Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-08-01 DOI: 10.16288/j.yczz.24-149

Ji-Long Wang, Qing Li, Ting-Zheng Zhan

{"title":"Principle and application of self-transcribing active regulatory region sequencing in enhancer discovery research.","authors":"Ji-Long Wang, Qing Li, Ting-Zheng Zhan","doi":"10.16288/j.yczz.24-149","DOIUrl":"https://doi.org/10.16288/j.yczz.24-149","url":null,"abstract":"Self-transcribing active regulatory region sequencing (STARR-seq) is a high-throughput sequencing method capable of simultaneously discovering and validating all enhancers within the genome. In this method, candidate sequences are inserted into plasmid vectors and electroporated into cells. Acting as both enhancers and target genes, the self-transcription of these sequences will also be enhanced by themselves. By sequencing the transcriptome and comparing the results with the non-inserted control, the locations and activity of enhancers can be determined. In traditional enhancer discovery strategies, the chromatin open regions and transcription active regions were sequenced and predicted as enhancers. However, the activity of these putative enhancers could only be validated one by one without a high-throughput method. STARR-seq solved this limitation, allowing simultaneous enhancers discovery and activity validation in a high-throughput manner. Since the introduction of STARR-seq, it has been widely used to discover enhancers and validate enhancer activity in a number of organisms and cells. In this review, we present the traditional enhancer prediction methods and the basic principles, development history, specific applications of STARR-seq, and its future prospects, aiming to provide a reference for researchers in related fields conducting enhancer studies.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 8","pages":"589-602"},"PeriodicalIF":0.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141976790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Effects of functional defects in the NMD pathway on rice phenotype and transcriptome. NMD 通路功能缺陷对水稻表型和转录组的影响

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-063

Yue-Yang Wu, Xiao-Yan Zhou, Yu-Feng Wu, Ju Huang

{"title":"Effects of functional defects in the NMD pathway on rice phenotype and transcriptome.","authors":"Yue-Yang Wu, Xiao-Yan Zhou, Yu-Feng Wu, Ju Huang","doi":"10.16288/j.yczz.24-063","DOIUrl":"https://doi.org/10.16288/j.yczz.24-063","url":null,"abstract":"Nonsense-mediated mRNA decay (NMD) is an important RNA quality control pathway. It aids in degrading harmful erroneous mRNA, thereby preserving a stable and healthy internal environment. In this study, we employed CRISPR/Cas9 and amiRNA technology to generate knock out or knock down mutants of realted genes in the rice NMD pathway. Through transcriptome sequencing and observing phenotype changes, the study explored the impact of NMD pathway defects on rice gene expression and alternative splicing. The results suggest that even partial defects will induce phenotypic changes such as plant height and pollen vitality to different degrees, showing necessity of NMD factors. Gene expression analysis reveals that most differentially expressed genes are upregulated in the mutants, with ko-upf1-like and kd-upf1 defects having a more significant impact than kd-upf2 and kd-upf3. Specifically, NMD pathway defects result in increased expression levels of rice defense response-related genes and decreased expression levels of secondary metabolism-related genes, with a wider range of affected genes observed in 60-day-old senescence mutants. Transcript analysis indicates that different NMD related genes defects alter hundreds of alternative splicing events, mostly enriched in genes involving alternative splicing regulatory pathways. Approximately half of these events are shared among different mutants, and a substantial number of affected transcripts show NMD target features. NMD could affect both the transcript abundance and their splicing subtypes to regulate the defense response and early-senescence associated pathways, which plays a vital role in rice growth and reproduction.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 7","pages":"540-551"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrating mRNA transcripts and genomic information into genomic prediction. 将 mRNA 转录本和基因组信息整合到基因组预测中。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-096

Yu-Long Hu, Fang Yang, Yan-Tong Chen, Shuo-Kai Shen, Yu-Bo Yan, Yue-Bo Zhang, Xiao-Lin Wu, Jia-Ming Wang, Jun He, Ning Gao

{"title":"Integrating mRNA transcripts and genomic information into genomic prediction.","authors":"Yu-Long Hu, Fang Yang, Yan-Tong Chen, Shuo-Kai Shen, Yu-Bo Yan, Yue-Bo Zhang, Xiao-Lin Wu, Jia-Ming Wang, Jun He, Ning Gao","doi":"10.16288/j.yczz.24-096","DOIUrl":"https://doi.org/10.16288/j.yczz.24-096","url":null,"abstract":"Genomic prediction has emerged as a pivotal technology for the genetic evaluation of livestock, crops, and for predicting human disease risks. However, classical genomic prediction methods face challenges in incorporating biological prior information such as the genetic regulation mechanisms of traits. This study introduces a novel approach that integrates mRNA transcript information to predict complex trait phenotypes. To evaluate the accuracy of the new method, we utilized a Drosophila population that is widely employed in quantitative genetics researches globally. Results indicate that integrating mRNA transcript data can significantly enhance the genomic prediction accuracy for certain traits, though it does not improve phenotype prediction accuracy for all traits. Compared with GBLUP, the prediction accuracy for olfactory response to dCarvone in male Drosophila increased from 0.256 to 0.274. Similarly, the accuracy for cafe in male Drosophila rose from 0.355 to 0.401. The prediction accuracy for survival_paraquat in male Drosophila is improved from 0.101 to 0.138. In female Drosophila, the accuracy of olfactory response to 1hexanol increased from 0.147 to 0.210. In conclusion, integrating mRNA transcripts can substantially improve genomic prediction accuracy of certain traits by up to 43%, with range of 7% to 43%. Furthermore, for some traits, considering interaction effects along with mRNA transcript integration can lead to even higher prediction accuracy.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 7","pages":"560-569"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Classification accuracy of machine learning algorithms for Chinese local cattle breeds using genomic markers. 利用基因组标记对中国地方牛种进行机器学习算法分类的准确性。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-059

Hui Liang, Xue Wang, Jing-Fang Si, Yi Zhang

{"title":"Classification accuracy of machine learning algorithms for Chinese local cattle breeds using genomic markers.","authors":"Hui Liang, Xue Wang, Jing-Fang Si, Yi Zhang","doi":"10.16288/j.yczz.24-059","DOIUrl":"https://doi.org/10.16288/j.yczz.24-059","url":null,"abstract":"Accurate breed classification is required for the conservation and utilization of farm animal genetic resources. Traditional classification methods mainly rely on phenotypic characterization. However, it is difficult to distinguish between the highly similar breeds due to the challenges in qualifying the phenotypic character. Machine learning algorithms show unique advantages in breed classification using genomic information. To evaluate the classification methods for Chinese cattle breeds, this study utilized genomic SNP data from 213 individuals across seven Chinese local breeds and compared the classification accuracies of three feature selection methods (FST value sorting and screening, mRMR, and Relief-F) and three machine learning algorithms (Random Forest, Support Vector Machine, and Naive Bayes). Results showed that: 1) using the FST method to screen more than 1500 SNPs, or using the mRMR algorithm to screen more than 1000 SNPs, the SVM classification algorithm can achieve more than 99.47% classification accuracy; 2) the most effective algorithm was SVM, followed by NB, while the best SNP selection method was FST and mRMR, followed by Relief-F; 3) species misclassification often occurs between breeds with high similarity. This study demonstrates that machine learning classification models combined with genomic data are effective methods for the classification of local cattle breeds, providing a technical basis for the rapid and accurate classification of cattle breeds in China.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 7","pages":"530-539"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627935","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Teaching genetics with integrative thoughts of conservation biology. 用保护生物学的综合思想教授遗传学。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-127

Jian-Qing Lin, Shao-Pan Ye, Shu-Qi Wang, Hong Du

引用次数: 0

Research progress on the effect of sperm chromatin integrity on function and its detection methods. 精子染色质完整性对功能的影响及其检测方法的研究进展。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-106

Daiyuan Liu, Zhao-Hui Zhang, Xian-Jiang Kang

引用次数: 0

A case study of Duchenne muscular dystrophy caused by Alu element insertion in DMD gene and analysis of its gray-hair symptoms. 由 DMD 基因中的 Alu 元素插入引起的杜兴氏肌肉萎缩症病例研究及其灰发症状分析。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-020

Hui Li, Ru-Yi Zhang, Chang-Ye Li, Xiao-Lin Zhang, Qing-Yin Zheng, Xiu-Zhen Liu

{"title":"A case study of Duchenne muscular dystrophy caused by Alu element insertion in DMD gene and analysis of its gray-hair symptoms.","authors":"Hui Li, Ru-Yi Zhang, Chang-Ye Li, Xiao-Lin Zhang, Qing-Yin Zheng, Xiu-Zhen Liu","doi":"10.16288/j.yczz.24-020","DOIUrl":"10.16288/j.yczz.24-020","url":null,"abstract":"Duchenne muscular dystrophy (DMD) is a severe X-linked recessive genetic disorder caused by mutations in the DMD gene, which leads to a deficiency of the dystrophin protein. The main mutation types of this gene include exon deletions and duplications, point mutations, and insertions. These mutations disrupt the normal expression of dystrophin, ultimately leading to the disease. In this study, we reported a case of DMD caused by an insertion mutation in exon 59 (E59) of the DMD gene. The affected child exhibited significant abnormalities in related biochemical markers, early symptoms of DMD, and multiple gray hair. His mother and sister were carriers with slightly abnormal biochemical markers. The mother had mild clinical symptoms, while the sister had no clinical symptoms. Other family members were genetically and physically normal. Sequencing and sequence alignment revealed that the inserted fragment was an Alu element from the AluYa5 subfamily. This insertion produced two stop codons and a polyadenylate (polyA) tail. To understand the impact of this insertion on the DMD gene and its association with clinical symptoms, exonic splicing enhancer (ESE) prediction indicated that the insertion did not affect the splicing of E59. Therefore, we speculated that the insertion sequence would be present in the mRNA sequence of the DMD gene. The two stop codons and polyA tail likely terminate translation, preventing the production of functional dystrophin protein, which may be the mechanism leading to DMD. In addition to typical DMD symptoms, the child also exhibited premature graying of hair. This study reports, for the first time, a case of DMD caused by the insertion of an Alu element into the coding region of the DMD gene. This finding provides clues for studying gene mutations induced by Alu sequence insertion and expands the understanding of DMD gene mutations.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 7","pages":"570-580"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The effect of centromere protein Fta2 phosphorylation during meiosis. 减数分裂过程中中心粒蛋白 Fta2 磷酸化的影响

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-07-01 DOI: 10.16288/j.yczz.24-038

Zi-Han Ni, Yu Min, Ling-Ling Ma, Yoshinori Watanabe

{"title":"The effect of centromere protein Fta2 phosphorylation during meiosis.","authors":"Zi-Han Ni, Yu Min, Ling-Ling Ma, Yoshinori Watanabe","doi":"10.16288/j.yczz.24-038","DOIUrl":"10.16288/j.yczz.24-038","url":null,"abstract":"During meiosis, defects in cohesin localization within the centromere region can result in various diseases. Accurate cohesin localization depends on the Mis4-Ssl3 loading complex. Although it is known that cohesin completes the loading process with the help of the loading complex, the mechanisms underlying its localization in the centromere region remain unclear. Previous studies suggest cohesin localization in the centromere is mediated by phosphorylation of centromeric proteins. In this study, we focused on the Fta2 protein, a component of the Sim4 centromere protein complex. Using bioinformatics methods, potential phosphorylation sites were identified, and fta2-9A and fta2-9D mutants were constructed in Schizosaccharomyces pombe. The phenotypes of these mutants were characterized through testing thiabendazole (TBZ) sensitivity and fluorescent microscopy localization. Results indicated that Fta2 phosphorylation did not impact mitosis but affected chromosome segregation during meiosis. This study suggests that Fta2 phosphorylation is vital for meiosis and may be related to the specific localization of cohesin during this process.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 7","pages":"552-559"},"PeriodicalIF":0.0,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141627940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Il34 rescues metronidazole-induced impairment of spinal cord regeneration in zebrafish central nervous system. Il34能挽救甲硝唑诱导的斑马鱼中枢神经系统脊髓再生障碍。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-06-20 DOI: 10.16288/j.yczz.24-083

Ji-Xiang Liu, Si-Ting Lai, Jing Bai, Jin Xu

{"title":"Il34 rescues metronidazole-induced impairment of spinal cord regeneration in zebrafish central nervous system.","authors":"Ji-Xiang Liu, Si-Ting Lai, Jing Bai, Jin Xu","doi":"10.16288/j.yczz.24-083","DOIUrl":"10.16288/j.yczz.24-083","url":null,"abstract":"Metronidazole (MTZ), a commonly used anti-infective drug in clinical practice, has also been employed as a prodrug in cell-targeted ablation systems in scientific research, exhibiting significant application value. However, it has been demonstrated that MTZ can induce neurotoxic symptoms to some extent during its use, and there is currently a lack of effective means to circumvent its toxicity in both clinical and research settings, which limits its application. Therefore, exploring the specific mechanisms underlying MTZ-induced neurotoxic symptoms and elucidating countermeasures will enhance the practical value of MTZ. In this study, using a zebrafish spinal cord injury regeneration model, we confirmed that MTZ neurotoxicity leads to impaired axon regeneration in the central nervous system. By overexpressing il34 in the central nervous system of zebrafish, we eliminated the inhibitory effect of MTZ on axonal regeneration and demonstrated that the pro-regenerative effect against MTZ neurotoxicity is not caused by excessive macrophages/microglia chemoattracted by interleukin 34(Il34). Transcriptome sequencing analysis and GO enrichment analysis of differentially expressed genes between groups revealed that Il34 may counteract MTZ neurotoxicity and promote spinal cord injury repair through biological processes that enhance cellular adhesion and cell location. In summary, our work uncovers a possible cause of MTZ neurotoxicity and provides a new perspective for eliminating MTZ toxicity.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 6","pages":"478-489"},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141421209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Retraction notice to "Tip60-FOXO regulates JNK signaling mediated apoptosis in Drosophila" [Yi Chuan 46(6) (2024) 490-501]. Tip60-FOXO调控果蝇中JNK信号介导的细胞凋亡》的撤稿通知[《易传》46(6) (2024) 490-501]。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-06-20 DOI: 10.16288/j.yczz.24-095

引用次数: 0

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