Journal of Genetics and Genomics

The Application of CRISPR-Cas9 Genome Editing in Caenorhabditis elegans

Suhong Xu

2015, 42(8): 413-421. doi: 10.1016/j.jgg.2015.06.005

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Abstract:
Genome editing using the Cas9 endonuclease of Streptococcus pyogenes has demonstrated unparalleled efficacy and facility for modifying genomes in a wide variety of organisms. Caenorhabditis elegans is one of the most convenient multicellular organisms for genetic analysis, and the application of this novel genome editing technique to this organism promises to revolutionize analysis of gene function in the future. CRISPR-Cas9 has been successfully used to generate imprecise insertions and deletions via non-homologous end-joining mechanisms and to create precise mutations by homology-directed repair from donor templates. Key variables are the methods used to deliver the Cas9 endonuclease and the efficiency of the single guide RNAs. CRISPR-Cas9-mediated editing appears to be highly specific in C. elegans, with no reported off-target effects. In this review, I briefly summarize recent progress in CRISPR-Cas9-based genome editing in C. elegans, highlighting technical improvements in mutagenesis and mutation detection, and discuss potential future applications of this technique.

Integrative Analysis Reveals Enhanced Regulatory Effects of Human Long Intergenic Non-Coding RNAs in Lung Adenocarcinoma

You Zhou, Kai Wu, Jianping Jiang, Jinfei Huang, Peiwei Zhang, Yufei Zhu, Guohong Hu, Jingyu Lang, Yufang Shi, Landian Hu, Tao Huang, Xiangyin Kong

2015, 42(8): 423-436. doi: 10.1016/j.jgg.2015.07.001

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Abstract:
Although there is an accumulating appreciation of the key roles that long intergenic non-coding RNAs (lincRNAs) play in diverse cellular processes, our knowledge of how lincRNAs function in cancer remains sparse. Here, we present a comprehensive landscape of RNA-seq transcriptome profiles of lung adenocarcinomas and their paired normal counterparts to unravel gene regulation rules of lincRNAs. Consistent with previous findings of co-expression between neighboring protein-coding genes, lincRNAs were typically co-expressed with their neighboring genes, which was found in both cancerous and normal tissues. By building a mathematical model based on correlated gene expression, we distinguished an additional subset of lincRNAs termed “regulatory lincRNAs”, representing their dominant roles in gene regulation. The number of regulatory lincRNAs was significantly higher in cancerous compared to normal tissues, and most of them positively regulated protein-coding genes intrans. Functional validation, using knockdown, determined that regulatory lincRNA, GAS5, affected its predicted protein-coding targets. Moreover, we discovered hundreds of differentially expressed regulatory lincRNAs with inclusion of some cancer-associated lincRNAs. Our integrated analysis reveals enhanced regulatory effects of lincRNAs and provides a resource for the study of regulatory lincRNAs that play critical roles in lung adenocarcinoma.

Generation of B Cell-Deficient Pigs by Highly Efficient CRISPR/Cas9-Mediated Gene Targeting

Fengjiao Chen, Ying Wang, Yilin Yuan, Wei Zhang, Zijian Ren, Yong Jin, Xiaorui Liu, Qiang Xiong, Qin Chen, Manling Zhang, Xiaokang Li, Lihua Zhao, Ze Li, Zhaoqiang Wu, Yanfei Zhang, Feifei Hu, Juan Huang, Rongfeng Li, Yifan Dai

2015, 42(8): 437-444. doi: 10.1016/j.jgg.2015.05.002

Abstract (88) HTML PDF (4)

Abstract:
Generating B cell-deficient mutant is the first step to produce human antibody repertoires in large animal models. In this study, we applied the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system to target the J_H region of the pig IgM heavy chain gene which is crucial for B cell development and differentiation. Transfection of IgM-targeting Cas9 plasmid in primary porcine fetal fibroblasts (PFFs) enabled inducing gene knock out (KO) in up to 53.3% of colonies analyzed, a quarter of which harbored biallelic modification, which was much higher than that of the traditional homologous recombination (HR). With the aid of somatic cell nuclear transfer (SCNT) technology, three piglets with the biallelic IgM heavy chain gene mutation were produced. The piglets showed no antibody-producing B cells which indicated that the biallelic mutation of the IgM heavy chain gene effectively knocked out the function of the IgM and resulted in a B cell-deficient phenotype. Our study suggests that the CRISPR/Cas9 system combined with SCNT technology is an efficient genome-editing approach in pigs.

SHEsisPCA: A GPU-Based Software to Correct for Population Stratification that Efficiently Accelerates the Process for Handling Genome-Wide Datasets

Jiawei Shen, Zhiqiang Li, Yongyong Shi

2015, 42(8): 445-453. doi: 10.1016/j.jgg.2015.06.007

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Abstract:
Population stratification is a problem in genetic association studies because it is likely to highlight loci that underlie the population structure rather than disease-related loci. At present, principal component analysis (PCA) has been proven to be an effective way to correct for population stratification. However, the conventional PCA algorithm is time-consuming when dealing with large datasets. We developed a Graphic processing unit (GPU)-based PCA software named SHEsisPCA (http://analysis.bio-x.cn/SHEsisMain.htm) that is highly parallel with a highest speedup greater than 100 compared with its CPU version. A cluster algorithm based on X-means was also implemented as a way to detect population subgroups and to obtain matched cases and controls in order to reduce the genomic inflation and increase the power. A study of both simulated and real datasets showed that SHEsisPCA ran at an extremely high speed while the accuracy was hardly reduced. Therefore, SHEsisPCA can help correct for population stratification much more efficiently than the conventional CPU-based algorithms.

Derivation of Non-Integration Induced Pluripotent Stem Cells from Fibroblast of Severe Deafness Patients with GJB2 Mutation

Xiaofeng Jin, Rui Fu, Wanwan Zhu, Zhengxin Liu, Tiantian Gu, Guanyi Jiao, Hua Yang, Qi Zhou, Zhiqiang Gao, Xiao-Yang Zhao

2015, 42(8): 455-458. doi: 10.1016/j.jgg.2015.06.002

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Abstract:

Characterization and Genome Changes of New Amphiploids from Wheat Wide Hybridization

Xiang Guo, Qinghua Shi, Jing Wang, Yanlin Hou, Yuhai Wang, Fangpu Han

2015, 42(8): 459-461. doi: 10.1016/j.jgg.2015.06.006

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Abstract:

2015 Vol. 42, No. 8