Article
Reproductive Biology
Gyeong-Min Gim, Kyeong-Hyun Uhm, Dong-Hyeok Kwon, Min-Ji Kim, Dae-Jin Jung, Dae-Hyun Kim, Jun-Koo Yi, Jae-Jung Ha, Soo-Young Yum, Woo-Jae Son, Ji-Hyun Lee, Ji-Hyun Park, Kil-Young Song, Won-Wu Lee, Goo Jang
Summary: This study assessed the germline transmission of MSTN mutations in F0 cattle and demonstrated successful transmission of the mutations to the next generation. Additionally, the study showed the possibility of further gene editing using electroporation in embryos fertilized with the mutant sperms.
Article
Cell Biology
Yukiko U. Inoue, Yuki Morimoto, Mayumi Yamada, Ryosuke Kaneko, Kazumi Shimaoka, Shinji Oki, Mayuko Hotta, Junko Asami, Eriko Koike, Kei Hori, Mikio Hoshino, Itaru Imayoshi, Takayoshi Inoue
Summary: Fluorescent reporter mouse lines and Cre/Flp recombinase driver lines are essential for investigating molecular functions in vivo. The study reverified and optimized the phospho-PCR method to obtain highly pure long ssDNAs for knock-in mouse generation, enabling successful generation of knock-in mice through microinjection and electroporation methods, thus broadening its applicability.
Article
Chemistry, Analytical
Xianfeng Wang, Xiaolong Chen, Chengxiang Chu, Yuanyi Deng, Mei Yang, Danqun Huo, Faliang Xu, Changjun Hou, Jiayi Lv
Summary: Cas-G4EX is a novel method for detecting single-stranded nucleic acids, combining the advantages of CRISPR/Cas9 and EXPAR, with outstanding site-specific recognition and high-performance amplification efficiency, applicable for the detection of any ssRNA or ssDNA. The method exhibits excellent discrimination for single-base mutation of single-stranded nucleic acids, providing a promising platform for applications in molecular diagnosis and pathological analysis.
Article
Biotechnology & Applied Microbiology
Tony P. Huang, Zachary J. Heins, Shannon M. Miller, Brandon G. Wong, Pallavi A. Balivada, Tina Wang, Ahmad S. Khalil, David R. Liu
Summary: Directed evolution has been used to create new compact Cas9 variants that can target most pyrimidine-rich PAM sequences. These variants were evolved using phage-assisted noncontinuous evolution and eVOLVER-supported phage-assisted continuous evolution. The resulting variants showed improved target specificity and activity in human cells compared to existing variants.
NATURE BIOTECHNOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Ying-Ying Zhang, Pu-Feng Du
Summary: The essentiality of genes can be defined at different levels and is context-dependent. While the essentiality of protein-coding genes has been well studied, the essentiality of non-coding genes remains poorly characterized. Experimental technologies like CRISPR-Cas9 provide insights into non-coding regions, but assessing the essentiality of non-coding genes in different contexts is still challenging. Machine learning algorithms have been successful in estimating the essentiality of protein-coding genes, but the development of algorithms for non-coding genes is in its early stages. Recent studies suggest that the essentiality of non-coding genes will be a new and fertile ground in bioinformatics, and this perspective article outlines potential research topics.
CURRENT BIOINFORMATICS
(2023)
Review
Genetics & Heredity
Qing Rex Lyu, Shikuan Zhang, Zhe Zhang, Zhiyu Tang
Summary: An effective loss-of-function study is necessary to investigate the biological function of lncRNA, and CRISPR-based genome editing is the most widely used method for inactivating lncRNA function at the genomic level. However, the complex genomic interplay between lncRNA and neighbor genes makes it challenging to accurately interpret lncRNA function. This article discusses the advantages and disadvantages of different lncRNA knockout methods and envisions potential future directions for lncRNA functional study.
FRONTIERS IN GENETICS
(2023)
Article
Cell Biology
Deshani C. Ranawakage, Keita Okada, Kota Sugio, Yuya Kawaguchi, Yuki Kuninobu-Bonkohara, Takuya Takada, Yusuke Kamachi
Summary: This study successfully demonstrated precise gene knock-ins with composite tags in the zebrafish genome using CRISPR-Cas9 technology, highlighting the importance of the structural and sequence characteristics of the donor templates for efficient knock-in.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chaya T. L. Yuen, Dawn G. L. Thean, Becky K. C. Chan, Peng Zhou, Cynthia C. S. Kwok, Hoi Yee Chu, Maggie S. H. Cheung, Bei Wang, Yee Man Chan, Silvia Y. L. Mak, Anskar Y. Leung, Gigi C. G. Choi, Zongli Zheng, Alan S. L. Wong
Summary: Researchers have enhanced editing accuracy and reduced off-target edits by re-engineering KKH-SaCas9 with a Y239H mutation and a set of additional mutations, demonstrating the feasibility of multi-domain combinatorial mutagenesis to optimize editing fidelity.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Jianli Shi, Shuxuan Zheng, Xiaoyan Wu, Zhe Peng, Chen Li, Shuo Wang, Changxun Xin, Shaojian Xu, Jun Li
Summary: The study successfully edited the PCV2 genome using the CRISPR/Cas9 system, suppressing its replication in cells; some sgRNAs efficiently edited the genome while others did not; these findings suggest that the CRISPR/Cas9 system may be a new approach in combating PCV2 infection in the future.
MOLECULAR IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yi-Li Feng, Si-Cheng Liu, Ruo-Dan Chen, Xiu-Na Sun, Jing-Jing Xiao, Ji-Feng Xiang, An-Yong Xie
Summary: In CRISPR/Cas9 genome editing, dCas9 can be loaded onto a DSB-adjacent site to stimulate HDR and suppress c-NHEJ, providing a control over genome editing. This method can increase HDR-mediated CRISPR genome editing without exacerbating off-target effects.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Cell Biology
Tian Tian, Xuanye Cao, Yongyan Chen, Lei Jin, Zhiwen Li, Xiao Han, Ying Lin, Bogdan J. Wlodarczyk, Richard H. Finnell, Zhengwei Yuan, Linlin Wang, Aiguo Ren, Yunping Lei
Summary: This study identified functional variants of MED genes associated with the etiology of some NTDs. Cellular functional studies showed that MED12 gene mutation affected the regulation of MED12 on the canonical-WNT signaling pathway. A Med12 p.Arg1784Cys knock-in mouse model exhibited exencephaly and spina bifida, validating the human findings in mice using CRISPR/Cas9 technology.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Barbora Vesela, Michael Killinger, Kamila Rihova, Petr Benes, Eva Svandova, Adela Kratochvilova, Filip Trcka, Karel Kleparnik, Eva Matalova
Summary: In this study, caspase-8 was eliminated in MC3T3-E1 cells using CRISPR/cas9 technology, and the consequences of caspase-8 deficiency on non-apoptotic pathways in osteoblastic cells were investigated. The results showed that caspase-8 deficiency inhibited osteogenic differentiation and affected the expression of osteogenic genes.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Shaun Spisak, Brett O'Brien, Marc Ostermeier
Summary: A single system has been developed for selecting both active and inactive dCas9 variants. Active variants are selected through growth in the presence of ampicillin, while cells lacking dCas9 activity are isolated through growth in M9 minimal media or media containing streptomycin. This system can enrich for rare dCas9 variants up to 9,000-fold and has potential utility in directed evolution experiments.
Article
Biochemistry & Molecular Biology
Audrey Jacq, Denis Becquet, Maria-Montserrat Bello-Goutierrez, Benedicte Boyer, Severine Guillen, Jean-Louis Franc, Anne-Marie Francois-Bellan
Summary: The long non-coding RNA Neat1 plays a crucial role in paraspeckle formation and may also be involved in regulating circadian rhythms. Deletion of the Neat1 gene affects the expression of a large number of RNAs, including those related to circadian rhythms and key biological processes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Multidisciplinary Sciences
Vanessa Chenouard, Isabelle Leray, Laurent Tesson, Severine Remy, Alasdair Allan, Daniel Archer, Adam Caulder, Agnes Fortun, Karine Bernardeau, Yacine Cherifi, Lydia Teboul, Laurent David, Ignacio Anegon
Summary: CRISPR-Cas9 cleavage efficacy and accuracy are influenced by the optimal formation of the ribonucleoprotein (RNP) complex. The study shows that an equimolar ratio of Cas9 and guide RNA (gRNA) is optimal for RNP complex formation. Increasing the Cas9/gRNA ratio does not improve knock-in (KI) efficiency, and excess gRNA leads to a decrease in point mutation KI efficiency and an increase in large deletions.
Article
Biochemistry & Molecular Biology
Shuqing Zheng, Feng Shao, Wenjing Tao, Zhilong Liu, Juan Long, Xiaoshuang Wang, Shuai Zhang, Qingyuan Zhao, Karen L. Carleton, Thomas D. Kocher, Li Jin, Zhijian Wang, Zuogang Peng, Deshou Wang, Yaoguang Zhang
Summary: The study constructed a chromosome-level draft genome of Southern catfish, predicted a significant number of protein-coding genes, and revealed a rod-dominated visual system in the catfish which is adapted for scotopic vision. Additionally, analysis identified the loss of certain genes which may be related to the small eyes in this species.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Yubing Luo, Jie Wang, Xiaoming Bai, Hesheng Xiao, Wenjing Tao, Linyan Zhou, Deshou Wang, Jing Wei
Summary: Two paralogous rec8 genes, OnRec8a and OnRec8b, were identified in Nile tilapia, showing differential expression patterns during spermatogenesis and oogenesis. The expression of both genes can be upregulated by RA signaling, suggesting their potential involvement in the RA-mediated meiosis program.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY
(2021)
Article
Developmental Biology
Shengfei Dai, Shuangshuang Qi, Xueyan Wei, Xingyong Liu, Yibing Li, Xin Zhou, Hesheng Xiao, Baoyue Lu, Deshou Wang, Minghui Li
Summary: Recent studies challenge the long-standing belief that germline sexual fate is determined by the somatic environment, showing instead that in tilapia, the sexual fate of germline is determined by the antagonistic interaction of dmrt1 and foxl3. Our findings suggest that the sexual plasticity of germ cells relies on the presence of both dmrt1 and foxl3, allowing environmental factors to influence sex fate decision in vertebrates.
Article
Biochemistry & Molecular Biology
Shuai Zhang, Lang Xie, Shuqing Zheng, Baoyue Lu, Wenjing Tao, Xiaoshuang Wang, Thomas D. Kocher, Linyan Zhou, Deshou Wang
Summary: This study conducted genome-wide identification and comprehensive analysis of the SDR superfamily in 29 animal species, revealing that the number of SDR genes in animals increased with whole genome duplication, and vertebrate SDRs were clustered into five categories. Tandem duplication of specific SDR genes was observed in different animal groups, and sexually dimorphic expression of certain SDRs in adult fish gonads was confirmed by in situ hybridization and qPCR, suggesting their potential roles in steroidogenesis and gonadal differentiation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Feilong Wang, Zuliang Qin, Zhiqiang Li, Shuangyi Yang, Tian Gao, Lina Sun, Deshou Wang
Summary: In this study, the precise expression patterns of dnmt3aa and dnmt3ab in tilapia gonads were elucidated. Mutation of dnmt3aa and dnmt3ab were achieved, showing that dnmt3aa(-/-) mutants exhibited lower GSI, increased apoptosis, and reduced sperm quality, while dnmt3ab(-/-) mutants displayed normal gonadal development. Results suggest that dnmt3aa, but not dnmt3ab, plays important roles in maintaining gametogenesis in teleosts.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Evolutionary Biology
Chenxu Wang, Baoyue Lu, Tao Li, Guangyuan Liang, Mengmeng Xu, Xingyong Liu, Wenjing Tao, Linyan Zhou, Thomas D. Kocher, Deshou Wang
Summary: The diverse color patterns of cichlid fishes are important in mate choice and speciation. Different genes control body and eye pigmentation in Nile tilapia. Several genes, including mitf, kita/kitlga, and pmel, are significant for color patterning in tilapia, making it an excellent model system for studying vertebrate color patterning.
JOURNAL OF HEREDITY
(2021)
Article
Biochemistry & Molecular Biology
Zhisheng Ma, Jing Yang, Qingqing Zhang, Chunmei Xu, Jing Wei, Lina Sun, Deshou Wang, Wenjing Tao
Summary: miR-133b, a member of the miR-133 family, plays a crucial role in tilapia oogenesis by regulating the expression of tagln2 gene and impacting estrogen synthesis. The study validates the role of miR-133b in fish reproduction through experiments in mice, laying the foundation for further exploration of the regulatory network in fish oogenesis.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY
(2021)
Article
Genetics & Heredity
Xingyong Liu, Shengfei Dai, Jiahong Wu, Xueyan Wei, Xin Zhou, Mimi Chen, Dejie Tan, Deyong Pu, Minghui Li, Deshou Wang
Summary: The study analyzed the expression and functions of amh duplicates in Nile tilapia. It was found that amhy is expressed earlier and at a higher level during sex determination, and it determines sex by repressing the transcription of cyp19a1a. Mutations in amhy lead to sex reversal and altered germ cell proliferation.
Article
Evolutionary Biology
Chenxu Wang, Jia Xu, Thomas D. Kocher, Minghui Li, Deshou Wang
Summary: In this study, researchers identified two pmel genes in Nile tilapia and demonstrated their importance in pigmentation. Homozygous mutation of pmela resulted in a yellowish body color with weak vertical bars, while mutation of pmelb had a milder effect. Double mutation of both genes led to a decrease in melanophores and an increase in xanthophores, resulting in a golden body color. The findings provide new strategies for breeding golden tilapia and offer a new model for studying pmel function in vertebrates.
JOURNAL OF HEREDITY
(2022)
Article
Biology
Shuqing Zheng, Wenjing Tao, Haowen Yang, Thomas D. Kocher, Zhijian Wang, Zuogang Peng, Li Jin, Deyong Pu, Yaoguang Zhang, Deshou Wang
Summary: Teleosts are important models for studying sex chromosomes and sex-determining genes. In this study, a high-contiguity chromosome-level genome assembly on a YY southern catfish was generated using Nanopore and Hi-C technologies. The study identified a candidate sex-determining gene in the sex-determining region and confirmed the role of amhr2y in male sex determination.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Chunmei Xu, Miao Yu, Qingqing Zhang, Zhisheng Ma, Kang Du, Huiqin You, Jing Wei, Deshou Wang, Wenjing Tao
Summary: In this study, the BRD gene family was identified and characterized in Nile tilapia, revealing sexually dimorphic expression patterns and their critical role in spermatogenesis. The findings provide insights into the understanding of sex differentiation and gonadal development in teleosts.
Correction
Biology
Shuqing Zheng, Wenjing Tao, Haowen Yang, Thomas D. Kocher, Zhijian Wang, Zuogang Peng, Li Jin, Deyong Pu, Yaoguang Zhang, Deshou Wang
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Xingyong Liu, Li Zhou, Wenbo Li, Jiahong Wu, Deshou Wang
Summary: In this study, it was found that GATA2 plays a critical role in lens morphogenesis in Nile tilapia. Mutations in the gata2a gene led to degeneration and apoptosis of lens fiber cells, causing progressive microphthalmia and blindness in adulthood. Transcriptome analysis revealed significant changes in the expression levels of genes encoding crystallin and genes involved in visual perception and metal ion binding after gata2a mutation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biology
Zeming Zhang, Jie Wang, Jianeng Li, Xiang Liu, Lei Liu, Changle Zhao, Wenjing Tao, Deshou Wang, Jing Wei
Summary: In this study, an integrated CRISPR/Cas9 system was established for gene knock-out and knock-in at a specific site in medaka. The system is simple, cost-effective, and efficient. The results showed that pCas9-mU6sgRNA driven by endogenous U6 promoter achieved high gene editing efficiency in medaka cultured cells, but not by exogenous U6 promoters. This study provides insights into other fish genome editing and promotes gene functional analysis.