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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":"<p><p>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.</p>","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
{"title":"KDM2A and KDM2B protect a subset of CpG islands from DNA methylation.","authors":"Yuan Liu, Ying Liu, Yunji Zhu, Di Hu, Hu Nie, Yali Xie, Rongrong Sun, Jin He, Honglian Zhang, Falong Lu","doi":"10.1016/j.jgg.2024.10.012","DOIUrl":"10.1016/j.jgg.2024.10.012","url":null,"abstract":"<p><p>In the mammalian genome, most CpGs are methylated. However, CpGs within the CpG islands (CGIs) are largely unmethylated, which are important for gene expression regulation. The mechanism underlying the low methylation levels at CGIs remains largely elusive. KDM2 proteins (KDM2A and KDM2B) are H3K36me2 demethylases known to bind specifically at CGIs. Here, we report that depletion of each or both KDM2 proteins, or mutation of all their JmjC domains that harbor the H3K36me2 demethylation activity, leads to an increase in DNA methylation at selective CGIs. The Kdm2a/2b double knockout shows a stronger increase in DNA methylation compared with the single mutant of Kdm2a or Kdm2b, indicating that KDM2A and KDM2B redundantly regulate DNA methylation at CGIs. In addition, the increase of CGI DNA methylation upon mutations of KDM2 proteins is associated with the chromatin environment. Our findings reveal that KDM2A and KDM2B function redundantly in regulating DNA methylation at a subset of CGIs in an H3K36me2 demethylation-dependent manner.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"39-50"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142632874","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
{"title":"Crop root system architecture in drought response.","authors":"Yanjun Zhang, Xi Wu, Xingrong Wang, Mingqiu Dai, Yunling Peng","doi":"10.1016/j.jgg.2024.05.001","DOIUrl":"10.1016/j.jgg.2024.05.001","url":null,"abstract":"<p><p>Drought is a natural disaster that profoundly impacts on global agricultural production, significantly reduces crop yields, and thereby poses a severe threat to worldwide food security. Addressing the challenge of effectively improving crop drought resistance (DR) to mitigate yield loss under drought conditions is a global issue. An optimal root system architecture (RSA) plays a pivotal role in enhancing the capacity of crops to efficiently uptake water and nutrients, which consequently strengthens their resilience against environmental stresses. In this review, we discuss the compositions and roles of crop RSA and summarize the most recent developments in augmenting drought tolerance in crops by manipulating RSA-related genes. Based on the current research, we propose the potential optimal RSA configuration that could be helpful in enhancing crop DR. Lastly, we discuss the existing challenges and future directions for breeding crops with enhanced DR capabilities through genetic improvements targeting RSA.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"4-13"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900336","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
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":"<p><p>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.</p>","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":"<p><p>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.</p>","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
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
{"title":"The future of zebrafish research: highlights from the 18th International Zebrafish Conference.","authors":"Chenyang Bian, Dongyuan Ma, Feng Liu","doi":"10.1016/j.jgg.2024.09.006","DOIUrl":"10.1016/j.jgg.2024.09.006","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"1-3"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301289","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
Zebrafish cartilage development atlas generated by longitudinal in vivo imaging. 通过纵向活体成像生成斑马鱼软骨发育图谱。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-11-15 DOI: 10.1016/j.jgg.2024.11.003
Shirong Jin, Hongfei Zhang, Jia Li, Huaxing Zi, Jiulin Du, Hongyu Li
{"title":"Zebrafish cartilage development atlas generated by longitudinal in vivo imaging.","authors":"Shirong Jin, Hongfei Zhang, Jia Li, Huaxing Zi, Jiulin Du, Hongyu Li","doi":"10.1016/j.jgg.2024.11.003","DOIUrl":"10.1016/j.jgg.2024.11.003","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"124-127"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645139","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 histone modifications and nuclear lamina in genome regulation. 组蛋白修饰与核薄层在基因组调控中的相互作用。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-10-18 DOI: 10.1016/j.jgg.2024.10.005
Chang Sun, Yanjing Zhao, Liping Guo, Juhui Qiu, Qin Peng
{"title":"The interplay between histone modifications and nuclear lamina in genome regulation.","authors":"Chang Sun, Yanjing Zhao, Liping Guo, Juhui Qiu, Qin Peng","doi":"10.1016/j.jgg.2024.10.005","DOIUrl":"10.1016/j.jgg.2024.10.005","url":null,"abstract":"<p><p>Gene expression is regulated by chromatin architecture and epigenetic remodeling in cell homeostasis and pathologies. Histone modifications act as the key factors to modulate the chromatin accessibility. Different histone modifications are strongly associated with the localization of chromatin. Heterochromatin primarily localizes at the nuclear periphery, where it interacts with lamina proteins to suppress gene expression. In this review, we summarize the potential bridges that have regulatory functions of histone modifications in chromatin organization and transcriptional regulation at the nuclear periphery. We use lamina-associated domains (LADs) as examples to elucidate the biological roles of the interactions between histone modifications and nuclear lamina in cell differentiation and development. In the end, we highlight the technologies that are currently used to identify and visualize histone modifications and LADs, which could provide spatiotemporal information for understanding their regulatory functions in gene expression and discovering new targets for diseases.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"24-38"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481282","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
TaNPF6.2 improves agronomic traits via enhancing nitrogen uptake efficiency in wheat. TaNPF6.2 通过提高小麦的氮吸收效率来改善农艺性状。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2025-01-01 Epub Date: 2024-11-14 DOI: 10.1016/j.jgg.2024.11.004
Huanhuan Wang, Yangyang Liu, Lifen Wu, Chuan Xia, Yaoyu Chen, Xiuying Kong, Feng Shi, Huili Li, Xifang Yang, Liang Ma, Jiaqiang Sun, Lichao Zhang, Zhencheng Xie
{"title":"TaNPF6.2 improves agronomic traits via enhancing nitrogen uptake efficiency in wheat.","authors":"Huanhuan Wang, Yangyang Liu, Lifen Wu, Chuan Xia, Yaoyu Chen, Xiuying Kong, Feng Shi, Huili Li, Xifang Yang, Liang Ma, Jiaqiang Sun, Lichao Zhang, Zhencheng Xie","doi":"10.1016/j.jgg.2024.11.004","DOIUrl":"10.1016/j.jgg.2024.11.004","url":null,"abstract":"","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"120-123"},"PeriodicalIF":6.6,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640299","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
Prospects for synthetic biology in 21st Century agriculture. 合成生物学在21世纪农业中的应用前景。
IF 6.6 2区 生物学
Journal of Genetics and Genomics Pub Date : 2024-12-30 DOI: 10.1016/j.jgg.2024.12.016
Xingyan Ye, Kezhen Qin, Alisdair R Fernie, Youjun Zhang
{"title":"Prospects for synthetic biology in 21<sup>st</sup> Century agriculture.","authors":"Xingyan Ye, Kezhen Qin, Alisdair R Fernie, Youjun Zhang","doi":"10.1016/j.jgg.2024.12.016","DOIUrl":"10.1016/j.jgg.2024.12.016","url":null,"abstract":"<p><p>Plant synthetic biology has emerged as a transformative field in agriculture, offering innovative solutions to enhance food security, provide resilience to climate change, and transition to sustainable farming practices. By integrating advanced genetic tools, computational modeling, and systems biology, researchers can precisely modify plant genomes to enhance traits such as yield, stress tolerance, and nutrient use efficiency. The ability to design plants with specific characteristics tailored to diverse environmental conditions and agricultural needs holds great potential to address global food security challenges. Here, we highlight recent advancements and applications of plant synthetic biology in agriculture, focusing on key areas such as photosynthetic efficiency, nitrogen fixation, drought tolerance, pathogen resistance, nutrient use efficiency, biofortification, climate resilience, microbiology engineering, synthetic plant genomes, and the integration of artificial intelligence (AI) with synthetic biology. These innovations aim to maximize resource use efficiency, reduce reliance on external inputs, and mitigate environmental impacts associated with conventional agricultural practices. Despite challenges related to regulatory approval and public acceptance, the integration of synthetic biology in agriculture holds immense promise for creating more resilient and sustainable agricultural systems, contributing to global food security and environmental sustainability. Rigorous multi-field testing of these approaches will undoubtedly be required to ensure reproducibility.</p>","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142916281","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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