基因组拷贝数变异研究进展

基因组结构变异分为两个层次:显微水平(microscopic)和亚显微水平(submicroscopic)。显微水平的基因组结构变异主要是指显微镜下可见的染色体畸变,包括整倍体或非整倍体、缺失、插入、倒位、易位、脆性位点等结构变异。亚显微水平的基因组结构变异是指DNA片段长度在1Kb-3Mb的基因组结构变异,包括缺失、插入、重复、重排、倒位、DNA拷贝数目变化(copy numbervariation,CNV),这些统称为CNV或者CNP(copy number polymorphisms,CNP)。对CNV的研究能够帮助研究者建立遗传检测假说,进而发现疾病易感基因,同时加深对表型变异的理解,为今后研究人类生物功能、进化、疾病奠定基础。本文主要从CNV的研究历史、分子机制、研究方法、研究意义等四个方面进行综述.。     

Genetic control of lipid transport in mice. II. Genes controlling structure of high density lipoproteins

Genetic factors controlling the structure of high density lipoproteins (HDL) in mice have been examined. Surveys of inbred strains of mice revealed genetic structural variations of the two major apolipoproteins of mouse HDL, apolipoproteins A-I and A-II. The structural variations alter the charge of the proteins as judged by isoelectric focusing of HDL under denaturing conditions. The structural variations are inherited as single Mendelian genes exhibiting co-dominant expression. The structural gene for mouse apolipoprotein A-II, designated Alp-2, resides on mouse chromosome 1, tightly linked to Ly-m20, a lymphocyte alloantigen locus. Previous studies, as well as our results, suggest that the structural gene for mouse apolipoprotein A-I, designated Alp-1, is on mouse chromosome 9. The genetic structural variation for apo-A-I results in a shift in the charge of the entire family of apo-A-I isoforms, indicating that they are all encoded by a common structural gene. The structure of intact HDL, examined primarily by electrophoretic techniques, exhibits numerous and complex phenotypes among different strains of mice. One variation, controlling the density and possibly the size of HDL, has been studied in two sets of recombinant inbred strains of mice. The results indicate that the variation is controlled by a single major gene that is either tightly linked to or identical with the Alp-2 gene on chromosome 1. In addition to structural variation, inbred strains of mice exhibited considerable quantitative variation of plasma HDL. Thus, the mouse provides a useful model system for examining the genetic control of mammalian HDL structure and regulation.     

Variant class II molecules from H-2 haplotypes in wild mouse populations: functional characteristics of closely related class II gene products

Independently derived haplotypes found in wild populations of mice often express class II molecules antigenically related to specific alleles of the A molecules defined in laboratory mice. Tryptic peptide fingerprint comparisons of these antigenically related molecules indicate that they have similar, or possibly identical, primary structures in the A alpha, A beta, or both subunits. By using the Ak and Ap families of independently derived, antigenically related A molecules, we examined the effect that minor structural variations in the A molecule have on allorecognition by T lymphocytes. Data obtained indicate that a) minor structural variations in the A molecule can effect, although not always, major functional changes in allorecognition, b) changes in allorecognition are always detected when the A beta subunit contains structural variations, but not necessarily when the A alpha subunit contains structural variations, and c) more than one site in the A molecule can be recognized by alloreactive T lymphocytes. These results can be interpreted as indicating that specific sites within the A molecule are critically involved in allorecognition and that structural variations must affect these sites to elicit major changes in allorecognition.     

Structural Variations Increase the Upper Limit of Colony Size of Microcystis: Implications from Laboratory Cultures and Field Investigations

Wild Microcystis have highly diverse colonial structures and sizes, including variable colony geometry, cell arrangement, and diameter. These structural and dimensional variations may play an important role in continual, frequent Microcystis blooms during summer and autumn, the cause of which still remains unclear. Here, laboratory cultures and field investigations were applied to assess mechanisms that drive variation in structure and size, as well as factors that influence diversity. The results demonstrated that colonies grew to large sizes at the expense of their structure being loose and inhomogeneous. Furthermore, colonies may spontaneously change structure to relieve the constraints of size in return. Influencing factors (nutrient limits and turbulent shear) tended to promote these variations. Our work highlights that the diversity of Microcystis colonies may be a result of structural variations as survival strategies for gaining a higher upper size limit. Therefore, during seasonal successions, large colonies commonly have porous or loosely arranged structures, such as in M. aeruginosa. Additionally, this study hypothesized three possible transition routes for better understanding structural diversity and variations in Microcystis.     

Identification of transposable element-mediated deletions in 27 Korean individuals based on whole genome sequencing data

The human genome has various genomic structural variations such as insertion/deletions between human individuals. These structural variations have led to genomic fluidity and rearrangements in individuals and populations. To investigate Korean-specific structural genomic variations, we performed next generation sequencing with 30× mean coverage from 27 Korean individuals using illumina-HiSeq 2000 platform. We collected a total of 119 deletion loci as transposable element-mediated Korean-specific deletion (KSD) candidates. Of the 119 loci, 35 were filtered out due to computational overlapping regions. A total of 78 loci were validated by PCR amplification with 27 Korean individuals and 80 human individuals from four different populations. We confirmed deletion breakpoints of the 78 loci using Sanger sequencing. We also investigated different deletion mechanisms based on sequencing alignment analysis. We found at least one KSD locus in 80 human individual panel. It has not been previously reported in human genomes. Here, for the first time, we report transposable element-mediated KSD study based on whole genome sequencing data of 27 Korean.     

Levodopa influences the regularity of the ankle joint kinematics in individuals with Parkinson’s disease

The aim of the investigation was to explore the influence of levodopa therapy on the regularity of the structural variations present in the lower extremity joints of individuals with Parkinson’s disease (PD). Ten participants with PD walked on a treadmill during the states of “off” and “on” levodopa. Approximate entropy was used to quantify the regularity of the structural variations present in the joint kinematics. Additionally, a pseudo-periodic surrogation analysis was used to evaluate if changes in the regularity of the joint’s movement were associated with a noisy or deterministic motor process. This investigation provided two key findings. The first was that the structural variations present in ankle joint were more regular with levodopa therapy. The second was that changes in the structural variations were related to a deterministic motor process. This indicated that the variations present in the walking patterns of individuals with PD most likely arose from higher-order neural couplings rather than noise in the motor process. Monitoring the regularity of the structural variations present in gait may help improve the management of PD.     

A Genome-Wide Analysis of Array-Based Comparative Genomic Hybridization (CGH) Data to Detect Intra-Species Variations and Evolutionary Relationships

Array-based comparative genomics hybridization (aCGH) has gained prevalence as an effective technique for measuring structural variations in the genome. Copy-number variations (CNVs) form a large source of genomic structural variation, but it is not known whether phenotypic differences between intra-species groups, such as divergent human populations, or breeds of a domestic animal, can be attributed to CNVs. Several computational methods have been proposed to improve the detection of CNVs from array CGH data, but few population studies have used CGH data for identification of intra-species differences. In this paper we propose a novel method of genome-wide comparison and classification using CGH data that condenses whole genome information, aimed at quantification of intra-species variations and discovery of shared ancestry. Our strategy included smoothing CGH data using an appropriate denoising algorithm, extracting features via wavelets, quantifying the information via wavelet power spectrum and hierarchical clustering of the resultant profile. To evaluate the classification efficiency of our method, we used simulated data sets. We applied it to aCGH data from human and bovine individuals and showed that it successfully detects existing intra-specific variations with additional evolutionary implications.     

CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations

Background  

Distantly related proteins adopt and retain similar structural scaffolds despite length variations that could be as much as two-fold in some protein superfamilies. In this paper, we describe an analysis of indel regions that accommodate length variations amongst related proteins. We have developed an algorithm CUSP, to examine multi-membered PASS2 superfamily alignments to identify indel regions in an automated manner. Further, we have used the method to characterize the length, structural type and biochemical features of indels in related protein domains.     

人类基因组结构变异检测方法

本研究介绍了基因组结构变异检测的生物信息学基本方法和前沿技术。对基于第二代测序技术的四种检测方法(读对方法,读深方法,分裂片段方法和序列拼接方法)的原理和特点进行了详细解读,分析了第二代测序技术应用在检测结构变异上的特点与发展趋势。最后介绍了三代测序、Linked-reads和光学物理图谱等新技术在基因组结构变异检测中的应用,论述了融合新技术的结构变异检测方法的特点与优势。     

Ultrastructural variations in frog muscles subjected to sciatectomy

Fine structural variations in two different types of muscles of frog (Rana cyanophlictis) subjected to sciatectomy were studied electronmicroscopically. Gastrocnemius muscle showed marked myofibrillar disarray and degeneration due to sciatectomy, while sartorius muscle was relatively less affected. The extent of sciatectomy induced fine structural variation was in proportion to the degree of denervation atrophy (as reflected by loss of wet muscle weight) in these muscles. Differences in the degree of degenerative changes in atrophying muscles may be attributed to variations in fiber type composition and stretch effects imposed during swimming movements.     

High Density LD-Based Structural Variations Analysis in Cattle Genome

Genomic structural variations represent an important source of genetic variation in mammal genomes, thus, they are commonly related to phenotypic expressions. In this work, ∼770,000 single nucleotide polymorphism genotypes from 506 animals from 19 cattle breeds were analyzed. A simple LD-based structural variation was defined, and a genome-wide analysis was performed. After applying some quality control filters, for each breed and each chromosome we calculated the linkage disequilibrium (r ²) of short range (≤100 Kb). We sorted SNP pairs by distance and obtained a set of LD means (called the expected means) using bins of 5 Kb. We identified 15,246 segments of at least 1 Kb, among the 19 breeds, consisting of sets of at least 3 adjacent SNPs so that, for each SNP, r ² within its neighbors in a 100 Kb range, to the right side of that SNP, were all bigger than, or all smaller than, the corresponding expected mean, and their P-value were significant after a Benjamini-Hochberg multiple testing correction. In addition, to account just for homogeneously distributed regions we considered only SNPs having at least 15 SNP neighbors within 100 Kb. We defined such segments as structural variations. By grouping all variations across all animals in the sample we defined 9,146 regions, involving a total of 53,137 SNPs; representing the 6.40% (160.98 Mb) from the bovine genome. The identified structural variations covered 3,109 genes. Clustering analysis showed the relatedness of breeds given the geographic region in which they are evolving. In summary, we present an analysis of structural variations based on the deviation of the expected short range LD between SNPs in the bovine genome. With an intuitive and simple definition based only on SNPs data it was possible to discern closeness of breeds due to grouping by geographic region in which they are evolving.     

Epigenetic silencing of genomic structural variations

A great amount of copy number variations (CNVs) are identified in the human genome. Most of them are neutral; nevertheless, the role of CNVs in the pathogenesis of hereditary diseases is still significant. Especially, this is important for neuropsychiatric disorders, such as intellectual disability and autism. When analyzing the CNV-associated diseases, the controversial question is to distinguish the pathogenic CNVs among common polymorphic variants and to predict the disease risk in other children of the family. Unfortunately, the mechanisms of phenotypic expression and incomplete penetrance of CNVs remain largely unknown. Currently, incomplete penetrance and variable expressivity of CNVs are attributed mainly to allelic interaction of different genetic variations. However, epigenetic mechanisms of gene expression regulation in the context of structural variation of the genome are poorly explored. It is possible that epigenetic modifications of the genome regions with CNVs may underlie the understanding of ways of phenotypic manifestations of structural variations in the human genome.     

Continuum secondary structure captures protein flexibility

The DSSP program assigns protein secondary structure to one of eight states. This discrete assignment cannot describe the continuum of thermal fluctuations. Hence, a continuous assignment is proposed. Technically, the continuum results from averaging over ten discrete DSSP assignments with different hydrogen bond thresholds. The final continuous assignment for a single NMR model successfully reflected the structural variations observed between all NMR models in the ensemble. The structural variations between NMR models were verified to correlate with thermal motion; these variations were captured by the continuous assignments. Because the continuous assignment reproduces the structural variation between many NMR models from one single model, functionally important variation can be extracted from a single X-ray structure. Thus, continuous assignments of secondary structure may affect future protein structure analysis, comparison, and prediction.     

Identification of large-scale genomic variation in cancer genomes using in silico reference models

Identifying large-scale structural variation in cancer genomes continues to be a challenge to researchers. Current methods rely on genome alignments based on a reference that can be a poor fit to highly variant and complex tumor genomes. To address this challenge we developed a method that uses available breakpoint information to generate models of structural variations. We use these models as references to align previously unmapped and discordant reads from a genome. By using these models to align unmapped reads, we show that our method can help to identify large-scale variations that have been previously missed.     

Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure

Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational variations in a protein and conformational differences in its homologues of known structure is still unclear. In this study, we have used a structural alphabet called Protein Blocks (PBs). PBs are used to perform abstraction of protein 3-D structures into a 1-D strings of 16 alphabets (a–p) based on dihedral angles of overlapping pentapeptides. We have analyzed the variations in local conformations in terms of PBs represented in the ensembles of 801 protein structures determined using NMR spectroscopy. In the analysis of concatenated data over all the residues in all the NMR ensembles, we observe that the overall nature of inherent local structural variations in NMR ensembles is similar to the nature of local structural differences in homologous proteins with a high correlation coefficient of .94. High correlation at the alignment positions corresponding to helical and β-sheet regions is only expected. However, the correlation coefficient by considering only the loop regions is also quite high (.91). Surprisingly, segregated position-wise analysis shows that this high correlation does not hold true to loop regions at the structurally equivalent positions in NMR ensembles and their homologues of known structure. This suggests that the general nature of local structural changes is unique; however most of the local structural variations in loop regions of NMR ensembles do not correlate to their local structural differences at structurally equivalent positions in homologues.     

Three-dimensional quantitative structure-activity relationship analyses of RGD mimetics as fibrinogen receptor antagonists

In order to better understand the structural requirements of fibrinogen receptor antagonists, variations in the platelet aggregation inhibitory activity of a series of RGD mimetics were examined using techniques for the analysis of three-dimensional quantitative structure activity relationship, such as CoMFA.     

The importance of aquaporin water channel protein structures

The history of the water channel and recent structural and functional analyses of aquaporins are reviewed. These ubiquitous channels are important for bacteria, plants and animals, exhibit a pronounced sequence homology and share functional as well as structural similarities. Aquaporins allow water or small specific solutes to pass unhindered, but block the passage of ions to prevent dissipation of the transmembrane potential. Besides advances in structure determination, recent experiments suggest that many of these channels are regulated by pH variations, phosphorylation and binding of auxiliary proteins.     

The influence of chromosome density variations on the increase in nuclear disorder strength in carcinogenesis

Microscopic structural changes have long been observed in cancer cells and used as a marker in cancer diagnosis. Recent development of an optical technique, partial-wave spectroscopy (PWS), enabled more sensitive detection of nanoscale structural changes in early carcinogenesis in terms of the disorder strength related to density variations. These nanoscale alterations precede the well-known microscopic morphological changes. We investigate the influence of nuclear density variations due to chromosome condensation on changes of disorder strength by computer simulations of model chromosomes. Nuclear configurations with different degrees of chromosome condensation are realized from simulations of decondensing chromosomes and the disorder strength is calculated for these nuclear configurations. We found that the disorder strength increases significantly for configurations with slightly more condensed chromosomes. Coupled with PWS measurements, the simulation results suggest that the chromosome condensation and the resulting spatial density inhomogeneity may represent one of the earliest events in carcinogenesis.     

合成型酵母基因组重排技术

基因组的结构变异是生物体表型进化的重要驱动力之一。设计与合成酵母基因组为人工基因组结构变异提供了新途径。人工合成酿酒酵母基因组(Sc2.0)通过系统性地引入重排元件,赋予了基因组柔性可变的功能,可诱导产生 DNA 片段的删除、反转、复制、移位等基因组结构变异。合成型酵母基因组重排技术可实现菌株性状的快速进化,并且为研究基因组结构变异与表型变化间的关系提供了一种快速、全新的方法。综述了合成型酵母基因组重排技术的研究热点和技术进展,并展示了其在创新菌种中的应用价值。