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Eijlers P, Al-Khafaji M, Soto-Martin E, Fasimoye R, Stead D, Wenzel M, Müller B, Pettitt J. A nematode-specific ribonucleoprotein complex mediates interactions between the major nematode spliced leader snRNP and its target pre-mRNAs. Nucleic Acids Res 2024:gkae321. [PMID: 38676950 DOI: 10.1093/nar/gkae321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 04/08/2024] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Spliced leader trans-splicing of pre-mRNAs is a critical step in the gene expression of many eukaryotes. How the spliced leader RNA and its target transcripts are brought together to form the trans-spliceosome remains an important unanswered question. Using immunoprecipitation followed by protein analysis via mass spectrometry and RIP-Seq, we show that the nematode-specific proteins, SNA-3 and SUT-1, form a complex with a set of enigmatic non-coding RNAs, the SmY RNAs. Our work redefines the SmY snRNP and shows for the first time that it is essential for nematode viability and is involved in spliced leader trans-splicing. SNA-3 and SUT-1 are associated with the 5' ends of most, if not all, nascent capped RNA polymerase II transcripts, and they also interact with components of the major nematode spliced leader (SL1) snRNP. We show that depletion of SNA-3 impairs the co-immunoprecipitation between one of the SL1 snRNP components, SNA-2, and several core spliceosomal proteins. We thus propose that the SmY snRNP recruits the SL1 snRNP to the 5' ends of nascent pre-mRNAs, an instrumental step in the assembly of the trans-spliceosome.
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Affiliation(s)
- Peter Eijlers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Mohammed Al-Khafaji
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Eva Soto-Martin
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Rotimi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - David Stead
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Rowett Institute, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Marius Wenzel
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ Scotland, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD Scotland, UK
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Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin. Arch Microbiol 2022; 204:461. [DOI: 10.1007/s00203-022-03085-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/08/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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3
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Philippe L, Pandarakalam GC, Fasimoye R, Harrison N, Connolly B, Pettitt J, Müller B. An in vivo genetic screen for genes involved in spliced leader trans-splicing indicates a crucial role for continuous de novo spliced leader RNP assembly. Nucleic Acids Res 2017; 45:8474-8483. [PMID: 28582530 PMCID: PMC5737717 DOI: 10.1093/nar/gkx500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/23/2017] [Accepted: 05/26/2017] [Indexed: 11/13/2022] Open
Abstract
Spliced leader (SL) trans-splicing is a critical element of gene expression in a number of eukaryotic groups. This process is arguably best understood in nematodes, where biochemical and molecular studies in Caenorhabditis elegans and Ascaris suum have identified key steps and factors involved. Despite this, the precise details of SL trans-splicing have yet to be elucidated. In part, this is because the systematic identification of the molecules involved has not previously been possible due to the lack of a specific phenotype associated with defects in this process. We present here a novel GFP-based reporter assay that can monitor SL1 trans-splicing in living C. elegans. Using this assay, we have identified mutants in sna-1 that are defective in SL trans-splicing, and demonstrate that reducing function of SNA-1, SNA-2 and SUT-1, proteins that associate with SL1 RNA and related SmY RNAs, impairs SL trans-splicing. We further demonstrate that the Sm proteins and pICln, SMN and Gemin5, which are involved in small nuclear ribonucleoprotein assembly, have an important role in SL trans-splicing. Taken together these results provide the first in vivo evidence for proteins involved in SL trans-splicing, and indicate that continuous replacement of SL ribonucleoproteins consumed during trans-splicing reactions is essential for effective trans-splicing.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Base Sequence
- Caenorhabditis elegans/genetics
- Caenorhabditis elegans/metabolism
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- Helminth Proteins/genetics
- Helminth Proteins/metabolism
- Microscopy, Fluorescence
- RNA Interference
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Helminth/genetics
- RNA, Helminth/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Spliced Leader/genetics
- RNA, Spliced Leader/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Trans-Splicing
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Affiliation(s)
- Lucas Philippe
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - George C. Pandarakalam
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Rotimi Fasimoye
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Neale Harrison
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Bernadette Connolly
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Jonathan Pettitt
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Berndt Müller
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Institute of Medical Sciences, Foresterhill, Aberdeen AB25 2ZD, UK
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4
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Abstract
The rapid development of high-throughput sequencing technologies and bioinformatics algorithms now enables detection and profiling of a large number of noncoding transcripts. Long noncoding RNAs (lncRNAs), which are longer than 200 nucleotides, are accumulating with important roles involved in biological processes and tissue physiology. In this chapter, we describe the use of NONCODEv4, a database that provide a comprehensive catalog of noncoding RNAs with particularly detailed annotations for lncRNAs. NONCODEv4 stores more than half million transcripts, of which more than 200,000 are lncRNAs. NONCODEv4 raises the concept of lncRNA genes and explores their expression and functions based on public transcriptome data. NONCODEv4 also integrated a series of online tools and have a web interface easy to use. NONCODEv4 is available at http://www.noncode.org/ http://www.bioinfo.org/ noncode.
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Velandia-Huerto CA, Gittenberger AA, Brown FD, Stadler PF, Bermúdez-Santana CI. Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum. BMC Genomics 2016; 17:691. [PMID: 27576499 PMCID: PMC5006418 DOI: 10.1186/s12864-016-2934-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 07/12/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to its status as a major invasive species. Non-coding RNAs, in particular microRNAs (miRNAs), are important regulatory genes that impact development and environmental adaptation. Beyond miRNAs, not much in known about tunicate ncRNAs. RESULTS We provide here a comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum. To this end we employed a combination of several computational approaches, including blast searches with a wide range of parameters, and secondary structured centered survey with infernal. The resulting candidate set was curated extensively to produce a high-quality ncRNA annotation of the first draft of the D. vexillum genome. It comprises 57 miRNA families, 4 families of ribosomal RNAs, 22 isoacceptor classes of tRNAs (of which more than 72 % of loci are pseudogenes), 13 snRNAs, 12 snoRNAs, and 1 other RNA family. Additionally, 21 families of mitochondrial tRNAs and 2 of mitochondrial ribosomal RNAs and 1 long non-coding RNA. CONCLUSIONS The comprehensive annotation of the D. vexillum non-coding RNAs provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians. Furthermore it provides a valuable research for efforts to establish detailed non-coding RNA annotations for other recently published and recently sequences in tunicate genomes.
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Affiliation(s)
- Cristian A. Velandia-Huerto
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C, Colombia
| | - Adriaan A. Gittenberger
- Institute of Biology, Leiden University, Leiden, P.O. Box 9505, 2300 RA Netherlands
- GiMaRIS, BioScience Park Leiden, J.H. Oortweg 21, 2333 CH, Leiden, Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Federico D. Brown
- Laboratorio de Biología del Desarrollo Evolutiva, Departamento de Ciencias Biológicas, Universidad de los Andes, Cra 1 No. 18A-12, Bogotá, Colombia
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Tr. 14 no. 101, São Paulo SP, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, Rod. Manuel Hypólito do Rego km. 131.5, Praia do Cabelo Gordo, São Sebastião, Brazil
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, Leipzig, D-04107 Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103 Germany
- Fraunhofer Institut for Cell Therapy and Immunology, Perlickstraße 1, Leipzig, D-04103 Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna, A-1090 Austria
- Center for non-coding RNA in Technology and Health, Grønegårdsvej 3, Frederiksberg C, DK-1870 Denmark
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501 USA
| | - Clara I. Bermúdez-Santana
- Biology Department, Universidad Nacional de Colombia, Carrera 45 # 26-85, Edif. Uriel Gutiérrez, Bogotá D.C, Colombia
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Xu D, Wei G, Lu P, Luo J, Chen X, Skogerbø G, Chen R. Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy. Protein Cell 2014; 5:770-82. [PMID: 24844773 PMCID: PMC4180458 DOI: 10.1007/s13238-014-0071-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 04/09/2014] [Indexed: 11/28/2022] Open
Abstract
In recent years, large numbers of non-coding RNAs (ncRNAs) have been identified in C. elegans but their functions are still not well studied. In C. elegans, CEP-1 is the sole homolog of the p53 family of genes. In order to obtain transcription profiles of ncRNAs regulated by CEP-1 under normal and UV stressed conditions, we applied the 'not-so-random' hexamers priming strategy to RNA sequencing in C. elegans, This NSR-seq strategy efficiently depleted rRNA transcripts from the samples and showed high technical replicability. We identified more than 1,000 ncRNAs whose apparent expression was repressed by CEP-1, while around 200 were activated. Around 40% of the CEP-1 activated ncRNAs promoters contain a putative CEP-1-binding site. CEP-1 regulated ncRNAs were frequently clustered and concentrated on the X chromosome. These results indicate that numerous ncRNAs are involved in CEP-1 transcriptional network and that these are especially enriched on the X chromosome in C. elegans.
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Affiliation(s)
- Derong Xu
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
- Graduate University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Guifeng Wei
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
- Graduate University of Chinese Academy of Sciences, Beijing, 100080 China
| | - Ping Lu
- Key Laboratory of Forest Protection, State Forestry
Administration/Research Institute of Forest Ecology, Environment and
Protection, Chinese Academy of Forestry, Beijing, 100091 China
| | - Jianjun Luo
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaomin Chen
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Geir Skogerbø
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
| | - Runsheng Chen
- Laboratory of Non-coding RNA, Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, 100101 China
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8
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Pettitt J, Philippe L, Sarkar D, Johnston C, Gothe HJ, Massie D, Connolly B, Müller B. Operons are a conserved feature of nematode genomes. Genetics 2014; 197:1201-11. [PMID: 24931407 PMCID: PMC4125394 DOI: 10.1534/genetics.114.162875] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/06/2014] [Indexed: 01/09/2023] Open
Abstract
The organization of genes into operons, clusters of genes that are co-transcribed to produce polycistronic pre-mRNAs, is a trait found in a wide range of eukaryotic groups, including multiple animal phyla. Operons are present in the class Chromadorea, one of the two main nematode classes, but their distribution in the other class, the Enoplea, is not known. We have surveyed the genomes of Trichinella spiralis, Trichuris muris, and Romanomermis culicivorax and identified the first putative operons in members of the Enoplea. Consistent with the mechanism of polycistronic RNA resolution in other nematodes, the mRNAs produced by genes downstream of the first gene in the T. spiralis and T. muris operons are trans-spliced to spliced leader RNAs, and we are able to detect polycistronic RNAs derived from these operons. Importantly, a putative intercistronic region from one of these potential enoplean operons confers polycistronic processing activity when expressed as part of a chimeric operon in Caenorhabditis elegans. We find that T. spiralis genes located in operons have an increased likelihood of having operonic C. elegans homologs. However, operon structure in terms of synteny and gene content is not tightly conserved between the two taxa, consistent with models of operon evolution. We have nevertheless identified putative operons conserved between Enoplea and Chromadorea. Our data suggest that operons and "spliced leader" (SL) trans-splicing predate the radiation of the nematode phylum, an inference which is supported by the phylogenetic profile of proteins known to be involved in nematode SL trans-splicing.
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Affiliation(s)
- Jonathan Pettitt
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Lucas Philippe
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Debjani Sarkar
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Christopher Johnston
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Henrike Johanna Gothe
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Diane Massie
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Bernadette Connolly
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Berndt Müller
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
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9
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Abstract
Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes. Several programs have been developed for identifying RNAs, including specific tools tailored to a particular RNA family as well as more general ones designed to work for any family. Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence, and structure of an RNA family. In this chapter, as an illustrative example, the Infernal software package and CMs from the Rfam database are used to identify RNAs in the genome of the archaeon Methanobrevibacter ruminantium, uncovering some additional RNAs not present in the genome's initial annotation. Analysis of the results and comparison with family-specific methods demonstrate some important strengths and weaknesses of this general approach.
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Affiliation(s)
- Eric P Nawrocki
- Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn, VA, 20147, USA
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10
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Rivas E. The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. RNA Biol 2013; 10:1185-96. [PMID: 23695796 PMCID: PMC3849167 DOI: 10.4161/rna.24971] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/06/2013] [Accepted: 05/08/2013] [Indexed: 12/31/2022] Open
Abstract
Any method for RNA secondary structure prediction is determined by four ingredients. The architecture is the choice of features implemented by the model (such as stacked basepairs, loop length distributions, etc.). The architecture determines the number of parameters in the model. The scoring scheme is the nature of those parameters (whether thermodynamic, probabilistic, or weights). The parameterization stands for the specific values assigned to the parameters. These three ingredients are referred to as "the model." The fourth ingredient is the folding algorithms used to predict plausible secondary structures given the model and the sequence of a structural RNA. Here, I make several unifying observations drawn from looking at more than 40 years of methods for RNA secondary structure prediction in the light of this classification. As a final observation, there seems to be a performance ceiling that affects all methods with complex architectures, a ceiling that impacts all scoring schemes with remarkable similarity. This suggests that modeling RNA secondary structure by using intrinsic sequence-based plausible "foldability" will require the incorporation of other forms of information in order to constrain the folding space and to improve prediction accuracy. This could give an advantage to probabilistic scoring systems since a probabilistic framework is a natural platform to incorporate different sources of information into one single inference problem.
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Affiliation(s)
- Elena Rivas
- Janelia Farm Research Campus; Howard Hughes Medical Institute; Ashburn, VA USA
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11
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Penev L, Hagedorn G, Mietchen D, Georgiev T, Stoev P, Sautter G, Agosti D, Plank A, Balke M, Hendrich L, Erwin T. Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID. Zookeys 2011:1-12. [PMID: 21594104 PMCID: PMC3084489 DOI: 10.3897/zookeys.90.1369] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 04/14/2011] [Indexed: 11/16/2022] Open
Abstract
Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors.
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Affiliation(s)
- Lyubomir Penev
- Institute of Biodiversity and Ecosystem Research, Sofia, Bulgaria
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Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res 2010; 39:D141-5. [PMID: 21062808 PMCID: PMC3013711 DOI: 10.1093/nar/gkq1129] [Citation(s) in RCA: 326] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community-derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk.
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Affiliation(s)
- Paul P Gardner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA.
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Menzel P, Gorodkin J, Stadler PF. The tedious task of finding homologous noncoding RNA genes. RNA (NEW YORK, N.Y.) 2009; 15:2075-82. [PMID: 19861422 PMCID: PMC2779685 DOI: 10.1261/rna.1556009] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
User-driven in silico RNA homology search is still a nontrivial task. In part, this is the consequence of a limited precision of the computational tools in spite of recent exciting progress in this area, and to a certain extent, computational costs are still problematic in practice. An important, and as we argue here, dominating issue is the dependence on good curated (secondary) structural alignments of the RNAs. These are often hard to obtain, not so much because of an inherent limitation in the available data, but because they require substantial manual curation, an effort that is rarely acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging: BLAST still works better or equally good as other methods unless extensive expert knowledge on the RNA family is included. However, when good curated data are available the recent development yields further improvements in finding remote homologs. Homology search beyond the reach of BLAST hence is not at all a routine task.
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Affiliation(s)
- Peter Menzel
- Section for Genetics and Bioinformatics, IBHV, and Center for Applied Bioinformatics, University of Copenhagen, DK-1870 Frederiksberg, Denmark
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15
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Gardner PP. The use of covariance models to annotate RNAs in whole genomes. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:444-50. [PMID: 19833700 DOI: 10.1093/bfgp/elp042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this review we discuss bioinformatic issues in non-coding RNA analysis, in particular the annotation of genome sequences using covariance models. Some recent innovations for improving the speed and accuracy of covariance models is discussed.
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Affiliation(s)
- Paul P Gardner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK.
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Stadler PF, Chen JJL, Hackermuller J, Hoffmann S, Horn F, Khaitovich P, Kretzschmar AK, Mosig A, Prohaska SJ, Qi X, Schutt K, Ullmann K. Evolution of Vault RNAs. Mol Biol Evol 2009; 26:1975-91. [DOI: 10.1093/molbev/msp112] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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