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Interconnected Codons: Unravelling the Epigenetic Significance of Flanking Sequences in CpG Dyads

JOURNAL OF MOLECULAR EVOLUTION 2024年第3期92卷 207-216页

作者： Creasey, Leo Douglas Tauber, Eran Univ Haifa Dept Evolutionary & Environm Biol 199 Abba Hushi Ave IL-3498838 Haifa Israel Univ Haifa Inst Evolut 199 Abba Hushi Ave IL-3498838 Haifa Israel

Hypothesizing that CpG codon dyads, formed by consecutive codons containing a cytosine-guanine pair (NNC-GNN), may play a crucial role in gene function, we conducted an extensive analysis to investigate their distribution and conservation within mammalian genes. Our findings reveal that genes characterized by a high density of CpG codon dyads are notably associated with homeobox domains and RNA polymerase II transcription factors. Conversely, genes exhibiting low CpG codon dyad density have links to dna damage repair and mitosis. Importantly, our study identifies a re-markable increase in expressed genes that harbor CpG during embryonic development, suggesting their potential involvement in gene regulation at these developmental stages. These results under-score the functional significance of CpG codon dyads in dna methylation and gene expression, fur-ther demonstrating the coevolution of consecutive codons and their contribution to codon usage bias.

关键词： dna methylation Epigenetics coding dna Codon usage bias

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Self-Organization Through Semiosis

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BIOLOGICAL THEORY 2023年第2期18卷 90-100页

作者： Beekman, Wim Jochemsen, Henk Wageningen Univ & Res Philosophy Grp Wageningen Netherlands

This article deals with the question of how self-organization in living organisms is realized. Self-organization may be observed in open systems that are out of equilibrium. Many disequilibria-conversion phenomena exist where free energy conversion occurs by spontaneously formed engines. However, how is self-organization realized in living entities? Living cells turn out to be self-organizing disequilibria-converting systems of a special kind. Disequilibrium conversion is realized in a typical way, through employing information specifying protein complexes acting as nano engines. The genetic code enables processing of information-derived from coding dna-to produce these molecular machines. Hence, information is at the core of living systems. Two promising approaches to explaining living cells containing sequences carrying information are mentioned. Also discussed is the question of whether a second concept of self-organization-namely, the Kantian concept-applies.

关键词： Biosemiotics Code biology coding dna Disequilibria conversion Information Kant Molecular machines Nano engines Self-organization Semiosis

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DWT based coding dna watermarking for dna copyright protection

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INFORMATION SCIENCES 2014年 273卷 263-286页

作者： Lee, Suk-Hwan Tongmyong Univ Dept Informat Secur Pusan South Korea

dna watermarking is a technique for copyright protection and ownership authentication of dna sequences and ensures the security of private genetic information. This paper addresses issues regarding watermarking dna coding sequences in the frequency domain that confer mutation resistance, amino acid conservation, and security. Multimedia watermarking is designed for robustness and invisibility mainly based on frequency domain representations. However, frequency domain watermarking for a coding dna sequence is significantly constrained because the transformation and inverse transformation must be performed while completely conserving the amino acid sequence. In this paper, we present a coding dna watermarking method in a lifting-based discrete wavelet transform (DWT) domain that focuses on the feasibility of frequency domain watermarking for dna sequences. Our method divides a coding dna sequence into a number of subsequences and allocates all codons in subsequences to a numerical code using the histogram ranks of the amino acids. Our method then calculates a set of DWT coefficients for subsequences of synonymous codons and finds a subsequence among them with DWT coefficients that are optimal for embedding watermark bits. Finally, our method substitutes this sequence for a subsequence of codons. To secure the watermark, our method generates the binary watermark based on nonlinear congruential - pseudorandom number generator (NC-PRNG) and randomly selects the embeddable position in the DWT domain of the subsequence. We experimentally verified that our method ensures not only amino acid conservation and security but also resists a point mutation rate of approximately 18.5% point mutations. (c) 2014 Elsevier Inc. All rights reserved.

关键词： dna watermarking dna copyright protection coding dna Lifting based DWT Genetic information security Mutation resistance

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Information stored in nanoscale: Encoding data in a single dna strand with Base64

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NANO TODAY 2020年 33卷 100871-100871页

作者： Zhang, Yi Kong, Linlin Wang, Fei Li, Bo Ma, Chao Chen, Dong Liu, Kai Fan, Chunhai Zhang, Hongjie Chinese Acad Sci Changchun Inst Appl Chem State Key Lab Rare Earth Resource Utilizat Changchun 130022 Peoples R China Zhejiang Univ Coll Energy Engn Inst Proc Equipment Hangzhou 310027 Peoples R China Zhejiang Univ State Key Lab Fluid Power & Mechatron Syst Hangzhou 310027 Peoples R China Univ Sci & Technol China Hefei 230026 Peoples R China Shanghai Jiao Tong Univ Sch Chem & Chem Engn Frontiers Sci Ctr Transformat Mol Shanghai 200240 Peoples R China Shanghai Jiao Tong Univ Renji Hosp Sch Med Inst Mol Med Shanghai 200240 Peoples R China Southern Med Univ Shanghai Jiao Tong Univ Affiliated Peoples Hosp 6 Affiliated Fengxian Hosp Joint Res Ctr Precis Med South Campus Shanghai 201499 Peoples R China Tsinghua Univ Dept Chem Beijing 100084 Peoples R China

dna as a storage medium has enormous potential because of its high storage density, but the produced redundancy limits this potential. The introduction of less error corrections to fully increase the storage density in dna remains a major challenge. To address this, an optimized Base64 method is developed and accordingly we realized a high specific storage density of 1.77 bits/nucleotide in a dna single strand. In this strategy, by Base64 encoding, code reshaping and balancing, and data mapping, some random text information was encoded into a dna sequence and the corresponding dna molecule was synthesized. It was then inserted into a circular plasmid for long-term information storage. This is also particularly suitable for information replication at an exponential rate when it is transformed in a bacterium. The introduction of balance codes during the transcoding process effectively controlled the GC content and continuous base repeat, which is important to reduce the error rates in the encoded dna synthesis and sequencing. Moreover, the circular plasmid platform enhanced the storage stability and sequencing accuracy. Therefore, our approach achieved a robust and high efficient storage and an accurate readout of digital data. (C) 2020 Elsevier Ltd. All rights reserved.

关键词： Information storage coding dna Base64 Logical storage density Double direction sequencing

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Visualization of Genetic Drift Processes Using the Conserved Collagen 11 GXY Domain

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JOURNAL OF MOLECULAR EVOLUTION 2019年第2-3期87卷 106-130页

作者： Kleinnijenhuis, Anne J. Triskelion Utrechtseweg 48 NL-3704 HE Zeist Netherlands

Speciation proceeds by the accumulation of dna differences in time. The genetic code changes as a result of genetic drift and by selective pressure. In variable domains, exposure to high selective pressure obscures the view on background mutations. Therefore, we characterized and visualized background mutations using the highly conserved collagen 11 GXY domain. Typical change routes were identified and the data set showed several indications that changes in the collagen 11 GXY domain have taken place randomly within a functionally restricted space. The types of nucleotide and codon group differences are similar across the vertebrate subphylum and gradually become less functionally neutral with increasing distance between species, which offers the opportunity for rapid visualization of evolutionary relations using a single domain. It was concluded that the findings and approach of the study could be important for analytical method development in authenticity research, especially when conserved domains are targeted.

关键词： Genetic drift Collagen 11 Molecular evolution coding dna Authenticity Functional restriction

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Genome-wide analysis of coding dna and amino acid variation in Saccharomyces cerevisiae

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YEAST 2008年第1期25卷 29-39页

作者： Tan, Haidong Wang, Jinxia Yang, Fan Zhao, Zongbao K. Chinese Acad Sci Dalian Inst Chem Phys Div Biotechnol Dalian 116023 Peoples R China

The possible causes of variation on amino acid composition in the yeast Saccharomyces cerevisiae were investigated genome-wide. The results indicated that: (a) the base composition of coding dna and amino acid composition was similar among all the chromosomes, which was in sharp contrast with the great varies of the composition of the individual's coding dna and amino acid;(b) some amino acids (e.g. Cys and Trp) were not present in all the proteins;and (c) amino acid bias was associated with a base bias (in terms of A-, G-, C- and T-rich codons). Based on the third rule and a proposed universal trend of amino acid gain and loss in protein evolution, the changing pattern of coding dna was predicted to be T- and C-accruing, whereas A and G were consistently reducing. All these results held the potential to reveal precisely how dna ongoing change has a major effect on the composition of proteins. Copyright (C) 2007 John Wiley & Sons, Ltd.

关键词： genome coding dna base composition amino acid composition Saccharomyces cerevisiae

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Word organization in coding dna: A mathematical model

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THEORY IN BIOSCIENCES 2006年第1期125卷 1-17页

作者： Mukhopadhyay, Indranil Som, Anup Sahoo, Satyabrata Univ Pittsburgh Dept Human Genet Pittsburgh PA 15261 USA Arizona State Univ Biodesign Inst Ctr Evolut Funct Genom Tempe AZ 85287 USA Raidighi Coll Dept Phys Raidighi 743383 India

This article deals with the relationship between vocabulary (total number of distinct oligomers or "words") and text-length (total number of oligomers or "words") for a coding dna sequence (CDS). For natural human languages, Heaps established a. mathematical formula known as Heaps' law, which relates vocabulary to text-length. Our analysis shows that Heaps' law fails to model this relationship for CDSs Here we develop a mathematical model to establish the relationship between the number of type of words (vocabulary) and the number of words sampled (text-length) for CDSs, when non-overlapping nucleotide strings with the same length are treated as words. We use tangent-hyperbolic function, which captures the saturation property of vocabulary. Based on the parameters of the model, we formulate a mathematical equation, known as "equation of word organization", whose parameters essentially indicate that nucleotide organization of coding sequences are different from one another. We also compare the word organization of CDSs with the random word distribution and conclude that a CDS is neither similar to a natural human language nor to a random one. Moreover, these sequences have their unique nucleotide organization and it is completely structured for specific biological functioning. (c) 2006 Elsevier GmbH. All rights reserved.

关键词： coding dna vocabulary text-length Heaps' law mathematical modeling

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Discriminating coding, non-coding and regulatory regions using rescaled range and detrended fluctuation analysis

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BIOSYSTEMS 2008年第1期91卷 183-194页

作者： te Boekhorst, Rene Abnizova, Irina Nehaniv, Chrystopher Univ Hertfordshire Sch Comp Sci Hatfield AL10 9AB Herts England MRC BSU Cambridge England

In this paper we analyse the efficiency of two methods, rescaled range analysis and detrended fluctuation analysis, in distinguishing between coding dna, regulatory dna and non-coding non-regulatory dna of Drosophila melanogaster. Both methods were used to estimate the degree of sequential dependence (or persistence) among nucleotides. We found that these three types of dna can be discriminated by both methods, although rescaled range analysis performs slightly better than detrended fluctuation analysis. On average, non-coding, non-regulatory dna has the highest degree of sequential persistence. coding dna could be characterised as being anti-persistent, which is in line with earlier findings of latent periodicity. Regulatory regions are shown to possess intermediate sequential dependency. Together with other available methods, rescaled range and detrended fluctuation analysis on the basis of a combined purine/pyrimidine and weak/strong classification of the nucleotides are useful tools for refined structural and functional segmentation of dna. (C) 2007 Elsevier Ireland Ltd. All rights reserved.

关键词： Hurst exponent rescaled range detrended fluctuation analysis coding dna regulatory regions

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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

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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

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A C-terminal region of RAG1 contacts the coding dna during V(D)J recombination

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MOLECULAR AND CELLULAR BIOLOGY 2001年第6期21卷 2038-2047页

作者： Mo, XM Bailin, T Sadofsky, MJ Med Coll Georgia Inst Mol Med & Genet Augusta GA 30912 USA

The site-specific dna rearrangement process, called V(D)J recombination, creates much of the diversity of immune receptor molecules in the adaptive immune system. Central to this reaction is the organization of the protein-dna. complex containing the proteins RAG1 and RAG2 and their dna targets. A long-term goal is to appreciate the three-dimensional relationships between the proteins and dna that allow the assembly of the appropriate reaction intermediates, resulting in concerted cleavage and directed rejoining of the dna ends. Previous cross-linking approaches have mapped RAG1 contacts on the dna. RAG1. protein contacts the dna at the conserved heptamer and nonamer sequences as well as at the coding dna adjacent to the heptamer. Here we subject RAGI, covalently cross-linked to dna substrates, to partial cyanogen bromide degradation or trypsin proteolysis in order to map contacts on the protein. We find that coding-sequence contacts occur near the C terminus of RAG1, while contacts made within the recombination signal sequence occur nearer the N terminus of the core region of RAG1. A deletion protein lacking the C-terminal dna-contacting region is still capable of making the N-terminal contacts. This suggests that the two binding interactions may exist on two separate domains of the protein. A trypsin cleavage pattern of the native protein supports this conclusion. A two-domain model for RAG1 is evaluated with respect to the larger recombination complex.

关键词： .cross-linking contacts C-Terminal Nonamer heptamer coding dna Region of RAG

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