Nodes occupying central positions in human tissue specific PPI networks are enriched with many splice variants

The functional repertoire of genes in the eukaryotic organisms is enhanced by the phenomenon of alternative splicing. Hence, a node in a tissue specific protein–protein interaction (TS PPIN) network can be thought of as an ensemble of various spliced protein products of the corresponding gene expressed in that tissue. Here we demonstrate that the nodes that occupy topologically central positions characterized by high degree, betweenness, closeness, and eigenvector centrality values in TS PPINs of Homo sapiens are associated with high number of splice variants. We also show that the high “centrality” of these genes/nodes could in part be explained by the presence of a large number of promiscuous domains.     

CDKN2B expression and subcutaneous adipose tissue expandability: Possible influence of the 9p21 atherosclerosis locus

Risk alleles within a gene desert at the 9p21 locus constitute the most prevalent genetic determinant of cardiovascular disease. Previous research has demonstrated that 9p21 risk variants influence gene expression in vascular tissues, yet the biological mechanisms by which this would mediate atherosclerosis merits further investigation. To investigate possible influences of this locus on other tissues, we explored expression patterns of 9p21-regulated genes in a panel of multiple human tissues and found that the tumor suppressor CDKN2B was highly expressed in subcutaneous adipose tissue (SAT). CDKN2B expression was regulated by obesity status, and this effect was stronger in carriers of 9p21 risk alleles. Covariation between expression of CDKN2B and genes implemented in adipogenesis was consistent with an inhibitory effect of CDKN2B on SAT proliferation. Moreover, studies of postprandial triacylglycerol clearance indicated that CDKN2B is involved in down-regulation of SAT fatty acid trafficking. CDKN2B expression in SAT correlated with indicators of ectopic fat accumulation, including markers of hepatic steatosis. Among genes regulated by 9p21 risk variants, CDKN2B appears to play a significant role in the regulation of SAT expandability, which is a strong determinant of lipotoxicity and therefore might contribute to the development of atherosclerosis.     

Methylation Modifications in Eukaryotic Messenger RNA

RNA methylation modifications have been found for decades of years, which occur at different RNA types of numerous species, and their distribution is species-specific. However, people rarely know their biological functions. There are several identified methylation modifications in eukaryotic messenger RNA （mRNA）, such as NT-methylguanosine （mVG） at the cap, Nr-methyl-2＇-O-methyladenosine （m6Am）, 2＇-O-methylation （Nm） within the cap and the internal positions, and internal N6-methyladenosine （m6A） and 5-methylcytosine （mSC）. Among them, mTG cap was studied more clearly and found to have vital roles in several important mRNA processes like mRNA translation, stability and nuclear export, m6A as the most abundant modification in mRNA was found in the 1970s and has been proposed to function in mRNA splicing, translation, stability, transport and so on. mrA has been discovered as the first RNA reversible modification which is demethylated directly by human fat mass and obesity associated protein （FRO） and its homolog protein, alkylation repair ho- molog 5 （ALKBH5）. b-TO has a special demethylation mechanism that demethylases m6A to A through two over-oxidative intermediate states： N6-hydroxymethyladenosine （hm6A） and Nr-formyladenosine （frA）. The two newly discovered m6A demethylases, bTO and ALKBH5, significantly control energy homeostasis and spermatogenesis, respectively, indicating that the dynamic and reversible mrA, analogous to DNA and histone modifications, plays broad roles in biological kingdoms and brings us an emerging field ＂RNA Epige- netics＂. 5-methylcytosine （5mC） as an epigenetic mark in DNA has been studied widely, but mSC in mRNA is seldom explored. The bisulfide sequencing showed mSC is another abundant modification in mRNA, suggesting that it might be another RNA epigenetic mark. This review focuses on the main methylation modifications in mRNA to describe their formation, distribution, function and demethylation from the current knowledge and to provide future 19erspectives on functional studies.     

hMMS2基因对结肠癌细胞耐药逆转的影响

为探讨hMMS2(Human methyl methanesulfonate sensitive mutant 2)基因对人结肠癌细胞耐药逆转的影响, 文章以人高分化耐奥沙利铂结肠癌细胞(THC8307/L-OHP)为实验材料, 采用脂质体-质粒转染技术构建了带有干扰目的基因hMMS2的miRNA片段并携带绿色荧光蛋白标记重组质粒(pcDNA6.2-GW/EmGFP-miR-MMS2)的细胞系, 通过实时荧光定量PCR(qRT-PCR)和免疫荧光技术(Immunostaining technique)检测该细胞系的干扰效率。选择hMMS2低表达具有统计学意义的上述细胞系作为实验组细胞, 同时将未曾作过处理的THC8307/ L-OHP细胞作为空白对照组, 转染绿色荧光蛋白空质粒(pcDNA6.2-GW/EmGFP-miR)的THC8307/L-OHP细胞作为阴性对照组, 以噻唑蓝比色分析实验(MTT colorimetric analysis assay)、克隆形成实验(Colony formation assay)对3组细胞的存活率和克隆形成率进行检测, 结果显示：实验组细胞的奥沙利铂半数抑制浓度(Half inhibition concentration, IC50)、耐药指数(Resistance index, RI)及克隆形成率(Colony-forming efficiency, CFE)均比对照组细胞明显降低(P＜0.05), 而相对逆转率(Relative reverse efficiency, RRE)增高(P＜0.05), 提示实验组细胞增殖能力减弱; 以罗丹明123实验(Rhodamine 123 assay)结合倒置荧光显微镜、流式细胞仪检测技术等观测细胞的凋亡变化, 结果显示, 实验组细胞的凋亡率较对照组细胞显著增高(P＜0.05); 两对照(空白、阴性)组间并无细胞增殖或凋亡的显著性差异。研究结果提示：下调hMMS2基因表达可逆转人高分化耐奥沙利铂结肠癌细胞对L-OHP的耐药性并促进结肠癌细胞的凋亡。