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

The lawc gene emerged de novo from conserved genomic elements and acquired a broad expression pattern in Drosophila. lawc基因从保守的基因组元件中重新出现，并在果蝇中获得了广泛的表达模式。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-27 DOI: 10.1016/j.jgg.2024.12.014

Roman O Cherezov, Julia E Vorontsova, Elena E Kuvaeva, Angelina A Akishina, Ekaterina L Zavoloka, Olga B Simonova

{"title":"The lawc gene emerged de novo from conserved genomic elements and acquired a broad expression pattern in Drosophila.","authors":"Roman O Cherezov, Julia E Vorontsova, Elena E Kuvaeva, Angelina A Akishina, Ekaterina L Zavoloka, Olga B Simonova","doi":"10.1016/j.jgg.2024.12.014","DOIUrl":"10.1016/j.jgg.2024.12.014","url":null,"abstract":"It has recently become evident that the de novo emergence of genes is widespread and documented for a variety of organisms. De novo genes frequently emerge in proximity to existing genes, forming gene overlaps. Here, we present an analysis of the evolutionary history of a putative de novo gene, lawc, which overlaps with the conserved Trf2 gene, which encodes a general transcription factor in Drosophila melanogaster. We demonstrate that lawc emerged approximately 68 million years ago in the 5'-untranslated region (UTR) of Trf2 and displays an extensive spatiotemporal expression pattern. One of the most remarkable features of the lawc evolutionary history is that its emergence was facilitated by the engagement of Drosophilidae-specific short, highly conserved regions located in Trf2 introns. This represents a unique example of putative de novo gene birth involving conserved DNA regions localized in introns of conserved genes. The observed lawc expression pattern may be due to the overlap of lawc with the 5'-UTR of Trf2. This study not only enriches our understanding of gene evolution but also highlights the complex interplay between genetic conservation and innovation.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904049","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

In vivo adenine base editing ameliorates Rho-associated autosomal dominant retinitis pigmentosa. 体内腺嘌呤碱基编辑可改善rho相关的常染色体显性视网膜色素变性。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-24 DOI: 10.1016/j.jgg.2024.12.012

Sihui Hu, Yuxi Chen, Yitong Zhou, Tianqi Cao, Simiao Liu, Chenhui Ding, Dongchun Xie, Puping Liang, Li Huang, Haiying Liu, Junjiu Huang

{"title":"In vivo adenine base editing ameliorates Rho-associated autosomal dominant retinitis pigmentosa.","authors":"Sihui Hu, Yuxi Chen, Yitong Zhou, Tianqi Cao, Simiao Liu, Chenhui Ding, Dongchun Xie, Puping Liang, Li Huang, Haiying Liu, Junjiu Huang","doi":"10.1016/j.jgg.2024.12.012","DOIUrl":"https://doi.org/10.1016/j.jgg.2024.12.012","url":null,"abstract":"Mutations in the Rhodopsin (RHO) gene are the main cause of autosomal dominant retinitis pigmentosa (adRP), 84% of which are pathogenic gain-of-function point mutations. Treatment strategies for adRP typically involve silencing or ablating the pathogenic allele, while normal RHO protein replacement has no meaningful therapeutic benefit. Here, we present an adenine base editor (ABE)-mediated therapeutic approach for adRP caused by RHO point mutations in vivo. The correctable pathogenic mutations are screened and verified, including T17M, Q344ter, and P347L. Two adRP animal models are created carrying the class 1 (Q344ter) and class 2 (T17M) mutations, and dual AAV-delivered ABE can effectively repair both mutations in vivo. The early intervention of ABE8e efficiently corrects the Q344ter mutation that causes a severe form of adRP, delays photoreceptor death, and restores retinal function and visual behavior. These results suggest that ABE is a promising alternative to treat RHO mutation-associated adRP. Our work provides an effective spacer-mediated point mutation correction therapy approach for dominantly inherited ocular disorders.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142900125","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

Unlocking the small RNAs: local and systemic modulators for advancing agronomic enhancement. 解锁小rna：促进农艺增强的局部和系统调节剂。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-21 DOI: 10.1016/j.jgg.2024.12.011

Wenqi Ouyang, Hongda Sun, Yuan Wang

{"title":"Unlocking the small RNAs: local and systemic modulators for advancing agronomic enhancement.","authors":"Wenqi Ouyang, Hongda Sun, Yuan Wang","doi":"10.1016/j.jgg.2024.12.011","DOIUrl":"10.1016/j.jgg.2024.12.011","url":null,"abstract":"Small regulatory RNAs (sRNAs) are essential regulators of gene expression across a wide range of organisms to precisely modulate gene activity based on sequence-specific recognition. In model plants like Arabidopsis thaliana, extensive research has primarily concentrated on 21 to 24-nucleotide (nt) sRNAs, particularly microRNAs (miRNAs). Recent advancements in cell and tissue isolation techniques, coupled with advanced sequencing technologies, are revealing a diverse array of preciously uncharacterized sRNA species. These include previously novel structural RNA fragments as well as numerous cell- and tissue-specific sRNAs that are active during distinct developmental stages, thereby enhancing our understanding of the precise and dynamic regulatory roles of sRNAs in plant development regulation. Additionally, a notable feature of sRNAs is their capacity for amplification and movement between cells and tissues, which facilitates long-distance communication-an adaptation critical to plants due to their sessile nature. In this review, we will discuss the classification and mechanisms of action of sRNAs, using legumes as a primary example due to their essential engagement for the unique organ establishment of root nodules and long-distance signaling, and further illustrating the potential applications of sRNAs in modern agricultural breeding and environmentally sustainable plant protection strategies.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142882980","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 testis-specific gene 1700030J22Rikis essential for sperm flagellar function and male fertility in mice. rik对小鼠精子鞭毛功能和雄性生育能力至关重要。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-20 DOI: 10.1016/j.jgg.2024.12.010

Damin Yun, Sheng Gao, Xinyao Li, Jie Shi, Lingling Wang, Tiao Bu, Xiwen Yang, Yunhao Wu, Xiaolong Wu, Fei Sun

引用次数: 0

High-quality genome of Firmiana hainanensis provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation. 海南枫的高质量基因组为研究锦葵科亚科的进化及其木材密度形成机制提供了新的思路。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-19 DOI: 10.1016/j.jgg.2024.12.009

Zeyu Dong, Shangkun Jin, Rui Fan, Pengcheng Sun, Lei Shao, Ting Zhao, Haojie Jiang, Zhiyuan Zhang, Haihong Shang, Xueying Guan, Yan Hu, Tianzhen Zhang, Fuyuan Zhu, Lei Fang

{"title":"High-quality genome of Firmiana hainanensis provides insights into the evolution of Malvaceae subfamilies and the mechanism of their wood density formation.","authors":"Zeyu Dong, Shangkun Jin, Rui Fan, Pengcheng Sun, Lei Shao, Ting Zhao, Haojie Jiang, Zhiyuan Zhang, Haihong Shang, Xueying Guan, Yan Hu, Tianzhen Zhang, Fuyuan Zhu, Lei Fang","doi":"10.1016/j.jgg.2024.12.009","DOIUrl":"10.1016/j.jgg.2024.12.009","url":null,"abstract":"The Malvaceae family, the most diverse family in the order Malvales, consists of nine subfamilies. Within the Firmiana genus of the Sterculioideae subfamily, most species are considered globally vulnerable, yet their genomes remain unexplored. Here, we present a chromosome-level genome assembly for a representative Firmiana species, F. hainanensis, 2n = 40, totaling 1536 Mb. Phylogenomic analysis shows that F. hainanensis and Durio zibethinus have the closest evolutionary relationship, with an estimated divergence time of approximately 21 MYA and distinct polyploidization events in their histories. Evolutionary trajectory analyses indicate that fissions and fusions may play a crucial role in chromosome number variation (2n = 14 to 2n = 96). Analysis of repetitive elements among Malvaceae reveals that the Tekay subfamily (belonging to the Gypsy group) contributes to variation in genome size (ranging from 324 Mb to 1620 Mb). Additionally, genes associated with P450, peroxidase, and microtubules, and thereby related to cell wall biosynthesis, are significantly contracted in F. hainanensis, potentially leading to its lower wood density relative to Hopea hainanensis. Overall, our study provides insights into the evolution of chromosome number, genome size, and the genetic basis of cell wall biosynthesis in Malvaceae species.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873456","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 : 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":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-18","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

Deep learning chromatin profiles reveal the cis-regulatory sequence code of the rice genome. 深度学习染色质谱揭示了水稻基因组的顺式调控序列代码。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-16 DOI: 10.1016/j.jgg.2024.12.007

Xinkai Zhou, Zhonghao Ruan, Chenlu Zhang, Kerstin Kaufmann, Dijun Chen

引用次数: 0

Foxo1 directs the transdifferentiation of mouse Sertoli cells into granulosa-like cells. Foxo1指导小鼠支持细胞向颗粒样细胞的转分化。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-15 DOI: 10.1016/j.jgg.2024.12.006

Junhua Chen, Changhuo Cen, Mengyue Wang, Shanshan Qin, Bowen Liu, Zhiming Shen, Xiuhong Cui, Xiaohui Hou, Fei Gao, Min Chen

{"title":"Foxo1 directs the transdifferentiation of mouse Sertoli cells into granulosa-like cells.","authors":"Junhua Chen, Changhuo Cen, Mengyue Wang, Shanshan Qin, Bowen Liu, Zhiming Shen, Xiuhong Cui, Xiaohui Hou, Fei Gao, Min Chen","doi":"10.1016/j.jgg.2024.12.006","DOIUrl":"10.1016/j.jgg.2024.12.006","url":null,"abstract":"Sertoli and granulosa cells, the initial differentiated somatic cells in bipotential gonads, play crucial roles in directing male and female gonad development, respectively. The transcription factor Foxo1 is involved in diverse cellular processes, and its expression in gonadal somatic cells is sex-dependent. While Foxo1 is abundantly expressed in ovarian granulosa cells, it is notably absent in testicular Sertoli cells. Nevertheless, its function in gonadal somatic cell differentiation remains elusive. In this study, we find that ectopic expression of Foxo1 in Sertoli cells leads to defects in testes development. Further study uncovers that the ectopic expression of Foxo1 induces the abundant expression of Foxl2 in Sertoli cells, along with the upregulation of other female-specific genes. In contrast, the expression of male-specific genes is reduced. Mechanistic studies indicate that Foxo1 directly binds to the promoter region of Foxl2, inducing its expression. Our findings highlight that Foxo1 serves as a key regulator for the lineage maintenance of ovarian granulosa cells. This study contributes valuable insights into understanding the regulatory mechanisms governing the lineage maintenance of gonadal somatic cells.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142840255","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

Regulation of tillering and panicle branching in rice and wheat. 调节水稻和小麦的分蘖和圆锥花序分枝。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-14 DOI: 10.1016/j.jgg.2024.12.005

Ning Zhang, Yuhao Liu, Songtao Gui, Yonghong Wang

引用次数: 0

Transcription factors BnaC09.FUL and BnaC06.WIP2 antagonistically regulate flowering time under long-day conditions in Brassica napus. 转录因子 BnaC09.FUL 和 BnaC06.WIP2 在长日照条件下拮抗调控甘蓝型油菜的开花时间。

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2024-12-12 DOI: 10.1016/j.jgg.2024.12.003

Yuanchang Min, Shuangcheng He, Xin Wang, Huan Hu, Shihao Wei, Ankang Ge, Lixi Jiang, Saiqi Yang, Yuan Guo, Zijin Liu, Mingxun Chen

{"title":"Transcription factors BnaC09.FUL and BnaC06.WIP2 antagonistically regulate flowering time under long-day conditions in Brassica napus.","authors":"Yuanchang Min, Shuangcheng He, Xin Wang, Huan Hu, Shihao Wei, Ankang Ge, Lixi Jiang, Saiqi Yang, Yuan Guo, Zijin Liu, Mingxun Chen","doi":"10.1016/j.jgg.2024.12.003","DOIUrl":"10.1016/j.jgg.2024.12.003","url":null,"abstract":"Appropriate flowering time in rapeseed (Brassica napus L.) is vital for preventing losses from weather, diseases, and pests. However, the molecular basis of its regulation remains largely unknown. Here, a genome-wide association study identifies BnaC09.FUL, a MADS-box transcription factor, as a promising candidate gene regulating flowering time in B. napus. BnaC09.FUL expression increases sharply in B. napus shoot apices near bolting. BnaC09.FUL overexpression results in early flowering, while BnaFUL mutation causes delayed flowering in B. napus. A zinc finger transcription factor, BnaC06.WIP2, is identified as an interaction partner of BnaC09.FUL, and BnaC06.WIP2 overexpression delays flowering in B. napus, with RNA sequencing revealing its influence on the expression of many flowering-associated genes. We further demonstrate that BnaC06.WIP2 directly represses the expression of BnaA05.SOC1, BnaC03.SOC1, BnaC04.SOC1, BnaC06.FT, BnaA06.LFY, BnaC07.FUL, BnaA08.CAL, and BnaC03.CAL and indirectly inhibits the expression of other flowering time-related genes. Genetic and molecular investigations highlight the antagonistic relationship between BnaC09.FUL and BnaC06.WIP2 in regulating the flowering time in B. napus through direct regulation of the expression of BnaC03.SOC1, BnaA08.CAL, and BnaC03.CAL. Overall, our findings provide a mechanism by which the BnaC09.FUL-BnaC06.WIP2 transcriptional regulatory module controls the flowering time in B. napus.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824889","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