遗传最新文献

{"title":"Progress and challenges in human developmental cell atlas.","authors":"Yi-Chen Que, Qing-Quan Liu, Yi-Chi Xu","doi":"10.16288/j.yczz.24-153","DOIUrl":"https://doi.org/10.16288/j.yczz.24-153","url":null,"abstract":"<p><p>Illustrating molecular mechanisms of human embryonic development has always been one of the most significant challenges in biology. The scarcity of human embryo samples, the difficulty in dissecting embryo samples, and the complex structures of human organs are the major obstacles in studying human embryogenesis. In recent years, with the rapid advancement of single-cell technology, humans can systematically analyze the dynamic changes in differentiation at various stages of the central dogma and achieve observation and research with spatial information. This has accelerated the progress in constructing a human developmental cell atlas, ultimately allowing us to depict the cell ontology, fate trajectories, and three-dimensional dynamic changes of human development. In this review, we first introduce the single-cell technologies used to construct the atlas, then summarize the latest progress in human developmental cell atlas, followed by identifying the main problems and challenges in this field so far. Finally, we discuss how to utilize the human developmental cell atlas to address key biological and medical issues. This review provides guidance for the optimal use of single-cell omics technology in constructing and applying a human developmental cell atlas.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 10","pages":"760-778"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509518","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}

{"title":"Research progress on single-cell expression quantitative trait loci.","authors":"Xiao-Peng Xu, Xiao-Ying Fan","doi":"10.16288/j.yczz.24-162","DOIUrl":"https://doi.org/10.16288/j.yczz.24-162","url":null,"abstract":"<p><p>Expression quantitative trait loci (eQTL) represent genetic variants that regulate gene expression levels. eQTL analysis has become a crucial method for identifying the functional roles of disease-associated genetic variants in the post-genome-wide association study (GWAS) era, yielding numerous significant discoveries. Traditional eQTL analysis relies on whole-genome sequencing combined with bulk RNA-seq, which obscures gene expression differences between cells and thus fails to identify cell type- or state-dependent eQTL. This limitation makes it challenging to elucidate the roles of disease-associated genetic variants under specific conditions. In recent years, with the development and widespread application of single-cell RNA sequencing (scRNA-seq) technology, scRNA-seq-based eQTL (sc-eQTL) research has emerged as a focal point. The advantage of this approach lies in its ability to leverage the resolution and granularity of single-cell sequencing to uncover eQTL that are dependent on cell type, cell state, and cellular dynamics. This significantly enhances our ability to analyze genetic variants associated with gene expression. Consequently, it holds substantial significance for advancing our understanding of the formation of complex organs and the mechanisms underlying disease onset, progression, intervention, and treatment. This review comprehensively examines the recent advancements in sc-eQTL studies, focusing on their development, experimental design strategies, modeling approaches, and current challenges. The aim is to offer researchers novel perspectives for identifying disease-associated loci and elucidating gene regulatory mechanisms.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 10","pages":"795-806"},"PeriodicalIF":0.0,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509519","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}

{"title":"CRISPR/Gal4BD-Cas donor adapting systems based on miniaturized Cas proteins for improved gene editing.","authors":"Sen Yang, Bao-Xia Ma, Hong-Run Qian, Jie-Yu Cui, Xiao-Jun Zhang, Li-da Li, Ze-Hui Wei, Zhi-Ying Zhang, Jian-Gang Wang, Kun Xu","doi":"10.16288/j.yczz.24-124","DOIUrl":"https://doi.org/10.16288/j.yczz.24-124","url":null,"abstract":"<p><p>Targeted precise point editing and knock-in can be achieved by homology-directed repair(HDR) based gene editing strategies in mammalian cells. However, the inefficiency of HDR strategies seriously restricts their application in precision medicine and molecular design breeding. In view of the problem that exogenous donor DNA cannot be efficiently recruited autonomously at double-stranded breaks(DSBs) when using HDR strategies for gene editing, the concept of donor adapting system(DAS) was proposed and the CRISPR/Cas9-Gal4BD DAS was developed previously. Due to the large size of SpCas9 protein, its fusion with the Gal4BD adaptor is inconvenient for protein expression, virus vector packaging and <i>in vivo</i> delivery. In this study, two novel CRISPR/Gal4BD-SlugCas9 and CRISPR/Gal4BD-AsCas12a DASs were further developed, using two miniaturized Cas proteins, namely SlugCas9-HF derived from <i>Staphylococcus lugdunensis</i> and AsCas12a derived from <i>Acidaminococcus</i> sp<i>.</i> Firstly, the SSA reporter assay was used to assess the targeting activity of different Cas-Gal4BD fusions, and the results showed that the fusion of Gal4BD with SlugCas9 and AsCas12a N-terminals had minimal distraction on their activities. Secondly, the HDR efficiency reporter assay was conducted for the functional verification of the two DASs and the corresponding donor patterns were optimized simultaneously. The results demonstrated that the fusion of the Gal4BD adaptor binding sequence at the 5'-end of intent dsDNA template (BS-dsDNA) was better for the CRISPR/Gal4BD-AsCas12a DAS, while for the CRISPR/Gal4BD-SlugCas9 DAS, the dsDNA-BS donor pattern was recommended. Finally, CRISPR/Gal4BD-SlugCas9 DAS was used to achieve gene editing efficiency of 24%, 37% and 31% respectively for <i>EMX1, NUDT5</i> and <i>AAVS1</i> gene loci in HEK293T cells, which was significantly increased compared with the controls. In conclusion, this study provides a reference for the subsequent optimization of the donor adapting systems, and expands the gene editing technical toolbox for the researches on animal molecular design breeding.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 9","pages":"716-726"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297199","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}

{"title":"Analysis of expression characteristics and identification of interaction proteins of transcription factor BnaABI5 in <i>Brassica napus</i>.","authors":"Qian-Qian Ao, Fang-Xiao Lu, Liu-Qing Yang, Chun Li, Zeng-Kang Zhai, Dong-Ye Jia, Yuan-Qing Jiang, Bo Yang","doi":"10.16288/j.yczz.24-064","DOIUrl":"10.16288/j.yczz.24-064","url":null,"abstract":"<p><p>Rapeseed is one important oil crop in China. However, its planting benefit is frequently affected by environmental stresses such as drought in the northwest region of China. The abscisic acid(ABA) signaling pathway plays an important role in plant abiotic stress response and tolerance, and ABFs/AREBs(ABA-responsive element binding factors/ABA-responsive element binding proteins) are the core transcription factors that regulate the expression of ABA-responsive genes. To dissect the key transcription factors mediated abiotic stress, we mainly characterized abscisic acid insensitive 5(BnaABI5) in rapeseed, including its subcellular localization, expression pattern in response to various stress and tissue-specific expression analysis, transcriptional activity analysis as well as interaction screening with BnaMPKs(mitogen-activated protein kinases). Our results showed that the BnaABI5-GFP fusion protein was localized in the nucleus, and its transcript level is induced by drought stress and was mainly expressed in the roots of rapeseed. Furthermore, BnaABI5 showed transcriptional activation activity through a yeast transactivation assay and it also activated the promoter activity of <i>EM6</i> target gene in the transient expression system in tobacco leaves. Moreover, BnaABI5 interacted with BnaMPK6 and BnaMPK13 through BiFC and Y2H analysis. This study preliminarily explored the expression characteristics of transcription factor BnaABI5 and its interaction with BnaMPKs, which might help us for further understanding the function of BnaABI5.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 9","pages":"737-749"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297198","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}

{"title":"Progress on CRISPR-Cas gene editing technology in sheep production.","authors":"Dong-Xia Pan, Hui Wang, Ben-Hai Xiong, Xiang-Fang Tang","doi":"10.16288/j.yczz.24-155","DOIUrl":"https://doi.org/10.16288/j.yczz.24-155","url":null,"abstract":"<p><p>Gene editing is a kind of genetic engineering technology that can modify the genome. In recent years, with the rapid development of molecular biotechnology, the clustered regularly interspaced short palindromic repeats associated protein system has been widely used as a powerful gene editing tool due to its high efficiency, accuracy and flexibility. The CRISPR-Cas system makes a significant contribution to different aspects of livestock production by introducing site-specific modifications such as insertions, deletions or single base replacements at specific genomic sites. In terms of sheep production applications, by establishing animal models that improve production economic traits and disease resistance, the function of key genes can be studied to accelerate the improvement of traits, thereby accelerating the improvement of traits. In this review, we summarize the mechanism and function of CRISPR-Cas system and its application in the production of reproductive traits, meat use traits, wool production traits, lactation traits and disease resistance traits of sheep and the establishment of sheep animal models.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 9","pages":"690-700"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297204","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}

{"title":"Identification of a pathogenic variant and pre-implantation genetic testing for a Chinese family affected with split-hand/foot malformation.","authors":"Li-Bin Mei, Yi-Yuan Zhang, Xian-Jing Huang, Hong Ji, Ping-Ping Qiu, Lu Ding, Xuemei He, Ping Li","doi":"10.16288/j.yczz.24-141","DOIUrl":"https://doi.org/10.16288/j.yczz.24-141","url":null,"abstract":"<p><p>Split-hand/foot malformation is a serious congenital limb malformation characterized by syndactyly and underdevelopment of the phalanges and metatarsals. In this study, we reported a case of a fetus with hand-foot cleft deformity. Whole exome and Sanger sequencing were used to filter out candidate gene mutation sites and provide pre-implantation genetic testing(PGT) for family members. Genetic testing results showed that there was a homozygous mutation c.786G>A (p.Trp262*) in the fetal <i>WNT10B</i>, and both parents were carriers of heterozygous mutations. PGT results showed that out of the two blastocysts, one was a heterozygous mutant and the other was a homozygous mutant. All the embryos had diploid chromosomes. The heterozygous embryo was transferred, and a singleton pregnancy was successfully achieved. This study suggests that homozygous mutations in <i>WNT10B</i> are the likely cause of hand-foot clefts in this family. For families with monogenic diseases, preimplantation genetic testing can effectively prevent the birth of an affected child only after identifying the pathogenic mutation.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 9","pages":"750-756"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297202","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}

{"title":"Progress on deep learning in genomics.","authors":"Yan-Chun Bao, Cai-Xia Shi, Chuan-Qiang Zhang, Ming-Juan Gu, Lin Zhu, Zai-Xia Liu, Le Zhou, Feng-Ying Ma, Ri-Su Na, Wen-Guang Zhang","doi":"10.16288/j.yczz.24-151","DOIUrl":"https://doi.org/10.16288/j.yczz.24-151","url":null,"abstract":"<p><p>With the rapid growth of data driven by high-throughput sequencing technologies, genomics has entered an era characterized by big data, which presents significant challenges for traditional bioinformatics methods in handling complex data patterns. At this critical juncture of technological progress, deep learning-an advanced artificial intelligence technology-offers powerful capabilities for data analysis and pattern recognition, revitalizing genomic research. In this review, we focus on four major deep learning models: Convolutional Neural Network(CNN), Recurrent Neural Network(RNN), Long Short-Term Memory(LSTM), and Generative Adversarial Network(GAN). We outline their core principles and provide a comprehensive review of their applications in DNA, RNA, and protein research over the past five years. Additionally, we also explore the use of deep learning in livestock genomics, highlighting its potential benefits and challenges in genetic trait analysis, disease prevention, and genetic enhancement. By delivering a thorough analysis, we aim to enhance precision and efficiency in genomic research through deep learning and offer a framework for developing and applying livestock genomic strategies, thereby advancing precision livestock farming and genetic breeding technologies.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 9","pages":"701-715"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297205","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}

{"title":"Effects of <i>SvAPETALA1-5</i> gene on floral organ development in <i>Senecio vulgaris</i>.","authors":"Yu-Na Zhang, Yan-Min Hao, Min-Long Cui, Chun-Lan Piao","doi":"10.16288/j.yczz.24-147","DOIUrl":"10.16288/j.yczz.24-147","url":null,"abstract":"<p><p>Asteraceae is a large class of eudicots with complex capitulum, and little is known regarding the molecular regulation mechanism of flower development. <i>APETALA1</i>(<i>AP1</i>) belongs to the MADS-box gene family and plays a key role in plant floral induction and floral organ development. In this study, the bioinformatics and tissue-specific expression of <i>AP1</i> homologous gene <i>SvAP1-5</i> in <i>Senecio vulgaris</i> were analyzed. Based on VIGS technology, <i>SvAP1-5</i> gene silencing plants were created, and <i>SvAP1-5</i> was overexpressed in <i>Solanum nigrum</i>. The results of bioinformatics analysis showed that <i>SvAP1-5</i> gene had typical MADS-box and K-box structure, and contains FUL motif and paleoAP1 motif at the C-terminal. <i>SvAP1-5</i> belongs to the euFUL branch of <i>AP1</i> gene. qRT-PCR results showed that <i>SvAP1-5</i> was expressed in bracts, petals and carpels, and was highly expressed in carpels. Compared with the control group, <i>SvAP1-5</i> gene silencing resulted in irregular petal dehiscence, increased stigma division, and carpel dysplasia. The fruit development of <i>SvAP1-5</i> overexpressing <i>S.nigrum</i> plants was abnormal, and the hyperplastic tissue similar to fruit appeared. In summary, <i>SvAP1-5</i> gene may be involved in the development of petals and carpels and plays an important role during the development of <i>S.vulgaris</i>.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 9","pages":"727-736"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297200","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}

{"title":"Progress on <i>SOX9</i> and its enhancers in mammalian sex determination.","authors":"Min Yang, Si-Yuan Lin, Chang-Qi Yang, Yao-Sheng Chen, Zu-Yong He","doi":"10.16288/j.yczz.24-146","DOIUrl":"10.16288/j.yczz.24-146","url":null,"abstract":"<p><p>The sex determination in mammals refers to the development of an initial bipotential organ, termed the bipotential gonad/genital ridge, into either a testis or an ovary at the early stages of embryonic development, under the precise regulation of transcription factors. SOX9 (SRY-box transcription factor 9) is a multifunctional transcription factor in mammalian development and plays a critical role in sex determination and subsequent male reproductive organs development. Recent studies have shown that several enhancers upstream of <i>SOX9</i> also play an important role in the process of sex determination. In this review, we summarize the progress on the role of <i>SOX9</i> and its gonadal enhancers in sex determination. This review will facilitate to understand the regulatory mechanism of sex determination of <i>SOX9</i> and provides a theoretical basis for the further development of animal sex manipulation technologies.</p>","PeriodicalId":35536,"journal":{"name":"遗传","volume":"46 9","pages":"677-689"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297203","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}

{"title":"Genetic diseases are not necessarily inherited: suggestion on its Chinese translation.","authors":"Pan-Hui Tian, Yue Xu, Yong-Qing Zhang, Tian-Yun Wang","doi":"10.16288/j.yczz.24-199","DOIUrl":"https://doi.org/10.16288/j.yczz.24-199","url":null,"abstract":"<p><p>From Mendel's discovery of the basic laws of genetics in 1865 to the widespread application of genomics in medicine today, medical genetics has made enormous progress, and the concept of genetic diseases has also been evolved. In 1972, the World Health Organization (WHO) expert group began to use \"Genetic Disease\" to define hereditary diseases, while early Chinese genetics textbooks used \"inferior inheritance\", and later introduced terms such as \"Genetic Disease\" and \"Inherited Disease\". In the early days, it was generally believed that genetic diseases were inherited from ancestors. However, research in recent years has found that genetic diseases are not necessarily inherited, and some diseases are actually caused by <i>de novo</i> mutations in the offspring. Although the occurrence of this type of genetic disease is related to genetic factors, it is not inherited from ancestors. If we still use \"Inherited Disease\" or \"Hereditary Disease\" to describe it, it is not accurate enough. In order to further standardize the translation and use of the concept of \"Genetic Disease\", this article briefly reviews its development process in both English and Chinese literature, discusses the difference between different Chinese translations, and provides guidance and suggestions for scientifically and accurately describing genetic diseases in Chinese, with a view to promote efficient exchange and cooperation in the field of medical genetics.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":"46 9","pages":"673-676"},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142297201","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}