拷贝数目变异:基因组遗传变异的新诠释

拷贝数目变异(copy-number variant, CNV)也称拷贝数目多态(copy-number polymorphism, CNP), 是一种大小介于1 kb至3 Mb的DNA片段的变异, 在人类基因组中广泛分布, 其覆盖的核苷酸总数大大超过单核苷酸多态性(single nucleotide polymorphisms, SNPs)的总数, 极大地丰富了基因组遗传变异的多样性。CNV对于物种特异的基因组构成、物种的演化和系统发育以及基因组某些特定区域基因的表达和调控可能具有非常重要的生物学意义。本文从CNV的多态性、CNV的检测方法、CNV的多态性与表型的关联分析以及CNV的进化四个方面综述了CNV的研究成果, 并就CNV在动物基因组中的研究进行了展望。     

果蝇心脏基因一个新人同源基因WNT-10A的研究初报

Ｗｇ基因是控制果蝇心脏前体细胞形成的一个关键基因,根据物种间同源异型基因结构上的保守性与功能上的相似性,我们运用计算机克隆的方法获得了一个新的人同源基因,命名为ＷＮＴ－１０Ａ。该基因有一富集ＧＣ碱基的启动子,ｍＲＮＡ全长约２．４ｋｂ,３′末端包含ＡＴＡＡＡ的加尾信号,编码一段长４１７个氨基酸的蛋白质,与小鼠Ｗｎｔ－１０ａ的编码蛋白高度相似。其心脏ＥＳＴ数目占正常组织ＥＳＴ总数的４５％,表明该基因在心脏组织高度表达,提示其可能与心脏发育有关。该基因与其基因家族成员具有相似的同源框序列,在肿瘤细胞中大量表达（占总ＥＳＴ的３１％）,表明该基因相似于其家族成员,可能与肿瘤的发生有关。     

果蝇基因剂量补偿的实现机制

雌、雄果蝇间的基因剂量补偿是通过雄性果蝇中X染色体相关基因的表达水平上调至雌性果蝇的2倍实现的,基因剂量补偿的实现机制存在2种模型.平衡模型认为是基因组的不一致导致了全基因的反式剂量效应,而MSL复合体将组蛋白修饰酶从常染色体隔离,阻止了常染色体上的基因上调,同时,通过抑制高水平的组蛋白修饰以防止X染色体上的过度补偿....     

柑桔种间原生质体融合植株再生及染色体数目变异的研究

为了获得具有抗病、优质丰产等优良性状的柑桔体细胞杂种,本研究应用当前推广良种朋娜脐橙胚性细胞原生质体和抗裂皮病、耐盐碱的红桔叶肉细胞原生质体作为亲本进行体细胞杂交研究。通过对原生质体分离,融合和培养过程中培养基调控等环节的研究,建立起原生质体融合及其后的胚状体再生系统,并从融合处理后的原生质体培养中获得了大最的胚状体,进而获得个别体细胞杂种植株。同时对融合后再生的胚状体染色体数目和同工酶分析,还揭示了在柑桔原生质体融合再生中,胚状体水平上存在淹广泛的遗传变异。其中有14.1%的胚状体为四倍体,近20%为超倍体的非整倍体,并讨论了变异发生及由胚状体再生植株困难的原因。     

双拷贝APP/BACE/DPsn转基因果蝇模型的建立及基因功能的研究

阿尔茨海默症 (Alzheimer′s disease, AD), 是一种以脑中β-淀粉样蛋白 (β-amyloid peptide, Aβ)沉积为主要病理改变的神经退行性疾病。在果蝇Drosophila模型中建立淀粉样蛋白前体蛋白 (amyloid precursor protein, APP)的剪切通路模拟Aβ的产生过程, 有望建立一种快速筛选治疗AD药物的动物模型。我们利用经典的Gal4/UAS系统, 将现有的APP/BACE/DPsn果蝇品系连续杂交, 通过同源重组的方法构建表达两个拷贝的APP/BACE/DPsn稳定可遗传的转基因果蝇新品系。进一步的实验结果表明： 与不表达APP/BACE/DPsn的对照果蝇w/y; APP/Cyo; BACE-DPsn/TM6BTb相比, 表达两拷贝APP/BACE/DPsn的 w/y; elav-APP; BACE-DPsn果蝇的最长寿命为52 d, 比对照组(69 d)缩短了17 d, 为对照组果蝇的75%; 中位生存时间为39 d, 比对照组(49 d)缩短了10 d, 为对照组的80%; 平均寿命为37 d, 比对照组(47 d)缩短了10 d, 为对照组的79%。同时, 表达两个拷贝APP/BACE/DPsn的果蝇所产卵的羽化时间比对照果蝇延长了3 d; 其羽化成虫的理论值为1∶9 (11%), 而实际羽化率仅为5.2%。结果提示, 由elav-Gal驱动在果蝇泛神经元内过表达APP/BACE/DPsn, 可以缩短果蝇寿命、 干扰果蝇胚胎正常发育。该果蝇有可能作为初步筛选AD治疗药物的动物模型, 为AD治疗新药的发现提供工具。     

科学家完成12种果蝇基因组对比研究“壮举”其中10种是首次测序；研究发现新基因和进化痕迹

要详尽刻画一种生物模型的特征,需要多少个基因组序列?对果蝇而言,一打可能是不错的开始。由美国国立人类基因组研究所(NHGRI)资助的一个国际科研组织11月8日宣布,他们完成了12种“近亲”果蝇的基因组对比研究工作,其中有10种果蝇的基因组是首次测序。对比分析确定出了数千个新     

银额果蝇的B染色体研究:1.昆明群体的Bs数目和频率

本研究发现银额果蝇昆明群体有丝分裂中期核型中存在B染色体,出现频率为69.1%。目前,在已研究过的来自各个地区的银额果蝇中,昆明群体的B染色体频率最高。B染色体数目为1-6条。该群体内单雌系间的B染色体数目不同,个体间和细胞间的B染色体数目也不同。在核型中,B染色体最小,形态稳定,点状,C-带和G-带呈阳性。     

打开经典实验的问号——以摩尔根果蝇杂交实验为例

在实际教学中,对教材所描述的"摩尔根的果蝇交配实验"存有不少疑惑。从最初发现的白眼果蝇进行了几次交配、摩尔根通过哪种测交进一步验证了假设、如何理解白眼的遗传与X染色体遗传相似等3个方面着手,尝试解开该经典实验的问号。     

抗果蝇zip基因产物抗体的制备和胚胎zip蛋白分布的研究

zip基因为果蝇晚期神经发生所必需。分子生物学研究表明,zip基因产物是一个膜上整合糖蛋白,可能作为神经细胞的识别或粘联分子参与神经系统的发生。通过基因工程的方法,我们提取了lacZ-zip融合蛋白,继而免疫兔子制备了抗lacZ-zip融合蛋白抗体。该抗体在经过蛋白质印迹鉴定后,用于整幅果蝇胚胎的标记。结果显示zip基因产物主要在胚带缩短后表达,表明zip基因可能参与了晚期神经的发生。抗zip抗体除了识别中枢神经系统(CNS)中的个别神经元外,还标记了侧神经纤维,证实了以前的推测,即在CNS中表达的zip基因可能参与神经纤维束化的建立和维持。     

基于同源基因的病原菌鉴定和分型靶位点的功能基因组学研究

利用病原菌序列差异,对病原菌特定基因和位点进行检测,可以快速发现和鉴别病原菌的分类和特征,对传染病快速诊断和溯源具有基础性意义和重要价值.本文旨在覆盖中国重要传染病的103种病原菌,寻找各分类阶元中特有的同源基因,并从中挑选出适合用于病原菌鉴定、分型的候选基因.利用生物信息学和基因组学方法,对已有全基因组序列的275株病原菌的836415个基因进行比对分析,进一步明确菌株的门、纲、目、科、属各分类阶元中特有的同源基因集合;通过COG功能分类方法,对同源基因集合进行功能注释,并分析在不同分类阶元内的保守基因功能的变化规律.本研究寻找到适合鉴定和分型的不同分类阶元（门、纲、目、科、属）的同源基因集合共19563个（门2891个、纲1016个、目3601个、科10130个、属1925个）.对同源基因功能的分析表明,适合对病原菌进行鉴定的基因在不同分类阶元中,表现的功能存在较大差异.革兰氏阳性和阴性病原菌在不同分类阶元中,同源基因表现出的功能也存在差异.该结果将为对在中国广泛存在的病原菌进行检测所涉及的探针、芯片设计提供理论依据,加快目标探针的筛选工作.同时,研究也是首次将世界范围内的全基因组数据和中国重大传染病涉及的病原菌紧密联系结合,为利用功能基因组学开展区域性、有针对性的病原检测和监测,提供候选基因和位点筛选的新方法.相关结果在细菌的元基因组学研究中也具有一定的应用价值.     

猪13号染色体上拷贝数变异区内基因信息发掘及遗传规律分析

拷贝数变异(Copy number variation, CNV)是染色体上发生的一种微结构变异, 已引起越来越多研究者的关注。本课题组前期已获得猪13号染色体上的32个CNV区域(CNV region, CNVR), 为了发掘CNVR内的基因信息, 文章在线检索了上述CNVR内的基因并进行基因本体(Gene Ontology)分析。结果共发现236个基因, 其中有注释基因169个, 主要参与蛋白质水解、细胞粘附、大分子降解等生物过程。为了探索这些基因拷贝数变异的遗传规律, 文章选择RCAN1(Regulators of calcineurin 1)基因为候选基因, 利用QPCR方法在莱芜猪群中检测了该基因的拷贝数, 并分析了CNV在莱芜猪3个家系中的遗传规律。结果表明, RCAN1基因在莱芜猪群体中存在拷贝数的缺失、重复现象, 其拷贝数变异的遗传规律符合孟德尔遗传方式。     

Maintenance of transposable element copy number in natural populations of Drosophila melanogaster and D. simulans

To investigate the main forces controlling the containment of transposable elements (TE) in natural populations, we analyzed the copia, mdg1, and 412 elements in various populations of Drosophila melanogaster and D. simulans. A lower proportion of insertion sites on the X chromosome in comparison with the autosomes suggests that selection against the detrimental effects of TE insertions is the major force containing TE copies in populations of Drosophila. This selection effect hypothesis is strengthened by the absence of the negative correlation between recombination rate and TE copy number along the chromosomes, which was expected under the alternative ectopic exchange model (selection against the deleterious rearrangements promoted by recombination between TE insertions). A cline in 412 copy number in relation to latitude was observed among the natural populations of D. simulans, with very high numbers existing in some local populations (around 60 copies in a sample from Canberra, Australia). An apparent absence of selection effects in this Canberra sample and a value of transposition rate equal to 1–2 × 10^-3 whatever the population and its copy number agree with the idea of recent but temporarily drastic TE movements in local populations. The high values of transposition rate in D. simulans clearly disfavor the hypothesis that the low amount of transposable elements in this species could result from a low transposition rate. This revised version was published online in August 2006 with corrections to the Cover Date.     

tRNA gene copy number variation in humans

The human tRNAome consists of more than 500 interspersed tRNA genes comprising 51 anticodon families of largely unequal copy number. We examined tRNA gene copy number variation (tgCNV) in six individuals; two kindreds of two parents and a child, using high coverage whole genome sequence data. Such differences may be important because translation of some mRNAs is sensitive to the relative amounts of tRNAs and because tRNA competition determines translational efficiency vs. fidelity and production of native vs. misfolded proteins. We identified several tRNA gene clusters with CNV, which in some cases were part of larger iterations. In addition there was an isolated tRNALysCUU gene that was absent as a homozygous deletion in one of the parents. When assessed by semiquantitative PCR in 98 DNA samples representing a wide variety of ethnicities, this allele was found deleted in hetero- or homozygosity in all groups at ~ 50% frequency. This is the first report of copy number variation of human tRNA genes. We conclude that tgCNV exists at significant levels among individual humans and discuss the results in terms of genetic diversity and prior genome wide association studies (GWAS) that suggest the importance of the ratio of tRNALys isoacceptors in Type-2 diabetes.     

Microarray karyotyping of maltose‐fermenting Saccharomyces yeasts with differing maltotriose utilization profiles reveals copy number variation in genes involved in maltose and maltotriose utilization

Aims: We performed an analysis of maltotriose utilization by 52 Saccharomyces yeast strains able to ferment maltose efficiently and correlated the observed phenotypes with differences in the copy number of genes possibly involved in maltotriose utilization by yeast cells. Methods and Results: The analysis of maltose and maltotriose utilization by laboratory and industrial strains of the species Saccharomyces cerevisiae and Saccharomyces pastorianus (a natural S. cerevisiae/Saccharomyces bayanus hybrid) was carried out using microscale liquid cultivation, as well as in aerobic batch cultures. All strains utilize maltose efficiently as a carbon source, but three different phenotypes were observed for maltotriose utilization: efficient growth, slow/delayed growth and no growth. Through microarray karyotyping and pulsed‐field gel electrophoresis blots, we analysed the copy number and localization of several maltose‐related genes in selected S. cerevisiae strains. While most strains lacked the MPH2 and MPH3 transporter genes, almost all strains analysed had the AGT1 gene and increased copy number of MALx1 permeases. Conclusions: Our results showed that S. pastorianus yeast strains utilized maltotriose more efficiently than S. cerevisiae strains and highlighted the importance of the AGT1 gene for efficient maltotriose utilization by S. cerevisiae yeasts. Significance and Impact of the Study: Our results revealed new maltotriose utilization phenotypes, contributing to a better understanding of the metabolism of this carbon source for improved fermentation by Saccharomyces yeasts.     

A systematic phenotypic screen of F-box genes through a tissue-specific RNAi-based approach in Drosophila

F-box proteins are components of the SCF(SkpA-Cullin 1-F-box) E3 ligase complexes,acting as the specificity-determinants in targeting substrate proteins for ubiquitination and degradation.In humans,at least 22 out of 75 F-box proteins have experimentally documented substrates,whereas in Drosophila 12 F-box proteins have been characterized with known substrates.To systematically investigate the genetic and molecular functions of F-box proteins in Drosophila,we performed a survey of the literature and databases.We identified 45 Drosophila genes that encode proteins containing at least one F-box domain.We collected publically available RNAi lines against these genes and used them in a tissue-specific RNAi-based phenotypic screen.Here,we present our systematic phenotypic dataset from the eye,the wing and the notum.This dataset is the first of its kind and represents a useful resource for future studies of the molecular and genetic functions of F-box genes in Drosophila.Our results show that,as expected,F-box genes in Drosophila have regulatory roles in a diverse array of processes including cell proliferation,cell growth,signal transduction,and cellular and animal survival.     

Rare copy number variation in extremely impulsively violent males

The genetic correlates of extreme impulsive violence are poorly understood, and there have been no studies that have systematically characterized a large group of affected individuals both clinically and genetically. We performed a genome‐wide rare copy number variant (CNV) analysis in 281 males from four Czech prisons who met strict clinical criteria for extreme impulsive violence. Inclusion criteria included age ≥ 18 years, an ICD‐10 diagnosis of Dissocial Personality Disorder, and the absence of an organic brain disorder. Participants underwent a structured psychiatric assessment to diagnose extreme impulsive violence and then provided a blood sample for genetic analysis. DNA was genotyped and CNVs were identified using Illumina HumanOmni2.5 single‐nucleotide polymorphism array platform. Comparing with 10851 external population controls, we identified 828 rare CNVs (frequency ≤ 0.1% among control samples) in 264 participants. The CNVs impacted 754 genes, with 124 genes impacted more than once (2‐25 times). Many of these genes are associated with autosomal dominant or X‐linked disorders affecting adult behavior, cognition, learning, intelligence, specifically expressed in the brain and relevant to synapses, neurodevelopment, neurodegeneration, obesity and neuropsychiatric phenotypes. Specifically, we identified 31 CNVs of clinical relevance in 31 individuals, 59 likely clinically relevant CNVs in 49 individuals, and 17 recurrent CNVs in 65 individuals. Thus, 123 of 281 (44%) individuals had one to several rare CNVs that were indirectly or directly relevant to impulsive violence. Extreme impulsive violence is genetically heterogeneous and genomic analysis is likely required to identify, further research and specifically treat the causes in affected individuals.     

A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method

The discovery of copy number variation (CNV) in the genome has provided new insight into genomic polymorphism. Studies with chickens have identified a number of large CNV segments using a 385k comparative genomic hybridization (CGH) chip (mean length >140 kb). We present a detailed CNV map for local Chinese chicken breeds and commercial chicken lines using an Agilent 400k array CGH platform with custom-designed probes. We identified a total of 130 copy number variation regions (CNVRs; mean length = 25.70 kb). Of these, 104 (80.0%) were novel segments reported for the first time in chickens. Among the 104 novel CNVRs, 56 (53.8%) of the segments were non-coding sequences, 65 (62.5%) showed the gain of DNA and 40 (38.5%) showed the loss of DNA (one locus showed both loss and gain). Overlapping with the formal selective sweep data and the quantitative trait loci data, we identified four loci that might be considered to be high-confidence selective segments that arose during the domestication of chickens. Compared with the CNVRs reported previously, genes for the positive regulation of phospholipase A2 activity were discovered to be significantly over-represented in the novel CNVRs reported here by gene ontology analysis. Availability of our results should facilitate further research in the study of the genetic variability in chicken breeds.