Tang, Yongqiang Yu, Tongda Xu

引用次数: 0

Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae. 麦属植物祖先基因组重建与染色体重排进化。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 DOI: 10.1016/j.jgg.2024.12.017

Xueqing Yan, Runxian Yu, Jinpeng Wang, Yuannian Jiao

{"title":"Ancestral genome reconstruction and the evolution of chromosomal rearrangements in Triticeae.","authors":"Xueqing Yan, Runxian Yu, Jinpeng Wang, Yuannian Jiao","doi":"10.1016/j.jgg.2024.12.017","DOIUrl":"10.1016/j.jgg.2024.12.017","url":null,"abstract":"Chromosomal rearrangements (CRs) often cause phenotypic variations. Although several major rearrangements have been identified in Triticeae, a comprehensive study of the order, timing, and breakpoints of CRs has not been conducted. Here, we reconstruct high-quality ancestral genomes for the most recent common ancestor (MRCA) of the Triticeae, and the MRCA of the wheat lineage (Triticum and Aegilops). The protogenes of MRCA of the Triticeae and the wheat lineage are 22,894 and 29,060, respectively, which were arranged in their ancestral order. By partitioning modern Triticeae chromosomes into sets of syntenic regions and linking each to the corresponding protochromosomes, we revisit the rye chromosome structural evolution and propose alternative evolutionary routes. The previously identified 4L/5L reciprocal translocation in rye and Triticum urartu are found to have occurred independently and are unlikely the result of chromosomal introgression following distant hybridization. We also clarify that the 4AL/7BS translocation in tetraploid wheat was a bidirectional rather than unidirectional translocation event. Lastly, we identify several breakpoints in protochromosomes that independently reoccur following Triticeae evolution, representing potential CR hotspots. This study demonstrates that these reconstructed ancestral genomes can serve as special comparative references and facilitate a better understanding of the evolution of structural rearrangements in Triticeae.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142924040","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

Rab1 and Syntaxin 17 regulate hematopoietic homeostasis through β-integrin trafficking in Drosophila. 果蝇体内的 Rab1 和 Syntaxin 17 通过β-整合素贩运调节造血稳态

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-11-13 DOI: 10.1016/j.jgg.2024.11.001

Fangzhou Luo, Luwei Sui, Ying Sun, Zhixian Lai, Chengcheng Zhang, Gaoqun Zhang, Bing Bi, Shichao Yu, Li Hua Jin

{"title":"Rab1 and Syntaxin 17 regulate hematopoietic homeostasis through β-integrin trafficking in Drosophila.","authors":"Fangzhou Luo, Luwei Sui, Ying Sun, Zhixian Lai, Chengcheng Zhang, Gaoqun Zhang, Bing Bi, Shichao Yu, Li Hua Jin","doi":"10.1016/j.jgg.2024.11.001","DOIUrl":"10.1016/j.jgg.2024.11.001","url":null,"abstract":"Hematopoiesis is crucial for organismal health, and Drosophila serves as an effective genetic model due to conserved regulatory mechanisms with vertebrates. In larvae, hematopoiesis primarily occurs in the lymph gland, which contains distinct zones, including the cortical zone, intermediate zone, medullary zone, and posterior signaling center (PSC). Rab1 is vital for membrane trafficking and maintaining the localization of cell adhesion molecules, yet its role in hematopoietic homeostasis is not fully understood. This study investigates the effects of Rab1 dysfunction on β-integrin trafficking within circulating hemocytes and lymph gland cells. Rab1 impairment disrupts the endosomal trafficking of β-integrin, leading to its abnormal localization on cell membranes, which promotes lamellocyte differentiation and alters progenitor dynamics in circulating hemocytes and lymph glands, respectively. We also show that the mislocalization of β-integrin is dependent on the adhesion protein DE-cadherin. The reduction of β-integrin at cell boundaries in PSC cells leads to fewer PSC cells and lamellocyte differentiation. Furthermore, Rab1 regulates the trafficking of β-integrin via the Q-SNARE protein Syntaxin 17 (Syx17). Our findings indicate that Rab1 and Syx17 regulate distinct trafficking pathways for β-integrin in different hematopoietic compartments and maintain hematopoietic homeostasis of Drosophila.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"51-65"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632878","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

KDM2A and KDM2B protect a subset of CpG islands from DNA methylation. KDM2A 和 KDM2B 保护一部分 CpG 岛免受 DNA 甲基化。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-11-08 DOI: 10.1016/j.jgg.2024.10.012

Yuan Liu, Ying Liu, Yunji Zhu, Di Hu, Hu Nie, Yali Xie, Rongrong Sun, Jin He, Honglian Zhang, Falong Lu

引用次数: 0

Prox1a promotes liver growth and differentiation by repressing cdx1b expression and intestinal fate transition in zebrafish. Prox1a通过抑制cdx1b的表达和斑马鱼肠道命运转变促进肝脏的生长和分化

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-09-27 DOI: 10.1016/j.jgg.2024.09.010

Yingying Hu, Zhou Luo, Meiwen Wang, Zekai Wu, Yunxing Liu, Zhenchao Cheng, Yuhan Sun, Jing-Wei Xiong, Xiangjun Tong, Zuoyan Zhu, Bo Zhang

{"title":"Prox1a promotes liver growth and differentiation by repressing cdx1b expression and intestinal fate transition in zebrafish.","authors":"Yingying Hu, Zhou Luo, Meiwen Wang, Zekai Wu, Yunxing Liu, Zhenchao Cheng, Yuhan Sun, Jing-Wei Xiong, Xiangjun Tong, Zuoyan Zhu, Bo Zhang","doi":"10.1016/j.jgg.2024.09.010","DOIUrl":"10.1016/j.jgg.2024.09.010","url":null,"abstract":"The liver is a key endoderm-derived multifunctional organ within the digestive system. Prospero homeobox 1 (Prox1) is an essential transcription factor for liver development, but its specific function is not well understood. Here, we show that hepatic development, including the formation of intrahepatic biliary and vascular networks, is severely disrupted in prox1a mutant zebrafish. We find that Prox1a is essential for liver growth and proper differentiation but not required for early hepatic cell fate specification. Intriguingly, prox1a depletion leads to ectopic initiation of a Cdx1b-mediated intestinal program and the formation of intestinal lumen-like structures within the liver. Morpholino knockdown of cdx1b alleviates liver defects in the prox1a mutant zebrafish. Finally, chromatin immunoprecipitation analysis reveals that Prox1a binds directly to the promoter region of cdx1b, thereby repressing its expression. Overall, our findings indicate that Prox1a is required to promote and protect hepatic development by repression of Cdx1b-mediated intestinal cell fate in zebrafish.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"66-77"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332645","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

Epigenetic basis for the establishment of ruminal tissue-specific functions in bovine fetuses and adults. 牛胎儿和成年牛瘤胃组织特异功能建立的表观遗传学基础

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-11-05 DOI: 10.1016/j.jgg.2024.10.008

Jing Wang, Wen Yuan, Fang Liu, Guangbo Liu, Xiaoxiong Geng, Chen Li, Chenchen Zhang, Nan Li, Xueling Li

{"title":"Epigenetic basis for the establishment of ruminal tissue-specific functions in bovine fetuses and adults.","authors":"Jing Wang, Wen Yuan, Fang Liu, Guangbo Liu, Xiaoxiong Geng, Chen Li, Chenchen Zhang, Nan Li, Xueling Li","doi":"10.1016/j.jgg.2024.10.008","DOIUrl":"10.1016/j.jgg.2024.10.008","url":null,"abstract":"Epigenetic regulation in the rumen, a unique ruminant organ, remains largely unexplored compared with other tissues studied in model species. In this study, we perform an in-depth analysis of the epigenetic and transcriptional landscapes across fetal and adult bovine tissues as well as pluripotent stem cells. Among the extensive methylation differences across various stages and tissues, we identify tissue-specific differentially methylated regions (tsDMRs) unique to the rumen, which are crucial for regulating epithelial development and energy metabolism. These tsDMRs cluster within super-enhancer regions that overlap with transcription factor (TF) binding sites. Regression models indicate that DNA methylation, along with H3K27me3 and H3K27ac, can be used to predict enhancer activity. Key upstream TFs, including SOX2, FOSL1/2, and SMAD2/3, primarily maintain an inhibitory state through bivalent modifications during fetal development. Downstream functional genes are maintained mainly in a stable repressive state via DNA methylation until differentiation is complete. Our study underscores the critical role of tsDMRs in regulating distal components of rumen morphology and function, providing key insights into the epigenetic regulatory mechanisms that may influence bovine production traits.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"78-92"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606724","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

Crop root system architecture in drought response. 作物根系结构对干旱的响应。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-05-08 DOI: 10.1016/j.jgg.2024.05.001

Yanjun Zhang, Xi Wu, Xingrong Wang, Mingqiu Dai, Yunling Peng

引用次数: 0

The future of zebrafish research: highlights from the 18th International Zebrafish Conference. 斑马鱼研究的未来：第 18 届国际斑马鱼大会亮点。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-09-14 DOI: 10.1016/j.jgg.2024.09.006

Chenyang Bian, Dongyuan Ma, Feng Liu

引用次数: 0