Journal of Genetics and Genomics最新文献

Coordinated regulation of cortical astrocyte maturation by OLIG1 and OLIG2 through BMP7 signaling modulation.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-24 DOI: 10.1016/j.jgg.2025.03.008

Ziwu Wang, Yu Tian, Tongye Fu, Feihong Yang, Jialin Li, Lin Yang, Wen Zhang, Wenhui Zheng, Xin Jiang, Zhejun Xu, Yan You, Xiaosu Li, Guoping Liu, Yunli Xie, Zhengang Yang, Dashi Qi, Zhuangzhi Zhang

{"title":"Coordinated regulation of cortical astrocyte maturation by OLIG1 and OLIG2 through BMP7 signaling modulation.","authors":"Ziwu Wang, Yu Tian, Tongye Fu, Feihong Yang, Jialin Li, Lin Yang, Wen Zhang, Wenhui Zheng, Xin Jiang, Zhejun Xu, Yan You, Xiaosu Li, Guoping Liu, Yunli Xie, Zhengang Yang, Dashi Qi, Zhuangzhi Zhang","doi":"10.1016/j.jgg.2025.03.008","DOIUrl":"https://doi.org/10.1016/j.jgg.2025.03.008","url":null,"abstract":"Astrocyte maturation is crucial for brain function, yet the mechanisms regulating this process remain poorly understood. In this study, we identify the bHLH transcription factors Olig1 and Olig2 as essential coordinators of cortical astrocyte maturation. We demonstrate that Olig1 and Olig2 work synergistically to regulate cortical astrocyte maturation by modulating Bmp7 expression. Genetic ablation of both Olig1 and Olig2 results in defective astrocyte morphology, including reduced process complexity and an immature gene expression profile. Single-cell RNA sequencing reveals a shift towards a less mature astrocyte state, marked by elevated levels of HOPX and GFAP, resembling human astrocytes. Mechanistically, Olig1 and Olig2 bind directly to the Bmp7 enhancer, repressing its expression to promote astrocyte maturation. Overexpression of Bmp7 in vivo replicates the astrocyte defects seen in Olig1/2 double mutants, confirming the critical role of BMP7 signaling in this process. These findings provide insights into the transcriptional and signaling pathways regulating astrocyte development and highlight Olig1 and Olig2 as key regulators of cortical astrocyte maturation, with potential implications for understanding glial dysfunction in neurological diseases.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733257","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

Characterization of zebrafish alas2 reporter for study on erythropoiesis, blood flow and erythroid disease.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-24 DOI: 10.1016/j.jgg.2025.03.009

Wenjuan Zhang, Shuang Wu, Yaxin Li, Mengye Cao, Biao Cao, Dantong Li, Kai Chen, Jian Zhao, Weijun Pan

引用次数: 0

The Cys2/His2 type zinc finger protein TaZFP21 functions as a repressor of drought response in wheat.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-18 DOI: 10.1016/j.jgg.2025.03.007

Yongliang Li, Zhenbing Ma, Ming Yu, Qiannan Wang, You Li, Shunxing Ye, Wenjun Xiao, Shuai Jiang, Xiaoxiao Zou, Hude Mao, Xinhong Guo

引用次数: 0

3' untranslated region somatic variants connect alternative polyadenylation dysregulation in human cancers.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-17 DOI: 10.1016/j.jgg.2025.03.006

Qiushi Xu, Xiaomeng Cheng, Qianru Li, Peng Yu, Xiaolan Zhou, Yu Chen, Limin Lin, Ting Ni, Zhaozhao Zhao

{"title":"3' untranslated region somatic variants connect alternative polyadenylation dysregulation in human cancers.","authors":"Qiushi Xu, Xiaomeng Cheng, Qianru Li, Peng Yu, Xiaolan Zhou, Yu Chen, Limin Lin, Ting Ni, Zhaozhao Zhao","doi":"10.1016/j.jgg.2025.03.006","DOIUrl":"https://doi.org/10.1016/j.jgg.2025.03.006","url":null,"abstract":"Somatic variants in the cancer genome influence gene expression through diverse mechanisms depending on their specific locations. However, a systematic evaluation of the effects of somatic variants located in 3' untranslated regions (3' UTRs) on alternative polyadenylation (APA) of mRNA remains lacking. In this study, we analyze 10,199 tumor samples across 32 cancer types and identify 1,333 somatic single nucleotide variants (SNVs) associated with abnormal 3' UTR APA. Mechanistically, these 3' UTR SNVs can alter cis-regulatory elements, such as the poly(A) signal and UGUA motif, leading to changes in APA. Minigene assays confirm that 3' UTR SNVs in multiple genes, including RPS23 and CHTOP, induce aberrant APA. Among affected genes, 62 exhibit differential stability between tandem 3' UTR isoforms, including HSPA4 and UCK2, validated by experimental assays. Finally, we establish that SNV-related abnormal APA usage serves as an additional layer of expression regulation for tumor-suppressor gene HMGN2 in breast cancer. Collectively, this study reveals 3' UTR APA as a critical mechanism mediating the functional impact of somatic noncoding variants in human cancers.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665385","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

Phenotypic advantages and improved genomic stability following selection in advanced selfing-generations of Brassica allohexaploids.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-14 DOI: 10.1016/j.jgg.2025.03.004

Yan Niu, Rui Yang, Zelong Li, Zhengxuan Huo, Shihao Chang, Entang Tian, Han Qin, Wallace A Cowling, Kadambot H M Siddique, Annaliese S Mason, Sheng Chen, Jun Zou

{"title":"Phenotypic advantages and improved genomic stability following selection in advanced selfing-generations of Brassica allohexaploids.","authors":"Yan Niu, Rui Yang, Zelong Li, Zhengxuan Huo, Shihao Chang, Entang Tian, Han Qin, Wallace A Cowling, Kadambot H M Siddique, Annaliese S Mason, Sheng Chen, Jun Zou","doi":"10.1016/j.jgg.2025.03.004","DOIUrl":"https://doi.org/10.1016/j.jgg.2025.03.004","url":null,"abstract":"Allopolyploids often exhibit advantages in vigor and adaptability compared to diploids. A long-term goal in the economically important Brassica genus has been to develop a new allohexaploid crop type (AABBCC) by combining different diploid and allotetraploid crop species. However, early-generation allohexaploids often face challenges like unstable meiosis and low fertility, and the phenotypic performance of these synthetic lines has rarely been assessed. This study analyzes agronomic traits, fertility, and genome stability in ArArBcBcCcCc lines derived from four crosses between B. carinata and B. rapa after 9-11 selfing generations. Our results demonstrate polyploid advantage in vigor and seed traits, considerable phenotypic variation, and high fertility and genome stability. Meanwhile, parental genotypes significantly influence outcomes in advanced allohexaploids. Structural variants, largely resulting from A-C homoeologous exchanges, contribute to genomic variation and influence hexaploid genome stability, with the A sub-genome showing the highest variability. Both positive and negative impacts of SVs on fertility and seed weight are observed. Pseudo-euploids, frequently appearing, do not significantly affect fertility or other agronomic traits compared to euploids, indicating a potential pathway toward a stable allohexaploid species. These findings provide insights into the challenge and potential for developing an adaptable and stable Brassica hexaploid through selection.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639896","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 profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-13 DOI: 10.1016/j.jgg.2025.03.005

Xiyu Tan, Wanyong Zeng, Yujian Yang, Zhansheng Lin, Fuquan Li, Jianhong Liu, Shaotong Chen, Yao-Guang Liu, Weibo Xie, Xianrong Xie

{"title":"Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations.","authors":"Xiyu Tan, Wanyong Zeng, Yujian Yang, Zhansheng Lin, Fuquan Li, Jianhong Liu, Shaotong Chen, Yao-Guang Liu, Weibo Xie, Xianrong Xie","doi":"10.1016/j.jgg.2025.03.005","DOIUrl":"https://doi.org/10.1016/j.jgg.2025.03.005","url":null,"abstract":"Short tandem repeats (STRs) modulate gene expression and contribute to trait variation. However, a systematic evaluation of the genomic characteristics of STRs has not been conducted, and their influence on gene expression in rice remains unclear. Here, we construct a map of 137,629 polymorphic STRs in the rice (Oryza sativa L.) genome using a population-scale resequencing dataset. A genome-wide survey encompassing 4,726 accessions shows that the occurrence frequency, mutational patterns, chromosomal distribution, and functional properties of STRs are correlated with the sequences and lengths of repeat motifs. Leveraging a transcriptome dataset from 127 rice accessions, we identify 44,672 expression STRs (eSTRs) by modeling gene expression in response to the length variation of STRs. These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures. Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1,726 tagged STRs that may be associated with agronomic traits. By editing the (ACT)7 STR in OsFD1 promoter, we further experimentally validate its role in regulating gene expression and phenotype. Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143634072","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 phospholipid scramblase PLSCR5 is regulated by POU4F3 and required for hair cell stereocilia homeostasis and auditory functions.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-09 DOI: 10.1016/j.jgg.2025.03.003

Sihao Gong, Qing Liu, Haibo Du, Linqing Zhang, Chengwen Zhu, Zhigang Xu, Xia Gao, Guang-Jie Zhu, Guoqiang Wan

引用次数: 0

Gap-free genome assembly and metabolomics analysis of common bean provide insights into genomic characteristics and metabolic determinants of seed coat pigmentation.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-08 DOI: 10.1016/j.jgg.2025.03.002

Bo Zhao, Hui Zhang, Qin Zhao, Rina Wu, Qian You, Bihui Wang, Yiming Wang, Zhilan Yan, Peng Wang, Chunguo Huang, Wei Zhang, Youmei Wang, Xiaopeng Hao, Jing Wu, Lixiang Wang, Zhaosheng Kong

引用次数: 0

Establishing a semi-homology-directed recombination method for precision gene integration in axolotls.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-06 DOI: 10.1016/j.jgg.2025.03.001

Liqun Wang, Yan Hu, Yuanhui Qiu, Huiting Lin, Xiang Li, Sulei Fu, Yan-Yun Zeng, Maria Ghouse, Cheng Long, Yanmei Liu, Ji-Feng Fei

{"title":"Establishing a semi-homology-directed recombination method for precision gene integration in axolotls.","authors":"Liqun Wang, Yan Hu, Yuanhui Qiu, Huiting Lin, Xiang Li, Sulei Fu, Yan-Yun Zeng, Maria Ghouse, Cheng Long, Yanmei Liu, Ji-Feng Fei","doi":"10.1016/j.jgg.2025.03.001","DOIUrl":"https://doi.org/10.1016/j.jgg.2025.03.001","url":null,"abstract":"The axolotl is broadly used in regenerative, developmental, and evolutionary biology research. Targeted gene knock-in is crucial for precision transgenesis, enabling disease modeling, visualization, tracking, and functional manipulation of specific cells or genes of interest (GOIs). Existing CRISPR/Cas9-mediated homology-independent method for gene knock-in often causes \"scars/indels\" at integration junctions. Here, we develop a CRISPR/Cas9-mediated semi-homology-directed recombination (HDR) knock-in method using a donor construct containing a single homology arm for precise GOI integration. This semi-HDR approach achieves seamless single-end integration of the Cherry reporter gene and a large inducible Cre cassette into intronless genes like Sox2 and Neurod6 in axolotls, which are challenging to modify with the homology-independent method. Additionally, we integrate the inducible Cre cassette into intron-containing loci (e.g., Nkx2.2 and FoxA2) without introducing indels via semi-HDR. GOIs are properly expressed in F0 founders, with approximately 5%-10% showing precise integration confirmed by genotyping. Furthermore, using the Nkx2.2:CreERT2 line, we fate-map spinal cord p3 neural progenitor cells, revealing that Nkx2.2+ cells adopt different lineages in development and regeneration, preferentially generating motoneurons over oligodendrocytes during regeneration. Overall, this semi-HDR method balances efficiency and precision in GOI integration, providing a valuable tool for generating knock-in axolotls and potentially extending to other species.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":""},"PeriodicalIF":6.6,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143588292","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

LG1 promotes preligule band formation through directly activating ZmPIN1 genes in maize.

IF 6.6 2区生物学

Journal of Genetics and Genomics Pub Date : 2025-03-01 Epub Date: 2025-01-27 DOI: 10.1016/j.jgg.2025.01.014

Zhuojun Zhong, Minhao Yao, Yingying Cao, Dexin Kong, Baobao Wang, Yanli Wang, Rongxin Shen, Haiyang Wang, Qing Liu

{"title":"LG1 promotes preligule band formation through directly activating ZmPIN1 genes in maize.","authors":"Zhuojun Zhong, Minhao Yao, Yingying Cao, Dexin Kong, Baobao Wang, Yanli Wang, Rongxin Shen, Haiyang Wang, Qing Liu","doi":"10.1016/j.jgg.2025.01.014","DOIUrl":"10.1016/j.jgg.2025.01.014","url":null,"abstract":"Increasing plant density is an effective strategy for enhancing crop yield per unit land area. A key architectural trait for crops adapting to high planting density is a smaller leaf angle (LA). Previous studies have demonstrated that LG1, a SQUAMOSA BINDING PROTEIN (SBP) transcription factor, plays a critical role in LA establishment. However, the molecular mechanisms underlying the regulation of LG1 on LA formation remain largely unclear. In this study, we conduct comparative RNA-seq analysis of the preligule band (PLB) region of wild type and lg1 mutant leaves. Gene Ontology (GO) term enrichment analysis reveals enrichment of phytohormone pathways and transcription factors, including three auxin transporter genes ZmPIN1a, ZmPIN1b, and ZmPIN1c. Further molecular experiments demonstrate that LG1 can directly bind to the promoter region of these auxin transporter genes and activate their transcription. We also show that double and triple mutants of these ZmPINs genes exhibit varying degrees of auricle size reduction and thus decreased LA. On the contrary, overexpression of ZmPIN1a causes larger auricle and LA. Taken together, our findings establish a functional link between LG1 and auxin transport in regulating PLB formation and provide valuable targets for genetic improvement of LA for breeding high-density tolerant maize cultivars.","PeriodicalId":54825,"journal":{"name":"Journal of Genetics and Genomics","volume":" ","pages":"356-366"},"PeriodicalIF":6.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069196","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