5.9
CiteScore
5.9
Impact Factor

2017 Vol. 44, No. 4

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Original research
Significant differences of function and expression of microRNAs between ground state and serum-cultured pluripotent stem cells
Ying Yan, Xi Yang, Ting-Ting Li, Kai-Li Gu, Jing Hao, Qiang Zhang, Yangming Wang
2017, 44(4): 179-189. doi: 10.1016/j.jgg.2017.01.005
Abstract (75) HTML PDF (5)
Abstract:
Serum- and 2i-cultured embryonic stem cells (ESCs) show different epigenetic landscapes and transcriptomic profiles. The difference in the function and expression of microRNAs (miRNAs) between these two states remains unclear. Here, we showed that 2i- and serum-cultured ESCs exhibited distinctive miRNA expression profiles with >100 miRNAs differentially expressed, and the expression changes were largely due to transcriptional regulation. We further characterized the function of miRNAs differentially expressed under two conditions and found that ESCs exhibited higher degree of dependency on miRNAs for rapid proliferation; since or but not wild-type ESCs showed slower growth rate and more accumulation in the G1 phase under 2i than serum condition. More interestingly, introduction of various self-renewal-silencing miRNAs in wild-type or ESCs failed to silence the self-renewal in 2i medium, but regained the ability to silence the self-renewal upon the addition of serum. Our findings reveal significant differences in the expression and function of miRNAs between serum- and 2i-cultured ESCs.
Expression profiling-based clustering of healthy subjects recapitulates classifications defined by clinical observation in Chinese medicine
Ruoxi Yu, Dan Liu, Yin Yang, Yuanyuan Han, Lingru Li, Luyu Zheng, Ji Wang, Yan Zhang, Yingshuai Li, Qian-Fei Wang, Qi Wang
2017, 44(4): 191-197. doi: 10.1016/j.jgg.2017.01.001
Abstract (88) HTML PDF (8)
Abstract:
Differences between healthy subjects and associated disease risks are of substantial interest in clinical medicine. Based on clinical presentations, Traditional Chinese Medicine (TCM) classifies healthy people into nine constitutions: Balanced, Qi, Yang or Yin deficiency, Phlegm-dampness, Damp-heat, Blood stasis, Qi stagnation, and Inherited special constitutions. In particular, Yang and Yin deficiency constitutions exhibit cold and heat aversion, respectively. However, the intrinsic molecular characteristics of unbalanced phenotypes remain unclear. To determine whether gene expression-based clustering can recapitulate TCM-based classification, peripheral blood mononuclear cells (PBMCs) were collected from Chinese Han individuals with Yang/Yin deficiency (n = 12 each) and Balanced (n = 8) constitutions, and global gene expression profiles were determined using the Affymetrix HG-U133A Plus 2.0 array. Notably, we found that gene expression-based classifications reflected distinct TCM-based subtypes. Consistent with the clinical observation that subjects with Yang deficiency tend toward obesity, series-clustering analysis detected several key lipid metabolic genes (diacylglycerol acyltransferase (DGAT2), acyl-CoA synthetase (ACSL1), and ATP-binding cassette subfamily A member 1 (ABCA1)) to be down- and up-regulated in Yin and Yang deficiency constitutions, respectively. Our findings suggest that Yin/Yang deficiency and Balanced constitutions are unique entities in their mRNA expression profiles. Moreover, the distinct physical and clinical characteristics of each unbalanced constitution can be explained, in part, by specific gene expression signatures.
Temperature effect on CRISPR-Cas9 mediated genome editing
Guanghai Xiang, Xingying Zhang, Chenrui An, Chen Cheng, Haoyi Wang
2017, 44(4): 199-205. doi: 10.1016/j.jgg.2017.03.004
Abstract (100) HTML PDF (4)
Abstract:
Zinc-finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR-Cas9) are the most commonly used genome editing tools. Previous studies demonstrated that hypothermia treatment increased the mutation rates induced by ZFNs and TALENs in mammalian cells. Here, we characterize the effect of different culture temperatures on CRISPR-Cas9 mediated genome editing and find that the genome editing efficiency of CRISPR-Cas9 is significantly hampered by hypothermia treatment, unlike ZFN and TALEN. In addition, hyperthermia culture condition enhances genome editing by CRISPR-Cas9 in some cell lines, due to the higher enzyme activity and sgRNA expression level at higher temperature. Our study has implications on CRISPR-Cas9 applications in a broad spectrum of species, many of which do not live at 37°C.
Method
A simple and efficient method for CRISPR/Cas9-induced mutant screening
Yufeng Hua, Chun Wang, Jian Huang, Kejian Wang
2017, 44(4): 207-213. doi: 10.1016/j.jgg.2017.03.005
Abstract (98) HTML PDF (15)
Abstract:
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system provides a technological breakthrough in mutant generation. Several methods such as the polymerase chain reaction (PCR)/restriction enzyme (RE) assay, T7 endonuclease I (T7EI) assay, Surveyor nuclease assay, PAGE-based genotyping assay, and high-resolution melting (HRM) analysis-based assay have been developed for screening CRISPR/Cas9-induced mutants. However, these methods are time- and labour-intensive and may also be sequence-limited or require very expensive equipment. Here, we described a cost-effective and sensitive screening technique based on conventional PCR, annealing at critical temperature PCR (ACT-PCR), for identifying mutants. ACT-PCR requires only a single PCR step followed by agarose gel electrophoresis. We demonstrated that ACT-PCR accurately distinguished CRISPR/Cas9-induced mutants from wild type in both rice and zebrafish. Moreover, the method can be adapted for accurately determining mutation frequency in cultured cells. The simplicity of ACT-PCR makes it particularly suitable for rapid, large-scale screening of CRISPR/Cas9-induced mutants in both plants and animals.
Letter to the editor
A 2-bp insertion (c.67_68insCC) in MC1R causes recessive white coat color in Bama miniature pigs
Qitao Jia, Chunwei Cao, Hai Tang, Ying Zhang, Qiantao Zheng, Xiao Wang, Rui Zhang, Xianlong Wang, Ailing Luo, Hong Wei, Anming Meng, Qi Zhou, Hongmei Wang, Jianguo Zhao
2017, 44(4): 215-217. doi: 10.1016/j.jgg.2017.02.003
Abstract (76) HTML PDF (8)
Abstract:
Molecular evolution of pancreatic ribonuclease gene (RNase1) in Rodentia
Da-Tian Lang, Xiao-Ping Wang, Lei Wang, Li Yu
2017, 44(4): 219-222. doi: 10.1016/j.jgg.2017.03.002
Abstract (73) HTML PDF (4)
Abstract: