Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-03-20 DOI: 10.16288/j.yczz.23-268

Yi Zhu, Xue-Qin Chen, Li-Zhi Leng, Ge Lin

{"title":"Early embryonic polarity establishment and implications for lineage differentiation.","authors":"Yi Zhu, Xue-Qin Chen, Li-Zhi Leng, Ge Lin","doi":"10.16288/j.yczz.23-268","DOIUrl":"10.16288/j.yczz.23-268","url":null,"abstract":"Polarity establishment is one of the key factors affecting early embryonic development. Polarity establishment begins with myosin phosphorylation in the 8-cell embryo, and phosphorylation activates actin leading to its initiation of contractility. Subsequently, actin undergoes reorganization to form an apical domain rich in microvilli on the non-contacting surface of each blastomere, and form the actomyosin ring that marks the maturation of the apical domain in conjunction with polar protein complexes and others. From the process of polarity establishment, it can be seen that the formation of the apical domain is influenced by actin-related proteins and polar protein complexes. Some zygote genome activation (ZGA) and lineage-specific genes also regulate polarity establishment. Polarity establishment underlies the first cell lineage differentiation during early embryonic development. It regulates lineage segregation and morphogenesis by affecting asymmetric cell division, asymmetric localization of lineage differentiation factors, and activity of the Hippo signaling pathway. In this review, we systematically summarize the mechanisms of early embryonic polarity establishment and its impact on lineage differentiation in mammals, and discuss the shortcomings of the currently available studies in terms of regulatory mechanisms and species, thereby providing clues and systematic perspectives for elucidating early embryonic polarity establishment.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 3","pages":"199-208"},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140867434","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

Frontiers of soybean pan-genome studies. 大豆泛基因组研究的前沿。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-03-20 DOI: 10.16288/j.yczz.23-321

Yu-Cheng Liu, Yan-Ting Shen, Zhi-Xi Tian

{"title":"Frontiers of soybean pan-genome studies.","authors":"Yu-Cheng Liu, Yan-Ting Shen, Zhi-Xi Tian","doi":"10.16288/j.yczz.23-321","DOIUrl":"10.16288/j.yczz.23-321","url":null,"abstract":"Artificial domestication provided the original motivation to the blooming of agriculture, following with the dramatic change of the genetic background of crops and livestock. According to theory and technology upgradation that contributing to the omics, we appreciate using the pan-genome instead of single reference genome for crop study. By comparison and integration of multiple genomes under the guidance of pan-genome theory, we can estimate the genomic information range of a species, leading to a global understanding of its genetic diversity. Combining pan-genome with large size chromosomal structural variations, high throughput population resequencing, and multi-omics data, we can profoundly study the genetic basis behind species traits we focus on. Soybean is one of the most important commercial crops over the world. It is also essential to our food security. Dissecting the formation of genetic diversity and the causal loci of key agricultural traits of soybean will make the modern soybean breeding more efficiently. In this review, we summarize the core idea of pan-genome and clarified the characteristics of construction strategies of pan-genome such as de novo/mapping assembly, iterative assembly and graph-based genome. Then we used the soybean pan-genome work as a case study to introduce the general way to study pan-genome. We highlighted the contribution of structural variation (SV) to the evolution/domestication of soybean and its value in understanding the genetic bases of agronomy traits. By those, we approved the value of graph-based pan-genome for data integration and SV calculation. Future research directions are also discussed for crop genomics and data science.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 3","pages":"183-198"},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140867595","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

N⁶-adenosine methylation and the regulatory mechanism on LINE-1. N6-腺苷甲基化与 LINE-1 的调控机制

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-03-20 DOI: 10.16288/j.yczz.23-248

Ao Zhang, Shan Cen, Xiao-Yu Li

{"title":"N6-adenosine methylation and the regulatory mechanism on LINE-1.","authors":"Ao Zhang, Shan Cen, Xiao-Yu Li","doi":"10.16288/j.yczz.23-248","DOIUrl":"10.16288/j.yczz.23-248","url":null,"abstract":"Long interspersed elements-1(LINE-1) is the only autonomous transposon in human genome，and its retrotransposition results in change of cellular genome structure and function, leading occurrence of various severe diseases. As a central key intermediated component during life cycle of LINE-1 retrotransposition, the host modification of LINE-1 mRNA affects the LINE-1 transposition directly. N6-adenosine methylation(m6A), the most abundant epigenetic modification on eukaryotic RNA, is dynamically reversible. m6A modification is also found on LINE-1 mRNA, and it participants regulation of the whole LINE-1 replication cycle, with affecting LINE-1 retrotransposition as well as its adjacent genes expression, followed by influencing genomic stability, cellular self-renewal, and differentiation potential, which plays important roles in human development and diseases. In this review, we summarize the research progress in LINE-1 m6A modification, including its modification positions, patterns and related mechanisms, hoping to provide a new sight on the mechanism research and treatment of related diseases.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 3","pages":"209-218"},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140872170","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

Effect of mutation at c.493T>C locus of transcription factor HNF1α gene on its protein level. 转录因子 HNF1α 基因 c.493T>C 位点突变对其蛋白水平的影响

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-03-20 DOI: 10.16288/j.yczz.23-274

Shu-Jie Liang, Yi-Hua Peng, Jia-Hong Lei, Ai-Min Jia, Hong Jiang, Yan Cai

{"title":"Effect of mutation at c.493T>C locus of transcription factor HNF1α gene on its protein level.","authors":"Shu-Jie Liang, Yi-Hua Peng, Jia-Hong Lei, Ai-Min Jia, Hong Jiang, Yan Cai","doi":"10.16288/j.yczz.23-274","DOIUrl":"10.16288/j.yczz.23-274","url":null,"abstract":"Hepatocyte nuclear factor 1α (HNF1α) is a transcription factor that is crucial for the regulation to maintain the function of pancreatic β-cell, hepatic lipid metabolism, and other processes. Mature-onset diabetes of the young type 3 is a monogenic form of diabetes caused by HNF1α mutations. Although several mutation sites have been reported, the specific mechanisms remain unclear, such hot-spot mutation as the P291fsinsC mutation and the P112L mutation and so on. In preliminary studies, we discovered one MODY3 patient carrying a mutation at the c.493T>C locus of the HNF1α gene. In this study, we analyzed the pathogenic of the mutation sites by using the Mutation Surveyor software and constructed the eukaryotic expression plasmids of the wild-type and mutant type of HNF1α to detect variations in the expression levels and stability of HNF1α protein by using Western blot. The analyses of the Mutation Surveyor software showed that the c.493T>C site mutation may be pathogenic gene and the results of Western blot showed that both the amount and stability of HNF1α protein expressed by the mutation type plasmid were reduced significantly compared to those by the wild type plasmid (P<0.05). This study suggests that the c.493T>C (p.Trp165Arg) mutation dramatically impacts HNF1α expression, which might be responsible for the development of the disease and offers fresh perspectives for the following in-depth exploration of MODY3's molecular pathogenic process.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 3","pages":"256-262"},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140871065","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

Progress on CRISPR/Cas9 system in the genetic improvement of livestock and poultry. CRISPR/Cas9 系统在畜禽遗传改良方面的进展。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-03-20 DOI: 10.16288/j.yczz.24-021

Yan-Chun Bao, Ling-Li Dai, Zai-Xia Liu, Feng-Ying Ma, Yu Wang, Yong-Bin Liu, Ming-Juan Gu, Ri-Su Na, Wen-Guang Zhang

引用次数: 0

Generation and analysis of TPI deficiency zebrafish model. 生成并分析 TPI 缺乏症斑马鱼模型。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-03-20 DOI: 10.16288/j.yczz.23-316

Piao Sun, Ying Li, Fan Liu, Lu Wang

引用次数: 0

Genome-wide identification of GRF transcription factors and their expression profile in stem meristem of broomcorn millet (Panicum miliaceum L.). GRF转录因子的全基因组鉴定及其在锦鸡儿粟（Panicum miliaceum L.）茎分生组织中的表达谱。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-03-20 DOI: 10.16288/j.yczz.23-210

Heng Wei, Tian-Peng Liu, Ji-Hong He, Kong-Jun Dong, Rui-Yu Ren, Lei Zhang, Ya-Wei Li, Zi-Yi Hao, Tian-Yu Yang

{"title":"Genome-wide identification of GRF transcription factors and their expression profile in stem meristem of broomcorn millet (Panicum miliaceum L.).","authors":"Heng Wei, Tian-Peng Liu, Ji-Hong He, Kong-Jun Dong, Rui-Yu Ren, Lei Zhang, Ya-Wei Li, Zi-Yi Hao, Tian-Yu Yang","doi":"10.16288/j.yczz.23-210","DOIUrl":"10.16288/j.yczz.23-210","url":null,"abstract":"To understand the genome-wide information of the GRF family genes in broomcorn millet and their expression profile in the vegetative meristems, bioinformatic methods and transcriptome sequencing were used to analyze the characteristics, physical and chemical properties, phylogenetic relationship, chromosome distribution, gene structure, cis-acting elements and expression profile in stem meristem for the GRF family members. The results showed that the GRF gene family of millet contains 21 members, and the PmGRF gene is unevenly distributed on 12 chromosomes. The lengths of PmGRF proteins vary from 224 to 618 amino acids, and the isoelectric points are between 4.93-9.69. Each member of the family has 1-4 introns and 2-5 exons. The protein PmGRF13 is localized in both the nucleus and chloroplast, and the rest PmGRF proteins are located in the nucleus. Phylogenetic analysis showed that the 21 GRF genes were divided into 4 subfamilies (A,B,C and D) in broomcorn millet. The analysis of cis-acting elements showed that there were many cis-acting elements involved in light response, hormone response, drought induction, low temperature response and other environmental stress responses in the 2000 bp sequence upstream of the GRF genes. Transcriptome sequencing and qRT-PCR analyses showed that the expression levels of PmGRF3 and PmGRF12 in the dwarf variety Zhang778 were significantly higher than those of the tall variety Longmi12 in the internode and node meristems at the jointing stage, while the expression patterns of PmGRF4, PmGRF16 and PmGRF21 were reverse. In addition, the expression levels of PmGRF2 and PmGRF5 in the internode of Zhang778 were significantly higher than Longmi12. The other GRF genes were not or insignificantly expressed. These results indicated that seven genes, PmGRF2, PmGRF3, PmGRF4, PmGRF5, PmGRF12, PmGRF16 and PmGRF21, were related to the formation of plant height in broomcorn millet.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 3","pages":"242-255"},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140868314","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

Progress on the quality control technology of next generation sequencing library. 新一代测序文库质量控制技术的进展。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-02-20 DOI: 10.16288/j.yczz.23-262

Meng-Nan Cui, Yan Guo, Ya-Rong Wu, Guang-Qian Pei, Yu-Jun Cui

{"title":"Progress on the quality control technology of next generation sequencing library.","authors":"Meng-Nan Cui, Yan Guo, Ya-Rong Wu, Guang-Qian Pei, Yu-Jun Cui","doi":"10.16288/j.yczz.23-262","DOIUrl":"10.16288/j.yczz.23-262","url":null,"abstract":"As a key supporting technology in the fields of life sciences and medicine, high-throughput sequencing has developed rapidly and become increasingly mature. The workflow of this technology can be divided into nucleic acid extraction, library construction, sequencing, and data analysis. Among these, library construction is a pivotal step that bridges the previous and subsequent stages. The effectiveness of library construction is contingent on the quality of upstream samples and also impacts the data analysis following sequence data output. The selection and implementation of library construction quality control techniques are crucial for enhancing the reliability of results and reducing errors in sequencing data. This review provides an in-depth discussion of library construction quality control techniques, summarizing and evaluating their principles, advantages and disadvantages, and applicability. It also discusses the selection of relevant technologies in practical application scenarios. The aim is to offer theoretical foundations and references for researchers, disease prevention and control personnel, and others when choosing library quality control techniques, thereby promoting the quality and efficiency of high-throughput sequencing work.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"140-148"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716483","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

Choroid plexus and its relations with age-related diseases. 脉络丛及其与老年性疾病的关系。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-02-20 DOI: 10.16288/j.yczz.23-294

Yun-Fei Yang, Yi-Dong Shen

引用次数: 0

Application of next-generation sequencing in the detection of low-abundance mutations. 应用新一代测序技术检测低丰度突变。

Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji Pub Date : 2024-02-20 DOI: 10.16288/j.yczz.23-309

Yang Luan, Xin-Yue You, Jin Yang

{"title":"Application of next-generation sequencing in the detection of low-abundance mutations.","authors":"Yang Luan, Xin-Yue You, Jin Yang","doi":"10.16288/j.yczz.23-309","DOIUrl":"10.16288/j.yczz.23-309","url":null,"abstract":"Mutation accumulation in somatic cells contributes to cancer development, aging and many non-malignant diseases. The true mutation frequency in normal cells is extremely low, which presents a challenge in detecting these mutations at such low frequencies. The emergence of next-generation sequencing (NGS) technology enables direct detection of rare mutations across the entire genome of any species. This breakthrough overcomes numerous limitations of traditional mutation detection techniques that rely on specific detection models and sites. However, conventional NGS is limited in its application for detecting low-frequency mutations due to its high sequencing error rate. To address this challenge, high-accuracy NGS sequencing techniques based on molecular consensus sequencing strategies have been developed. These techniques have the ability to correct sequencing errors, resulting in error rates lower than 10-7, are expected to serve as effective tools for low-frequency mutation detection. Error-corrected NGS (ecNGS) techniques hold great potential in various areas, including safety evaluation and research on environmental mutagens, risk assessment of cell and gene therapy drugs, population health risk monitoring, and fundamental research in life sciences. This review highlights a comprehensive review of the research progress in low-frequency mutation detection techniques based on NGS, and provides a glimpse into their potential applications. It also offers an outlook on the potential applications of these techniques, thereby providing valuable insights for further development, research, and application of this technology in relevant fields.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 2","pages":"126-139"},"PeriodicalIF":0.0,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139716468","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

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