Journal of Genetics and Genomics

Single-Cell Sequencing Technologies: Current and Future

Jialong Liang, Wanshi Cai, Zhongsheng Sun

2014, 41(10): 513-528. doi: 10.1016/j.jgg.2014.09.005

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Abstract:
Intensively developed in the last few years, single-cell sequencing technologies now present numerous advantages over traditional sequencing methods for solving the problems of biological heterogeneity and low quantities of available biological materials. The application of single-cell sequencing technologies has profoundly changed our understanding of a series of biological phenomena, including gene transcription, embryo development, and carcinogenesis. However, before single-cell sequencing technologies can be used extensively, researchers face the serious challenge of overcoming inherent issues of high amplification bias, low accuracy and reproducibility. Here, we simply summarize the techniques used for single-cell isolation, and review the current technologies used in single-cell genomic, transcriptomic, and epigenomic sequencing. We discuss the merits, defects, and scope of application of single-cell sequencing technologies and then speculate on the direction of future developments.

TRAP1 Shows Clinical Significance and Promotes Cellular Migration and Invasion through STAT3/MMP2 Pathway in Human Esophageal Squamous Cell Cancer

Yunwei Ou, Lingyan Liu, Liyan Xue, Wei Zhou, Zitong Zhao, Bainan Xu, Yongmei Song, Qimin Zhan

2014, 41(10): 529-537. doi: 10.1016/j.jgg.2014.08.004

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Abstract:
Tumor necrosis factor receptor-associated protein 1 (TRAP1), an important member of mitochondrial heat shock protein 90 family, is involved in multiple biological processes in several types of tumors. However, its pathological role in esophageal squamous cell cancer (ESCC) remains unknown. Herein, we demonstrated the clinical value of TRAP1, and its role in apoptosis and motility in ESCC. The clinical potential of TRAP1 was investigated through immunohistochemical analysis in 328 ESCC samples, which revealed that strong TRAP1 expression was associated with increased risk of lymph node metastasis, while high TRAP1 expression correlated with poor prognosis. Expression of TRAP1 was found to be an independent prognostic factor for patients with ESCC. Additionally, the upregulation of TRAP1 antagonized cisplatin-induced apoptosis while its downregulation sensitized cells to cisplatin-induced apoptosis. As revealed by the transwell assay, TRAP1 overexpression promoted cellular migration and invasion as compared to the control groups. In contrast, silencing of endogenous TRAP1 expression attenuated the ability of migration and invasion. Finally, the molecular mechanism investigated in the present study demonstrated that TRAP1-mediated migration and invasion occurred through STAT3/MMP2 signaling pathway. In conclusion, TRAP1 may be considered as a molecular predictive marker for prognosis and a novel molecular candidate for therapeutic target in ESCC.

STRIPE2 Encodes a Putative dCMP Deaminase that Plays an Important Role in Chloroplast Development in Rice

Jing Xu, Yiwen Deng, Qun Li, Xudong Zhu, Zuhua He

2014, 41(10): 539-548. doi: 10.1016/j.jgg.2014.05.008

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Abstract:
Mutants with abnormal leaf coloration are good genetic materials for understanding the mechanism of chloroplast development and chlorophyll biosynthesis. In this study, a rice mutant st2 (stripe2) with stripe leaves was identified from the γ-ray irradiated mutant pool. The st2 mutant exhibited decreased accumulation of chlorophyll and aberrant chloroplasts. Genetic analysis indicated that the st2 mutant was controlled by a single recessive locus. The ST2 gene was finely confined to a 27-kb region on chromosome 1 by the map-based cloning strategy and a 5-bp deletion inOs01g0765000 was identified by sequence analysis. The deletion happened in the joint of exon 3 and intron 3 and led to new spliced products of mRNA. Genetic complementation confirmed that Os01g0765000 is the ST2 gene. We found that the ST2 gene was expressed ubiquitously. Subcellular localization assay showed that the ST2 protein was located in mitochondria. ST2 belongs to the cytidine deaminase-like family and possibly functions as the dCMP deaminase, which catalyzes the formation of dUMP from dCMP by deamination. Additionally, exogenous application of dUMP could partially rescue the st2 phenotype. Therefore, our study identified a putative dCMP deaminase as a novel regulator in chloroplast development for the first time.

A New-Nipponbare Rice Germplasm with High Seed-Setting Rate

Jiang Hu, Guojun Dong, Yunxia Fang, Yuchun Rao, Jie Xu, Dawei Xue, Haiping Yu, Changwei Ge, Zhenyuan Shi, Jiangjie Pan, Li Zhu, Dali Zeng, Guangheng Zhang, Longbiao Guo, Qian Qian

2014, 41(10): 549-552. doi: 10.1016/j.jgg.2014.07.001

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Abstract:

Identification and Profiling of Known and Novel Fiber MicroRNAs during the Secondary Wall Thickening Stage in Cotton (Gossypium hirsutum) via High-Throughput Sequencing

Dingwei Yu, Yanmei Wang, Wei Xue, Shuli Fan, Shuxun Yu, Jin-Yuan Liu

2014, 41(10): 553-556. doi: 10.1016/j.jgg.2014.08.002

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Abstract:

Identification of QTLs for Branch Number in Oilseed Rape (Brassica napus L.)

Jinsong Xu, Xi Song, Yong Cheng, Xiling Zou, Liu Zeng, Xing Qiao, Guangyuan Lu, Guiping Fu, Zhen Qu, Xuekun Zhang

2014, 41(10): 557-559. doi: 10.1016/j.jgg.2014.06.006

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Abstract:

Cellular Serpents and Dreaming Spires: New Frontiers in Arginine and Pyrimidine Biology

Gabriel N. Aughey, Ömür Y. Tastan, Ji-Long Liu

2014, 41(10): 561-565. doi: 10.1016/j.jgg.2014.08.006

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2014 Vol. 41, No. 10