检索结果-内蒙古大学图书馆

Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences

JOURNAL OF THEORETICAL BIOLOGY 2007年第4期244卷 621-630页

作者： Knibbe, Carole Mazet, Olivier Chaudier, Fabien Fayard, Jean-Michel Beslon, Guillaume Inst Natl Sci Appl Dept Comp Sci F-69621 Villeurbanne France Inst Natl Sci Appl INRA UMR 203 Lab Biol Fonct Insectes & Interact F-69621 Villeurbanne France Inst Natl Sci Appl Camille Jordan Inst Math F-69621 Villeurbanne France Inst Natl Sci Appl Dept Biosci F-69621 Villeurbanne France

The phenotypic effects of random mutations depend on both the architecture of the genome and the gene-trait relationships. Both levels thus play a key role in the mutational variability of the phenotype, and hence in the long-term evolutionary success of the lineage. Here, by simulating the evolution of organisms with flexible genomes, we show that the need for an appropriate phenotypic variability induces a relationship between the deleteriousness of gene mutations and the quantity of non-coding sequences maintained in the genome. The more deleterious the gene mutations, the shorter the intergenic sequences. Indeed, in a shorter genome, fewer genes are affected by rearrangements (duplications, deletions, inversions, translocations) at each replication, which compensates for the higher impact of each gene mutation. This spontaneous adjustment of genome structure allows the organisms to retain the same average fitness loss per replication, despite the higher impact of single gene mutations. These results show how evolution can generate unexpected couplings between distinct organization levels. (c) 2006 Elsevier Ltd. All rights reserved.

关键词： genome evolution non-coding dna mutation effect variability robustness

来源：评论

学校读者我要写书评

暂无评论

dna octaplex formation with an I-motif of water-mediated A-quartets:: Reinterpretation of the crystal structure of d(gcGAAAgc)

引用

JOURNAL OF BIOCHEMISTRY 2006年第6期140卷 759-762页

作者： Sato, Yoshiteru Mitomi, Kenta Sunami, Tomoko Kondo, Jiro Takenaka, Akio Tokyo Inst Technol Grad Sch Biosci & Biotechnol Yokohama Kanagawa 2268501 Japan Univ Strasbourg CNRS Inst Biol Mol & Cellulaire F-67084 Strasbourg France

The crystal structure of the tetragonal form of d(gcGAAAgc) has been revised and reasonably refined including the disordered residues. The two dna strands form a base-intercalated duplex, and the four duplexes are assembled according to the crystallographic 222 symmetry to form an octaplex. In the central region, the eight strands are associated by I-motif of double A-quartets. Furthermore, eight hydrated-magnesium cations link the four duplexes to support the octaplex formation. Based on these structural features, a proposal that folding of d(GAAA)(n), found in the non-coding region of genomes, into an octaplex can induce slippage during replication to facilitate length polymorphism is presented.

关键词： A-quartet dna octaplex non-coding dna VNTR X-ray analysis

来源：评论

学校读者我要写书评

暂无评论

Natural genome-editing competences of viruses

引用

ACTA BIOTHEORETICA 2006年第4期54卷 235-253页

作者： Witzany, Guenther Philosoph Praxis A-5111 Salzburg Austria

It is becoming increasingly evident that the driving forces of evolutionary novelty are not randomly derived chance mutations of the genetic text, but a precise genome editing by omnipresent viral agents. These competences integrate the whole toolbox of natural genetic engineering, replication, transcription, translation, genomic imprinting, genomic creativity, enzymatic inventions and all types of genetic repair patterns. Even the non-coding, repetitive dna sequences which were interpreted as being ancient remnants of former evolutionary stages are now recognized as being of viral descent and crucial for higher-order regulatory and constitutional functions of protein structural vocabulary. In this article I argue that non-randomly derived natural genome editing can be envisioned as (a) combinatorial (syntactic), (b) context-specific (pragmatic) and (c) content-sensitive (semantic) competences of viral agents. These three-leveled biosemiotic competences could explain the emergence of complex new phenotypes in single evolutionary events. After short descriptions of the non-coding regulatory networks, major viral life strategies and pre-cellular viral life three of the major steps in evolution serve as examples: There is growing evidence that natural genome-editing competences of viruses are essential (1) for the evolution of the eukaryotic nucleus, (2) the adaptive immune system and (3) the placental mammals.

关键词： non-coding dna repetitive elements genome editing persistent viral life-style

来源：评论

学校读者我要写书评

暂无评论

Why repetitive dna is essential to genome function

引用

BIOLOGICAL REVIEWS 2005年第2期80卷 227-250页

作者： Shapiro, JA von Sternberg, R Univ Chicago Dept Biochem & Mol Biol Chicago IL 60637 USA NIH Natl Ctr Biotechnol Informat Bethesda MD 20894 USA Natl Museum Nat Hist Smithsonian Inst Dept Syst Biol Washington DC 20013 USA

There are clear theoretical reasons and many well-documented examples which show that repetitive dna is essential for genome function. Generic repeated signals in the dna are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive dna sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive dna in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist' perspective on repetitive dna leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive dna component is often greater than the coding sequence component.

关键词： transposable element non-coding dna satellite dna junk dna transcriptional regulation chromatin domains evolution biocomputing systems biology data storage

来源：评论

学校读者我要写书评

暂无评论

Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast dna markers and the utility of non-coding dna at higher taxonomic levels

引用

MOLECULAR PHYLOGENETICS AND EVOLUTION 2002年第2期24卷 274-301页

作者： Bremer, B Bremer, K Heidari, N Erixon, P Olmstead, RG Anderberg, AA Källersjö, M Barkhordarian, E Evolutionary Biol Ctr Dept Systemat Bot SE-75236 Uppsala Sweden Univ Washington Dept Bot Seattle WA 98195 USA Swedish Museum Nat Hist Dept Phanerogam Bot SE-10405 Stockholm Sweden Swedish Museum Nat Hist Lab Mol Systemat SE-10405 Stockholm Sweden Royal Swedish Acad Sci Bergius Fdn SE-10405 Stockholm Sweden

Asterids comprise 1/4-1/3 of all flowering plants and are classified in 10 orders and >100 families. The phylogeny of asterids is here explored with jackknife parsimony analysis of chloroplast dna from 132 genera representing 103 families and all higher groups of asterids. Six different markers were used, three of the markers represent protein coding genes, rbcL, ndhF, and matK, and three other represent non-coding dna;a region including trnL exons and the intron and intergenic spacers between trnT (UGU) to trnF (GAA);another region including trnV exons and intron, trnM and intergenic spacers between trnV (UAC) and atpE, and the rps16 intron. The three non-coding markers proved almost equally useful as the three coding genes in phylogenetic reconstruction at the high level of orders and families in asterids, and in relation to the number of aligned positions the non-coding markers were even more effective. Basal interrelationships among Cornales, Ericales, lamiids (new name replacing euasterids 1), and campanulids (new name replacing euasterids 11) are resolved with strong support. Family interrelationships are fully or almost fully resolved with medium to strong support in Cornales, Garryales, Gentianales, Solanales, Aquifoliales, Apiales, and Dipsacales. Within the three large orders Ericales, Lamiales, and Asterales, family interrelationships remain partly unclear. The analysis has contributed to reclassification of several families, e.g., Tetrameristaceae, Ebenaceae, Styracaceae, Montiniaceae, Orobanchaceae, and Scrophulariaceae (by inclusion of Pellicieraceae, Lissocarpaceae, Halesiaceae, Kaliphoraceae, Cyclocheilaceae, and Myoporaceae + Buddlejaceae, respectively), and to the placement of families that were unplaced in the APG-system, e.g., Sladeniaceae, Pentaphylacaceae, Plocospermataceae, Cardiopteridaceae, and Adoxaceae (in Ericales, Ericales, Lamiales, Aquifoliales, and Dipsacales, respectively), and Paracryphiaceae among campanulids. Several families of e

关键词： asterids phylogeny rbcL ndhF matK trnT-F trnV-atpE rps16 coding dna non-coding dna

来源：评论

学校读者我要写书评

暂无评论

Strategies for characterising cis-regulatory elements in Xenopus

引用

Briefings in Functional Genomics and Proteomics 2005年第1期4卷 58-68页

作者： Khokha, Mustafa K. Loots, Gabriela G. Department of Molecular and Cell Biology University of California Berkeley CA United States Department of Pediatrics University of California San Francisco CA United States Genome Biology Division Biosciences Department Lawrence Livermore National Laboratory Livermore CA 94550 7000 East Avenue United States

Understanding the cis-regulatory architecture of metazoan organisms is the greatest challenge facing genome biology today. In vertebrate organisms, distinct sequence elements mediate transcriptional regulation and are scattered throughout the genome, either proximal or distal to promoters. The identification of transcriptional enhancers has proven rather difficult by conventional experimental approaches. In the past decade, the rapid generation of genomic sequences for multiple vertebrate organisms, accompanied by sophisticated comparative tools, has facilitated the identification of non-coding evolutionarily conserved regions that may encode cis-regulatory elements. Validating computational predictions and characterising cis-regulatory elements in vivo, however, has been a major bottleneck, mainly because the most commonly used organism for these experiments has been the mouse, and generating transgenic mice or modifying the mouse genome continues to be a labour-intensive, low-throughput, expensive process. This has led to the use of Xenopus, which holds great promise for high-throughput interrogation of putative cis-regulatory elements. In particular, Xenopus tropicalis may become particularly powerful for elucidating regulatory networks, chiefly because it is amenable to genetic manipulations, and its genome is being sequenced. © Henry Stewart Publications.

关键词： Cis-regulatory elements Comparative genomics Evolutionary conserved elements non-coding dna Transcriptional regulation Xenopus transgenics

来源：评论

学校读者我要写书评

暂无评论

Within-intron correlation with base composition of adjacent exons in different genomes

引用

GENE 2001年第1-2期276卷 143-151页

作者： Vinogradov, AE Russian Acad Sci Inst Cytol St Petersburg 194064 Russia

Within-intron difference of correlation with base composition of the adjacent exons was studied in the genomes of 34 species. For this purpose, GC-percent was determined for segments of 50 bp in length taken at both intron margins and in the internal part of the intron. It was found that in certain genomes the coefficient of correlation with GC-percent of the adjacent exon was significantly higher for the intron margin than for the internal part of the intron (homeotherms, cereals,). Only part of this difference can be explained by unequal probability of insertion of transposable elements. Those multicellular organisms which have a low or no within-intron difference in correlation with the adjacent exons (anamniotes, invertebrates, dicots) show a higher local compositional heterogeneity (a greater exon/intron contrast in the GC-content). These results are evidence against the mutational bias being a possible explanation for the compositional genome heterogeneity. Thus, in the genomes with a high global heterogeneity there seems to be a selective force for compliance of intron base composition with the adjacent exons. This force is stronger in those parts of the intron that are closer to exons. In addition, the previously found positive general correlation between the genome size and average intron length was confirmed with a much larger dataset. However, within separate phylogenetic groups this rule can be broken, as it occurs in the cereals (family Poaceae), where a negative correlation was found. (C) 2001 Published by Elsevier Science B.V.

关键词： non-coding dna isochores genome compositional heterogeneity mutation bias genome evolution retroposon insertion

来源：评论

学校读者我要写书评

暂无评论

引用

GENE 1999年第1期232卷 87-95页

作者： Frontali, C Pizzi, E Ist Super Sanita Cell Biol Lab I-00161 Rome Italy

A method is presented which allows detection of a sequence correlation effect not related to patchiness in base composition or to preferences in codon usage. Recurrence plots providing local views of oligonucleotide recurrence regimen show that introns and intergenic regions are often characterised by a highly recurrent use of oligonucleotides. By window analysis it is possible to score a long sequence for the recurrence of a given subset of oligos while filtering away the effects of short-range correlations. Long-range exploration of chromosome III from Caenorhabditis elegans reveals that consistent use of recurrent oligonucleotides in introns and intergenic regions generates a correlation effect that extends over several megabases. (C) 1999 Elsevier Science B.V. All rights reserved.

关键词： Caenorhabditis elegans correlation structure genome organisation non-coding dna recurrence sequence analysis

来源：评论

学校读者我要写书评

暂无评论

Hairpins create minute inversions in non-coding regions of chloroplast dna

引用

CURRENT GENETICS 1996年第3期30卷 259-262页

作者： Kelchner, SA Wendel, JF IOWA STATE UNIV DEPT BOTAMESIA 50011

Minute inversions (4 bp in length), associated with probable hairpin secondary structures, were inferred from comparative analysis of rp116 intron sequences from the chloroplast genomes of Chusquea species and related bamboos (Poaceae). The inverted sequences, which appear to have arisen independently on several occasions, comprise entire loops of the putative hairpins. The process of inversion seems dependent upon the stem length of the hairpin and its estimated free energy of formation. A similar inversion was uncovered for other plants in a previously published data set for a different non-coding region of the chloroplast genome, suggesting that the inversional process may be a common feature of non-coding dna evolution. Several implications for phylogenetic analysis are noted.

关键词： inversions non-coding dna phylogenetics molecular evolution rpl16 intron

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：