2016 Vol. 7, No. 4

Chances and challenges in China
Boris Tefsen
2016, 7(4): 233-235. doi: 10.1007/s13238-015-0235-4
Research articles
The key role of CYC2 during meiosis in Tetrahymena thermophila
Qianlan Xu, Ruoyu Wang, A. R. Ghanam, Guanxiong Yan, Wei Miao, Xiaoyuan Song
2016, 7(4): 236-249. doi: 10.1007/s13238-016-0254-9
Meiotic recombination is carried out through a specialized pathway for the formation and repair of DNA double-strand breaks (DSBs) made by the Spo11 protein. The present study shed light on the functional role of cyclin, CYC2, in Tetrahymena thermophila which has transcriptionally high expression level during meiosis process. Knocking out the CYC2 gene results in arrest of meiotic conjugation process at 2.5-3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. To investigate the underlying mechanism of this phenomenon, a complete transcriptome profile was performed between wild-type strain and CYC2 knock-out strain. Functional analysis of RNA-Seq results identifies related differentially expressed genes (DEGs) including SPO11 and these DEGs are enriched in DNA repair/mismatch repair (MMR) terms in homologous recombination (HR), which indicates that CYC2 could play a crucial role in meiosis by regulating SPO11 and participating in HR.
Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome
Zhuoya Gu, Ke Jin, M. James C. Crabbe, Yang Zhang, Xiaolin Liu, Yanyan Huang, Mengyi Hua, Peng Nan, Zhaolei Zhang, Yang Zhong
2016, 7(4): 250-266. doi: 10.1007/s13238-015-0240-7
Transposable elements (TEs) have no longer been totally considered as "junk DNA" for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C (chromosome conformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC:r=0.9, P < 2.2×1016; IMR90 fibroblasts:r=0.94, P < 2.2×1016) and also have a significant positive correlation with some remote functional DNA elements like enhancers and promoters (Enhancer:hESC:r=0.997, P=2.3×10-4; IMR90:r=0.934, P=2×10-2; Promoter:hESC:r=0.995, P=3.8×10-4; IMR90:r=0.996, P=3.2×10-4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes.
In vitro assembly of the bacterial actin protein MamK from ‘Candidatus Magnetobacterium casensis’ in the phylum Nitrospirae
Aihua Deng, Wei Lin, Nana Shi, Jie Wu, Zhaopeng Sun, Qinyun Sun, Hua Bai, Yongxin Pan, Tingyi Wen
2016, 7(4): 267-280. doi: 10.1007/s13238-016-0253-x
Magnetotactic bacteria (MTB), a group of phylogenetically diverse organisms that use their unique intracellular magnetosome organelles to swim along the Earth's magnetic field, play important roles in the biogeochemical cycles of iron and sulfur. Previous studies have revealed that the bacterial actin protein MamK plays essential roles in the linear arrangement of magnetosomes in MTB cells belonging to the Proteobacteria phylum. However, the molecular mechanisms of multiple-magnetosome-chain arrangements in MTB remain largely unknown. Here, we report that the MamK filaments from the uncultivated ‘Candidatus Magnetobacterium casensis’ (Mcas) within the phylum Nitrospirae polymerized in the presence of ATP alone and were stable without obvious ATP hydrolysis-mediated disassembly. MamK in Mcas can convert NTP to NDP and NDP to NMP, showing the highest preference to ATP. Unlike its Magnetospirillum counterparts, which form a single magnetosome chain, or other bacterial actins such as MreB and ParM, the polymerized MamK from Mcas is independent of metal ions and nucleotides except for ATP, and is assembled into well-ordered filamentous bundles consisted of multiple filaments. Our results suggest a dynamically stable assembly of MamK from the uncultivated Nitrospirae MTB that synthesizes multiple magnetosome chains per cell. These findings further improve the current knowledge of biomineralization and organelle biogenesis in prokaryotic systems.
Autophagy induction by SIRT6 is involved in oxidative stress-induced neuronal damage
Jiaxiang Shao, Xiao Yang, Tengyuan Liu, Tingting Zhang, Qian Reuben Xie, Weiliang Xia
2016, 7(4): 281-290. doi: 10.1007/s13238-016-0257-6
SIRT6 is a NAD+-dependent histone deacetylase and has been implicated in the regulation of genomic stability, DNA repair, metabolic homeostasis and several diseases. The effect of SIRT6 in cerebral ischemia and oxygen/glucose deprivation (OGD) has been reported, however the role of SIRT6 in oxidative stress damage remains unclear. Here we used SH-SY5Y neuronal cells and found that overexpression of SIRT6 led to decreased cell viability and increased necrotic cell death and reactive oxygen species (ROS) production under oxidative stress. Mechanistic study revealed that SIRT6 induced autophagy via attenuation of AKT signaling and treatment with autophagy inhibitor 3-MA or knockdown of autophagy-related protein Atg5 rescued H2O2-induced neuronal injury. Conversely, SIRT6 inhibition suppressed autophagy and reduced oxidative stressinduced neuronal damage. These results suggest that SIRT6 might be a potential therapeutic target for neuroprotection.
Death receptor 6 is a novel plasmacytoid dendritic cell-specific receptor and modulates type I interferon production
Jingyun Li, Qiumei Du, Rui Hu, Yanbing Wang, Xiangyun Yin, Haisheng Yu, Peishuang Du, Joël Plumas, Laurence Chaperot, Yong-jun Liu, Liguo Zhang
2016, 7(4): 291-294. doi: 10.1007/s13238-015-0239-0
Overexpression of SIRT3 disrupts mitochondrial proteostasis and cell cycle progression
Xiaofei Wang, Haiping Tang, Yuling Chen, Binghuan Chi, Shiyu Wang, Yang Lv, Di Wu, Renshan Ge, Haiteng Deng
2016, 7(4): 295-299. doi: 10.1007/s13238-016-0251-z
Structural basis of interaction between the hepatitis C virus p7 channel and its blocker hexamethylene amiloride
Linlin Zhao, Shuqing Wang, Lingyu Du, Jyoti Dev, Liujuan Zhou, Zhijun Liu, James J. Chou, Bo OuYang
2016, 7(4): 300-304. doi: 10.1007/s13238-016-0256-7
MiR-181a-5p promotes anoikis by suppressing autophagy during detachment induction in the mammary epithelial cell line MCF10A
Jia-li Wei, Yuan-cheng Li, Zhong-liang Ma, You-xin Jin
2016, 7(4): 305-309. doi: 10.1007/s13238-016-0255-8