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THE DISTRIBUTION OF GENES IN THE HUMAN GENOME

GENE 1991年第C期100卷 181-187页

作者： MOUCHIROUD, D DONOFRIO, G AISSANI, B MACAYA, G GAUTIER, C BERNARDI, G INST JACQUES MONOD GENET MOLEC LAB2 PL JUSSIEUF-75251 PARIS 05FRANCE UNIV CLAUDE BERNARD LYON 1 BIOMETRIE GENET & BIOL POPULAT LABURA 243F-69600 VILLEURBANNEFRANCE

Previous investigations on the human genome determined: (i) the base compositions (GC levels) and the relative amounts of its isochore families;(ii) the compositional correlations (i.e., the correlations between GC levels) between third codon positions of a set of genes and the DNA fractions in which the genes were localized;and (iii) the compositional correlations between (a) third and first + second codon positions, as well as that between (b) introns and exons from the set of 'localized genes' and from all the coding sequences and genes (genomic sequences of exons + introns) available in gene banks. Here, we have shown that the correlations (iii, a and b) for 'localized genes' and genes from the bank are in full agreement, indicating that the former set is representative of the latter. We haven then used the data (i) and the correlation (ii) to estimate the distribution of genes in isochore families. We have found that 34% of the genes are located in the GC-poor isochores (which represent 62% of the genome), 38% in the GC-rich isochores (31% of the genome) and 28% in the GC-richest isochores (3% of the genome). There is, therefore, a compositional gradient of gene concentration in the human genome. The gene density in the GC-richest 3% of the genome is about eight times higher than in the GC-rich 31%, and about 16 times higher than in the GC-poorest 62%.

关键词： GENE COMPOSITION ISOCHORES CODON POSITIONS INTRONS coding sequences

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4 SYNONYMOUS GENES ENCODE CALMODULIN IN THE TELEOST FISH, MEDAKA (ORYZIAS-LATIPES) - CONSERVATION OF THE MULTIGENE ONE-PROTEIN PRINCIPLE

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GENE 1992年第2期119卷 279-281页

作者： MATSUO, K SATO, K IKESHIMA, H SHIMODA, K TAKANO, T KEIO UNIV SCH MED CTR LAB ANIM SHINJUKU KU TOKYO 160 JAPAN

We cloned four distinct calmodulin (CaM)-encoding cDNAs from a small teleost fish, medaka (Oryzias latipes). The deduced amino acid (aa) sequences were exactly the same in these four genes and identical to the aa sequence of mammalian CaM, because of synonymous codon usages. The four cDNAs from medaka, termed CaM-A, -B, -C and -D, corresponded to mRNAs of 1.8, 1.4, 2.5 and 1.8 kb, respectively, in Northern blot analysis. Our results demonstrated that the 'multigene one-protein' principle of CaM synthesis is applicable to medaka, as well as to mammals whose CaM is encoded by at least three different genes.

关键词： RECOMBINANT DNA POLYMERASE CHAIN REACTION coding sequences GENE EVOLUTION

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Protocol to obtain targeted transcript sequence data from snake venom samples collected in the Colombian field

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TOXICON 2018年 148卷 1-6页

作者： Fonseca, Alejandra Renjifo-Ibanez, Camila Manuel Renjifo, Juan Cabrera, Rodrigo Fdn Cardioinfantil Inst Cardiol Lab Biol Mol & Pruebas Diagnost Alta Complejidad Calle 163A 13B-60 Bogota 110131 Colombia Ctr Invest Tibaitata Corp Colombiana Invest Agr Corpo Kilometro 14Via Mosquera Cundinamarca 250047 Colombia Univ Magdalena Lab Herpetol & Anfibios Cl 32 22-08 Santa Marta Magdalena Colombia

Snake venoms are a mixture of different molecules that can be used in the design of drugs for various diseases. The study of these venoms has relied on strategies that use complete venom extracted from animals in captivity or from venom glands that require the sacrifice of the animals. Colombia, a country with political and geographical conflicts has difficult access to certain regions. A strategy that can prevent the sacrifice of animals and could allow the study of samples collected in the field is necessary. We report the use of lyophilized venom from Crotalus durissus cumanensis as a model to test, for the first time, a protocol for the amplification of complete toxins from Colombian venom samples collected in the field. In this protocol, primers were designed from conserved region from Crotalus sp. mRNA and EST regions to maximize the likelihood of coding sequence amplification. We obtained the sequences of Metalloproteinases II, Disintegrins, Disintegrin-Like, Phospholipases A(2), C-type Lectins and Serine proteinases from Crotalus durissus cumanensis and compared them to different Crotalus sp sequences available on databases obtaining concordance between the toxins amplified and those reported. Our strategy allows the use of lyophilized venom to obtain complete toxin sequences from samples collected in the field and the study of poorly characterized venoms in challenging environments. (C) 2018 Elsevier Ltd. All rights reserved.

关键词： Toxins Transcriptomic Lyophilized venom Pit-vipers coding sequences

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Eukaryotic noncoding DNA sequences provide genes with an additional protection against chemical mutagens

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RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2006年第4期32卷 368-372页

作者： Patrushev, L. I. Minkevich, I. G. Russian Acad Sci Shemyakin Ovchinnikov Inst Bioorg Chem Moscow 117997 Russia Russian Acad Sci Skryabin Inst Biochem & Physiol Microorg Pushchino 142290 Moscow Oblast Russia

A quantitative model was developed that identified a new function of noncoding sequences in the eukaryotic genome, namely, the protection of coding sequences against chemical (mainly endogenous) mutagens. It was shown that, under common ecological conditions, the number of nucleotides damaged by endogenous and exogenous reactive species in coding sequences of the genome is inversely proportional to the size of their noncoding parts. Noncoding sequences can differently protect single genetic loci from chemical modification by the formation of specific spatial structures of the protected loci in the interphase nuclei. The significant differences in genome sizes between species (C-value paradox) can be explained by different contributions of noncoding sequences to the total effect of genome protection from endogenous chemical mutagens.

关键词： coding sequences evolution genome noncoding sequences mutations C-value paradox

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Analysis of genetic variations across regulatory and coding regions of kappa-casein gene of Indian native cattle (Bos indicus) and buffalo (Bubalus bubalis)

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META GENE 2014年 2卷 769-781页

作者： Kishore, Amit Mukesh, M. Sobti, R. C. Kataria, R. S. Mishra, B. P. Sodhi, Monika Natl Bur Anim Genet Resources POB 129 Karnal 132001 Haryana India Panjab Univ Dept Biotechnol Chandigarh 160014 India

The promoter region of kappa- casein (k-CN) gene in Indian native cattle and buffalo breeds was sequenced and analyzed for nucleotide variations. Sequence comparison across breeds of Indian cattle revealed a total of 7 variations in the promoter region, ofwhich-515 G/T,- 427 C/T,- 385 C/T,- 283 A/G and- 251 C/T were locatedwithin consensus binding sites for octamer-binding protein (OCT1)/pregnancy specific mammary nuclear factor (PMF), activator protein-2 (AP2), hepatocyte nuclear factor (HNF-1) and GAL4 transcription factors (TFs), respectively. These variations might be involved in gain or loss of potential transcription factor binding sites (TFBSs). Unlike the other 4 variants, the - 283 (A/G) variant located within HNF-1 TFBS was specific to Indian cattle as this change has not been observed in the Bos taurus sequence. Other TFBSs viz., MGF, TBP, NF-1, milk box and C/EBP were conserved across species. For the Indian native buffalo breeds, only 3 changes were identified in the promoter region;- 305 (A/C), - 160 (T/C) and - 141 (A/G) and most of the TFBSs were found to be conserved. However, deletion of two adjacent nucleotides located in and around binding site for C/EBP TF was identified in buffalo when compared with promoter sequence of bovine k-CN. For k-CN of Indian native cattle, a strong linkage disequilibrium (LD) was observed for variations 515 G/T, - 427 C/T and - 385 C/T in the promoter region;and for variations at codons 136 and 148 of exon-IV. Further, among intragenic haplotypes, variation - 427 C/T was found to be in LD with variations at codons 136 and 148. The information generated in the present work provides comprehensive characterization of k-CN gene promoter and coding regions in Indian cattle and buffaloes and reported variations could become important candidates for carrying out further research in dairy traits. (C) 2014 Published by Elsevier B.V.

关键词： Kappa casein Molecular characterization Genetic variability Promoter region coding sequences Linkage disequilibrium

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A novel terahertz beam splitter using ultrathin flexible transmission-type coding metasurface

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JOURNAL OF OPTOELECTRONICS AND ADVANCED MATERIALS 2019年第7-8期21卷 443-449页

作者： Liang, L. Wang, J. Yan, X. Gao, S. Lv, Y. Xiao, L. Li, Y. Wei, D. Wang, M. Wang, X. Zhang, Y. Yao, J. Zaozhuang Univ Sch Optoelect Engn Zaozhuang 277160 Peoples R China Tianjin Univ Coll Precis Instrument & Optoelect Engn Tianjin 300072 Peoples R China Zaozhuang Univ Key Lab Optoelect Informat Proc & Display Univ Sh Zaozhuang 277160 Peoples R China

A new flexible and simple transmission-type coding metasurface was proposed and characterized, which can generate different transmitted beam patterns by coding sequences of "0" and "1" digital elements. The two digital elements with almost identical transmission amplitude are composed of three metallic layers and three dielectric layers, and their transmission phase difference is approximately 180 degrees at 0.95 THz. The characterizations and working mechanisms of the coding metasurface were investigated through theoretical analysis and electromagnetic (EM) simulation. The simulation and theoretical analysis results show that the normally incident waves will be realized a single beam, two main beams and four main beams, respectively using different transmission-type coding sequences. And the amplitude modulation of transmission beam was realized by an optical pump beam. This work reveals a new and simple route for designing novel terahertz beam splitter and offers widespread applications.

关键词： Beam splitter coding metasurface Transmission-type Digital elements coding sequences

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Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect

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MOLECULAR ECOLOGY 2016年第14期25卷 3356-3369页

作者： Ament-Velasquez, S. L. Figuet, E. Ballenghien, M. Zattara, E. E. Norenburg, J. L. Fernandez-Alvarez, F. A. Bierne, J. Bierne, N. Galtier, N. Univ Montpellier Inst Evolutionary Sci CNRS IRDEPHE Pl Eugene Bataillon F-34095 Montpellier France Uppsala Univ Dept Organismal Biol Systemat Biol POB 256 SE-75105 Uppsala Sweden Indiana Univ Dept Biol 107 S Indiana Ave Bloomington IN 47405 USA Smithsonian Inst Natl Museum Nat Hist Dept Invertebrate Zool 10th St & Constitut Ave NW Washington DC 20560 USA CSIC Barcelona Inst Ciencies Mar Barcelona 08003 Spain Univ Reims Lab Biol Cellulaire & Mol 9 Blvd Paix F-51100 Reims France

Comparative population genetics in asexual vs. sexual species offers the opportunity to investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence polymorphism and divergence patterns in the fascinating Lineus ribbon worms, a group of marine, carnivorous nemerteans with unusual regeneration abilities, and in which asexual reproduction by fissiparity is documented. The population genomics of the fissiparous L. pseudolacteus is characterized by an extremely high level of heterozygosity and unexpectedly elevated pi(N)/pi(S) ratio, in apparent agreement with theoretical expectations under clonal evolution. Analysis of among-species allele sharing and read-count distribution, however, reveals that L. pseudolacteus is a triploid hybrid between Atlantic populations of L. sanguineus and L. lacteus. We model and quantify the relative impact of hybridity, polyploidy and asexuality on molecular variation patterns in L. pseudolacteus and conclude that (i) the peculiarities of L. pseudolacteus population genomics result in the first place from hybridization and (ii) the accumulation of new mutations through the Meselson effect is more than compensated by processes of heterozygosity erosion, such as gene conversion or gene copy loss. This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L. pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context.

关键词： clonality coding sequences hybridization polyploidy population genomics

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POTENTIAL GENE SEQUENCE ISOLATION AND REGIONAL MAPPING IN HUMAN CHROMOSOME-21

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AMERICAN JOURNAL OF MEDICAL GENETICS 1990年第S7期37卷 120-124页

作者： BRAHE, C TASSONE, F MILLINGTONWARD, A SERRA, A GARDINER, K A GEMELLI SCH MED INST HUMAN GENETROMEITALY LEIDEN STATE UNIV DEPT HUMAN GENET2312 AV LEIDENNETHERLANDS ELEANOR ROOSEVELT INST CANC RES DENVERCO

The transcription start sites of many genes are associated with CpG-rich DNA regions (CpG islands) containing clusters of rare cutting, methylation-sensitive restriction enzyme sites [Bird, 1986]. To detect gene sequences from human chromosome 21, we have screened closed DNA fragments from a chromosome 21-specific cosmid library for the presence of such restriction sites. Several DNA fragments containing rare cutter sites, including Sac II, were isolated and five of them partially characterized. The average insert size of the fragments was 38.4 kb. By using a panel of somatic cell hybrids, one insert was assigned to the distal part of region 21q21, three fragments to the region 21q22.1, and one sequence to the segment 21q22.2-22.3. Restriction mapping showed clusters of rare cutter sites in at least three of the cloned fragments, suggesting the presence of CpG islands. These fragments are thus good candidates for carriers of coding sequences.

关键词： CPG ISLANDS coding sequences COSMID LIBRARY

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The Landscape and Perspectives of the Human Gut Metaproteomics

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MOLECULAR & CELLULAR PROTEOMICS 2024年第5期23卷 100763页

作者： Sun, Zhongzhi Ning, Zhibin Figeys, Daniel Univ Ottawa Fac Med Sch Pharmaceut Sci Ottawa ON Canada Univ Ottawa Fac Med Dept Biochem Microbiol & Immunol Ottawa ON Canada

The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by reanalyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.

关键词： metaproteomics human gut microbiome proteome coverage functional annotation CDS coding sequences COG Cluster of Orthologous Groups DDA data-dependent acquisition DIA data-independent acquisition GO Gene Ontology LCA lowest common ancestor LC-MS/MS liquid chromatography and tandem mass spectrometry PASEF Parallel Accumulation-Serial Fragmentation PTMs post-translation modifications UHGG Unified Human Gastrointestinal Genome

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The complete chloroplast genome assembly ofCommelina carolinianaWalter (Commelinaceae)

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Mitochondrial DNA Part B 2024年第4期9卷

作者： Eun Su Kang Sang-Chul Kim Se Ryeong Lee Beom Kyun Park Dong Chan Son Forest Biodiversity Division Korea National Arboretum Pocheon-si Gyeonggi-do Republic of Korea

We sequenced and published the chloroplast genome ofCommelina carolinianaWalter, which was previously misidentified asC. diffusaowing to their morphological similarities until 1989. The genome ofC. carolinianais 160,857 bp long [large single copy region: 88,064 bp; a small single copy region: 18,549 bp; two inverted repeat regions: 27,122 bp] and has a GC content of 35.7%. The genome comprises 133 genes, including 87 coding sequences (CDSs), 38 tRNAs, and eight rRNAs. The phylogenetic relationship betweenC. carolinianaand related species was analyzed using the maximum likelihood method based on the 79 CDSs of the chloroplast genome. Phylogenetic analysis revealed thatC. carolinianais closely related toC. communis. Our findings will contribute to studies on species identification and phylogenetic and evolutionary research. These results enhance our understanding of theCommelinagenus.

关键词： Plastome coding sequences Commelina phylogenetic relationship

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