2015 Vol. 6, No. 5

Urgency to rein in the gene-editing technology
Xiaoxue Zhang
2015, 6(5): 313-313. doi: 10.1007/s13238-015-0161-5
Current aging research in China
Ruijuan Sun, Heqi Cao, Xudong Zhu, Jun-Ping Liu, Erdan Dong
2015, 6(5): 314-321. doi: 10.1007/s13238-015-0145-5
The mini-review stemmed from a recent meeting on national aging research strategies in China discusses the components and challenges of aging research in China. Highlighted are the major efforts of a number of research teams, funding situations and outstanding examples of recent major research achievements. Finally, authors discuss potential targets and strategies of aging research in China.
SIRTain regulators of premature senescence and accelerated aging
Shrestha Ghosh, Zhongjun Zhou
2015, 6(5): 322-333. doi: 10.1007/s13238-015-0149-1
The sirtuin proteins constitute class Ⅲ histone deacetylases (HDACs). These evolutionarily conserved NAD+-dependent enzymes form an important component in a variety of cellular and biological processes with highly divergent as well as convergent roles in maintaining metabolic homeostasis, safeguarding genomic integrity, regulating cancer metabolism and also inflammatory responses. Amongst the seven known mammalian sirtuin proteins, SIRT1 has gained much attention due to its widely acknowledged roles in promoting longevity and ameliorating age-associated pathologies. The contributions of other sirtuins in the field of aging are also gradually emerging. Here, we summarize some of the recent discoveries in sirtuins biology which clearly implicate the functions of sirtuin proteins in the regulation of premature cellular senescence and accelerated aging. The roles of sirtuins in various cellular processes have been extrapolated to draw inter-linkage with anti-aging mechanisms. Also, the latest findings on sirtuins which might have potential effects in the process of aging have been reviewed.
The physiological role of drug transporters
Yu Liang, Siqi Li, Ligong Chen
2015, 6(5): 334-350. doi: 10.1007/s13238-015-0148-2
Transporters comprise the largest family of membrane proteins in human organism, including members of solute carrier transporter and ATP-binding cassette transporter families. They play pivotal roles in the absorption, distribution and excretion of xenobiotic and endogenous molecules. Transporters are widely expressed in various human tissues and are routinely evaluated during the process of drug development and approval. Over the past decade, increasing evidence shows that drug transporters are important in both normal physiology and disease. Currently, transporters are utilized as therapeutic targets to treat numerous diseases such as diabetes, major depression, hypertension and constipation. Despite the steady growth of the field of transporter biology, more than half of the members in transporter superfamily have little information available about their endogenous substrate(s) or physiological functions. This review outlines current research methods in transporter studies, and summarizes the drug-transporter interactions including drug-drug and drug-endogenous substrate interactions. In the end, we also discuss the therapeutic perspective of transporters based on their physiological and pathophysiological roles.
Research articles
Insight into the Ebola virus nucleocapsid assembly mechanism:crystal structure of Ebola virus nucleoprotein core domain at 1.8 Å resolution
Shishang Dong, Peng Yang, Guobang Li, Baocheng Liu, Wenming Wang, Xiang Liu, Boran Xia, Cheng Yang, Zhiyong Lou, Yu Guo, Zihe Rao
2015, 6(5): 351-362. doi: 10.1007/s13238-015-0163-3
Ebola virus (EBOV) is a key member of Filoviridae family and causes severe human infectious diseases with high morbidity and mortality. As a typical negative-sense single-stranded RNA (-ssRNA) viruses, EBOV possess a nucleocapsid protein (NP) to facilitate genomic RNA encapsidation to form viral ribonucleoprotein complex (RNP) together with genome RNA and polymerase, which plays the most essential role in virus proliferation cycle. However, the mechanism of EBOV RNP formation remains unclear. In this work, we solved the high resolution structure of core domain of EBOV NP. The polypeptide of EBOV NP core domain (NPcore) possesses an N-lobe and C-lobe to clamp a RNA binding groove, presenting similarities with the structures of the other reported viral NPs encoded by the members from Mononegavirales order. Most strikingly, a hydrophobic pocket at the surface of the C-lobe is occupied by an α-helix of EBOV NPcore itself, which is highly conserved among filoviridae family. Combined with other biochemical and biophysical evidences, our results provides great potential for understanding the mechanism underlying EBOV RNP formation via the mobility of EBOV NP element and enables the development of antiviral therapies targeting EBOV RNP formation.
CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes
Puping Liang, Yanwen Xu, Xiya Zhang, Chenhui Ding, Rui Huang, Zhen Zhang, Jie Lv, Xiaowei Xie, Yuxi Chen, Yujing Li, Ying Sun, Yaofu Bai, Zhou Songyang, Wenbin Ma, Canquan Zhou, Junjiu Huang
2015, 6(5): 363-372. doi: 10.1007/s13238-015-0153-5
Genome editing tools such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated system (Cas) have been widely used to modify genes in model systems including animal zygotes and human cells, and hold tremendous promise for both basic research and clinical applications. To date, a serious knowledge gap remains in our understanding of DNA repair mechanisms in human early embryos, and in the efficiency and potential off-target effects of using technologies such as CRISPR/Cas9 in human pre-implantation embryos. In this report, we used tripronuclear (3PN) zygotes to further investigate CRISPR/Cas9-mediated gene editing in human cells. We found that CRISPR/Cas9 could effectively cleave the endogenous β-globin gene (HBB). However, the efficiency of homologous recombination directed repair (HDR) of HBB was low and the edited embryos were mosaic. Off-target cleavage was also apparent in these 3PN zygotes as revealed by the T7E1 assay and whole-exome sequencing. Furthermore, the endogenous delta-globin gene (HBD), which is homologous to HBB, competed with exogenous donor oligos to act as the repair template, leading to untoward mutations. Our data also indicated that repair of the HBB locus in these embryos occurred preferentially through the non-crossover HDR pathway. Taken together, our work highlights the pressing need to further improve the fidelity and specificity of the CRISPR/Cas9 platform, a prerequisite for any clinical applications of CRSIPR/Cas9-mediated editing.
Phylogenomics of non-model ciliates based on transcriptomic analyses
Xiao Chen, Xiaolu Zhao, Xiaohui Liu, Alan Warren, Fangqing Zhao, Miao Miao
2015, 6(5): 373-385. doi: 10.1007/s13238-015-0147-3
Ciliates are one of the oldest living eukaryotic unicellular organisms, widely distributed in the waters around the world. As a typical marine oligotrich ciliate, Strombidium sulcatum plays an important role in marine food webs and energy flow. Here we report the first deep sequencing and analyses of RNA-Seq data from Strombidium sulcatum. We generated 42,640 unigenes with an N50 of 1,451 bp after de novo assembly and removing rRNA, mitochondrial and bacteria contaminants. We employed SPOCS to detect orthologs from S. sulcatum and 17 other ciliates, and then carried out the phylogenomic reconstruction using 127 single copy orthologs. In phylogenomic analyses, concatenated trees have similar topological structures with concordance tree on the class level. Together with phylogenetic networks analysis, it aroused more doubts about the placement of Protocruzia, Mesodinium and Myrionecta. While epiplasmic proteins are known to be related to morphological characteristics, we found the potential relationship between gene expression of epiplasmic proteins and morphological characteristics. This work supports the use of high throughput approaches for phylogenomic analysis as well as correlation analysis between expression level of target genes and morphological characteristics.
A widely adaptable approach to generate integration-free iPSCs from non-invasively acquired human somatic cells
Zhichao Ding, Lina Sui, Ruotong Ren, Yanjun Liu, Xiuling Xu, Lina Fu, Ruijun Bai, Tingting Yuan, Ying Hao, Weiqi Zhang, Huize Pan, Wensu Liu, Han Yu, Concepcion Rodriguez Esteban, Xiaobing Yu, Ze Yang, Jian Li, Xiaomin Wang, Juan Carlos Izpisua Belmonte, Guang-Hui Liu, Fei Yi, Jing Qu
2015, 6(5): 386-389. doi: 10.1007/s13238-014-0117-1