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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/28633360/expression-properties-exhibit-correlated-patterns-with-the-fate-of-duplicated-genes-their-divergence-and-transcriptional-plasticity-in-saccharomycotina
#3
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
#4
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
#5
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
#6
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/28575165/genome-wide-profiling-of-sus-scrofa-circular-rnas-across-nine-organs-and-three-developmental-stages
#7
Guoming Liang, Yalan Yang, Guanglin Niu, Zhonglin Tang, Kui Li
The spatio-temporal expression patterns of Circular RNA (circRNA) across organs and developmental stages are critical for its function and evolution analysis. However, they remain largely unclear in mammals. Here, we comprehensively analysed circRNAs in nine organs and three skeletal muscles of Guizhou miniature pig (S. scrofa), a widely used biomedical model animal. We identified 5,934 circRNAs and analysed their molecular properties, sequence conservation, spatio-temporal expression pattern, potential function, and interaction with miRNAs...
May 29, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28541388/the-genome-sequence-of-sweet-cherry-prunus-avium-for-use-in-genomics-assisted-breeding
#8
Kenta Shirasawa, Kanji Isuzugawa, Mitsunobu Ikenaga, Yutaro Saito, Toshiya Yamamoto, Hideki Hirakawa, Sachiko Isobe
We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site-associated DNA sequencing...
May 25, 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
#9
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...
May 11, 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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/28338730/genetic-variability-of-the-activity-of-bidirectional-promoters-a-pilot-study-in-bovine-muscle
#14
Cédric Meersseman, Rabia Letaief, Véronique Léjard, Emmanuelle Rebours, Gabriel Guillocheau, Diane Esquerré, Anis Djari, Amanda Chamberlain, Christy Vander Jagt, Christophe Klopp, Mekki Boussaha, Gilles Renand, Abderrahman Maftah, Daniel Petit, Dominique Rocha
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28170034/comparative-analyses-of-the-major-royal-jelly-protein-gene-cluster-in-three-apis-species-with-long-amplicon-sequencing
#15
Sophie Helbing, H Michael G Lattorff, Robin F A Moritz, Anja Buttstedt
The western honeybee, Apis mellifera is a prominent model organism in the field of sociogenomics and a recent upgrade substantially improved annotations of the reference genome. Nevertheless, genome assemblies based on short-sequencing reads suffer from problems in regions comprising e.g. multi-copy genes. We used single-molecule nanopore-based sequencing with extensive read-lengths to reconstruct the organization of the major royal jelly protein (mrjp) region in three species of the genus Apis. Long-amplicon sequencing provides evidence for lineage-specific evolutionary fates of Apis mrjps...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28168289/ribo-seq-enlightens-codon-usage-bias
#16
Damien Paulet, Alexandre David, Eric Rivals
Codon usage is biased between lowly and highly expressed genes in a genome-specific manner. This universal bias has been well assessed in some unicellular species, but remains problematic to assess in more complex species. We propose a new method to compute codon usage bias based on genome wide translational data. A new technique based on sequencing of ribosome protected mRNA fragments (Ribo-seq) allowed us to rank genes and compute codon usage bias with high precision for a great variety of species, including mammals...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28158431/prediction-of-bipartite-transcriptional-regulatory-elements-using-transcriptome-data-of-arabidopsis
#17
Yoshiharu Y Yamamoto, Hiroyuki Ichida, Ayaka Hieno, Daichi Obata, Mutsutomo Tokizawa, Mika Nomoto, Yasuomi Tada, Kazutaka Kusunoki, Hiroyuki Koyama, Natsuki Hayami
In our previous study, a methodology was established to predict transcriptional regulatory elements in promoter sequences using transcriptome data based on a frequency comparison of octamers. Some transcription factors, including the NAC family, cannot be covered by this method because their binding sequences have non-specific spacers in the middle of the two binding sites. In order to remove this blind spot in promoter prediction, we have extended our analysis by including bipartite octamers that are composed of '4 bases-a spacer with a flexible length-4 bases'...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28130382/integrated-high-density-consensus-genetic-map-of-pyrus-and-anchoring-of-the-bartlett-v1-0-pyrus-communis-genome
#18
Leiting Li, Cecilia H Deng, Mareike Knäbel, David Chagné, Satish Kumar, Jiangmei Sun, Shaoling Zhang, Jun Wu
Genetic maps are essential tools for pear genetics and genomics research. In this study, we first constructed an integrated simple sequence repeat (SSR) and single nucleotide polymorphism (SNP)-based consensus genetic map for pear based on common SSR markers between nine published maps. A total of 5,085 markers, including 1,232 SSRs and 3,853 SNPs, were localized on a consensus map spanning 3,266.0 cM in total, with an average marker interval of 0.64 cM, which represents the highest density consensus map of pear to date...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28119334/genome-wide-analysis-of-cis-regulatory-element-structure-and-discovery-of-motif-driven-gene-co-expression-networks-in-grapevine
#19
Darren Chern Jan Wong, Rodrigo Lopez Gutierrez, Gregory Alan Gambetta, Simone Diego Castellarin
Coordinated transcriptional and metabolic reprogramming ensures a plant's continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters...
June 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28460080/a-genomic-landscape-of-mitochondrial-dna-insertions-in-the-pig-nuclear-genome-provides-evolutionary-signatures-of-interspecies-admixture
#20
Giuseppina Schiavo, Orsolya Ivett Hoffmann, Anisa Ribani, Valerio Joe Utzeri, Marco Ciro Ghionda, Francesca Bertolini, Claudia Geraci, Samuele Bovo, Luca Fontanesi
Nuclear DNA sequences of mitochondrial origin (numts) are derived by insertion of mitochondrial DNA (mtDNA), into the nuclear genome. In this study, we provide, for the first time, a genome picture of numts inserted in the pig nuclear genome. The Sus scrofa reference nuclear genome (Sscrofa10.2) was aligned with circularized and consensus mtDNA sequences using LAST software. A total of 430 numt sequences that may represent 246 different numt integration events (57 numt regions determined by at least two numt sequences and 189 singletons) were identified, covering about 0...
April 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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