Journal of Genetics and Genomics

Cotton functional genomics reveals global insight into genome evolution and fiber development

Zhiguo Wu, Yan Yang, Gai Huang, Jing Lin, Yuying Xia, Yuxian Zhu

2017, 44(11): 511-518. doi: 10.1016/j.jgg.2017.09.009

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Abstract:
Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution. Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDα1 were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.

A glycolysis-based ten-gene signature correlates with the clinical outcome, molecular subtype and IDH1 mutation in glioblastoma

Cong Chen, Yu Shi, Yong Li, Zhi-Cheng He, Kai Zhou, Xiao-Ning Zhang, Kai-Di Yang, Jin-Rong Wu, Hsiang-Fu Kung, Yi-Fang Ping, Xiu-Wu Bian

2017, 44(11): 519-530. doi: 10.1016/j.jgg.2017.05.007

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Abstract:
Reprogrammed metabolism is a hallmark of cancer. Glioblastoma (GBM) tumor cells predominantly utilize aerobic glycolysis for the biogenesis of energy and intermediate nutrients. However, in GBM, the clinical significance of glycolysis and its underlying relations with the molecular features such asIDH1 mutation and subtype have not been elucidated yet. Herein, based on glioma datasets including TCGA (The Cancer Genome Atlas), REMBRANDT (Repository for Molecular Brain Neoplasia Data) and GSE16011, we established a glycolytic gene expression signature score (GGESS) by incorporating ten glycolytic genes. Then we performed survival analyses and investigated the correlations between GGESS and IDH1 mutation as well as the molecular subtypes in GBMs. The results showed that GGESS independently predicted unfavorable prognosis and poor response to chemotherapy of GBM patients. Notably, GGESS was high in GBMs of mesenchymal subtype but low in IDH1-mutant GBMs. Furthermore, we found that the promoter regions of tumor-promoting glycolytic genes were hypermethylated in IDH1-mutant GBMs. Finally, we found that high GGESS also predicted poor prognosis and poor response to chemotherapy when investigating IDH1-wildtype GBM patients only. Collectively, glycolysis represented by GGESS predicts unfavorable clinical outcome of GBM patients and is closely associated with mesenchymal subtype and IDH1 mutation in GBMs.

Site-specific transfer of chromosomal segments and genes in wheat engineered chromosomes

Jing Yuan, Qinghua Shi, Xiang Guo, Yalin Liu, Handong Su, Xianrui Guo, Zhenling Lv, Fangpu Han

2017, 44(11): 531-539. doi: 10.1016/j.jgg.2017.08.005

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Abstract:
Recently, engineered minichromosomes have been produced using a telomere-mediated truncation technique in some plants. However, the study on transferring genes to minichromosomes is very limited. Here, telomere-mediated truncation was successfully performed in common wheat (Triticum aestivum) to generate stable truncated chromosomes accompanied by a relatively high frequency of chromosomal rearrangements. After the cross between transgenic parents, a promoter-less DsRed gene in a chromosome from one parent was transferred to another chromosome from the other parent at the site behind a maize ubiquitin promoter via the Cre/lox system. DsRed transcripts and red fluorescent proteins were detected in the recombinant plants. In one such seedling, transgenic signals were detected at the centric terminus of chromosome 4D and the distal terminus of chromosome 3A. Clear translocations could be detected at the transgenic loci of these two chromosomes. Intriguingly, signals of centric-specific sequences were co-localized with the translocated D-group chromosomal segment in the terminal region of chromosome 3A. Our results indicate that the Cre/lox system induces the gene swapping to the target chromosome and non-homologous chromosomal recombination simultaneously. These approaches could offer a platform to transfer large DNA fragments or even terminal chromosomal segments to other chromosomes of the natural genome.

Harnessing the native type I-B CRISPR-Cas for genome editing in a polyploid archaeon

Feiyue Cheng, Luyao Gong, Dahe Zhao, Haibo Yang, Jian Zhou, Ming Li, Hua Xiang

2017, 44(11): 541-548. doi: 10.1016/j.jgg.2017.09.010

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Abstract:
Research on CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated protein) systems has led to the revolutionary CRISPR/Cas9 genome editing technique. However, for most archaea and half of bacteria, exploitation of their native CRISPR-Cas machineries may be more straightforward and convenient. In this study, we harnessed the native type I-B CRISPR-Cas system for precise genome editing in the polyploid haloarchaeon Haloarcula hispanica. After testing different designs, the editing tool was optimized to be a single plasmid that carries both the self-targeting mini-CRISPR and a 600–800 bp donor. Significantly, chromosomal modifications, such as gene deletion, gene tagging or single nucleotide substitution, were precisely introduced into the vast majority of the transformants. Moreover, we showed that simultaneous editing of two genomic loci could also be readily achieved by one step. In summary, our data demonstrate that the haloarchaeal CRISPR-Cas system can be harnessed for genome editing in this polyploid archaeon, and highlight the convenience and efficiency of the native CRISPR-based genome editing strategy.

Ataxin-10 is involved in Golgi membrane dynamics

Jie Tian, Yingxin Shi, Shanshan Nai, Qizhi Geng, Leiliang Zhang, Gong-Hong Wei, Xingzhi Xu, Jing Li

2017, 44(11): 549-552. doi: 10.1016/j.jgg.2017.11.002

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Abstract:

Short body length phenotype is compensated by the upregulation of nidogen family members in a deleterious nid1a mutation of zebrafish

Peipei Zhu, Zhipeng Ma, Liwei Guo, Wei Zhang, Qinghe Zhang, Ting Zhao, Kunpeng Jiang, Jinrong Peng, Jun Chen

2017, 44(11): 553-556. doi: 10.1016/j.jgg.2017.09.011

Abstract (103) HTML PDF (3)

Abstract:

2017 Vol. 44, No. 11