SLC2A12 of SLC2 Gene Family in Bird Provides Functional Compensation for the Loss of SLC2A4 Gene in Other Vertebrates

Avian genomes are small and lack some genes that are conserved in the genomes of most other vertebrates including nonavian sauropsids. One hypothesis stated that paralogs may provide biochemical or physiological compensation for certain gene losses; however, no functional evidence has been reported to date. By integrating evolutionary analysis, physiological genomics, and experimental gene interference, we clearly demonstrate functional compensation for gene loss. A large-scale phylogenetic analysis of over 1,400 SLC2 gene sequences identifies six new SLC2 genes from nonmammalian vertebrates and divides the SLC2 gene family into four classes. Vertebrates retain class III SLC2 genes but partially lack the more recent duplicates of classes I and II. Birds appear to have completely lost the SLC2A4 gene that encodes an important insulin-sensitive GLUT in mammals. We found strong evidence for positive selection, indicating that the N-termini of SLC2A4 and SLC2A12 have undergone diversifying selection in birds and mammals, and there is a significant correlation between SLC2A12 functionality and basal metabolic rates in endotherms. Physiological genomics have uncovered that SLC2A12 expression and allelic variants are associated with insulin sensitivity and blood glucose levels in wild birds. Functional tests have indicated that SLC2A12 abrogation causes hyperglycemia, insulin resistance, and high relative activity, thus increasing energy expenditures that resemble a diabetic phenotype. These analyses suggest that the SLC2A12 gene not only functionally compensates insulin response for SLC2A4 loss but also affects daily physical behavior and basal metabolic rate during bird evolution, highlighting that older genes retain a higher level of functional diversification.     

Functional Coding Variants in SLC6A15, a Possible Risk Gene for Major Depression

SLC6A15 is a neuron-specific neutral amino acid transporter that belongs to the solute carrier 6 gene family. This gene family is responsible for presynaptic re-uptake of the majority of neurotransmitters. Convergent data from human studies, animal models and pharmacological investigations suggest a possible role of SLC6A15 in major depressive disorder. In this work, we explored potential functional variants in this gene that could influence the activity of the amino acid transporter and thus downstream neuronal function and possibly the risk for stress-related psychiatric disorders. DNA from 400 depressed patients and 400 controls was screened for genetic variants using a pooled targeted re-sequencing approach. Results were verified by individual re-genotyping and validated non-synonymous coding variants were tested in an independent sample (N = 1934). Nine variants altering the amino acid sequence were then assessed for their functional effects by measuring SLC6A15 transporter activity in a cellular uptake assay. In total, we identified 405 genetic variants, including twelve non-synonymous variants. While none of the non-synonymous coding variants showed significant differences in case-control associations, two rare non-synonymous variants were associated with a significantly increased maximal ³H proline uptake as compared to the wildtype sequence. Our data suggest that genetic variants in the SLC6A15 locus change the activity of the amino acid transporter and might thus influence its neuronal function and the risk for stress-related psychiatric disorders. As statistically significant association for rare variants might only be achieved in extremely large samples (N >70,000) functional exploration may shed light on putatively disease-relevant variants.     

SLC6A4基因多态性与海洛因依赖的关联性研究

目的:探讨5-羟色胺转运体基因(solute carrier family 6 member 4,SLC6A4)基因4个单核苷酸多态性(single nucleotide polymorphism,SNP)位点与海洛因依赖之间的关系。方法:严格按照诊断标准,选取无亲缘关系的海洛因依赖个体397例(病例组)及健康对照个体402例(对照组)提取基因组DNA,采用SNaPshot SNP分型技术对SLC6A4基因4个SNP位点(rs1042173,rs3813034,rs6354,rs7224199)进行基因分型,比较病例-对照组间各位点等位基因、基因型频率的差异。结果:病例组和对照组SLC6A4基因rs1042173和rs3813034位点的基因型和等位基因频率比较存在显著性差异(P0.05),rs1042173的C等位基因(P=0.031,OR=1.317,95%CI=1.026-1.691)及rs3813034的C等位基因(P=0.013,OR=1.375,95%CI=1.069-1.768)是海洛因依赖的危险因素。病例组TCC单倍型(rs7224199、rs3813034和rs1042173)的比例较对照组显著增高(P0.05)。结论:SLC6A4基因rs1042173和rs3813034多态性可能与海洛因成瘾有关,携带有rs1042173的C等位基因和rs3813034的C等位基因的个体及携带TCC单倍型的个体可能更容易对海洛因产生依赖。     

DNA甲基化及其与胃癌相关研究进展

DNA甲基化是表观遗传学中的研究热点,与肿瘤的发生、发展、诊断、治疗、预后等相关。胃癌的发生、发展与DNA甲基化状态改变关系密切,研究胃癌相关基因DNA甲基化状态的改变有助于胃癌的早期发现、诊断、治疗及预后。因此,研究胃癌相关基因的甲基化状态具有一定的临床价值。     

DNA 甲基化及其与胃癌相关研究进展

DNA甲基化是表观遗传学中的研究热点,与肿瘤的发生、发展、诊断、治疗、预后等相关。胃癌的发生、发展与DNA甲基化状态改变关系密切,研究胃癌相关基因DNA甲基化状态的改变有助于胃癌的早期发现、诊断、治疗及预后。因此,研究胃癌相关基因的甲基化状态具有一定的临床价值。     

人二倍体化合子的DNA 甲基化变化模式

目的:探讨人类三原核合子及二倍体化合子中DNA甲基化模式的变化情况。方法:我们采用显微操作技术去除三原核合子中两个雄原核中的一个,观察恢复了二倍体状态的胚胎的发育情况,并检测了三原核和二倍体化的合子及早期胚胎中DNA甲基化模式的动态变化。结果:二倍体化的合子的囊胚形成率与三原核合子的囊胚形成率无显著性差异;在人三原核合子中两个雄原核发生主动地DNA去甲基化而雌原核在受精后的20h后仍保持甲基化。三原核与二倍体化合子中,DNA甲基化模式没有差别。结论:去除一个雄原核不会影响合子和胚胎的DNA甲基化模式。去除多余雄原核并不能改善胚胎的发育。     

DNA甲基化模式及其在癌症中的作用

随着对癌症研究的不断深入,表观遗传调控在癌症发生发展中的作用也越来越受到人们的关注。DNA基化作为一种重要的表观遗传修饰机制,在基因表达调控中起着十分重要的作用。该文对DNA基化模式及其在癌症中的作用作了综述,并对DNA甲基化作为癌症早期诊断的生物标记以及癌症表观治疗的新策略作了总结和展望。     

The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis

Recently it has been observed that cancer tissue is characterised by an increased variability in DNA methylation patterns. However, how the correlative patterns in genome-wide DNA methylation change during the carcinogenic progress has not yet been explored. Here we study genome-wide inter-CpG correlations in DNA methylation, in addition to single site variability, during cervical carcinogenesis. We demonstrate how the study of changes in DNA methylation covariation patterns across normal, intra-epithelial neoplasia and invasive cancer allows the identification of CpG sites that indicate the risk of neoplastic transformation in stages prior to neoplasia. Importantly, we show that the covariation in DNA methylation at these risk CpG loci is maximal immediately prior to the onset of cancer, supporting the view that high epigenetic diversity in normal cells increases the risk of cancer. Consistent with this, we observe that invasive cancers exhibit increased covariation in DNA methylation at the risk CpG sites relative to normal tissue, but lower levels relative to pre-cancerous lesions. We further show that the identified risk CpG sites undergo preferential DNA methylation changes in relation to human papilloma virus infection and age. Results are validated in independent data including prospectively collected samples prior to neoplastic transformation. Our data are consistent with a phase transition model of carcinogenesis, in which epigenetic diversity is maximal prior to the onset of cancer. The model and algorithm proposed here may allow, in future, network biomarkers predicting the risk of neoplastic transformation to be identified.     

A Potential Role for CHH DNA Methylation in Cotton Fiber Growth Patterns

DNA methylation controls many aspects of plant growth and development. Here, we report a novel annual growth potential change that may correlate with changes in levels of the major DNA demethylases and methyltransferases in cotton ovules harvested at different times of the year. The abundances of DNA demethylases, at both the mRNA and protein levels, increased significantly from February to August and decreased during the remainder of the 12-month period, with the opposite pattern observed for DNA methyltransferases. Over the course of one year, substantial changes in methylcytosine content was observed at certain CHH sites (H = A, C, or T) in the promoter regions of the ETHYLENE RESPONSIVE FACTOR 6 (ERF6), SUPPRESSION OF RVS 161 DELTA 4 (SUR4) and 3-KETOACYL-COA SYNTHASE 13 (KCS13), which regulate cotton fiber growth. Three independent techniques were used to confirm the annual fluctuations in DNA methylation. Furthermore, in homozygous RNAi lines specifically targeting REPRESSOR OF SILENCING 1 (ROS1, a conserved DNA demethylase domain), promotion of DNA methylation significantly reduced fiber growth during August.     

Association Study of Serotonin Transporter SLC6A4 Gene with Chinese Han Irritable Bowel Syndrome

Objective

Irritable bowel syndrome (IBS) is a common clinical gastrointestinal dysfunction disorders. 5-sertonon (5-hydroxytryptamine, 5-HT) is a very important neurotransmitter, which is involved in gastrointestinal motion and sensation. Solute carrier family 6 member 4 (SLC6A4) gene encode serotonin transporter (SERT) which function is to rapidly reuptake the most of 5-HT. Therefore, it is needed to explore the association between SLC6A4 gene polymorphisms and IBS.

Methods

119 patients and 238 healthy controls were administrated to detect the SLC6A4 gene polymorphisms including 5-HT-transporter-gene-linked polymorphic region (5-HTTLPR), variable number of tandem repeats (VNTRs) and three selected tag Single Nucleotide Polymorphisms (SNPs) rs1042173, rs3794808, rs2020936 by using polymerase chain reaction (PCR) and TaqMan® SNP Genotyping.

Results

There were significant difference for 5-HTTLPR between IBS and control groups (X2 = 106.168, P<0.0001). In control group, genotypes were mainly L/L (58.4%), however, the genotypes in IBS were S/S (37.8%). The significant difference was shown in D-IBS subjects when compared to the controls (X² = 50.850, P<0.0001) for 5-HTTLPR. For STin2 VNTR, rs1042173, rs3794808, and rs2020936 polymorphisms, there were no any significant differences between IBS and control groups. There were no statistical significantly haplotypes for 5-HTTLPR, VNTRs and the three SNPs between IBS and controls.

Conclusion

The S allele in 5-HTTLPR was a susceptible allele with Chinese Han IBS, but other associations of VNTRs, three selected Tag SNPs and positive haplotype with IBS were not found. It is indicated that much research are needed to study the relationship between other polymorphisms in SLC6A4 gene and IBS.     

乳腺癌相关基因的DNA甲基化

乳腺癌是女性最常见的恶性肿瘤之一。DNA甲基化作为哺乳动物细胞基因组修饰和表达调控的表观遗传学方式,在肿瘤的发生发展过程中总体水平降低,但同时又伴随某些基因的高甲基化。在乳腺癌中,多种关键基因的表达缺失都与其CpG岛高甲基化有关。     

植物中DNA甲基化模式及其相关机制

DNA甲基化是表观遗传修饰的重要形式之一,是植物中较早发现的DNA共价修饰方式。在植物的正常生长发育中,DNA甲基化与植物基因组维持、体细胞无性系变异、外来基因防御、内源基因的表达、转基因沉默以及基因印迹之间有着极大的关系,因此,植物DNA甲基化的研究对植物基因工程的发展有着举足轻重的作用。本文介绍了参与DNA甲基化的各种酶和蛋白质,阐述了DNA甲基化相关机制的最新研究进展。     

Prenatal Exposure to Maternal Depressed Mood and the MTHFR C677T Variant Affect SLC6A4 Methylation in Infants at Birth

Background

Prenatal and early postnatal exposure to maternal depression may “program” childhood behavior via epigenetic processes such as DNA methylation. Methylenetetrahydro-folate reductase (MTHFR) is an important enzyme in the generation of methyl groups for DNA methylation. The common MTHFR C677T variant is associated with depression in men and non-pregnant women, and with global changes in DNA methylation. This study investigated the effect of maternal MTHFR C677T genotype on antenatal maternal mood, and their impact on the gene-specific methylation in pregnant women and their newborn infants. The methylation status of SLC6A4, which encodes the transmembrane serotonin transporter, and BDNF, which encodes brain derived neurotrophic factor, were assessed because of their potential role in behaviour.

Methods/Principal Findings

Depressed mood was assessed by the Edinburgh Postnatal Depression Scale (EPDS) and the Hamilton Rating Scale for Depression (HAM-D) in women (n = 82, all taking folate) during the 2^nd and 3^rd trimesters of pregnancy. The methylation status of SLC6A4 and BDNF were assessed in 3rd trimester maternal peripheral leukocytes and in umbilical cord leukocytes collected from their infants at birth. Women with the MTHFR 677TT genotype had greater 2^nd trimester depressed mood (p<0.05). Increased 2^nd trimester maternal depressed mood (EPDS scores) was associated with decreased maternal and infant SLC6A4 promoter methylation (p<0.05), but had no effect on BDNF promoter methylation.

Conclusions

These findings show that the MTHFR C677T variant is associated with greater depressed mood during pregnancy. We further showed that prenatal exposure to maternal depressed mood affects gene-specific DNA methylation patterns. These findings support the concept that alterations in epigenetic processes may contribute to developmental programming of behaviour by maternal depression.     

Nell-1基因启动子区甲基化在胃癌中的研究*

目的:探讨Nell-1基因启动子区不同甲基化位点与胃癌患者术后病理分期及淋巴结转移度之间相关性。方法:收集2012年4月至2012年9月在哈尔滨医科大学附属第四临床医院肿瘤外科25例接受胃癌根治术的病人资料,运用配对t检验及线性回归统计方法,分析Nell-1基因启动子区不同甲基化位点与胃癌患者临床病理资料之间的相关因素。结果:Nell-1基因启动子区不同甲基化位点的胃癌组织组和胃正常组织组甲基化率之间的差别有统计学意义(第1号位点及第38号位点),简单线性回归结果分析显示在第1号位点随着患者术后病理分期逐渐降低,胃癌组织组和胃正常组织组甲基化率之间的差值会逐渐增大(负相关);而在第38号位点随着淋巴结转移度的逐渐增大,胃癌组织组和胃正常组织组甲基化率之间的差值会逐渐增大(正相关)。结论:胃癌的发生受诸多因素的影响,不同甲基化位点其甲基化率不同,其与胃癌患者临床病理资料之间存在一定相关性。     

Identifying Neural Patterns of Functional Dyspepsia Using Multivariate Pattern Analysis: A Resting-State fMRI Study

Background

Previous imaging studies on functional dyspepsia (FD) have focused on abnormal brain functions during special tasks, while few studies concentrated on the resting-state abnormalities of FD patients, which might be potentially valuable to provide us with direct information about the neural basis of FD. The main purpose of the current study was thereby to characterize the distinct patterns of resting-state function between FD patients and healthy controls (HCs).

Methodology/Principal Findings

Thirty FD patients and thirty HCs were enrolled and experienced 5-mintue resting-state scanning. Based on the support vector machine (SVM), we applied multivariate pattern analysis (MVPA) to investigate the differences of resting-state function mapped by regional homogeneity (ReHo). A classifier was designed by using the principal component analysis and the linear SVM. Permutation test was then employed to identify the significant contribution to the final discrimination. The results displayed that the mean classifier accuracy was 86.67%, and highly discriminative brain regions mainly included the prefrontal cortex (PFC), orbitofrontal cortex (OFC), supplementary motor area (SMA), temporal pole (TP), insula, anterior/middle cingulate cortex (ACC/MCC), thalamus, hippocampus (HIPP)/parahippocamus (ParaHIPP) and cerebellum. Correlation analysis revealed significant correlations between ReHo values in certain regions of interest (ROI) and the FD symptom severity and/or duration, including the positive correlations between the dmPFC, pACC and the symptom severity; whereas, the positive correlations between the MCC, OFC, insula, TP and FD duration.

Conclusions

These findings indicated that significantly distinct patterns existed between FD patients and HCs during the resting-state, which could expand our understanding of the neural basis of FD. Meanwhile, our results possibly showed potential feasibility of functional magnetic resonance imaging diagnostic assay for FD.     

Variations in DNA Methylation Patterns During the Cell Cycle of HeLa Cells

DNA methylation has been viewed as a stable component of the epigenome, which is established during development and fixed thereafter. We show here using nearest neighbor analysis, immunocytochemistry, and high performance capillary electrophoresis that the DNA methylation pattern varies in HeLa cells during a single cell cycle. Immunocytochemical analysis in primary human fibroblasts shows similar variations. The global levels of DNA methylation decreased in G1 and increase during the S phase of the cell cycle. Since there was little change in the DNA methylation levels in repetitive sequences throughout the cell cycle, we examined the DNA methylation pattern of unique sequences using a human CpG island microarray. Hybridization with methylated DNA from G1 and S phase of the cell cycle revealed that 174 CG-containing sequences were differentially methylated between G1 and S. 75% of all the variations in DNA methylation detected in unique sequences represented hypomethylation at G0, with changes occurring in both CpG islands and non-CpG islands. Bisulfite mapping confirmed these changes in methylation in the regions identified by the microarray. This is the first demonstration of a dynamic DNA methylation pattern within a single cell cycle of a mature somatic cell. These data are important for our understanding of the stability of DNA methylation patterns in somatic cells.