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DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes

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https://www.readbyqxmd.com/read/28679166/a-convenient-method-to-pre-screen-candidate-guide-rnas-for-crispr-cas9-gene-editing-by-nhej-mediated-integration-of-a-self-cleaving-gfp-expression-plasmid
#1
András Tálas, Péter István Kulcsár, Nóra Weinhardt, Adrienn Borsy, Eszter Tóth, Kornélia Szebényi, Sarah Laura Krausz, Krisztina Huszár, István Vida, Ádám Sturm, Bianka Gordos, Orsolya Ivett Hoffmann, Petra Bencsura, Antal Nyeste, Zoltán Ligeti, Elfrieda Fodor, Ervin Welker
The efficacies of guide RNAs (gRNAs), the short RNA molecules that bind to and determine the sequence specificity of the Streptococcus pyogenes Cas9 nuclease, to mediate DNA cleavage vary dramatically. Thus, the selection of appropriate target sites, and hence spacer sequence, is critical for most applications. Here, we describe a simple, unparalleled method for experimentally pre-testing the efficiencies of various gRNAs targeting a gene. The method explores NHEJ-cloning, genomic integration of a GFP-expressing plasmid without homologous arms and linearized in-cell...
June 30, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28679169/differential-dna-methylation-and-gene-expression-in-reciprocal-hybrids-between-solanum-lycopersicum-and-s-pimpinellifolium
#2
Muhammad Ammar Raza, Ningning Yu, Dan Wang, Liwen Cao, Susheng Gan, Liping Chen
Wide hybridization is a common and efficient breeding strategy for enhancing crop yield and quality. An interesting phenomenon is that the reciprocal hybrids usually show different phenotypes, and its underlying mechanism is not well understood. Here, we reported our comparative analysis of the DNA methylation patterns in Solanum lycopersicum, Solanum pimpinellifolium and their reciprocal hybrids by methylated DNA immunoprecipitation sequencing. The reciprocal hybrids had lower levels of DNA methylation in CpG islands and LTR retroelements when compared with those of their parents...
June 29, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28854689/identification-and-characterization-of-a-subtelomeric-satellite-dna-in-callitrichini-monkeys
#3
Naiara Pereira Araújo, Leonardo Gomes de Lima, Guilherme Borges Dias, Gustavo Campos Silva Kuhn, Alan Lane de Melo, Yatiyo Yonenaga-Yassuda, Roscoe Stanyon, Marta Svartman
Repetitive DNAs are abundant fast-evolving components of eukaryotic genomes, which often possess important structural and functional roles. Despite their ubiquity, repetitive DNAs are poorly studied when compared with the genic fraction of genomes. Here, we took advantage of the availability of the sequenced genome of the common marmoset Callithrix jacchus to assess its satellite DNAs (satDNAs) and their distribution in Callitrichini. After clustering analysis of all reads and comparisons by similarity, we identified a satDNA composed by 171 bp motifs, named MarmoSAT, which composes 1...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28498906/heap-a-highly-sensitive-and-accurate-snp-detection-tool-for-low-coverage-high-throughput-sequencing-data
#4
Masaaki Kobayashi, Hajime Ohyanagi, Hideki Takanashi, Satomi Asano, Toru Kudo, Hiromi Kajiya-Kanegae, Atsushi J Nagano, Hitoshi Tainaka, Tsuyoshi Tokunaga, Takashi Sazuka, Hiroyoshi Iwata, Nobuhiro Tsutsumi, Kentaro Yano
Recent availability of large-scale genomic resources enables us to conduct so called genome-wide association studies (GWAS) and genomic prediction (GP) studies, particularly with next-generation sequencing (NGS) data. The effectiveness of GWAS and GP depends on not only their mathematical models, but the quality and quantity of variants employed in the analysis. In NGS single nucleotide polymorphism (SNP) calling, conventional tools ideally require more reads for higher SNP sensitivity and accuracy. In this study, we aimed to develop a tool, Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28449100/integrated-analysis-of-individual-codon-contribution-to-protein-biosynthesis-reveals-a-new-approach-to-improving-the-basis-of-rational-gene-design
#5
Juan C Villada, Otávio José Bernardes Brustolini, Wendel Batista da Silveira
Gene codon optimization may be impaired by the misinterpretation of frequency and optimality of codons. Although recent studies have revealed the effects of codon usage bias (CUB) on protein biosynthesis, an integrated perspective of the biological role of individual codons remains unknown. Unlike other previous studies, we show, through an integrated framework that attributes of codons such as frequency, optimality and positional dependency should be combined to unveil individual codon contribution for protein biosynthesis...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430897/genetic-variants-associated-with-the-root-system-architecture-of-oilseed-rape-brassica-napus-l-under-contrasting-phosphate-supply
#6
Xiaohua Wang, Yanling Chen, Catherine L Thomas, Guangda Ding, Ping Xu, Dexu Shi, Fabian Grandke, Kemo Jin, Hongmei Cai, Fangsen Xu, Bin Yi, Martin R Broadley, Lei Shi
Breeding crops with ideal root system architecture for efficient absorption of phosphorus is an important strategy to reduce the use of phosphate fertilizers. To investigate genetic variants leading to changes in root system architecture, 405 oilseed rape cultivars were genotyped with a 60K Brassica Infinium SNP array in low and high P environments. A total of 285 single-nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels. Nine single-nucleotide polymorphisms corroborate a previous linkage analysis of root system architecture quantitative trait loci in the BnaTNDH population...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430886/intrinsic-protein-disorder-reduces-small-scale-gene-duplicability
#7
Sanghita Banerjee, Felix Feyertag, David Alvarez-Ponce
Whereas the rate of gene duplication is relatively high, only certain duplications survive the filter of natural selection and can contribute to genome evolution. However, the reasons why certain genes can be retained after duplication whereas others cannot remain largely unknown. Many proteins contain intrinsically disordered regions (IDRs), whose structures fluctuate between alternative conformational states. Due to their high flexibility, IDRs often enable protein-protein interactions and are the target of post-translational modifications...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28369217/evolutionary-adaptation-revealed-by-comparative-genome-analysis-of-woolly-mammoths-and-elephants
#8
Sean D Smith, Joseph K Kawash, Spyros Karaiskos, Ian Biluck, Andrey Grigoriev
Comparative genomics studies typically limit their focus to single nucleotide variants (SNVs) and that was the case for previous comparisons of woolly mammoth genomes. We extended the analysis to systematically identify not only SNVs but also larger structural variants (SVs) and indels and found multiple mammoth-specific deletions and duplications affecting exons or even complete genes. The most prominent SV found was an amplification of RNase L (with different copy numbers in different mammoth genomes, up to 9-fold), involved in antiviral defense and inflammasome function...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338930/expath-tool-a-system-for-comprehensively-analyzing-regulatory-pathways-and-coexpression-networks-from-high-throughput-transcriptome-data
#9
Han-Qin Zheng, Nai-Yun Wu, Chi-Nga Chow, Kuan-Chieh Tseng, Chia-Hung Chien, Yu-Cheng Hung, Guan-Zhen Li, Wen-Chi Chang
Next generation sequencing (NGS) has become the mainstream approach for monitoring gene expression levels in parallel with various experimental treatments. Unfortunately, there is no systematical webserver to comprehensively perform further analysis based on the huge amount of preliminary data that is obtained after finishing the process of gene annotation. Therefore, a user-friendly and effective system is required to mine important genes and regulatory pathways under specific conditions from high-throughput transcriptome data...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338901/characterization-of-the-genuine-type-2-chromatic-acclimation-in-the-two-geminocystis-cyanobacteria
#10
Yuu Hirose, Naomi Misawa, Chinatsu Yonekawa, Nobuyoshi Nagao, Mai Watanabe, Masahiko Ikeuchi, Toshihiko Eki
Certain cyanobacteria can adjust the wavelengths of light they absorb by remodeling their photosynthetic antenna complex phycobilisome via a process called chromatic acclimation (CA). Although several types of CA have been reported, the diversity of the molecular mechanisms of CA among the cyanobacteria phylum is not fully understood. Here, we characterized the molecular process of CA of Geminocystis sp. strains National Institute of Environmental Studies (NIES)-3708 and NIES-3709. Absorption and fluorescence spectroscopy revealed that both strains dramatically alter their phycoerythrin content in response to green and red light...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338832/evidence-of-translation-efficiency-adaptation-of-the-coding-regions-of-the-bacteriophage-lambda
#11
Eli Goz, Oriah Mioduser, Alon Diament, Tamir Tuller
Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338826/the-evolutionary-fate-of-the-chloroplast-and-nuclear-rps16-genes-as-revealed-through-the-sequencing-and-comparative-analyses-of-four-novel-legume-chloroplast-genomes-from-lupinus
#12
J Keller, M Rousseau-Gueutin, G E Martin, J Morice, J Boutte, E Coissac, M Ourari, M Aïnouche, A Salmon, F Cabello-Hurtado, A Aïnouche
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28633360/expression-properties-exhibit-correlated-patterns-with-the-fate-of-duplicated-genes-their-divergence-and-transcriptional-plasticity-in-saccharomycotina
#13
Florian Mattenberger, Beatriz Sabater-Muñoz, Christina Toft, Gaurav Sablok, Mario A Fares
Gene duplication is an important source of novelties and genome complexity. What genes are preserved as duplicated through long evolutionary times can shape the evolution of innovations. Identifying factors that influence gene duplicability is therefore an important aim in evolutionary biology. Here, we show that in the yeast Saccharomyces cerevisiae the levels of gene expression correlate with gene duplicability, its divergence, and transcriptional plasticity. Genes that were highly expressed before duplication are more likely to be preserved as duplicates for longer evolutionary times and wider phylogenetic ranges than genes that were lowly expressed...
June 15, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28605512/low-coverage-resequencing-detects-meiotic-recombination-pattern-and-features-in-tomato-rils
#14
Lars S de Haas, Roy Koopmans, Cilia L C Lelivelt, Remco Ursem, Rob Dirks, Geo Velikkakam James
Traditional plant breeding relies on meiotic recombination for mixing of parental alleles to create novel allele combinations. Detailed analysis of recombination patterns in model organisms shows that recombination is tightly regulated within the genome, but frequencies vary extensively along chromosomes. Despite being a model organism for fruit developmental studies, high-resolution recombination patterns are lacking in tomato. In this study, we developed a novel methodology to use low-coverage resequencing to identify genome-wide recombination patterns and applied this methodology on 60 tomato Recombinant Inbred Lines (RILs)...
June 9, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28586432/locus-specific-chip-combined-with-ngs-analysis-reveals-genomic-regulatory-regions-that-physically-interact-with-the-pax5-promoter-in-a-chicken-b-cell-line
#15
Toshitsugu Fujita, Fusako Kitaura, Miyuki Yuno, Yutaka Suzuki, Sumio Sugano, Hodaka Fujii
Chromosomal interactions regulate genome functions, such as transcription, via dynamic chromosomal organization in the nucleus. In this study, we attempted to identify genomic regions that physically bind to the promoter region of the Pax5 gene, which encodes a master regulator for B cell lineage commitment, in a chicken B cell line, DT40, with the goal of obtaining mechanistic insight into transcriptional regulation through chromosomal interaction. We found that the Pax5 promoter bound to multiple genomic regions using locus-specific chromatin immunoprecipitation (locus-specific ChIP), a method for locus-specific isolation of target genomic regions, in combination with next-generation sequencing (NGS)...
June 6, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28575160/dynamic-changes-in-methylome-and-transcriptome-patterns-in-response-to-methyltransferase-inhibitor-5-azacytidine-treatment-in-citrus
#16
Jidi Xu, Xia Wang, Hongbo Cao, Haidan Xu, Qiang Xu, Xiuxin Deng
DNA methylation is known to play an important role in various developmental processes in plants. However, there is a general lack of understanding about the possible functions of DNA methylation in fruit trees. Using callus as a model, methylome, transcriptome and metabolite changes were assessed after treatment with the DNA methyltransferase inhibitor 5-azacytidine (5azaC). Genome-wide methylome analysis revealed the demethylation of a diverse of genes, including many genes encoding transcription factors (TFs), genes involved in biological processes, and the up-regulation of a wide range of transposable elements (TEs)...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28419256/chloromitocu-codon-patterns-across-organelle-genomes-for-functional-genomics-and-evolutionary-applications
#17
Gaurav Sablok, Ting-Wen Chen, Chi-Ching Lee, Chi Yang, Ruei-Chi Gan, Jill L Wegrzyn, Nicola L Porta, Kinshuk C Nayak, Po-Jung Huang, Claudio Varotto, Petrus Tang
Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338918/integrated-mirna-and-mrna-expression-profiling-reveals-the-response-regulators-of-a-susceptible-tomato-cultivar-to-early-blight-disease
#18
Deepti Sarkar, Ranjan Kumar Maji, Sayani Dey, Arijita Sarkar, Zhumur Ghosh, Pallob Kundu
Early blight, caused by the fungus Alternaria solani, is a devastating foliar disease of tomatoes, causes massive yield loss each year worldwide. Molecular basis of the compatible host-pathogen interaction was elusive. We adopted next generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed during Alternaria-stress in tomato. Some of the interesting findings were also validated by alternative techniques. Our analysis revealed 181 known-miRNAs, belonging to 121 miRNA families, of which 67 miRNAs showed at least 2-fold change in expression level with the majority being downregulated...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338834/comparative-genomics-of-microsporidian-genomes-reveals-a-minimal-non-coding-rna-set-and-new-insights-for-transcription-in-minimal-eukaryotic-genomes
#19
Abdel Belkorchia, Jean-François Pombert, Valérie Polonais, Nicolas Parisot, Frédéric Delbac, Jean-François Brugère, Pierre Peyret, Christine Gaspin, Eric Peyretaillade
Microsporidia are ubiquitous intracellular pathogens whose opportunistic nature led to their increased recognition with the rise of the AIDS pandemic. As the RNA world was largely unexplored in this parasitic lineage, we developed a dedicated in silico methodology to carry out exhaustive identification of ncRNAs across the Encephalitozoon and Nosema genera. Thus, the previously missing U1 small nuclear RNA (snRNA) and small nucleolar RNAs (snoRNAs) targeting only the LSU rRNA were highlighted and were further validated using 5' and 3'RACE-PCR experiments...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338745/circadian-oscillations-of-microbial-and-functional-composition-in-the-human-salivary-microbiome
#20
Lena Takayasu, Wataru Suda, Kageyasu Takanashi, Erica Iioka, Rina Kurokawa, Chie Shindo, Yasue Hattori, Naoko Yamashita, Suguru Nishijima, Kenshiro Oshima, Masahira Hattori
The human microbiomes across the body evidently interact with various signals in response to biogeographical physiological conditions. To understand such interactions in detail, we investigated how the salivary microbiome in the oral cavity would be regulated by host-related signals. Here, we show that the microbial abundance and gene participating in keeping the human salivary microbiome exhibit global circadian rhythm. Analysis of the 16S rRNA sequences of salivary microbial samples of six healthy adults collected at 4-h intervals for three days revealed that the microbial genera accounting for 68...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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