Article
Biochemistry & Molecular Biology
Wenli Huang, Aihong Zheng, Huanhuan Huang, Zhifeng Chen, Jie Ma, Xiangxiang Li, Qiannan Liang, Ling Li, Ruobin Liu, Zhi Huang, Yaoguo Qin, Yi Tang, Huanxiu Li, Fen Zhang, Qiaomei Wang, Bo Sun
Summary: The study developed an efficient CRISPR/Cas9 system for gene editing in Chinese kale using multiple sgRNAs and two promoters. The system targeted BoaZDS and BoaCRTISO genes in Chinese kale protoplasts and cotyledons. The study also found that simultaneous targeting of BoaZDS and BoaCRTISO resulted in lower editing efficiency.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Si-Wei Wang, Chao Gao, Yi-Min Zheng, Li Yi, Jia-Cheng Lu, Xiao-Yong Huang, Jia-Bin Cai, Peng-Fei Zhang, Yue-Hong Cui, Ai-Wu Ke
Summary: The CRISPR/Cas9 gene editing technology has made significant progress in oncological research, providing a powerful tool for exploring the mechanism of cancer, establishing tumor models, and studying drug targets.
Article
Plant Sciences
Chong Ren, Yanfei Liu, Yuchen Guo, Wei Duan, Peige Fan, Shaohua Li, Zhenchang Liang
Summary: This study identified multiple effective promoters in grapevine and achieved multiplex genome editing by optimizing the CRISPR/Cas9 system, leading to increased editing efficiency. Simultaneous editing of TMT1 and TMT2 genes resulted in reduced sugar levels in grapes, highlighting the role of these genes in sugar accumulation. The findings provide valuable materials for the optimization of CRISPR/Cas9 system and expand the toolbox of grape genome editing for basic research and molecular breeding.
HORTICULTURE RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
X. -y. Ni, W. -j. Lu, X. Qiao, J. Huang
Summary: The study found that all four promoters could be used with variable efficiency to drive mutagenesis of the white gene in Drosophila suzukii. Among the four DsU6 promoters tested, DsU6-3 had the highest genome editing efficiency. In comparison, the DmU6:3 promoter showed lower efficiency. These findings expand the options for promoters to express gRNAs in D. suzukii, facilitating both basic and applied research on this important pest.
INSECT MOLECULAR BIOLOGY
(2021)
Review
Materials Science, Multidisciplinary
Shao Wei Hu, Tao Ding, Honghai Tang, Huiping Guo, Wenguo Cui, Yilai Shu
Summary: With the advancement of genome editing techniques, gene therapy is increasingly being used for the treatment of various human diseases. Nanomaterials have shown great potential in improving the efficiency and safety of gene editing in gene therapy. This review introduces three gene editing tools, with a particular focus on the development and optimization of the CRISPR system. It also discusses the recent application of nanobiomaterials in gene therapy, along with the prospects and remaining challenges. Lastly, future directions for gene editing tools, nanobiomaterial vectors, and gene therapy are presented.
Article
Biochemistry & Molecular Biology
Jianduo Zhang, Jiaxin Xing, Qili Mi, Wenwu Yang, Haiying Xiang, Li Xu, Wanli Zeng, Jin Wang, Lele Deng, Jiarui Jiang, Guangyu Yang, Qian Gao, Xuemei Li
Summary: CRISPR/Cas9 genome-editing technology has revolutionized plant science, showing great potential for crop improvement. By editing the NtPDS gene in tobacco, researchers have demonstrated that incorporating an OsU3-tRNA promoter combination into the CRISPR/Cas9 system can enhance editing efficiency. The optimized tobacco CRISPR/Cas9 system, named pOREU3TR, successfully produced transgene-free and homozygous gene-edited plants with significant differences in plant height and amino acid content. This OsU3-tRNA-sgRNA/AtUb10-Ros1 system provides essential improvements for increasing the efficiency of plant genome editing.
Article
Biology
Ganna Reint, Zhuokun Li, Kornel Labun, Salla Keskitalo, Inkeri Soppa, Katariina Mamia, Eero Tolo, Monika Szymanska, Leonardo A. Meza-Zepeda, Susanne Lorenz, Artur Cieslar-Pobuda, Xian Hu, Diana L. Bordin, Judith Staerk, Eivind Valen, Bernhard Schmierer, Markku Varjosalo, Jussi Taipale, Emma Haapaniemi
Summary: Precision CRISPR gene editing can be improved by fusing DNA repair proteins with Cas9, with different fusion proteins showing varying effects based on cell type and genomic site. Optimization is necessary to account for the diverse factors contributing to locus-specific genome editing outcomes.
Review
Biotechnology & Applied Microbiology
Congting Guo, Xiaoteng Ma, Fei Gao, Yuxuan Guo
Summary: Gene editing involves precise changes to specific nucleic acid sequences. The CRISPR/Cas9 system has revolutionized gene editing, making it efficient, convenient, and programmable. However, off-target effects remain a major concern, leading to unexpected alterations in the genome. Various methods have been developed to detect and mitigate these off-target effects, advancing the precision of CRISPR/Cas9 derivatives. This review summarizes these technological advancements and discusses the challenges in managing off-target effects for future gene therapy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
J. Boutin, J. Rosier, D. Cappellen, F. Prat, J. Toutain, P. Pennamen, J. Bouron, C. Rooryck, J. P. Merlio, I. Lamrissi-Garcia, G. Cullot, S. Amintas, V. Guyonnet-Duperat, C. Ged, J. M. Blouin, E. Richard, S. Dabernat, F. Moreau-Gaudry, A. Bedel
Summary: The study reveals the genotoxicity caused by CRISPR-Cas9 leading to loss of heterozygosity changes, while also highlighting the potential safety concerns of this technology for gene therapy.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Guo-Qing Song, Grace Urban, John T. Ryner, Gan-Yuan Zhong
Summary: This study evaluated chimeric editing in gene editing, using a transgenic tobacco line and a CRISPR-Cas9 editing vector. It was found that chimeric editing primarily occurred during or after cell regeneration. Further transformation was conducted to enhance editing efficiency. The findings provide valuable information for understanding gene editing in plant cells using constitutively expressed CRISPR-Cas9 and gRNAs.
Review
Cell Biology
Heba M. Mansour, Aiman S. El-Khatib
Summary: This article reviews the pathogenesis of Parkinson's disease (PD) and its association with CRISPR/Cas9 gene editing technology. It introduces the kinases encoding genes related to PD and targeted control by CRISPR/Cas9 technology. It also discusses the off-target effects of the CRISPR/Cas9 system and how to address them, as well as the challenges and future directions in kinase research for PD.
AGEING RESEARCH REVIEWS
(2023)
Article
Biochemical Research Methods
Stefan J. Tekel, Nicholas Brookhouser, Kylie Standage-Beier, Xiao Wang, David A. Brafman
Summary: The introduction of transient reporters of editing enrichment (TREE) has enabled highly efficient single-base editing of human cells using a transient episomal fluorescent reporter, allowing for rapid generation of clonal editing efficiencies exceeding 80% in biallelic or multiplexed edited isogenic human pluripotent stem cell lines within approximately 3-4 weeks.
Review
Biochemistry & Molecular Biology
Chin-Kai Chuang, Wei-Ming Lin
Summary: Cas9-sgRNA is a key tool for genome editing, with its simplicity, unique RNA-guided DNA recognition activity, and independent nuclease activities. Different variants of Cas9, in combination with sgRNA, can achieve various effects on target site breakage. Additionally, engineered enzyme activities can be introduced using Cas9 derivatives, and methods for transient expression and biosafety have been developed to address off-target effects.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Chengpeng Wang, Yang Li, Na Wang, Qin Yu, Yonghong Li, Junping Gao, Xiaofeng Zhou, Nan Ma
Summary: We established a platform for CRISPR/Cas9-mediated gene editing in rose using suspension cells, and successfully edited a gene involved in the ethylene signaling pathway. Our optimized CRISPR/Cas9 system provides a powerful tool for functional genomics, molecular breeding, and synthetic biology in rose.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Review
Cell Biology
Manuel M. Vicente, Miguel Chaves-Ferreira, Joao M. P. Jorge, Joao T. Proenca, Vasco M. Barreto
Summary: The repurposing of the CRISPR/Cas bacterial defense system as molecular tools has revolutionized gene editing, and efforts have been made since 2013 to decrease the frequency of unwanted mutations during CRISPR-based gene editing.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zongji Wang, Jilin Zhang, Xiaoman Xu, Christopher Witt, Yuan Deng, Guangji Chen, Guanliang Meng, Shaohong Feng, Luohao Xu, Tamas Szekely, Guojie Zhang, Qi Zhou
Summary: The sex chromosome evolution of paleognathous birds shows different rates and patterns. The Z-linked regions of paleognaths have an excess of species-specific autosomal duplicated genes, while the W chromosome suffers more serious functional gene loss. This defeminization of the Z chromosome and slow divergence of sex chromosomes might be related to the distinctive mode of sexual selection targeting females in their common ancestors.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Plant Sciences
Jianling You, Stephen C. Lougheed, Yao Zhao, Guojie Zhang, Wensheng Liu, Fan Lu, Yuguo Wang, Wenju Zhang, Ji Yang, La Qiong, Zhiping Song
Summary: Introgressive hybridization and incomplete lineage sorting play important roles in the phylogeography of plant species that experienced rapid diversification in the Qinghai-Tibetan Plateau and the Hengduan Mountains.
Article
Ornithology
Emily L. Cavill, Shyam Gopalakrishnan, Lara C. Puetz, Angela M. Ribeiro, Sarah S. T. Mak, Rute R. da Fonseca, George Pacheco, Bronwyn Dunlop, Wilna Accouche, Nirmal Shah, Anna Zora, Licia Calabrese, Martin Genner, Gareth Jones, Chunxue Guo, Guojie Zhang, M. Thomas P. Gilbert
Summary: The Seychelles Magpie-Robin is an endangered species endemic to the Seychelles with a population history of genetic bottleneck leading to inbreeding. Translocations have resulted in decreased genetic diversity in three out of four populations, as well as the establishment of population structure within these populations. Continued genetic monitoring is crucial for informed management decisions for the conservation of this species.
Article
Biochemistry & Molecular Biology
Fang Li, Rahul Rane, Victor Luria, Zijun Xiong, Jiawei Chen, Zimai Li, Renee A. Catullo, Philippa C. Griffin, Michele Schiffer, Stephen Pearce, Siu Fai Lee, Kerensa McElroy, Ann Stocker, Jennifer Shirriffs, Fiona Cockerell, Chris Coppin, Carla M. Sgro, Amir Karger, John W. Cain, Jessica A. Weber, Gabriel Santpere, Marc W. Kirschner, Ary A. Hoffmann, John G. Oakeshott, Guojie Zhang
Summary: The study developed a high-quality assembly database for 46 Drosophila species and one closely related Zaprionus for evolutionary genomic research. Results indicate that adaptation to different climates in the genus Drosophila has been associated with large-scale and multifaceted genomic changes.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemistry & Molecular Biology
Akihiro Itoigawa, Takashi Hayakawa, Yang Zhou, Adrian D. Manning, Guojie Zhang, Frank Grutzner, Hiroo Imai
Summary: The molecular evolution of bitter taste receptors in egg-laying mammals, such as platypus and echidna, is associated with their feeding habits. The receptive ranges of TAS2Rs differ between the two species, reflecting their distinct diets. Furthermore, the ability to detect beta-glucosides and other substances might be shared and ancestral among mammals.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Editorial Material
Ecology
Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, Jose A. Godoy, Jacob Hoglund, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila J. Mazzoni, Erich D. Jarvis, Miklos Balint
Summary: Progress in genome sequencing has enabled the generation of large-scale reference genomes, representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, allowing comprehensive analyses in population and functional genomics, and are expected to revolutionize conservation genomics.
TRENDS IN ECOLOGY & EVOLUTION
(2022)
Article
Physiology
Guo Ding, Qionghua Gao, Jun Chen, Jie Zhao, Guojie Zhang, Weiwei Liu
Summary: This study validates reliable reference genes for RT-qPCR analysis in pharaoh ants and lays the foundation for future research.
FRONTIERS IN PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Luis Ferrandez-Peral, Xiaoyu Zhan, Marina Alvarez-Estape, Cristina Chiva, Paula Esteller-Cucala, Raquel Garcia-Perez, Eva Julia, Esther Lizano, Oscar Fornas, Eduard Sabido, Qiye Li, Tomas Marques-Bonet, David Juan, Guojie Zhang
Summary: Transcriptomic diversity plays a significant role in disease, lineage-specific biology, and environmental adaptation. This study combines long- and short-read sequencing with mass spectrometry proteomics to analyze human, great apes, and rhesus macaque lymphoblastoid cell lines, resulting in the largest primate full-length isoform catalog to date. The findings reveal numerous transcriptomic innovations and isoform usage changes related to immune function and immunological disorders.
Editorial Material
Biochemical Research Methods
Yafei Mao, Guojie Zhang
Summary: The release of the first telomere-to-telomere human genome sequence is a significant milestone in human genomics research, offering potential insights for evolutionary genomics. This article describes the advances of this new genome assembly and discusses the challenges of applying this sequencing strategy to various extant species.
Correction
Biochemical Research Methods
Yafei Mao, Guojie Zhang
Article
Multidisciplinary Sciences
Ming-Li Li, Sheng Wang, Penghui Xu, Hang-Yu Tian, Mixue Bai, Ya-Ping Zhang, Yong Shao, Zi-Jun Xiong, Xiao-Guang Qi, David N. Cooper, Guojie Zhang, He Helen Zhu, Dong-Dong Wu
Summary: Lorises are globally threatened primates with unique physiological and behavioral features. Through genome sequencing and functional studies, specific gene expansions related to detoxification, muscle development, and circadian rhythm were found in the pygmy loris. The pygmy loris also exhibited evolutionary convergence with the koala in genes involved in metabolism and muscle development. Additionally, population genomics analysis revealed an inverse relationship in demographic trends between two coexisting loris species.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Iker Rivas-Gonzalez, Marjolaine Rousselle, Fang Li, Long Zhou, Julien Y. Dutheil, Kasper Munch, Yong Shao, Dongdong Wu, Mikkel H. Schierup, Guojie Zhang
Summary: Incomplete lineage sorting (ILS) was investigated in 29 major ancestral nodes of the primate phylogeny. Up to 64% of the genome was found to be affected by ILS. ILS was used to estimate speciation times and ancestral population sizes, which showed agreement with the fossil record.
Article
Multidisciplinary Sciences
Xupeng Bi, Long Zhou, Jin-Jin Zhang, Shaohong Feng, Mei Hu, David N. Cooper, Jiangwei Lin, Jiali Li, Dong-Dong Wu, Guojie Zhang
Summary: Understanding the mechanisms underlying phenotypic innovation is a key goal of comparative genomic studies. By comparing the genomes of 49 primate species, this study identified many novel lineage-specific accelerated regions (LinARs) associated with brain development or disease in humans, and also revealed detailed maps of LinARs in other primate lineages. Functional experimentation showed that gibbon LinARs could be involved in the developmental regulation of their unique limb structures, while some LinARs in the Colobinae were associated with metabolite detoxification, possibly adaptive to their leaf-eating diet. Overall, this study expands our knowledge of the functional roles of LinARs in primate evolution.
Article
Microbiology
Paul A. O'Brien, Shangjin Tan, Pedro R. Frade, Steven J. Robbins, J. Pamela Engelberts, Sara C. Bell, Inka Vanwonterghem, David J. Miller, Nicole S. Webster, Guojie Zhang, David G. Bourne
Summary: This article investigates the role of the sponge microbiome in supporting host function by providing and recycling essential nutrients. Genomic analysis of three common coral reef sponges reveals the central microbial functions involved in carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism, and B-vitamin supplementation. The study also uncovers new microbial taxa that contribute to the health of the sponge host via nutrient exchange.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Juwan Kim, Chul Lee, Byung June Ko, Dong Ahn Yoo, Sohyoung Won, Adam M. Phillippy, Olivier Fedrigo, Guojie Zhang, Kerstin Howe, Jonathan Wood, Richard Durbin, Giulio Formenti, Samara Brown, Lindsey Cantin, Claudio V. Mello, Seoae Cho, Arang Rhie, Heebal Kim, Erich D. Jarvis
Summary: This study evaluates the improvements of new vertebrate genome reference assemblies compared to previous assemblies. They found that up to 11% of genomic sequence was missing in the previous assemblies, while the new reference assemblies revealed underestimated regulatory landscapes and protein coding sequences.
