依赖于5′端非编码区高级结构的真核生物mRNA翻译调控

翻译水平的调控是真核基因表达调控的重要环节.近年来的研究表明,许多真核基因的翻译依赖于RNA5′端非编码区的结构元件.一些小结构元件,如铁离子反应元件,具有1个茎环结构,由铁离子介导控制转铁蛋白的翻译.核糖开关通过结合特定代谢分子在2种结构状态下切换,调控可变剪接和翻译起始.另1个高度结构化的mRNA元件是内部核糖体进入位点,通过富集核糖体和起始因子促进基因的表达.本文综述了依赖于小结构元件、内部核糖体进入位点和核糖开关的真核基因翻译起始调控相应的研究成果和研究方法.对于研究的前景以及可能存在的挑战也作出阐述.     

依赖于5′端非编码区高级结构的真核生物mRNA翻译调控

翻译水平的调控是真核基因表达调控的重要环节.近年来的研究表明,许多真核基因的翻译依赖于RNA 5′端非编码区的结构元件.一些小结构元件,如铁离子反应元件,具有1个茎环结构,由铁离子介导控制转铁蛋白的翻译. 核糖开关通过结合特定代谢分子在2种结构状态下切换,调控可变剪接和翻译起始.另1个高度结构化的mRNA元件是内部核糖体进入位点,通过富集核糖体和起始因子促进基因的表达.本文综述了依赖于小结构元件、内部核糖体进入位点和核糖开关的真核基因翻译起始调控相应的研究成果和研究方法.对于研究的前景以及可能存在的挑战也作出阐述.     

Yeast基因组编码区特征参数的研究

以碱基成分偏移量D值为基本参数定义参数d,以d为Yeast编码区的特征参数,对Yeast的第1、2、3类ORF（open reading frame)进行了统计,得到d的特征参数区间,并且,以此区间为标准为Yeast的6类ORF,以及5′帽、3′尾、内含子、组分随机序列等非编码序列进行了检验。结果表明,d作编码区的特征参数是可行的,它可以很好地区分编码序列和非编码序列。别外,又讨论了参数d与基因表达水平（用CAI值来衡量）的关系。发现,参数d与基因表达水平成很好的正相关关系。发现密码子的第1位点和第2位点的某些碱基分布与基因表达水平有关。     

大肠杆菌编码区碱基片段的分析研究

对大肠杆菌1231个编码开始区域和1307个编码终止区域内的6碱基片段、4碱基片段和3碱基片段进行了统计,发现绝大多数4碱基和3碱基模式出现在盯对频率小于2的范围之内;在这两个区域中,出现最多的碱基片段是多聚A;编码开始区域和编码终止区域的碱基构成模式有明显区别;编码开始区域里GGA类的稀有片段恰恰是SD区域最偏好的碱基片段;以TAG或CTA构造的3碱基模式为编码开始区和编码终止区的禁用模式。     

基于DNA非编码区序列探讨罗布麻的分类问题

通过测定中国产罗布红麻、大叶白麻和白麻的ITSt、rnL内含子和trnL-F非编码区序列,并与其它相关植物的相应序列比较,探讨“罗布麻”的系统分类。结果显示:罗布红麻、大叶白麻和白麻3种植物的ITS序列完全一致,而与罗布麻属加拿大麻的ITS序列相差较大;在trnL内含子和trnL-F非编码区,大叶白麻和白麻的完全一致,与罗布红麻之间仅有3个位点的变异,而加拿大麻与美国茶叶花在这3个位点却和白麻属的完全一致等。以上结果显示在ITSt、rnL内含子和trnL-F非编码区,白麻属和罗布麻属之间没有本质区别,罗布红麻与大叶白麻和白麻之间的亲缘关系可能较罗布红麻与罗布麻属内其它物种间的亲缘关系更近。遗传距离与系统树的分析结果进一步支持以上推论。建议撤销白麻属,将大叶白麻和白麻合并到罗布麻属。     

丙型肝炎病毒基因组5‘非编码区结构与功能研究进展

丙型肝炎病毒是经血源传播的一类肝炎病毒,其基因组为单股正链ＲＮＡ,全长约为 ９．５ｋｂ,结构组成与黄热病毒和瘟病毒相似,它的５、非编码区相对较长,一般为３２４－３４１个碱基。内含有数个小的开放阅读框。不同分离株在此区的同源性可高达９８％,其一级结构高度保守,并可形成特定的二级结构,在病毒基因的表达和复制中起重要的调节作用。     

真核生物mRNA 3'非翻译区的功能

真核牛物mRNA的3'非翻译区的功能复杂多样,不仅能调控其mRNA的稳定性、控制mRNA的亚细胞定位,而且还在特定氨基酸的编码过程中起着指导作用.一些真核生物mRNA的3'非翻译区内的突变可引起疾病的发生.近几年的研究义发现,一些真核生物mRNA的3'非翻译区还具有抑制肿瘤生长的功能.     

蛋白质编码区与非编码区的特征与识别

在核苷酸序列分析中,一个重要的问题是如何识别一段未知序列中的编码区和非编码区．近年来提出了一些方法,但效果都不够理想．本文在对编码区与非编码区特征进行大量统计分析的基础上,提出一种加权距离判别法,并对该方法的精度进行了评价．     

基因非编码区与转录调控元件的识别研究

随着后基因组时代的到来,非编码区的研究已经成为科学家面临的挑战,对基因非编码区的一个主要研究方向就是对调控元件的研究。识别转录调控元件是理解基因转录机制和表达模式的关键。较全面地介绍了基因非编码区以及调控元件,包括功能和作用,常用识别算法,并对常用数据库进行介绍,提出可能的研究方法和发展方向。     

真核生物mRNA 3′非翻译区的功能

真核生物mRNA的3′非翻译区的功能复杂多样,不仅能调控其mRNA的稳定性、控制mRNA的亚细胞定位,而且还在特定氨基酸的编码过程中起着指导作用.一些真核生物mRNA的3′非翻译区内的突变可引起疾病的发生.近几年的研究又发现,一些真核生物mRNA的3′非翻译区还具有抑制肿瘤生长的功能.     

The Influence of Specific Neighboring Bases on Substitution Bias in Noncoding Regions of the Plant Chloroplast Genome

Substitutions occurring in noncoding sequences of the plant chloroplast genome violate the independence of sites that is assumed by substitution models in molecular evolution. The probability that a substitution at a site is a transversion, as opposed to a transition, increases significantly with increasing A + T content of the two adjacent nucleotides. In the present study, this dependency of substitutions on local context is examined further in a number of noncoding regions from the chloroplast genome of members of the grass family (Poaceae). Two features were examined; the influence of specific neighboring bases, as opposed to the general A + T content, on transversion proportion and an influence on substitutions by nucleotides other than the two immediately adjacent to the site of substitution. In both cases, a significant effect was found. In the case of specific nucleotides, transversion proportion is significantly higher at sites with a pyrimidine immediately 5′ on either strand. Substitutions at sites of the type YNR, where N is the site of substitution, have the highest rate of transversion. This specific effect is secondary to the A + T content effect such that, in terms of proportion of substitutions that are transversions, the nucleotides are ranked T > A > C > G as to their effect when they are immediately 5′ to the site of substitution. In the case of nucleotides other than the immediate neighbors, a significant influence on substitution dynamics is observed in the case where the two neighboring bases are both A and/or T. Thus, substitutions are primarily, but not exclusively, influenced by the composition of the two nucleotides that are immediately adjacent. These results indicate that the pattern of molecular evolution of the plant chloroplast genome is extremely complex as a result of a variety of inter-site dependencies. Received: 18 October 1996 / Accepted: 12 April 1997     

Polymorphism of the Noncoding Region of the Mitochondrial Genome in Three Kazakh Populations Inhabiting Different Areas of Kazakhstan and in DNA Samples from Ancient Populations of the Kazakhstani Altai

The polymorphism of the major noncoding region of mitochondrial DNA (mtDNA D loop, 528 bp) has been studied in samples from three modern Kazakh populations (from Almaty, the Semipalatinsk Region, and the Altai Mountains) and in DNA samples of ancient human populations of the Kazakhstani Altai. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis for 13 restriction sites, including BamHI, EcoRV, Sau3AI (one site each), KpnI (two sites), HaeIII (three sites), and RsaI (five sites) were used. The frequency distributions of all sites have been determined. The gene diversity (h) and the genetic distances between different Kazakh populations and other populations of the world have been calculated. The RFLP analysis of the mtDNA control region of fossil samples has been performed similarly to the analysis of modern mtDNA samples. Two fossil mtDNA samples from burial mound 11 are monomorphic with respect to all restriction sites analyzed.     

非编码长链RNA与基因表达调控

近年来,在小鼠全长cDNA文库大规模测序中发现一类新的转录物——非编码长链RNA(long noncoding RNA,lncRNA),引起了科学界的关注.lncRNA长度大于200个核苷酸,无蛋白质编码功能,在真核细胞基因组中被普遍转录.lncRNA种类繁多,数量庞大,占哺乳动物基因组转录物的绝大部分.相对于研究较多的非编码小RNA,lncRNA的功能目前尚不完全清楚.但越来越多的研究发现,lncRNA在多个水平调控基因的表达,在胚胎发育、物种进化、细胞分化和某些疾病如神经退行性疾病及肿瘤的发生过程中起着重要作用.本文在简要介绍lncRNA基本概念的基础上,结合当前研究成果,就lncRNA在转录水平、转录后水平和表观遗传水平调控基因表达的机制作一综述.     

Selection on Accessible Chromatin Regions in Capsella grandiflora

Accurate estimates of genome-wide rates and fitness effects of new mutations are essential for an improved understanding of molecular evolutionary processes. Although eukaryotic genomes generally contain a large noncoding fraction, functional noncoding regions and fitness effects of mutations in such regions are still incompletely characterized. A promising approach to characterize functional noncoding regions relies on identifying accessible chromatin regions (ACRs) tightly associated with regulatory DNA. Here, we applied this approach to identify and estimate selection on ACRs in Capsella grandiflora, a crucifer species ideal for population genomic quantification of selection due to its favorable population demography. We describe a population-wide ACR distribution based on ATAC-seq data for leaf samples of 16 individuals from a natural population. We use population genomic methods to estimate fitness effects and proportions of positively selected fixations (α) in ACRs and find that intergenic ACRs harbor a considerable fraction of weakly deleterious new mutations, as well as a significantly higher proportion of strongly deleterious mutations than comparable inaccessible intergenic regions. ACRs are enriched for expression quantitative trait loci (eQTL) and depleted of transposable element insertions, as expected if intergenic ACRs are under selection because they harbor regulatory regions. By integrating empirical identification of intergenic ACRs with analyses of eQTL and population genomic analyses of selection, we demonstrate that intergenic regulatory regions are an important source of nearly neutral mutations. These results improve our understanding of selection on noncoding regions and the role of nearly neutral mutations for evolutionary processes in outcrossing Brassicaceae species.     

Compositional evolution of noncoding DNA in the human and chimpanzee genomes

We have examined the compositional evolution of noncoding DNA in the primate genome by comparison of lineage-specific substitutions observed in 1.8 Mb of genomic alignments of human, chimpanzee, and baboon with 6542 human single-nucleotide polymorphisms (SNPs) rooted using chimpanzee sequence. The pattern of compositional evolution, measured in terms of the numbers of GC-->AT and AT-->GC changes, differs significantly between fixed and polymorphic sites, and indicates that there is a bias toward fixation of AT-->GC mutations, which could result from weak directional selection or biased gene conversion in favor of high GC content. Comparison of the frequency distributions of a subset of the SNPs revealed no significant difference between GC-->AT and AT-->GC polymorphisms, although AT-->GC polymorphisms in regions of high GC segregate at slightly higher frequencies on average than GC-->AT polymorphisms, which is consistent with a fixation bias favoring high GC in these regions. However, the substitution data suggest that this fixation bias is relatively weak, because the compositional structure of the human and chimpanzee genomes is becoming homogenized, with regions of high GC decreasing in GC content and regions of low GC increasing in GC content. The rate and pattern of nucleotide substitution in 333 Alu repeats within the human-chimpanzee-baboon alignments are not significantly affected by the GC content of the region in which they are inserted, providing further evidence that, since the time of the human-chimpanzee ancestor, there has been little or no regional variation in mutation bias.     

森林群落复杂性分析:以广东黑石顶森林为例

本文将森林群落复杂性定义为消除群落中任意一个树木个体的种名及层次不确定性所需的平均信息量,提出用联合熵H(X,Y)测度群落复杂性.H(X,Y)=H(X)+H(Y|X),其中H(X)=-∑Si=1(ni)/(N)log2((ni)/(N)),H(Y|X)=-∑Si=1(ni)/(N)∑4j=1(nij)/(ni)log2((nij)/(ni)),分别为树种组成复杂性和树种结构复杂性.式中S为森林群落树种数,N为森林群落的树木总株数,ni(i=1,2,...,S)为第i个树种的株数,nij(j=1,2,3,4)为第i个树种在第j层次的株数.用联合熵分析了广东省封开县黑石顶自然保护区针叶林、针阔混交林和常绿阔叶林等3种典型森林类型的复杂性.结果表明,群落复杂性的顺序为常绿阔叶林>针阔混交林>针叶林.同时,各森林类型的群落复杂性H(X,Y)与取样尺度之间具有较好的分形关系.     

The Effect of the Nucleotide Context on Induction of Mutations in Hypervariable Segment 1 of Human Mitochondrial DNA

The distribution of unstable nucleotide positions with a higher frequency of homoplastic mutations was analyzed in hypervariable segment 1 (HVS1) of the major noncoding region of human mtDNA. Three motifs (GTAC, ACCC, CCTC) proved to be associated with a higher rate of point substitutions at unstable positions. The motifs were often arranged in direct, including tandem, repeats. Motifs CCTC and ACCC were found in extended poly(C) tracts, which form direct repeats associated with deletions and tandem duplications. The results suggested that the inconstancy of the human mitochondrial genome is to a great extent determined by context-dependent mutations.     

Admissible Regions in a Simplex of Identity Coefficients

Genealogical relationships between any number of individuals are characterized, from the genetic point of view, by the probabilitiea of ell poeeible gene identity states occuning at an autosomel locus. However, only a eubepece of the apace of all probabilities ie in fact accemible to any relationehip. Badon a theorem of THOMPSON (1076). a characterization of the admissible region in the simplex of all condeneed identity coefficients of two non-inbred individuals is presented. Further s similar result in the caae of detailed coefficients is given.     

中国主要农区稻田稗草分类与多样性研究

将采自中国15个省和1个直辖市的206份稗属（Echinochloa）植物种子分别播种在相同栽培条件下,获得了206份子代样本及其21项形态性状数据,基于这些形态性状对206份稗属植物样本进行了聚类和主成分分析。结果表明：（1）从206份稗属植物样本中鉴别出了形态性状相对一致的8个分类群（G1-G8）,依次对应于湖南稗子（Echinochloa frumentaceae,2份样本）、水田稗（E.oryzoides,5份）、细叶旱稗（E.crus-galli var.praticola,6份）、硬稃稗（E.glabrescens,14份）、光头稗（E.colona,2份）、长芒稗（E.caudata,16份）、孔雀稗（E.cruspavonis,8份）、稗复合群（稗原变种E.crus-galli var.crus-galli、稗的变种无芒稗var.mitis、短芒稗var.breviseta和西来稗var.zelayensis,共150份）,还有3份样本没有聚合成组。它们依次占总样本量的0.97%、0.97%、2.42%、2.91%、3.88%、7.77%、6.80%、72.81%和1.46%,反映出中国主要农区稻田稗属植物主要以稗及其变种为主;（2）单因素方差分析表明,9个数量性状,包括叶长、叶宽、圆锥花序长度、总状花序长度、小穗芒长、小穗长度、第1颖长度/小穗长度、主茎直径和株高,在稗属植物的8个分类群（G1-G8）之间有显著差异;（3）根据8个分类群之间的形态性状特点及差异,给出了鉴别中国主要农区稻田稗属植物的分种检索表;（4）由于细叶旱稗具有总状花序简单、小穗无芒、叶较宽、植株高大、小穗紫黑色等独特形态性状,在206份稗属植物样本的聚类图上单独聚成一组,故建议将细叶旱稗作为独立种处理。     

Genome analysis: A new approach for visualization of sequence organization in genomes

In this article we describe and demonstrate the versatility of a computer program, GENOME MAPPING, that uses interactive graphics and runs on an IRIS workstation. The program helps to visualize as well as analyse global and local patterns of genomic DNA sequences. It was developed keeping in mind the requirements of the human genome sequencing programme, which requires rapid analysis of the data. Using GENOME MAPPING one can discern signature patterns of different kinds of sequences and analyse such patterns for repetitive as well as rare sequence strings. Further, one can visualize the extent of global homology between different genomic sequences. An application of our method to the published yeast mitochondrial genome data shows similar sequence organizations in the entire sequence and in smaller subsequences