1
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Abstract
The 7SK RNA is a small nuclear RNA that is involved in the regulation of Pol-II transcription. It is very well conserved in vertebrates, but shows extensive variations in both sequence and structure across invertebrates. A systematic homology search extended the collection of 7SK genes in both Arthropods and Lophotrochozoa making use of the large number of recently published invertebrate genomes. The extended data set made it possible to infer complete consensus structures for invertebrate 7SK RNAs. These show that not only the well-conserved 5'- and 3'- domains but all the interior Stem A domain is universally conserved. In contrast, Stem B region exhibits substantial structural variation and does not adhere to a common structural model beyond phylum level.
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Affiliation(s)
- Ali M Yazbeck
- a Bioinformatics Group, Department of Computer Science , Leipzig University , Härtelstraße 16-18, Leipzig , Germany.,b Lebanese University, Doctoral School for Science and Technology, Rafic Hariri University Campus , Hadath , Lebanon
| | - Kifah R Tout
- b Lebanese University, Doctoral School for Science and Technology, Rafic Hariri University Campus , Hadath , Lebanon
| | - Peter F Stadler
- a Bioinformatics Group, Department of Computer Science , Leipzig University , Härtelstraße 16-18, Leipzig , Germany.,c Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases , Leipzig University.,d Department of Diagnostics , Fraunhofer Institute for Cell Therapy and Immunology - IZI , Perlickstraße 1, D-04103 Leipzig , Germany.,e Max Planck Institute for Mathematics in the Sciences , Inselstraße 22, D-04103 Leipzig , Germany.,f Department of Theoretical Chemistry , University of Vienna , Währingerstraße 17, A-1090 Wien , Austria.,g Center for non-coding RNA in Technology and Health , University of Copenhagen , Grønnegårdsvej 3, DK-1870 Frederiksberg C , Denmark.,h Santa Fe Institute , 1399 Hyde Park Rd., Santa Fe , NM 87501 , USA
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2
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Targeted CRISPR disruption reveals a role for RNase MRP RNA in human preribosomal RNA processing. Genes Dev 2017; 31:59-71. [PMID: 28115465 PMCID: PMC5287113 DOI: 10.1101/gad.286963.116] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 12/20/2016] [Indexed: 12/03/2022]
Abstract
In this study, Goldfarb et al. used CRISPR–Cas9 genome editing to eliminate MRP RNA—a ribonucleoprotein complex with an RNA subunit that is conserved across eukarya—in the majority of cells. Analysis by RNA FISH, Northerns, and RNA sequencing demonstrates an accumulation of ribosomal RNA precursor and thus establishes a role for RNase MRP in human pre-rRNA processing. MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR–Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor—analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing—implicates MRP RNA in pre-rRNA processing. Amelioration of pre-rRNA imbalance is achieved through rescue of MRP RNA levels by ectopic expression. Furthermore, affinity-purified MRP ribonucleoprotein (RNP) from HeLa cells cleaves the human pre-rRNA in vitro at at least one site used in cells, while RNP isolated from cells with CRISPR-edited MRP loci loses this activity, and ectopic MRP RNA expression restores cleavage activity. Thus, a role for RNase MRP in human pre-rRNA processing is established. As demonstrated here, targeted CRISPR disruption is a valuable tool for functional studies of essential noncoding RNAs that are resistant to RNAi and RNase H-based degradation.
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3
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Gupta Y, Witte M, Möller S, Ludwig RJ, Restle T, Zillikens D, Ibrahim SM. ptRNApred: computational identification and classification of post-transcriptional RNA. Nucleic Acids Res 2014; 42:e167. [PMID: 25303994 PMCID: PMC4267668 DOI: 10.1093/nar/gku918] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED Non-coding RNAs (ncRNAs) are known to play important functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as classification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity and specificity. We here present ptRNApred, a tool to detect and classify subclasses of non-coding RNA that are involved in the regulation of post-transcriptional modifications or DNA replication, which we here call post-transcriptional RNA (ptRNA). It (i) detects RNA sequences coding for post-transcriptional RNA from the genomic sequence with an overall sensitivity of 91% and a specificity of 94% and (ii) predicts ptRNA-subclasses that exist in eukaryotes: snRNA, snoRNA, RNase P, RNase MRP, Y RNA or telomerase RNA. AVAILABILITY The ptRNApred software is open for public use on http://www.ptrnapred.org/.
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Affiliation(s)
- Yask Gupta
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Mareike Witte
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Steffen Möller
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Ralf J Ludwig
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Tobias Restle
- Institute for Molecular Medicine, University of Lübeck, 23538 Lübeck, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Saleh M Ibrahim
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
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4
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Abstract
Many RNA families, i.e., groups of homologous RNA genes, belong to RNA classes, such as tRNAs, snoRNAs, or microRNAs, that are characterized by common sequence motifs and/or common secondary structure features. The detection of new members of RNA classes, as well as the comprehensive annotation of genomes with members of RNA classes is a challenging task that goes beyond simple homology search. Computational methods addressing this problem typically use a three-tiered approach: In the first step an efficient and sensitive filter is employed. In the second step the candidate set is narrowed down using computationally expensive methods geared towards specificity. In the final step the hits are annotated with class-specific features and scored. Here we review the tools that are currently available for a diverse set of RNA classes.
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5
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Esakova O, Perederina A, Berezin I, Krasilnikov AS. Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate. Nucleic Acids Res 2013; 41:7084-91. [PMID: 23700311 PMCID: PMC3737539 DOI: 10.1093/nar/gkt432] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/25/2013] [Accepted: 04/27/2013] [Indexed: 01/19/2023] Open
Abstract
Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed.
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Affiliation(s)
| | | | | | - Andrey S. Krasilnikov
- Department of Biochemistry and Molecular Biology and Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
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6
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Dieci G, Conti A, Pagano A, Carnevali D. Identification of RNA polymerase III-transcribed genes in eukaryotic genomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:296-305. [PMID: 23041497 DOI: 10.1016/j.bbagrm.2012.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/20/2012] [Accepted: 09/21/2012] [Indexed: 12/16/2022]
Abstract
The RNA polymerase (Pol) III transcription system is devoted to the production of short, generally abundant noncoding (nc) RNAs in all eukaryotic cells. Previously thought to be restricted to a few housekeeping genes easily detectable in genome sequences, the set of known Pol III-transcribed genes (class III genes) has been expanding in the last ten years, and the issue of their detection, annotation and actual expression has been stimulated and revived by the results of recent high-resolution genome-wide location analyses of the mammalian Pol III machinery, together with those of Pol III-centered computational studies and of ncRNA-focused transcriptomic approaches. In this article, we provide an outline of distinctive features of Pol III-transcribed genes that have allowed and currently allow for their detection in genome sequences, we critically review the currently practiced strategies for the identification of novel class III genes and transcripts, and we discuss emerging themes in Pol III transcription regulation which might orient future transcriptomic studies. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy.
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7
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Hernandez-Cid A, Aguirre-Sampieri S, Diaz-Vilchis A, Torres-Larios A. Ribonucleases P/MRP and the expanding ribonucleoprotein world. IUBMB Life 2012; 64:521-8. [PMID: 22605678 DOI: 10.1002/iub.1052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
One of the hallmarks of life is the widespread use of certain essential ribozymes. The ubiquitous ribonuclease P (RNase P) and eukaryotic RNase MRP are essential complexes where a structured, noncoding RNA acts in catalysis. Recent discoveries have elucidated the three-dimensional structure of the ancestral ribonucleoprotein complex, suggested the possibility of a protein-only composition in organelles, and even noted the absence of RNase P in a non-free-living organism. With respect to these last two findings, import mechanisms for RNases P/MRP into mitochondria have been demonstrated, and RNase P is present in organisms with some of the smallest known genomes. Together, these results have led to an ongoing debate regarding the precise definition of how "essential" these ribozymes truly are.
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Affiliation(s)
- Aaron Hernandez-Cid
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico
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8
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Lessa FA, Raiol T, Brigido MM, Martins Neto DSB, Walter MEMT, Stadler PF. Clustering rfam 10.1: clans, families, and classes. Genes (Basel) 2012; 3:378-90. [PMID: 24704975 PMCID: PMC3899987 DOI: 10.3390/genes3030378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 06/04/2012] [Accepted: 06/15/2012] [Indexed: 11/16/2022] Open
Abstract
The Rfam database contains information about non-coding RNAs emphasizing their secondary structures and organizing them into families of homologous RNA genes or functional RNA elements. Recently, a higher order organization of Rfam in terms of the so-called clans was proposed along with its “decimal release”. In this proposition, some of the families have been assigned to clans based on experimental and computational data in order to find related families. In the present work we investigate an alternative classification for the RNA families based on tree edit distance. The resulting clustering recovers some of the Rfam clans. The majority of clans, however, are not recovered by the structural clustering. Instead, they get dispersed into larger clusters, which correspond roughly to Genes 2012, 3 379 well-described RNA classes such as snoRNAs, miRNAs, and CRISPRs. In conclusion, a structure-based clustering can contribute to the elucidation of the relationships among the Rfam families beyond the realm of clans and classes.
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Affiliation(s)
- Felipe A Lessa
- Department of Computer Science, Institute of Exact Sciences, University of Brasília, Brasília 70910-900, Brazil.
| | - Tainá Raiol
- Department of Cellular Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil.
| | - Marcelo M Brigido
- Department of Cellular Biology, Institute of Biology, University of Brasília, Brasília 70910-900, Brazil.
| | | | - Maria Emília M T Walter
- Department of Computer Science, Institute of Exact Sciences, University of Brasília, Brasília 70910-900, Brazil.
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
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9
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Chen XS, Penny D, Collins LJ. Characterization of RNase MRP RNA and novel snoRNAs from Giardia intestinalis and Trichomonas vaginalis. BMC Genomics 2011; 12:550. [PMID: 22053856 PMCID: PMC3228867 DOI: 10.1186/1471-2164-12-550] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 11/06/2011] [Indexed: 12/02/2022] Open
Abstract
Background Eukaryotic cells possess a complex network of RNA machineries which function in RNA-processing and cellular regulation which includes transcription, translation, silencing, editing and epigenetic control. Studies of model organisms have shown that many ncRNAs of the RNA-infrastructure are highly conserved, but little is known from non-model protists. In this study we have conducted a genome-scale survey of medium-length ncRNAs from the protozoan parasites Giardia intestinalis and Trichomonas vaginalis. Results We have identified the previously 'missing' Giardia RNase MRP RNA, which is a key ribozyme involved in pre-rRNA processing. We have also uncovered 18 new H/ACA box snoRNAs, expanding our knowledge of the H/ACA family of snoRNAs. Conclusions Results indicate that Giardia intestinalis and Trichomonas vaginalis, like their distant multicellular relatives, contain a rich infrastructure of RNA-based processing. From here we can investigate the evolution of RNA processing networks in eukaryotes.
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Affiliation(s)
- Xiaowei S Chen
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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10
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Perederina A, Khanova E, Quan C, Berezin I, Esakova O, Krasilnikov AS. Interactions of a Pop5/Rpp1 heterodimer with the catalytic domain of RNase MRP. RNA (NEW YORK, N.Y.) 2011; 17:1922-31. [PMID: 21878546 PMCID: PMC3185923 DOI: 10.1261/rna.2855511] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/27/2011] [Indexed: 05/22/2023]
Abstract
Ribonuclease (RNase) MRP is a multicomponent ribonucleoprotein complex closely related to RNase P. RNase MRP and eukaryotic RNase P share most of their protein components, as well as multiple features of their catalytic RNA moieties, but have distinct substrate specificities. While RNase P is practically universally found in all three domains of life, RNase MRP is essential in eukaryotes. The structural organizations of eukaryotic RNase P and RNase MRP are poorly understood. Here, we show that Pop5 and Rpp1, protein components found in both RNase P and RNase MRP, form a heterodimer that binds directly to the conserved area of the putative catalytic domain of RNase MRP RNA. The Pop5/Rpp1 binding site corresponds to the protein binding site in bacterial RNase P RNA. Structural and evolutionary roles of the Pop5/Rpp1 heterodimer in RNases P and MRP are discussed.
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Affiliation(s)
- Anna Perederina
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Elena Khanova
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Chao Quan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Igor Berezin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Olga Esakova
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrey S. Krasilnikov
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Corresponding author.E-mail .
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11
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Abstract
Nuclear ribonuclease (RNase) P is a ubiquitous essential ribonucleoprotein complex, one of only two known RNA-based enzymes found in all three domains of life. The RNA component is the catalytic moiety of RNases P across all phylogenetic domains; it contains a well-conserved core, whereas peripheral structural elements are diverse. RNA components of eukaryotic RNases P tend to be less complex than their bacterial counterparts, a simplification that is accompanied by a dramatic reduction of their catalytic ability in the absence of protein. The size and complexity of the protein moieties increase dramatically from bacterial to archaeal to eukaryotic enzymes, apparently reflecting the delegation of some structural functions from RNA to proteins and, perhaps, in response to the increased complexity of the cellular environment in the more evolutionarily advanced organisms; the reasons for the increased dependence on proteins are not clear. We review current information on RNase P and the closely related universal eukaryotic enzyme RNase MRP, focusing on their functions and structural organization.
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Affiliation(s)
- Olga Esakova
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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12
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Jarrous N, Gopalan V. Archaeal/eukaryal RNase P: subunits, functions and RNA diversification. Nucleic Acids Res 2010; 38:7885-94. [PMID: 20716516 PMCID: PMC3001073 DOI: 10.1093/nar/gkq701] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
RNase P, a catalytic ribonucleoprotein (RNP), is best known for its role in precursor tRNA processing. Recent discoveries have revealed that eukaryal RNase P is also required for transcription and processing of select non-coding RNAs, thus enmeshing RNase P in an intricate network of machineries required for gene expression. Moreover, the RNase P RNA seems to have been subject to gene duplication, selection and divergence to generate two new catalytic RNPs, RNase MRP and MRP-TERT, which perform novel functions encompassing cell cycle control and stem cell biology. We present new evidence and perspectives on the functional diversification of the RNase P RNA to highlight it as a paradigm for the evolutionary plasticity that underlies the extant broad repertoire of catalytic and unexpected regulatory roles played by RNA-driven RNPs.
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Affiliation(s)
- Nayef Jarrous
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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13
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Yusuf D, Marz M, Stadler PF, Hofacker IL. Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics 2010; 11:432. [PMID: 20626900 PMCID: PMC2996960 DOI: 10.1186/1471-2164-11-432] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 07/13/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Effective bioinformatics solutions are needed to tackle challenges posed by industrial-scale genome annotation. We present Bcheck, a wrapper tool which predicts RNase P RNA genes by combining the speed of pattern matching and sensitivity of covariance models. The core of Bcheck is a library of subfamily specific descriptor models and covariance models. RESULTS Scanning all microbial genomes in GenBank identifies RNase P RNA genes in 98% of 1024 microbial chromosomal sequences within just 4 hours on single CPU. Comparing to existing annotations found in 387 of the GenBank files, Bcheck predictions have more intact structure and are automatically classified by subfamily membership. For eukaryotic chromosomes Bcheck could identify the known RNase P RNA genes in 84 out of 85 metazoan genomes and 19 out of 21 fungi genomes. Bcheck predicted 37 novel eukaryotic RNase P RNA genes, 32 of which are from fungi. Gene duplication events are observed in at least 20 metazoan organisms. Scanning of meta-genomic data from the Global Ocean Sampling Expedition, comprising over 10 million sample sequences (18 Gigabases), predicted 2909 unique genes, 98% of which fall into ancestral bacteria A type of RNase P RNA and 66% of which have no close homolog to known prokaryotic RNase P RNA. CONCLUSIONS The combination of efficient filtering by means of a descriptor-based search and subsequent construction of a high-quality gene model by means of a covariance model provides an efficient method for the detection of RNase P RNA genes in large-scale sequencing data. Bcheck is implemented as webserver and can also be downloaded for local use from http://rna.tbi.univie.ac.at/bcheck.
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Affiliation(s)
- Dilmurat Yusuf
- Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria
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14
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Hands-Taylor KLD, Martino L, Tata R, Babon JJ, Bui TT, Drake AF, Beavil RL, Pruijn GJM, Brown PR, Conte MR. Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA. Nucleic Acids Res 2010; 38:4052-66. [PMID: 20215441 PMCID: PMC2896528 DOI: 10.1093/nar/gkq141] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Rpp20 and Rpp25 are two key subunits of the human endoribonucleases RNase P and MRP. Formation of an Rpp20–Rpp25 complex is critical for enzyme function and sub-cellular localization. We present the first detailed in vitro analysis of their conformational properties, and a biochemical and biophysical characterization of their mutual interaction and RNA recognition. This study specifically examines the role of the Rpp20/Rpp25 association in the formation of the ribonucleoprotein complex. The interaction of the individual subunits with the P3 arm of the RNase MRP RNA is revealed to be negligible whereas the 1:1 Rpp20:Rpp25 complex binds to the same target with an affinity of the order of nM. These results unambiguously demonstrate that Rpp20 and Rpp25 interact with the P3 RNA as a heterodimer, which is formed prior to RNA binding. This creates a platform for the design of future experiments aimed at a better understanding of the function and organization of RNase P and MRP. Finally, analyses of interactions with deletion mutant proteins constructed with successively shorter N- and C-terminal sequences indicate that the Alba-type core domain of both Rpp20 and Rpp25 contains most of the determinants for mutual association and P3 RNA recognition.
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Affiliation(s)
- Katherine L. D. Hands-Taylor
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Luigi Martino
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Renée Tata
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Jeffrey J. Babon
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Tam T. Bui
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Alex F. Drake
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Rebecca L. Beavil
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Ger J. M. Pruijn
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Paul R. Brown
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | - Maria R. Conte
- Randall Division of Cell and Molecular Biophysics, King’s College London, New Hunt’s House, Guy’s Campus, London SE1 1UL, UK, Structural Biology Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville 3052, VIC, Australia, Pharmaceutical Science Division, King’s College London, The Wolfson Wing, Hodgkin Building, Guy's Campus, London SE1 1UL, UK and Department of Biomolecular Chemistry, Nijmegen Centre for Molecular Life Sciences, Institute for Molecules and Materials, Radboud University of Nijmegen, Nijmegen, The Netherlands
- *To whom correspondence should be addressed. Tel: +44 20 7848 6194; Fax: +44 20 7848 6435;
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Lu Q, Wierzbicki S, Krasilnikov AS, Schmitt ME. Comparison of mitochondrial and nucleolar RNase MRP reveals identical RNA components with distinct enzymatic activities and protein components. RNA (NEW YORK, N.Y.) 2010; 16:529-37. [PMID: 20086051 PMCID: PMC2822918 DOI: 10.1261/rna.1893710] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 11/20/2009] [Indexed: 05/22/2023]
Abstract
RNase MRP is a ribonucleoprotein endoribonuclease found in three cellular locations where distinct substrates are processed: the mitochondria, the nucleolus, and the cytoplasm. Cytoplasmic RNase MRP is the nucleolar enzyme that is transiently relocalized during mitosis. Nucleolar RNase MRP (NuMRP) was purified to homogeneity, and we extensively purified the mitochondrial RNase MRP (MtMRP) to a single RNA component identical to the NuMRP RNA. Although the protein components of the NuMRP were identified by mass spectrometry successfully, none of the known NuMRP proteins were found in the MtMRP preparation. Only trace amounts of the core NuMRP protein, Pop4, were detected in MtMRP by Western blot. In vitro activity of the two enzymes was compared. MtMRP cleaved only mitochondrial ORI5 substrate, while NuMRP cleaved all three substrates. However, the NuMRP enzyme cleaved the ORI5 substrate at sites different than the MtMRP enzyme. In addition, enzymatic differences in preferred ionic strength confirm these enzymes as distinct entities. Magnesium was found to be essential to both enzymes. We tested a number of reported inhibitors including puromycin, pentamidine, lithium, and pAp. Puromycin inhibition suggested that it binds directly to the MRP RNA, reaffirming the role of the RNA component in catalysis. In conclusion, our study confirms that the NuMRP and MtMRP enzymes are distinct entities with differing activities and protein components but a common RNA subunit, suggesting that the RNA must be playing a crucial role in catalytic activity.
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Affiliation(s)
- Qiaosheng Lu
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, USA
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16
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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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17
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Copeland CS, Marz M, Rose D, Hertel J, Brindley PJ, Santana CB, Kehr S, Attolini CSO, Stadler PF. Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. BMC Genomics 2009; 10:464. [PMID: 19814823 PMCID: PMC2770079 DOI: 10.1186/1471-2164-10-464] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Accepted: 10/08/2009] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA) plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available. RESULTS A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs. CONCLUSION The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.
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Affiliation(s)
- Claudia S Copeland
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
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18
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An Overview of the Introns-First Theory. J Mol Evol 2009; 69:527-40. [DOI: 10.1007/s00239-009-9279-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
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19
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Cartilage-hair hypoplasia: molecular basis and heterogeneity of the immunological phenotype. Curr Opin Allergy Clin Immunol 2009; 8:534-9. [PMID: 18978468 DOI: 10.1097/aci.0b013e328310fe7d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW To report on the expanding clinical and immunological spectrum associated with ribonuclease mitochondrial RNA-processing mutations and to review the cellular and molecular mechanisms involved in the pathophysiology of cartilage-hair hypoplasia (CHH) and related disorders in humans. RECENT FINDINGS Different types of mutations are associated with skeletal or extraskeletal manifestations of CHH, respectively. In particular, severe immunodeficiency is mostly associated with mutations that alter cyclin B2 mRNA cleavage and thus are likely to reflect disturbances in cell cycle control. The first cases of ribonuclease mitochondrial RNA-processing mutations with severe immunodeficiency, but no skeletal abnormalities, have been identified. SUMMARY Abnormalities of ribosome biogenesis have been shown to cause distinct bone marrow failure syndromes, including CHH. However, the specific role of ribosomal and extraribosomal defects in the pathophysiology of the various phenotypic features of CHH remains undefined. Development of suitable animal models is needed to address this important issue.
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20
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de Nooijer S, Holland BR, Penny D. The emergence of predators in early life: there was no Garden of Eden. PLoS One 2009; 4:e5507. [PMID: 19492046 PMCID: PMC2685975 DOI: 10.1371/journal.pone.0005507] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 03/30/2009] [Indexed: 11/25/2022] Open
Abstract
Background Eukaryote cells are suggested to arise somewhere between 0.85∼2.7 billion years ago. However, in the present world of unicellular organisms, cells that derive their food and metabolic energy from larger cells engulfing smaller cells (phagocytosis) are almost exclusively eukaryotic. Combining these propositions, that eukaryotes were the first phagocytotic predators and that they arose only 0.85∼2.7 billion years ago, leads to an unexpected prediction of a long period (∼1–3 billion years) with no phagocytotes – a veritable Garden of Eden. Methodology We test whether such a long period is reasonable by simulating a population of very simple unicellular organisms - given only basic physical, biological and ecological principles. Under a wide range of initial conditions, cellular specialization occurs early in evolution; we find a range of cell types from small specialized primary producers to larger opportunistic or specialized predators. Conclusions Both strategies, specialized smaller cells and phagocytotic larger cells are apparently fundamental biological strategies that are expected to arise early in cellular evolution. Such early predators could have been ‘prokaryotes’, but if the earliest cells on the eukaryote lineage were predators then this explains most of their characteristic features.
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Affiliation(s)
- Silvester de Nooijer
- Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
| | - Barbara R. Holland
- Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
| | - David Penny
- Allan Wilson Center for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
- * E-mail:
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21
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Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF. Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res 2009; 37:1602-15. [PMID: 19151082 PMCID: PMC2655684 DOI: 10.1093/nar/gkn1084] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 12/22/2008] [Accepted: 12/23/2008] [Indexed: 02/06/2023] Open
Abstract
A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs--in particular rRNAs, tRNAs and some snRNAs--we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.
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Affiliation(s)
- Jana Hertel
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Danielle de Jong
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Manja Marz
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Dominic Rose
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Hakim Tafer
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Andrea Tanzer
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Bernd Schierwater
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
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Collins LJ, Penny D. The RNA infrastructure: dark matter of the eukaryotic cell? Trends Genet 2009; 25:120-8. [PMID: 19171405 DOI: 10.1016/j.tig.2008.12.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Revised: 12/16/2008] [Accepted: 12/17/2008] [Indexed: 11/29/2022]
Abstract
Eukaryotes express many functional non-protein-coding RNAs (ncRNAs) that participate in the processing and regulation of other RNA molecules. By focusing on connections between RNA-based processes, common patterns emerge that form a network-like RNA infrastructure. Owing to the intracellular movement of RNA during its processing (both between nuclear compartments and between the nucleus and cytoplasm), the RNA infrastructure contains both spatial and temporal connections. As research moves away from being protein-centric and focuses more on genomics, it is timely to explore these often 'hidden' aspects of the eukaryotic cell. The general and ancestral nature of most basic RNA-processing steps places a new focus on the generality of the spatial and temporal steps in RNA processing.
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Affiliation(s)
- Lesley J Collins
- Allan Wilson Centre for Molecular Ecology and Evolution and Institute of Molecular BioSciences, Private Bag 11222, Massey University, 4442 Palmerston North, New Zealand.
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23
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Homology Search with Fragmented Nucleic Acid Sequence Patterns. LECTURE NOTES IN COMPUTER SCIENCE 2007. [DOI: 10.1007/978-3-540-74126-8_31] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Chen X(S, Rozhdestvensky TS, Collins LJ, Schmitz J, Penny D. Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis. Nucleic Acids Res 2007; 35:4619-28. [PMID: 17586815 PMCID: PMC1950533 DOI: 10.1093/nar/gkm474] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Non-protein-coding RNAs represent a large proportion of transcribed sequences in eukaryotes. These RNAs often function in large RNA-protein complexes, which are catalysts in various RNA-processing pathways. As RNA processing has become an increasingly important area of research, numerous non-messenger RNAs have been uncovered in all the model eukaryotic organisms. However, knowledge on RNA processing in deep-branching eukaryotes is still limited. This study focuses on the identification of non-protein-coding RNAs from the diplomonad parasite Giardia intestinalis, showing that a combined experimental and computational search strategy is a fast method of screening reduced or compact genomes. The analysis of our Giardia cDNA library has uncovered 31 novel candidates, including C/D-box and H/ACA box snoRNAs, as well as an unusual transcript of RNase P, and double-stranded RNAs. Subsequent computational analysis has revealed additional putative C/D-box snoRNAs. Our results will lead towards a future understanding of RNA metabolism in the deep-branching eukaryote Giardia, as more ncRNAs are characterized.
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Affiliation(s)
- Xiaowei (Sylvia) Chen
- Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand and Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - Timofey S. Rozhdestvensky
- Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand and Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - Lesley J. Collins
- Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand and Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
- *To whom correspondence should be addressed.+64 6 350 9099-7345+64 6 350 5626
| | - Jürgen Schmitz
- Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand and Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
| | - David Penny
- Allan Wilson Centre, IMBS, Massey University, Palmerston North, New Zealand and Institute of Experimental Pathology (ZMBE), University of Münster, Münster, Germany
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25
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Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA. The evolution of eukaryotes. Science 2007; 316:542-3; author reply 542-3. [PMID: 17463271 DOI: 10.1126/science.316.5824.542c] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Philippe H, Blanchette M. Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada. BMC Evol Biol 2007; 7 Suppl 1:S1-16. [PMID: 17288567 PMCID: PMC1796603 DOI: 10.1186/1471-2148-7-s1-s1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The First Phylogenomics Conference was held in Ste-Adèle (Québec, Canada) in March 2006. Selected papers appear in this special issue of BMC Evolutionary Biology. Here, we give an introduction to the field and provide an overview of the articles presented in this issue.
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Affiliation(s)
- Hervé Philippe
- Canadian Institute for Advanced Research, Centre Robert Cedergren, Département de Biochimie, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, Québec, H3T 1J4, Canada
| | - Mathieu Blanchette
- McGill Centre for Bioinformatics, McGill University, 3775 University Steet, Montréal, Québec, H3A 2B4, Canada
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