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Genes, Volume 9, Issue 6 (June 2018)

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Open AccessArticle CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads
Received: 11 April 2018 / Revised: 12 June 2018 / Accepted: 13 June 2018 / Published: 20 June 2018
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Abstract
With the rapid development of high-throughput sequencing technology, the analysis of metagenomic sequencing data and the accurate and efficient estimation of relative microbial abundance have become important ways to explore the microbial composition and function of microbes. In addition, the accuracy and efficiency
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With the rapid development of high-throughput sequencing technology, the analysis of metagenomic sequencing data and the accurate and efficient estimation of relative microbial abundance have become important ways to explore the microbial composition and function of microbes. In addition, the accuracy and efficiency of the relative microbial abundance estimation are closely related to the algorithm and the selection of the reference sequence for sequence alignment. We introduced the microbial core genome as the reference sequence for potential microbes in a metagenomic sample, and we constructed a finite mixture and latent Dirichlet models and used the Gibbs sampling algorithm to estimate the relative abundance of microorganisms. The simulation results showed that our approach can improve the efficiency while maintaining high accuracy and is more suitable for high-throughput metagenomic data. The new approach was implemented in our CoreProbe package which provides a pipeline for an accurate and efficient estimation of the relative abundance of microbes in a community. This tool is available free of charge from the CoreProbe’s website: Access the Docker image with the following instruction: sudo docker pull panhongfei/coreprobe:1.0. Full article
(This article belongs to the Section Technologies and Resources for Genetics)
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Open AccessCommunication The Case of X and Y Localization of Nucleolus Organizer Regions (NORs) in Tragulus javanicus (Cetartiodactyla, Mammalia)
Received: 7 May 2018 / Revised: 14 June 2018 / Accepted: 18 June 2018 / Published: 20 June 2018
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Abstract
There are differences in number and localization of nucleolus organizer regions (NORs) in genomes. In mammalian genomes, NORs are located on autosomes, which are often situated on short arms of acrocentric chromosomes and more rarely in telomeric, pericentromeric, or interstitial regions. In this
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There are differences in number and localization of nucleolus organizer regions (NORs) in genomes. In mammalian genomes, NORs are located on autosomes, which are often situated on short arms of acrocentric chromosomes and more rarely in telomeric, pericentromeric, or interstitial regions. In this work, we report the unique case of active NORs located on gonоsomes of a eutherian mammal, the Javan mouse-deer (Tragulus javanicus). We have investigated the position of NORs by FISH experiments with ribosomal DNA (rDNA) sequences (18S, 5.8S, and 28S) and show the presence of a single NOR site on the X and Y chromosomes. The NOR is localized interstitially on the p-arm of the X chromosome in close proximity with prominent C-positive heterochromatin blocks and in the pericentromeric area of mostly heterochromatic Y. The NOR sites are active on both the X and Y chromosomes in the studied individual and surrounded by GC enriched heterochromatin. We hypothesize that the surrounding heterochromatin might have played a role in the transfer of NORs from autosomes to sex chromosomes during the karyotype evolution of the Javan mouse-deer. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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Open AccessArticle Genome-Wide Identification and Functional Prediction of Novel Drought-Responsive lncRNAs in Pyrus betulifolia
Received: 2 May 2018 / Revised: 14 June 2018 / Accepted: 14 June 2018 / Published: 20 June 2018
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Abstract
Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes in plants. However, identification of lncRNAs in Pyrus betulifolia is limited compared with studies of functional gene expression. Using high-throughput sequencing technology, the transcriptome
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Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes in plants. However, identification of lncRNAs in Pyrus betulifolia is limited compared with studies of functional gene expression. Using high-throughput sequencing technology, the transcriptome of P. betulifolia under drought stress was analyzed to identify lncRNAs. A total of 14,478 lncRNAs were identified, of which 251 were found to be drought-responsive. The putative target genes of these differentially expressed lncRNAs were significantly enriched in metabolic processes, organic substance metabolic processes, macromolecule metabolic processes, and heterocyclic compound binding. Real-time quantitative polymerase chain reaction validation suggested that the results of the RNA sequencing data analysis were reliable. This study will provide genetic resources for pear breeding and provide reference to other pomological studies. Full article
(This article belongs to the Section Plant Genetics and Genomics)
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Open AccessReview H1.0 Linker Histone as an Epigenetic Regulator of Cell Proliferation and Differentiation
Received: 29 May 2018 / Accepted: 18 June 2018 / Published: 20 June 2018
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Abstract
H1 linker histones are a class of DNA-binding proteins involved in the formation of supra-nucleosomal chromatin higher order structures. Eleven non-allelic subtypes of H1 are known in mammals, seven of which are expressed in somatic cells, while four are germ cell-specific. Besides having
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H1 linker histones are a class of DNA-binding proteins involved in the formation of supra-nucleosomal chromatin higher order structures. Eleven non-allelic subtypes of H1 are known in mammals, seven of which are expressed in somatic cells, while four are germ cell-specific. Besides having a general structural role, H1 histones also have additional epigenetic functions related to DNA replication and repair, genome stability, and gene-specific expression regulation. Synthesis of the H1 subtypes is differentially regulated both in development and adult cells, thus suggesting that each protein has a more or less specific function. The somatic variant H1.0 is a linker histone that was recognized since long ago to be involved in cell differentiation. Moreover, it has been recently found to affect generation of epigenetic and functional intra-tumor heterogeneity. Interestingly, H1.0 or post-translational forms of it have been also found in extracellular vesicles (EVs) released from cancer cells in culture, thus suggesting that these cells may escape differentiation at least in part by discarding H1.0 through the EV route. In this review we will discuss the role of H1.0 in development, differentiation, and stem cell maintenance, also in relation with tumorigenesis, and EV production. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessReview Production of Plant Secondary Metabolites: Examples, Tips and Suggestions for Biotechnologists
Received: 30 May 2018 / Revised: 12 June 2018 / Accepted: 20 June 2018 / Published: 20 June 2018
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Abstract
Plants are sessile organisms and, in order to defend themselves against exogenous (a)biotic constraints, they synthesize an array of secondary metabolites which have important physiological and ecological effects. Plant secondary metabolites can be classified into four major classes: terpenoids, phenolic compounds, alkaloids and
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Plants are sessile organisms and, in order to defend themselves against exogenous (a)biotic constraints, they synthesize an array of secondary metabolites which have important physiological and ecological effects. Plant secondary metabolites can be classified into four major classes: terpenoids, phenolic compounds, alkaloids and sulphur-containing compounds. These phytochemicals can be antimicrobial, act as attractants/repellents, or as deterrents against herbivores. The synthesis of such a rich variety of phytochemicals is also observed in undifferentiated plant cells under laboratory conditions and can be further induced with elicitors or by feeding precursors. In this review, we discuss the recent literature on the production of representatives of three plant secondary metabolite classes: artemisinin (a sesquiterpene), lignans (phenolic compounds) and caffeine (an alkaloid). Their respective production in well-known plants, i.e., Artemisia, Coffea arabica L., as well as neglected species, like the fibre-producing plant Urtica dioica L., will be surveyed. The production of artemisinin and caffeine in heterologous hosts will also be discussed. Additionally, metabolic engineering strategies to increase the bioactivity and stability of plant secondary metabolites will be surveyed, by focusing on glycosyltransferases (GTs). We end our review by proposing strategies to enhance the production of plant secondary metabolites in cell cultures by inducing cell wall modifications with chemicals/drugs, or with altered concentrations of the micronutrient boron and the quasi-essential element silicon. Full article
(This article belongs to the Special Issue Plant Metabolic Engineering of High Value Bioactive Products)
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Open AccessArticle Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly
Received: 17 March 2018 / Revised: 19 May 2018 / Accepted: 4 June 2018 / Published: 20 June 2018
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Abstract
The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of
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The genome of a red fox (Vulpes vulpes) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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Open AccessArticle The Quorum Sensing System of Yersinia enterocolitica 8081 Regulates Swimming Motility, Host Cell Attachment, and Virulence Plasmid Maintenance
Received: 31 May 2018 / Accepted: 12 June 2018 / Published: 20 June 2018
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Abstract
Although Yersinia enterocolitica genomes are highly heterogeneous, they contain a conserved N-acylhomoserine lactone-dependent (AHL) quorum sensing (QS) system consisting of the luxR and luxI orthologs yenR and yenI respectively. Certain hypervirulent strains also contain a putative orphan luxR gene, ycoR, that
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Although Yersinia enterocolitica genomes are highly heterogeneous, they contain a conserved N-acylhomoserine lactone-dependent (AHL) quorum sensing (QS) system consisting of the luxR and luxI orthologs yenR and yenI respectively. Certain hypervirulent strains also contain a putative orphan luxR gene, ycoR, that is not linked to an AHL synthase. To explore the contribution of yenR/yenI/ycoR to QS-dependent phenotypes in Yersinia enterocolitica strain 8081, single and multiple mutants were constructed. AHL profiling identified N-(3-oxohexanoyl) homoserine lactone, N-hexanoylhomoserine lactone, and N-(3-oxoseptanoyl) homoserine lactone as the most abundant. The AHL profiles of the yenR, ycoR and yenR/ycoR mutants were similar to the parent suggesting that the two LuxR homologues do not regulate AHL production while the yenI mutants were AHL-negative. A role for QS in swimming motility and cell attachment was demonstrated. Down-regulation of the virulence plasmid partition gene, spyA, in yenI and yenI/yenR/ycoR mutants is consistent with the greater loss of the Y. enterocolitica pYVe virulence plasmid in the yenI mutant during serial passage at 37 °C but not at 22 °C. A role for QS-regulated spyA in virulence plasmid maintenance is suggested. Full article
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Open AccessArticle From Chromosomes to Genome: Insights into the Evolutionary Relationships and Biogeography of Old World Knifefishes (Notopteridae; Osteoglossiformes)
Received: 23 May 2018 / Revised: 13 June 2018 / Accepted: 15 June 2018 / Published: 19 June 2018
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Abstract
In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the
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In addition to its wide geographical distribution, osteoglossiform fishes represent one of the most ancient freshwater teleost lineages; making it an important group for systematic and evolutionary studies. These fishes had a Gondwanan origin and their past distribution may have contributed to the diversity present in this group. However, cytogenetic and genomic data are still scarce, making it difficult to track evolutionary trajectories within this order. In addition, their wide distribution, with groups endemic to different continents, hinders an integrative study that allows a globalized view of its evolutionary process. Here, we performed a detailed chromosomal analysis in Notopteridae fishes, using conventional and advanced molecular cytogenetic methods. Moreover, the genetic distances of examined species were assessed by genotyping using diversity arrays technology sequencing (DArTseq). These data provided a clear picture of the genetic diversity between African and Asian Notopteridae species, and were highly consistent with the chromosomal, geographical, and historical data, enlightening their evolutionary diversification. Here, we discuss the impact of continental drift and split of Pangea on their recent diversity, as well as the contribution to biogeographical models that explain their distribution, highlighting the role of the Indian subcontinent in the evolutionary process within the family. Full article
(This article belongs to the Section Animal Genetics and Genomics)
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Open AccessArticle MiRAR—miRNA Activity Reporter for Living Cells
Received: 6 June 2018 / Revised: 8 June 2018 / Accepted: 15 June 2018 / Published: 19 June 2018
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Abstract
microRNA (miRNA) activity and regulation are of increasing interest as new therapeutic targets. Traditional approaches to assess miRNA levels in cells rely on RNA sequencing or quantitative PCR. While useful, these approaches are based on RNA extraction and cannot be applied in real-time
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microRNA (miRNA) activity and regulation are of increasing interest as new therapeutic targets. Traditional approaches to assess miRNA levels in cells rely on RNA sequencing or quantitative PCR. While useful, these approaches are based on RNA extraction and cannot be applied in real-time to observe miRNA activity with single-cell resolution. We developed a green fluorescence protein (GFP)-based reporter system that allows for a direct, real-time readout of changes in miRNA activity in live cells. The miRNA activity reporter (MiRAR) consists of GFP fused to a 3′ untranslated region containing specific miRNA binding sites, resulting in miRNA activity-dependent GFP expression. Using qPCR, we verified the inverse relationship of GFP fluorescence and miRNA levels. We demonstrated that this novel optogenetic reporter system quantifies cellular levels of the tumor suppressor miRNA let-7 in real-time in single Human embryonic kidney 293 (HEK 293) cells. Our data shows that the MiRAR can be applied to detect changes in miRNA levels upon disruption of miRNA degradation pathways. We further show that the reporter could be adapted to monitor another disease-relevant miRNA, miR-122. With trivial modifications, this approach could be applied across the miRNome for quantification of many specific miRNA in cell cultures, tissues, or transgenic animal models. Full article
(This article belongs to the Special Issue Synthetic DNA and RNA Programming)
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Open AccessReview Membrane Proteins in Trypanosomatids Involved in Ca2+ Homeostasis and Signaling
Received: 31 May 2018 / Revised: 11 June 2018 / Accepted: 14 June 2018 / Published: 19 June 2018
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Abstract
Calcium ion (Ca2+) serves as a second messenger for a variety of cell functions in trypanosomes. Several proteins in the plasma membrane, acidocalcisomes, endoplasmic reticulum, and mitochondria are involved in its homeostasis and in cell signaling roles. The plasma membrane has
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Calcium ion (Ca2+) serves as a second messenger for a variety of cell functions in trypanosomes. Several proteins in the plasma membrane, acidocalcisomes, endoplasmic reticulum, and mitochondria are involved in its homeostasis and in cell signaling roles. The plasma membrane has a Ca2+ channel for its uptake and a plasma membrane-type Ca2+-ATPase (PMCA) for its efflux. A similar PMCA is also located in acidocalcisomes, acidic organelles that are the primary Ca2+ store and that possess an inositol 1,4,5-trisphosphate receptor (IP3R) for Ca2+ efflux. Their mitochondria possess a mitochondrial calcium uniporter complex (MCUC) for Ca2+ uptake and a Ca2+/H+ exchanger for Ca2+ release. The endoplasmic reticulum has a sarcoplasmic-endoplasmic reticulum-type Ca2+-ATPase (SERCA) for Ca2+ uptake but no Ca2+ release mechanism has been identified. Additionally, the trypanosomatid genomes contain other membrane proteins that could potentially bind calcium and await further characterization. Full article
(This article belongs to the Special Issue Membrane Proteins in Parasitic Protozoa)
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Open AccessArticle Integrative Analysis of Dysregulated lncRNA-Associated ceRNA Network Reveals Functional lncRNAs in Gastric Cancer
Received: 3 May 2018 / Revised: 28 May 2018 / Accepted: 12 June 2018 / Published: 18 June 2018
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Abstract
Mounting evidence suggests that long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNA (ceRNA). However, the regulatory mechanisms of lncRNA as ceRNA in gastric cancer (GC) are not fully understood. Here, we first
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Mounting evidence suggests that long noncoding RNAs (lncRNAs) play important roles in the regulation of gene expression by acting as competing endogenous RNA (ceRNA). However, the regulatory mechanisms of lncRNA as ceRNA in gastric cancer (GC) are not fully understood. Here, we first constructed a dysregulated lncRNA-associated ceRNA network by integrating analysis of gene expression profiles of lncRNAs, microRNAs (miRNAs), and messenger RNAs (mRNAs). Then, we determined three lncRNAs (RP5-1120P11, DLEU2, and DDX11-AS1) as hub lncRNAs, in which associated ceRNA subnetworks were involved in cell cycle-related processes and cancer-related pathways. Furthermore, we confirmed that the two lncRNAs (DLEU2 and DDX11-AS1) were significantly upregulated in GC tissues, promote GC cell proliferation, and negatively regulate miRNA expression, respectively. The hub lncRNAs (DLEU2 and DDX11-AS1) could have oncogenic functions, and act as potential ceRNAs to sponge miRNA. Our findings not only provide novel insights on ceRNA regulation in GC, but can also provide opportunities for the functional characterization of lncRNAs in future studies. Full article
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Open AccessReview Towards Long-Range RNA Structure Prediction in Eukaryotic Genes
Received: 27 April 2018 / Revised: 13 June 2018 / Accepted: 13 June 2018 / Published: 15 June 2018
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Abstract
The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and
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The ability to form an intramolecular structure plays a fundamental role in eukaryotic RNA biogenesis. Proximate regions in the primary transcripts fold into a local secondary structure, which is then hierarchically assembled into a tertiary structure that is stabilized by RNA-binding proteins and long-range intramolecular base pairings. While the local RNA structure can be predicted reasonably well for short sequences, long-range structure at the scale of eukaryotic genes remains problematic from the computational standpoint. The aim of this review is to list functional examples of long-range RNA structures, to summarize current comparative methods of structure prediction, and to highlight their advances and limitations in the context of long-range RNA structures. Most comparative methods implement the “first-align-then-fold” principle, i.e., they operate on multiple sequence alignments, while functional RNA structures often reside in non-conserved parts of the primary transcripts. The opposite “first-fold-then-align” approach is currently explored to a much lesser extent. Developing novel methods in both directions will improve the performance of comparative RNA structure analysis and help discover novel long-range structures, their higher-order organization, and RNA–RNA interactions across the transcriptome. Full article
(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)
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Open AccessArticle Decision Variants for the Automatic Determination of Optimal Feature Subset in RF-RFE
Received: 25 April 2018 / Revised: 30 May 2018 / Accepted: 6 June 2018 / Published: 15 June 2018
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Abstract
Feature selection, which identifies a set of most informative features from the original feature space, has been widely used to simplify the predictor. Recursive feature elimination (RFE), as one of the most popular feature selection approaches, is effective in data dimension reduction and
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Feature selection, which identifies a set of most informative features from the original feature space, has been widely used to simplify the predictor. Recursive feature elimination (RFE), as one of the most popular feature selection approaches, is effective in data dimension reduction and efficiency increase. A ranking of features, as well as candidate subsets with the corresponding accuracy, is produced through RFE. The subset with highest accuracy (HA) or a preset number of features (PreNum) are often used as the final subset. However, this may lead to a large number of features being selected, or if there is no prior knowledge about this preset number, it is often ambiguous and subjective regarding final subset selection. A proper decision variant is in high demand to automatically determine the optimal subset. In this study, we conduct pioneering work to explore the decision variant after obtaining a list of candidate subsets from RFE. We provide a detailed analysis and comparison of several decision variants to automatically select the optimal feature subset. Random forest (RF)-recursive feature elimination (RF-RFE) algorithm and a voting strategy are introduced. We validated the variants on two totally different molecular biology datasets, one for a toxicogenomic study and the other one for protein sequence analysis. The study provides an automated way to determine the optimal feature subset when using RF-RFE. Full article
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Open AccessArticle Automated Recognition of RNA Structure Motifs by Their SHAPE Data Signatures
Received: 27 April 2018 / Revised: 4 June 2018 / Accepted: 13 June 2018 / Published: 14 June 2018
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Abstract
High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA, an algorithm for rapidly
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High-throughput structure profiling (SP) experiments that provide information at nucleotide resolution are revolutionizing our ability to study RNA structures. Of particular interest are RNA elements whose underlying structures are necessary for their biological functions. We previously introduced patteRNA, an algorithm for rapidly mining SP data for patterns characteristic of such motifs. This work provided a proof-of-concept for the detection of motifs and the capability of distinguishing structures displaying pronounced conformational changes. Here, we describe several improvements and automation routines to patteRNA. We then consider more elaborate biological situations starting with the comparison or integration of results from searches for distinct motifs and across datasets. To facilitate such analyses, we characterize patteRNA’s outputs and describe a normalization framework that regularizes results. We then demonstrate that our algorithm successfully discerns between highly similar structural variants of the human immunodeficiency virus type 1 (HIV-1) Rev response element (RRE) and readily identifies its exact location in whole-genome structure profiles of HIV-1. This work highlights the breadth of information that can be gleaned from SP data and broadens the utility of data-driven methods as tools for the detection of novel RNA elements. Full article
(This article belongs to the Special Issue Computational Analysis of RNA Structure and Function)
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Open AccessCommunication Cytogenetics in Arctica islandica (Bivalvia, Arctidae): the Longest Lived Non-Colonial Metazoan
Received: 29 May 2018 / Revised: 8 June 2018 / Accepted: 12 June 2018 / Published: 13 June 2018
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Abstract
Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic
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Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic aspects but nothing is known about their chromosomes. In this work, the chromosomes of the ocean quahog Arctica islandica were analysed by means of 4′,6-diamidino-2-phenylindole (DAPI)/propidium iodide (PI) staining and fluorescent in situ hybridization (FISH) with rDNA, histone gene and telomeric probes. Whilst both 5S rDNA and 45S rDNA were clustered at single subcentromeric locations on the long arms of chromosome pairs 2 and 12, respectively, histone gene clusters located on the short arms of chromosome pairs 7, 10 and 17. As happens with most bivalves, the location of the vertebrate type telomeric sequence clusters was restricted to chromosome ends. The knowledge of the karyotype can facilitate the anchoring of genomic sequences to specific chromosome pairs in this species. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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