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Genome Biology

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https://www.readbyqxmd.com/read/29041960/substantial-contribution-of-genetic-variation-in-the-expression-of-transcription-factors-to-phenotypic-variation-revealed-by-erd-gwas
#1
Hung-Ying Lin, Qiang Liu, Xiao Li, Jinliang Yang, Sanzhen Liu, Yinlian Huang, Michael J Scanlon, Dan Nettleton, Patrick S Schnable
BACKGROUND: There are significant limitations in existing methods for the genome-wide identification of genes whose expression patterns affect traits. RESULTS: The transcriptomes of five tissues from 27 genetically diverse maize inbred lines were deeply sequenced to identify genes exhibiting high and low levels of expression variation across tissues or genotypes. Transcription factors are enriched among genes with the most variation in expression across tissues, as well as among genes with higher-than-median levels of variation in expression across genotypes...
October 17, 2017: Genome Biology
https://www.readbyqxmd.com/read/29020979/perfectly-matched-20-nucleotide-guide-rna-sequences-enable-robust-genome-editing-using-high-fidelity-spcas9-nucleases
#2
Dingbo Zhang, Huawei Zhang, Tingdong Li, Kunling Chen, Jin-Long Qiu, Caixia Gao
High-fidelity SpCas9 variants (eSpCas9 and SpCas9-HF1) have been engineered to reduce off-target effects. We found that changes in guide RNA length induced significant reductions in the editing activities of SpCas9 variants in plant cells. Single guide RNAs harboring precise, perfectly matched 20-nucleotide guide sequences are necessary for high on-target editing activities of eSpCas9 and SpCas9-HF1. Precise 20-nucleotide guide sequences derived from tRNA-sgRNA precursors enable robust on-target editing by these variants with enhanced specificity...
October 11, 2017: Genome Biology
https://www.readbyqxmd.com/read/29017520/the-nuclear-receptor-er%C3%AE-engages-ago2-in-regulation-of-gene-transcription-rna-splicing-and-risc-loading
#3
Roberta Tarallo, Giorgio Giurato, Giuseppina Bruno, Maria Ravo, Francesca Rizzo, Annamaria Salvati, Luca Ricciardi, Giovanna Marchese, Angela Cordella, Teresa Rocco, Valerio Gigantino, Biancamaria Pierri, Giovanni Cimmino, Luciano Milanesi, Concetta Ambrosino, Tuula A Nyman, Giovanni Nassa, Alessandro Weisz
BACKGROUND: The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities, antagonizing hormone-induced carcinogenesis and inhibiting growth and oncogenic functions in luminal-like breast cancers (BCs), where its expression correlates with a better prognosis of the disease...
October 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28985763/crossing-enhanced-and-high-fidelity-spcas9-nucleases-to-optimize-specificity-and-cleavage
#4
Péter István Kulcsár, András Tálas, Krisztina Huszár, Zoltán Ligeti, Eszter Tóth, Nóra Weinhardt, Elfrieda Fodor, Ervin Welker
BACKGROUND: The propensity for off-target activity of Streptococcus pyogenes Cas9 (SpCas9) has been considerably decreased by rationally engineered variants with increased fidelity (eSpCas9; SpCas9-HF1). However, a subset of targets still generate considerable off-target effects. To deal specifically with these targets, we generated new "Highly enhanced Fidelity" nuclease variants (HeFSpCas9s) containing mutations from both eSpCas9 and SpCas9-HF1 and examined these improved nuclease variants side by side to decipher the factors that affect their specificities and to determine the optimal nuclease for applications sensitive to off-target effects...
October 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28985744/correction-to-remixt-clone-specific-genomic-structure-estimation-in-cancer
#5
Andrew W McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P E de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S Cenk Sahinalp, Sohrab P Shah
No abstract text is available yet for this article.
October 6, 2017: Genome Biology
https://www.readbyqxmd.com/read/28974263/metagen-reference-free-learning-with-multiple-metagenomic-samples
#6
Xin Xing, Jun S Liu, Wenxuan Zhong
A major goal of metagenomics is to identify and study the entire collection of microbial species in a set of targeted samples. We describe a statistical metagenomic algorithm that simultaneously identifies microbial species and estimates their abundances without using reference genomes. As a trade-off, we require multiple metagenomic samples, usually ≥10 samples, to get highly accurate binning results. Compared to reference-free methods based primarily on k-mer distributions or coverage information, the proposed approach achieves a higher species binning accuracy and is particularly powerful when sequencing coverage is low...
October 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28974235/alignment-free-sequence-comparison-benefits-applications-and-tools
#7
REVIEW
Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M Karlowski
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis. However, many researchers are unclear about how these methods work, how they compare to alignment-based methods, and what their potential is for use for their research...
October 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28969707/massive-a-to-i-rna-editing-is-common-across-the-metazoa-and-correlates-with-dsrna-abundance
#8
Hagit T Porath, Binyamin A Knisbacher, Eli Eisenberg, Erez Y Levanon
BACKGROUND: Adenosine to inosine (A-to-I) RNA editing is a post-transcriptional modification catalyzed by the ADAR (adenosine deaminase that acts on RNA) enzymes, which are ubiquitously expressed among metazoans. Technical requirements have limited systematic mapping of editing sites to a small number of organisms. Thus, the extent of editing across the metazoan lineage is largely unknown. RESULTS: Here, we apply a computational procedure to search for RNA-sequencing reads containing clusters of editing sites in 21 diverse organisms...
October 2, 2017: Genome Biology
https://www.readbyqxmd.com/read/28950915/from-structure-to-function-how-bioinformatics-help-to-reveal-functions-of-our-genomes
#9
Xiaoqi Zheng, Sheng Zhong
A report on the 13th International Bioinformatics Workshop held in Harbin, China, 5-6 August 2017.
September 26, 2017: Genome Biology
https://www.readbyqxmd.com/read/28950880/abundant-expression-of-somatic-transposon-derived-pirnas-throughout-tribolium-castaneum-embryogenesis
#10
Maria Ninova, Sam Griffiths-Jones, Matthew Ronshaugen
BACKGROUND: Piwi-interacting RNAs (piRNAs) are a class of short (~26-31-nucleotide) non-protein-coding RNAs expressed in the metazoan germline. The piRNA pathway in arthropods is best understood in the ovary of Drosophila melanogaster, where it acts to silence active transposable elements (TEs). Maternal loading of piRNAs in oocytes is further required for the inheritance of piRNA-mediated transposon defence. However, our understanding of the diversity, evolution and function of the piRNA complement beyond drosophilids is limited...
September 26, 2017: Genome Biology
https://www.readbyqxmd.com/read/28942733/dna-methylation-dynamics-during-early-plant-life
#11
Daniel Bouyer, Amira Kramdi, Mohamed Kassam, Maren Heese, Arp Schnittger, François Roudier, Vincent Colot
BACKGROUND: Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. RESULTS: Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development...
September 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934976/desman-a-new-tool-for-de-novo-extraction-of-strains-from-metagenomes
#12
Christopher Quince, Tom O Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E Darling, Gavin Collins, A Murat Eren
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934964/comprehensive-benchmarking-and-ensemble-approaches-for-metagenomic-classifiers
#13
Alexa B R McIntyre, Rachid Ounit, Ebrahim Afshinnekoo, Robert J Prill, Elizabeth Hénaff, Noah Alexander, Samuel S Minot, David Danko, Jonathan Foox, Sofia Ahsanuddin, Scott Tighe, Nur A Hasan, Poorani Subramanian, Kelly Moffat, Shawn Levy, Stefano Lonardi, Nick Greenfield, Rita R Colwell, Gail L Rosen, Christopher E Mason
BACKGROUND: One of the main challenges in metagenomics is the identification of microorganisms in clinical and environmental samples. While an extensive and heterogeneous set of computational tools is available to classify microorganisms using whole-genome shotgun sequencing data, comprehensive comparisons of these methods are limited. RESULTS: In this study, we use the largest-to-date set of laboratory-generated and simulated controls across 846 species to evaluate the performance of 11 metagenomic classifiers...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28931413/topological-organization-and-dynamic-regulation-of-human-trna-genes-during-macrophage-differentiation
#14
Kevin Van Bortle, Douglas H Phanstiel, Michael P Snyder
BACKGROUND: The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing...
September 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/28927436/genomic-imprinting-beyond-dna-methylation-a-role-for-maternal-histones
#15
Courtney W Hanna, Gavin Kelsey
Inheritance of DNA methylation states from gametes determines genomic imprinting in mammals. A new study shows that repressive chromatin in oocytes can also confer imprinting.
September 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28927434/sifit-inferring-tumor-trees-from-single-cell-sequencing-data-under-finite-sites-models
#16
Hamim Zafar, Anthony Tzen, Nicholas Navin, Ken Chen, Luay Nakhleh
Single-cell sequencing enables the inference of tumor phylogenies that provide insights on intra-tumor heterogeneity and evolutionary trajectories. Recently introduced methods perform this task under the infinite-sites assumption, violations of which, due to chromosomal deletions and loss of heterozygosity, necessitate the development of inference methods that utilize finite-sites models. We propose a statistical inference method for tumor phylogenies from noisy single-cell sequencing data under a finite-sites model...
September 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28923089/dna-epigenome-editing-using-crispr-cas-suntag-directed-dnmt3a
#17
Yung-Hsin Huang, Jianzhong Su, Yong Lei, Lorenzo Brunetti, Michael C Gundry, Xiaotian Zhang, Mira Jeong, Wei Li, Margaret A Goodell
BACKGROUND: DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global patterns of DNA methylation and gene expression. RESULTS: Here, we utilize nuclease-deactivated Cas9 protein fused to repetitive peptide epitopes (SunTag) recruiting multiple copies of antibody-fused de novo DNA methyltransferase 3A (DNMT3A) (dCas9-SunTag-DNMT3A) to amplify the local DNMT3A concentration to methylate genomic sites of interest...
September 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28911331/dynamic-dna-methylation-reconfiguration-during-seed-development-and-germination
#18
Taiji Kawakatsu, Joseph R Nery, Rosa Castanon, Joseph R Ecker
BACKGROUND: Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming erases and re-establishes DNA methylation during development. However, knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared time-series methylomes of dry and germinating seeds to publicly available seed development methylomes...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28911330/extensive-transcriptomic-and-epigenomic-remodelling-occurs-during-arabidopsis-thaliana-germination
#19
Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G Lewsey, James Whelan
BACKGROUND: Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28911336/genome-build-information-is-an-essential-part-of-genomic-track-files
#20
LETTER
Chakravarthi Kanduri, Diana Domanska, Eivind Hovig, Geir Kjetil Sandve
Genomic locations are represented as coordinates on a specific genome build version, but the build information is frequently missing when coordinates are provided. We show that this information is essential to correctly interpret and analyse the genomic intervals contained in genomic track files. Although not a substitute for best practices, we also provide a tool to predict the genome build version of genomic track files.
September 14, 2017: Genome Biology
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