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Whisson SC, Avrova AO, Lavrova O, Pritchard L. Families of short interspersed elements in the genome of the oomycete plant pathogen, Phytophthora infestans. Fungal Genet Biol 2005; 42:351-65. [PMID: 15749054 DOI: 10.1016/j.fgb.2005.01.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Revised: 12/06/2004] [Accepted: 01/06/2005] [Indexed: 10/25/2022]
Abstract
The first known families of tRNA-related short interspersed elements (SINEs) in the oomycetes were identified by exploiting the genomic DNA sequence resources for the potato late blight pathogen, Phytophthora infestans. Fifteen families of tRNA-related SINEs, as well as predicted tRNAs, and other possible RNA polymerase III-transcribed sequences were identified. The size of individual elements ranges from 101 to 392 bp, representing sequences present from low (1) to highly abundant (over 2000) copy number in the P. infestans genome, based on quantitative PCR analysis. Putative short direct repeat sequences (6-14 bp) flanking the elements were also identified for eight of the SINEs. Predicted SINEs were named in a series prefixed infSINE (for infestans-SINE). Two SINEs were apparently present as multimers of tRNA-related units; four copies of a related unit for infSINEr, and two unrelated units for infSINEz. Two SINEs, infSINEh and infSINEi, were typically located within 400 bp of each other. These were also the only two elements identified as being actively transcribed in the mycelial stage of P. infestans by RT-PCR. It is possible that infSINEh and infSINEi represent active retrotransposons in P. infestans. Based on the quantitative PCR estimates of copy number for all of the elements identified, tRNA-related SINEs were estimated to comprise 0.3% of the 250 Mb P. infestans genome. InfSINE-related sequences were found to occur in species throughout the genus Phytophthora. However, seven elements were shown to be exclusive to P. infestans.
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Affiliation(s)
- Stephen C Whisson
- Plant-Pathogen Interactions Program, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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102
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Rooney AP, Ward TJ. Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth and death of a concerted evolution paradigm. Proc Natl Acad Sci U S A 2005; 102:5084-9. [PMID: 15784739 PMCID: PMC555991 DOI: 10.1073/pnas.0409689102] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2004] [Indexed: 11/18/2022] Open
Abstract
In eukaryotes, the primary components of the ribosome are encoded by multicopy nuclear ribosomal RNA (rRNA) genes: 28/26S, 18S, 5.8S, and 5S. Copies of these genes are typically localized within tandem arrays and homogenized within a genome. As a result, nuclear rRNA gene families have become a paradigm of concerted evolution. In filamentous fungi of the subphylum Pezizomycotina, 5S rRNA genes exist as a large and dispersed multigene family, with between 50 and 100 copies per genome. To determine whether these genes defy the concerted evolution paradigm, we examined the patterns of evolution of these genes by using sequences from the complete genomes of four species. Analyses of these sequences revealed (i) multiple 5S gene types within a genome, (ii) interspecies clustering of gene types, (iii) multiple identical gene types shared among species, (iv) multiple pseudogenes within a genome, and (v) presence/absence variation of individual 5S copies in comparisons of closely related species. These results demonstrate that the 5S family in these species is characterized by birth-and-death evolution under strong purifying selection. Furthermore, our results suggest that birth-and-death evolution occurs at different rates in the genera examined, and that the multiplication and movement of 5S genes across the genome are highly dynamic. As such, we hypothesize that a mechanism resembling retroposition controls 5S rRNA gene amplification, dispersal, and integration in the genomes of filamentous fungi.
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Affiliation(s)
- Alejandro P Rooney
- Microbial Genomics and Bioprocessing Research Unit, Agricultural Research Service, US Department of Agriculture, Peoria, IL 61604, USA.
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103
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Schmidt FR. About the nature of RNA interference. Appl Microbiol Biotechnol 2005; 67:429-35. [PMID: 15703909 DOI: 10.1007/s00253-004-1882-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Revised: 12/17/2004] [Accepted: 12/17/2004] [Indexed: 10/25/2022]
Abstract
In the context of yet unclarified issues of RNA interference (RNAi), it is discussed that RNAi-induced histone modification may not only have the purpose of inactivating native genes by blocking their transcription in the sense direction but may also simultaneously trigger transcription of the corresponding antisense strand to form double-stranded RNA for posttranscriptional gene-silencing in cells lacking RNA replicase activities. Invading foreign genetic traits may be posttranscriptionally silenced through complementary transcripts from specific, highly variable genomic regions, which are able to finally match any given sequence by the appropriate recombination and processing of their transcripts. The information to fight these traits may additionally become anchored in the genome, to provide at least a temporary "immunity" and may be inherited at least for a few generations. It is further proposed that: (1) RNA viruses evolved from constituents of the RNAi machinery through the capture of functions essential for their maintenance and replication and (2) viruses and RNAi are mutually interacting components of a universal and predominant genetic steering system that is involved in the modulation of gene expression on the cellular level and simultaneously constitutes a driving force for evolution, particularly in imperfect organisms. Such a model would deliver explanations for yet unresolved issues of RNAi, the clarification of which will have a significant impact on its future medical and biotechnological application.
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Affiliation(s)
- F R Schmidt
- Sanofi-Aventis Deutschland, Biocenter H 780, Industriepark Höchst, Frankfurt am Main.
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104
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da Silva R, Lucchinetti E, Pasch T, Schaub MC, Zaugg M. Ischemic but not pharmacological preconditioning elicits a gene expression profile similar to unprotected myocardium. Physiol Genomics 2004; 20:117-30. [PMID: 15494475 DOI: 10.1152/physiolgenomics.00166.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Pharmacological (PPC) and ischemic preconditioning (IschPC) provide comparable protection against ischemia in the heart. However, the genomic phenotype may depend on the type of preconditioning. Isolated perfused rat hearts were used to evaluate transcriptional responses to PPC and IschPC in the presence (mediator/effector response) or absence (trigger response) of 40 min of test ischemia using oligonucleotide microarrays. IschPC was induced by 3 cycles of 5 min of ischemia, and PPC by 15 min of 2.1 vol% isoflurane. Unsupervised analysis methods were used to identify gene expression patterns. PPC and IschPC were accompanied by marked alterations in gene expression. PPC and IschPC shared only approximately 25% of significantly up- and downregulated genes after triggering. The two types of preconditioning induced a more uniform genomic response after ischemia/reperfusion. Numerous genes separated preconditioned from unprotected ischemic hearts. Three stable gene clusters were identified in the trigger response to preconditioning, while eight stable clusters related to cytoprotection, inflammation, remodeling, and long interspersed nucleotide elements (LINEs) were delineated after prolonged ischemia. A single stable sample cluster emerged from cluster analysis for both IschPC and unprotected myocardium, indicating a close molecular relationship between these two treatments. Principal component analysis revealed differences between PPC vs. IschPC, and trigger vs. mediator/effector responses in transcripts predominantly related to biosynthesis and apoptosis. IschPC and PPC similarly but distinctly reprogram the genetic response to ischemic injury. IschPC elicits a postischemic gene expression profile closer to unprotected myocardium than PPC, which may be therefore more advantageous as therapeutic strategy in cardioprotection.
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Affiliation(s)
- Rafaela da Silva
- Institute of Pharmacology and Toxicology, University of Zurich, Switzerland
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105
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Williams WP, Tamburic L, Astell CR. Increased levels of B1 and B2 SINE transcripts in mouse fibroblast cells due to minute virus of mice infection. Virology 2004; 327:233-41. [PMID: 15351211 DOI: 10.1016/j.virol.2004.06.040] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 02/12/2004] [Accepted: 06/11/2004] [Indexed: 10/26/2022]
Abstract
Minute virus of mice (MVM), an autonomous parvovirus, has served as a model for understanding parvovirus infection including host cell response to infection. In this paper, we report the effect of MVM infection on host cell gene expression in mouse fibroblast cells (LA9 cells), analyzed by differential display. Somewhat surprisingly, our data reveal that few cellular protein-coding genes appear to be up- or downregulated and identify the murine B1 and B2 short interspersed element (SINE) transcripts as being increased upon MVM infection. Primer extension assays confirm the effect of MVM infection on SINE expression and demonstrate that both SINEs are upregulated in a roughly linear fashion throughout MVM infection. They also demonstrate that the SINE response was due to RNA polymerase III transcription and not contaminating DNA or RNA polymerase II transcription. Furthermore, expression of MVM NS1, the major nonstructural protein, by transient transfection also leads to an increase in both murine SINEs. We believe this is the first time that the B1 and B2 SINEs have been shown to be altered by viral infection and the first time parvovirus infection has been shown to increase SINE expression. The increase in SINE transcripts caused by MVM infection does not appear to be due to an increase in either of the basal transcription factors TFIIIC110 or 220, in contrast to that which has been shown for other viruses.
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Affiliation(s)
- Warren P Williams
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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106
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Nelson PN, Hooley P, Roden D, Davari Ejtehadi H, Rylance P, Warren P, Martin J, Murray PG. Human endogenous retroviruses: transposable elements with potential? Clin Exp Immunol 2004; 138:1-9. [PMID: 15373898 PMCID: PMC1809191 DOI: 10.1111/j.1365-2249.2004.02592.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2004] [Indexed: 12/20/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are a significant component of a wider family of retroelements that constitute part of the human genome. These viruses, perhaps representative of previous exogenous retroviral infection, have been integrated and passed through successive generations within the germ line. The retention of HERVs and isolated elements, such as long-terminal repeats, could have the potential to harm. In this review we describe HERVs within the context of the family of known transposable elements and survey these viruses in terms of superantigens and molecular mimics. It is entirely possible that these mechanisms provide the potential for undesired immune responses.
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Affiliation(s)
- P N Nelson
- Research Institute in Healthcare Science, University of Wolverhampton, UK.
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107
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108
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Pélissier T, Bousquet-Antonelli C, Lavie L, Deragon JM. Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. Nucleic Acids Res 2004; 32:3957-66. [PMID: 15282328 PMCID: PMC506818 DOI: 10.1093/nar/gkh738] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite the ubiquitous distribution of tRNA-related short interspersed elements (SINEs) in eukaryotic species, very little is known about the synthesis and processing of their RNAs. In this work, we have characterized in detail the different RNA populations resulting from the expression of a tRNA-related SINE S1 founder copy in Arabidopsis thaliana. The main population is composed of poly(A)-ending (pa) SINE RNAs, while two minor populations correspond to full-length (fl) or poly(A) minus [small cytoplasmic (sc)] SINE RNAs. Part of the poly(A) minus RNAs is modified by 3'-terminal addition of C or CA nucleotides. All three RNA populations accumulate in the cytoplasm. Using a mutagenesis approach, we show that the poly(A) region and the 3' end unique region, present at the founder locus, are both important for the maturation and the steady-state accumulation of the different S1 RNA populations. The observation that primary SINE transcripts can be post-transcriptionally processed in vivo into a poly(A)-ending species introduces the possibility that this paRNA is used as a retroposition intermediate.
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MESH Headings
- 3' Untranslated Regions
- Arabidopsis/genetics
- Base Sequence
- Cytoplasm/metabolism
- Gene Expression Regulation, Plant
- Molecular Sequence Data
- Polyadenylation
- RNA Processing, Post-Transcriptional
- RNA, Plant/biosynthesis
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Transfer/biosynthesis
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Regulatory Sequences, Ribonucleic Acid
- Short Interspersed Nucleotide Elements
- Transcription, Genetic
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Affiliation(s)
- Thierry Pélissier
- CNRS UMR 6547 BIOMOVE and GDR 2157, Université Blaise Pascal Clermont-Ferrand II, 63177 Aubière Cedex, France
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109
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Meshorer E, Toiber D, Zurel D, Sahly I, Dori A, Cagnano E, Schreiber L, Grisaru D, Tronche F, Soreq H. Combinatorial Complexity of 5′ Alternative Acetylcholinesterase Transcripts and Protein Products. J Biol Chem 2004; 279:29740-51. [PMID: 15123727 DOI: 10.1074/jbc.m402752200] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To explore the scope and significance of alternate promoter usage and its putative inter-relationship to alternative splicing, we searched expression sequence tags for the 5' region of acetylcholinesterase (ACHE) genes. Three and five novel first exons were identified in human and mouse ACHE genes, respectively. Reverse transcription-PCR and in situ hybridization validated most of the predicted transcripts, and sequence analyses of the corresponding genomic DNA regions suggest evolutionarily conserved promoters for each of the novel exons identified. Distinct tissue specificity and stress-related expression patterns of these exons predict combinatorial complexity with known 3' alternative AChE mRNA transcripts. Unexpectedly one of the 5' exons encodes an extended N terminus in-frame with the known AChE sequence, extending the increased complexity to the protein level. The resultant membrane variant(s), designated N-AChE, is developmentally regulated in human brain neurons and blood mononuclear cells. Alternative promoter usage combined with alternative splicing may thus lead to stress-dependent combinatorial complexity of AChE mRNA transcripts and their protein products.
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Affiliation(s)
- Eran Meshorer
- Department of Biological Chemistry and the Israel Center of Neuronal Computation, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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110
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Frenkel FE, Chaley MB, Korotkov EV, Skryabin KG. Evolution of tRNA-like sequences and genome variability. Gene 2004; 335:57-71. [PMID: 15194190 DOI: 10.1016/j.gene.2004.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2003] [Revised: 02/16/2004] [Accepted: 03/05/2004] [Indexed: 11/24/2022]
Abstract
Transfer RNA (tRNA)-like sequences were searched for in the nine basic taxonomic divisions of GenBank-121 (viruses, phages, bacteria, plants, invertebrates, vertebrates, rodents, mammals, and primates) by an original program package implementing a dynamic profile alignment approach for the genetic texts' analysis, in using 22 profiles of tRNAs of different isotypes. In total, 175,901 previously unknown tRNA-like sequences were revealed. The locations of the tRNA-likes were considered over the regions whose functional meaning is described by standard Feature Keys in GenBank. Many regions containing the tRNA-like sequences were recognized as known repeats. A mode of distribution of the tRNA-like sequences in a genome was proposed as expansion in a content of the various transposable elements. An analysis of the integrity of RNA polymerase III inner promoters in the tRNA-like sequences over the GenBank divisions has shown a high possibility of generating new copies of short interspersed nuclear element (SINE) repeats in all divisions, excepting primates. The numerous tRNA-likes found in the regions of RNA polymerase II promoters have suggested an adaptation of RNA polymerase III promoter to a binding of RNA polymerase II.
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Affiliation(s)
- Felix E Frenkel
- Centre Bioengineering RAS, Prospekt 60-letiya Oktyabrya, 7/1, Moscow 117312, Russia.
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111
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Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, Huang H, Wang H, Xing H, Daniels S, Gietzen D, Schmidt J, Stevens K, Vitt U, Wingrove J, Camara F, Mar Albà M, Abril JF, Guigo R, Smit A, Dubchak I, Rubin EM, Couronne O, Poliakov A, Hübner N, Ganten D, Goesele C, Hummel O, Kreitler T, Lee YA, Monti J, Schulz H, Zimdahl H, Himmelbauer H, Lehrach H, Jacob HJ, Bromberg S, Gullings-Handley J, Jensen-Seaman MI, Kwitek AE, Lazar J, Pasko D, Tonellato PJ, Twigger S, Ponting CP, Duarte JM, Rice S, Goodstadt L, Beatson SA, Emes RD, Winter EE, Webber C, Brandt P, Nyakatura G, Adetobi M, Chiaromonte F, Elnitski L, Eswara P, Hardison RC, Hou M, Kolbe D, Makova K, Miller W, Nekrutenko A, Riemer C, Schwartz S, Taylor J, Yang S, Zhang Y, Lindpaintner K, Andrews TD, Caccamo M, Clamp M, Clarke L, Curwen V, Durbin R, Eyras E, Searle SM, Cooper GM, Batzoglou S, Brudno M, Sidow A, Stone EA, Venter JC, Payseur BA, Bourque G, López-Otín C, Puente XS, Chakrabarti K, Chatterji S, Dewey C, Pachter L, Bray N, Yap VB, Caspi A, Tesler G, Pevzner PA, Haussler D, Roskin KM, Baertsch R, Clawson H, Furey TS, Hinrichs AS, Karolchik D, Kent WJ, Rosenbloom KR, Trumbower H, Weirauch M, Cooper DN, Stenson PD, Ma B, Brent M, Arumugam M, Shteynberg D, Copley RR, Taylor MS, Riethman H, Mudunuri U, Peterson J, Guyer M, Felsenfeld A, Old S, Mockrin S, Collins F. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 2004; 428:493-521. [PMID: 15057822 DOI: 10.1038/nature02426] [Citation(s) in RCA: 1524] [Impact Index Per Article: 76.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2003] [Accepted: 02/20/2004] [Indexed: 01/16/2023]
Abstract
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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Affiliation(s)
- Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu
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112
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Giles KE, Caputi M, Beemon KL. Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes. RNA (NEW YORK, N.Y.) 2004; 10:299-307. [PMID: 14730028 PMCID: PMC1370541 DOI: 10.1261/rna.2150604] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Retroviruses specifically package two copies of their RNA genome in each viral particle, along with some small cellular RNAs, including tRNAs and 7S L RNA. We show here that Rous sarcoma virus (RSV) also packages U6 snRNA at approximately one copy per virion. In addition, trace amounts of U1 and U2 snRNAs were detected in purified virus by Northern blotting. U6 snRNA comigrated with the RSV 70S genomic RNA dimer on sucrose gradients. We observed reverse transcription of U6 snRNA in an endogenous reaction in which RSV particles were the source of both reverse transcriptase and RNA substrates. This finding led us to examine mammalian genomic sequences for the presence of snRNA pseudogenes. A survey of the human, mouse, and rat genomes revealed a high number of spliceosomal snRNA pseudogenes. U6 pseudogenes were the most abundant, with approximately 200 copies in each genome. In the human genome, 67% of U6 snRNA pseudogenes, and a significant number of the other snRNA pseudogenes, were associated with LINE, SINE, or retroviral LTR repeat sequences. We propose that the packaging of snRNAs in retroviral particles leads to their reverse transcription in an infected cell and the integration of snRNA/viral recombinants into the host genome.
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Affiliation(s)
- Keith E Giles
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
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113
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Bernardino-Sgherri J, Flagiello D, Dutrillaux B. Overall DNA methylation and chromatin structure of normal and abnormal X chromosomes. Cytogenet Genome Res 2004; 99:85-91. [PMID: 12900549 DOI: 10.1159/000071578] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2003] [Accepted: 01/20/2003] [Indexed: 11/19/2022] Open
Abstract
DNA methylation patterns were studied at the chromosome level in normal and abnormal X chromosomes using an anti-5-methylcytosine antibody. In man, except for the late-replicating X of female cells, the labeled chromosome structures correspond to R- and T-bands and heterochromatin. Depending on the cell type, the species, and cell culture conditions, the late-replicating X in female cells appears to be more or less undermethylated. Under normal conditions, the only structures that remain methylated on the X chromosomes correspond to pseudoautosomal regions, which harbor active genes. Thus, active genes are usually hypomethylated but are located in methylated chromatin. Structural rearrangements of the X chromosome, such as t(X;X)(pter;pter), induce a Turner syndrome-like phenotype that is inconsistent with the resulting triple-X constitution. This suggests a position effect controlling gene inactivation. The derivative chromosomes are always late replicating, and their duplicated short arms, which harbor pseudoautosomal regions, replicate later than the normal late-replicating X chromosomes. The compaction or condensation of this segment is unusual, with a halo of chromatin surrounding a hypocondensed chromosome core. The chromosome core is hypomethylated, but the surrounding chromatin is slightly labeled. Thus, unusual DNA methylation and chromatin condensation are associated with the observed position effect. This strengthens the hypothesis that DNA methylation at the chromosome level is associated with both chromatin structure and gene expression.
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Affiliation(s)
- J Bernardino-Sgherri
- Laboratoire de radiosensibilité des cellules germinales, Département de Radiobiologie et Radiopathologie, CEA/DSV/DRR/SEGG/LRCG, Fontenay-aux-Roses, France.
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114
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Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 2003; 4:R74. [PMID: 14611660 PMCID: PMC329124 DOI: 10.1186/gb-2003-4-11-r74] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Revised: 09/02/2003] [Accepted: 09/25/2003] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Abundant pseudogenes are a feature of mammalian genomes. Processed pseudogenes (PPs) are reverse transcribed from mRNAs. Recent molecular biological studies show that mammalian long interspersed element 1 (L1)-encoded proteins may have been involved in PP reverse transcription. Here, we present the first comprehensive analysis of human PPs using all known human genes as queries. RESULTS The human genome was queried and 3,664 candidate PPs were identified. The most abundant were copies of genes encoding keratin 18, glyceraldehyde-3-phosphate dehydrogenase and ribosomal protein L21. A simple method was developed to estimate the level of nucleotide substitutions (and therefore the age) of PPs. A Poisson-like age distribution was obtained with a mean age close to that of the Alu repeats, the predominant human short interspersed elements. These data suggest a nearly simultaneous burst of PP and Alu formation in the genomes of ancestral primates. The peak period of amplification of these two distinct retrotransposons was estimated to be 40-50 million years ago. Concordant amplification of certain L1 subfamilies with PPs and Alus was observed. CONCLUSIONS We suggest that a burst of formation of PPs and Alus occurred in the genome of ancestral primates. One possible mechanism is that proteins encoded by members of particular L1 subfamilies acquired an enhanced ability to recognize cytosolic RNAs in trans.
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Affiliation(s)
- Kazuhiko Ohshima
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
| | - Masahira Hattori
- RIKEN Genomic Sciences Center, 1-7-22, Suehiro Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Laboratory of Genome Information, Kitasato Institute for Life Science, Kitasato University, 1-15-1, Kitasato, Sagamihara, Kanagawa 228-8555, Japan
| | - Tetsusi Yada
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Takashi Gojobori
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Sakaki
- RIKEN Genomic Sciences Center, 1-7-22, Suehiro Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Norihiro Okada
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan
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115
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Wickstead B, Ersfeld K, Gull K. Repetitive elements in genomes of parasitic protozoa. Microbiol Mol Biol Rev 2003; 67:360-75, table of contents. [PMID: 12966140 PMCID: PMC193867 DOI: 10.1128/mmbr.67.3.360-375.2003] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility.
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Affiliation(s)
- Bill Wickstead
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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116
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Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 2003; 35:41-8. [PMID: 12897783 DOI: 10.1038/ng1223] [Citation(s) in RCA: 741] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2003] [Accepted: 07/08/2003] [Indexed: 11/08/2022]
Abstract
Alu elements are the most successful transposons in humans. They are 300-bp non-coding sequences transcribed by RNA polymerase III (Pol III) and are expected to retrotranspose with the aid of reverse transcriptases of cellular origin. We previously showed that human LINEs can generate cDNA copies of any mRNA transcript by means of a retroposition process involving reverse transcription and integration by the LINE-encoded endonuclease and reverse transcriptase. Here we show mobility of marked Alu sequences in human HeLa cells with the canonical features of a retrotransposition process, including splicing out of an autocatalytic intron introduced into the marked sequence, target site duplications of varying lengths and integrations into consensus A-rich sequences. We further show that the poly-A stretch at the Alu 3' end is essential for mobility, that LINEs are required for transposition and that the rate of retroposition is 100-1,000 times higher for Alu transcripts than for control mRNAs, thus accounting for the high mutational activity of these elements observed in humans.
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Affiliation(s)
- Marie Dewannieux
- Unité des Rétrovirus Endogènes et Eléments Rétroïdes des Eucaryotes Supérieurs, UMR 8122 CNRS, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif Cedex, France
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117
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Schramke V, Allshire R. Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing. Science 2003; 301:1069-74. [PMID: 12869699 DOI: 10.1126/science.1086870] [Citation(s) in RCA: 225] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The expression of short hairpin RNAs in several organisms silences gene expression by targeted mRNA degradation. This RNA interference (RNAi) pathway can also affect the genome, as DNA methylation arises at loci homologous to the target RNA in plants. We demonstrate in fission yeast that expression of a synthetic hairpin RNA is sufficient to silence the homologous locus in trans and causes the assembly of a patch of silent Swi6 chromatin with cohesin. This requires components of the RNAi machinery and Clr4 histone methyltransferase for small interfering RNA generation. A similar process represses several meiotic genes through nearby retrotransposon long terminal repeats (LTRs). These analyses directly implicate interspersed LTRs in regulating gene expression during cellular differentiation.
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Affiliation(s)
- Vera Schramke
- Wellcome Trust Centre for Cell Biology, Institute of Cell and Molecular Biology, King's Buildings, University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
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118
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Bhattacharya A, Bhattacharya S, Ackers JP. Nontranslated polyadenylated RNAs from Entamoeba histolytica. Trends Parasitol 2003; 19:286-9. [PMID: 12855374 DOI: 10.1016/s1471-4922(03)00121-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protozoan parasites display a range of unusual molecular mechanisms that could be helpful for their survival in Nature. Among these parasites, Entamoeba histolytica is one of the most prevalent in developing countries such as India. Entamoeba histolytica produces at least four different unusual transcripts, IE, Tr, ehapt1 and UEE1, that are polyadenylated, but do not have significant open reading frames. Availability of large-scale sequence information has helped us to understand the nature of these sequences and their possible role. Entamoeba histolytica also encodes at least three classes of non-long-terminal-repeats containing retrotransposons, similar to mammalian long retrotransposable elements. This article describes the current status of our understanding of these transcripts and suggests a relationship between some of these transcripts and short retrotransposable element-like retro-elements present in many eukaryotes.
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Affiliation(s)
- Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, 110 067, New Delhi, India
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119
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Schluter SF, Marchalonis JJ. Cloning of shark RAG2 and characterization of the RAG1/RAG2 gene locus. FASEB J 2003; 17:470-2. [PMID: 12551847 DOI: 10.1096/fj.02-0565fje] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The recombination-activating genes (RAG) encode a site-specific recombinase that is centrally responsible for the rearrangement of genomic V(D)J exons necessary to form functional immunoglobulin and T-cell receptor genes. To help elucidate the origins of the RAG genes, we have cloned the RAG2 gene from the sandbar shark (Carcharhinus plumbeus) and characterized the entire RAG1/RAG2 gene locus. The shark RAG2 protein consists of 520 amino acids, is approximately 50% identical with RAG2 proteins from other vertebrates, and contains the same three domains identified in mammalian RAG2. Residues critical for RAG2 function are conserved in the shark sequence. In common with other vertebrate species, the shark RAG2 coding region lacks introns and is closely linked in opposite orientation to the RAG1 gene. The intergenic region is 9.4 kb, which is considerably larger than of teleosts (2-3 kb) and is comparable to that of tetrapods. This length is partially explained by the presence of several SINE and LINE fragments. The ancestors of the sharks were apparently the first vertebrates in phylogeny to have RAG genes, and our results confirm that the RAG genes have been highly conserved during evolution both in terms of sequence and gene organization.
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Affiliation(s)
- Samuel F Schluter
- Department of Microbiology and Immunology, University of Arizona, Tucson, Arizona 85724, USA
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120
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Brosius J. The contribution of RNAs and retroposition to evolutionary novelties. CONTEMPORARY ISSUES IN GENETICS AND EVOLUTION 2003. [DOI: 10.1007/978-94-010-0229-5_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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121
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Pavlícek A, Paces J, Zíka R, Hejnar J. Length distribution of long interspersed nucleotide elements (LINEs) and processed pseudogenes of human endogenous retroviruses: implications for retrotransposition and pseudogene detection. Gene 2002; 300:189-94. [PMID: 12468100 DOI: 10.1016/s0378-1119(02)01047-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Deciphering the human genome includes reliable identification and structural characterization of individual retrotransposon elements. The most active group of autonomous transposable elements, the long interspersed nuclear elements (LINE), transpose themselves as well as other RNAs, including those of human endogenous retroviruses (HERV). During this transposition, however, the LINE-encoded reverse transcriptase (RT) often abortively dissociates from the RNA template, leaving a prematurely terminated, 5' truncated copy. We have analyzed the length distributions of LINEs and of processed pseudogenes derived from HERV-W. As expected, we have found that the majority of 5' truncated LINEs and HERV-W processed pseudogenes show a prevalence of very short elements terminated close to the 3' end. On the other hand, the number of complete elements is far above the expectation. The characteristic distribution in both cases indicates two important conclusions: (i) dissociation of LINE RT from the template cannot be fully explained by low processivity of RT modelled as a stochastic, Poisson-type process. (ii) Currently cited numbers of pseudogenes within the human genome are underestimated, since a large percentage of pseudogenes are terminated in the 3' untranslated region and remain undetectable in translated homology searches of protein databases against the human genome.
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Affiliation(s)
- Adam Pavlícek
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague 6, CZ-16637, Czech Republic
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122
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Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis SE, Rubin GM, Ashburner M, Celniker SE. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol 2002; 3:RESEARCH0084. [PMID: 12537573 PMCID: PMC151186 DOI: 10.1186/gb-2002-3-12-research0084] [Citation(s) in RCA: 387] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2002] [Revised: 11/11/2002] [Accepted: 11/25/2002] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species. RESULTS We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes. CONCLUSIONS This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.
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Affiliation(s)
- Joshua S Kaminker
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
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