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PubMed2000

MaskerAid: a performance enhancement to RepeatMasker.

UNLABELLED: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid, a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting. AVAILABILITY: On request from the authors (see http://sapiens.wustl.edu/MaskerAid). CONTACT: maskeraid@watson.wustl.edu

Animals↗

PubMed2004

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.

The rates at which human genomic DNA changes by neutral substitution and insertion of certain families of transposable elements covary in large, megabase-sized segments. We used the rat, mouse, and human genomic DNA sequences to examine these processes in more detail in comparisons over both shorter (rat-mouse) and longer (rodent-primate) times, and demonstrated the generality of the covariation. Different families of transposable elements show distinctive insertion preferences and patterns of variation with substitution rates. SINEs are more abundant in GC-rich DNA, but the regional GC preference for insertion (monitored in young SINEs) differs between rodents and humans. In contrast, insertions in the rodent genomes are predominantly LINEs, which prefer to insert into AT-rich DNA in all three mammals. The insertion frequency of repeats other than SINEs correlates strongly positively with the frequency of substitutions in all species. However, correlations with SINEs show the opposite effects. The correlations are explained only in part by the GC content, indicating that other factors also contribute to the inherent tendency of DNA segments to change over evolutionary time.

Animals↗

PubMed2002

Gene-containing regions of wheat and the other grass genomes.

Deletion line-based high-density physical maps revealed that the wheat (Triticum aestivum) genome is partitioned into gene-rich and -poor compartments. Available deletion lines have bracketed the gene-containing regions to about 10% of the genome. Emerging sequence data suggest that these may further be partitioned into "mini" gene-rich and gene-poor regions. An average of about 10% of each gene-rich region seem to contain genes. Sequence analyses in various species suggest that uneven distribution of genes may be a characteristic of all grasses and perhaps all higher organisms. Comparison of the physical maps with genetic linkage maps showed that recombination in wheat and barley (Hordeum vulgare) is confined to the gene-containing regions. Number of genes, gene density, and the extent of recombination vary greatly among the gene-rich regions. The gene order, relative region size, and recombination are highly conserved within the tribe Triticeae and moderately conserved within the family. Gene-poor regions are composed of retrotransposon-like non-transcribing repeats and pseudogenes. Direct comparisons of orthologous regions indicated that gene density in wheat is about one-half compared with rice (Oryza sativa). Genome size difference between wheat and rice is, therefore, mainly because of amplification of the gene-poor regions. Presence of species-, genera-, and family-specific repeats reveal a repeated invasion of the genomes by different retrotransposons over time. Preferential transposition to adjacent locations and presence of vital genes flanking a gene-rich region may have restricted retrotransposon amplification to gene-poor regions, resulting into tandem blocks of non-transcribing repeats. Insertional inactivation by adjoining retro-elements and selection seem to have played a major role in stabilizing genomes.

Chromosome Mapping↗

PubMed2005

LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling.

Two major classes of retrotransposons have invaded eukaryotic genomes: the LTR retrotransposons closely resembling the proviral integrated form of infectious retroviruses, and the non-LTR retrotransposons including the widespread, autonomous LINE elements. Here, we review the modeling effects of the latter class of elements, which are the most active in humans, and whose enzymatic machinery is subverted to generate a large series of "secondary" retroelements. These include the processed pseudogenes, naturally present in all eukaryotic genomes possessing non-LTR retroelements, and the very successful SINE elements such as the human Alu sequences which have evolved refined parasitic strategies to efficiently bypass the original "protectionist" cis-preference of LINEs for their own retrotransposition.

Animals↗

PubMed2005

Isolation of the gene encoding the bovine neonatal Fc receptor.

The role of an IgG-Fc receptor (FcRn) that resembles a class I MHC Ag in transporting IgGs through epithelial cells was recently shown in selected species. Here we report our preliminary characterization of a clone encoding the alpha chain of the bovine FcRn from a BAC library. The recombinant BAC DNA was digested, analyzed by Southern blot hybridization and a bovine FcRn positive 9 kb long fragment was subcloned and partially sequenced. The exon/intron organization of the bovine FcRn alpha chain gene was deduced by comparison with its cDNA sequence. The sequence revealed a similar organization to the human and mouse FcRn alpha chain genes. The bovine FcRn alpha chain gene has acquired several repetitive sequences in its 5'-flanking region, including multiple SINE and LINE elements. Potential binding sites for transcription factors within the 5'-flanking sequence were identified using TESS and TFSEARCH programs. The 5'-flanking region of the bFcRn alpha chain gene was analyzed for its ability to directly express the luciferase reporter gene in bovine mammary gland epithelial cells. Transient transfection of a luciferase construct revealed that there was promoter activity in the region -1787 to +92 of the 5'-flanking sequence.

Animals↗

PubMed2002

Mobile genetic element activation and genotoxic cancer therapy: potential clinical implications.

Approximately one-quarter of the human genome is composed of short and long interspersed elements (SINEs and LINEs, respectively). These elements have spread throughout the genome by a process termed retrotransposition, consisting of transcription of an element into RNA, reverse transcription into cDNA, and reinsertion of the copied element into a new genomic location. Recombination events involving these elements, including novel insertions into active genes, have been associated with a number of human diseases. Despite the fact that these elements have replicated to hundreds of thousands of copies in the genome, under most conditions they remain transcriptionally silent, and therefore are not actively replicating. The signals controlling retrotransposable element activation in the genome have not been defined. Our laboratory recently found that exposure of cells to a variety of DNA-damaging agents, including several common chemotherapeutic drugs and gamma-radiation, is associated with dramatic induction of SINE transcription, and of a concomitant endogenous reverse transcriptase activity. As SINEs do not encode for reverse transcriptase, the latter finding suggests a more global activation of retrotransposable elements in response to DNA damage. Together these observations suggest that genotoxic exposure may lead to genomic mutation not only through direct DNA damage, but also through indirect activation of potentially mutagenic mobile elements in the genome. The nonrandom distribution of retrotransposable elements in the human genome may contribute to the pattern of characteristic translocation events associated with secondary malignancies in patients exposed to genotoxic agents. Here we describe these and other mechanisms by which retrotransposable elements can contribute to disease, and present an overview of what is known about this large, and largely unexplored, segment of the genome. Understanding the cellular responses to genotoxic stress may permit the development of a means of predicting the risks and preventing the development of secondary malignancy following cancer therapy.

Antineoplastic Agents↗

PubMed2000

Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs).

The presence of repetitive elements can create serious problems for sequence analysis, especially in the case of homology searches in nucleotide sequence databases. Repetitive elements should be treated carefully by using special programs and databases. In this paper, various aspects of SINE (short interspersed repetitive element) identification, analysis and evolution are discussed.

Animals↗

PubMed2005

Sequence of the canine major histocompatibility complex region containing non-classical class I genes.

We have sequenced a segment of 150,102 nucleotides of canine major histocompatibility complex (MHC) DNA, corresponding to the junction of the class I and class III regions. The distal portion contained five class III genes including two tumor necrosis factor genes and the proximal portion contained five genes or pseudogenes belonging to the class I region. The order of the class III region genes was conserved as in the porcine and human MHC regions. The order of the class Ib loci from the proximal side outwards was DLA-53, DLA-12a, DLA-64, stress-induced phosphoprotein-1, followed by DLA-12. Only DLA-64 and DLA-12 display an overall predicted protein sequence compatible with the expression of membrane-anchored glycoproteins. The other class 1b loci do not appear to be functional by sequence analysis. In all, these 10 genes spanned 24% of the total sequence. The remaining 76% comprised of a number of non-coding and repetitive DNA elements including long interspersed nuclear element (LINE) fragments, short interspersed nuclear elements (SINE), and microsatellites.

Animals↗

PubMed2005

Species- and strain-specific probes derived from repetitive DNA for distinguishing Entamoeba histolytica and Entamoeba dispar.

Entamoeba histolytica and Entamoeba dispar are two morphologically indistinguishable species that are found in the human gut. Of the two, E. histolytica is considered to be pathogenic while E. dispar is nonpathogenic. To generate molecular probes to detect and distinguish between the two species, we utilized repeat sequences present in Entamoeba genome. We have developed probes and primers from rDNA episomes, and unidentified Entamoeba EST1 repeat for this purpose, and used them for dot blot hybridization and PCR amplification. To investigate the possible existence of invasive and noninvasive strains of E. histolytica, the ability to differentiate individual isolates is necessary. For this purpose, we have utilized a modification of the AFLP procedure called 'Transposon display,' which generates and displays large number of genomic bands associated with a transposon. We have used the abundant retrotransposon, EhSINE1, for this purpose,and demonstrated its potential as a marker to study strain variation in E. histolytica. This technique could suitably be employed in carrying out significant molecular epidemiological studies and large-scale typing of this parasite.

Animals↗

PubMed1999

MosquI, a novel family of mosquito retrotransposons distantly related to the Drosophila I factors, may consist of elements of more than one origin.

A novel family of non-long-terminal-repeat (non-LTR) retrotransposons, named MosquI, was discovered in the yellow fever mosquito, Aedes aegypti. There were approximately 14 copies of MosquI in the A. aegypti genome. Four of the five analyzed MosquI elements were truncated at the 5' ends while one of them, MosquI-Aa2, was full-length. All five MosquI elements ended with 4-10 TAA tandem repeats, as the Drosophila I factors do. Interestingly, MosquI elements were often found near genes and other repetitive elements. The 6,623-bp MosquI-Aa2 contained two open reading frames (ORFs) flanked by a 404-bp 5' untranslated region and a 326-bp 3' untranslated region. The two ORFs code for nucleocapsids, endonuclease, reverse transcriptase, and RNase H domains. Although overall structural and sequence comparisons suggest that MosquI is highly similar to the Drosophila I factors, phylogenetic analysis based on the reverse transcriptase domains of 40 non-LTR retrotransposons indicate that MosquI and I factors are likely paralogous elements which may have been separated before the split between the ancestors of mollusca and arthropoda. Pairwise comparisons between the four truncated MosquI elements showed 96.7%-99.5% identity at the nucleotide level, while comparisons between the full-length MosquI-Aa2 and the truncated copies showed only 80.2%-81.8% identity. These comparisons and preliminary phylogenetic analyses suggest that the full-length and truncated MosquI elements may belong to two subfamilies originating from two source genes that diverged a long time ago. In contrast to the defective I factors in Drosophila melanogaster, which are likely very old components of the genome, the truncated MosquI elements seem to have been recently active. Finally, the genomic distribution and evolution of MosquI elements are analyzed in the context of other non-LTR retrotransposons in A. aegypti.

Aedes↗

PubMed2006

RNA editing level in the mouse is determined by the genomic repeat repertoire.

A-to-I RNA editing is the conversion of adenosine to inosine in double-stranded cellular and viral RNAs. Recently, abundant editing of human transcripts affecting thousands of genes has been reported. Most editing sites are confined to the primate-specific Alu repeats. Notably, the editing level in mouse was shown to be much lower. In order to find the reason for this dramatic difference, here we identify editing sites within mouse repeats and analyze the sequence properties required for RNA editing. Our results show that the overall rate of RNA editing is determined by specific properties of different repeat families such as abundance, length, and divergence. We show that the striking difference in editing levels between human and mouse is mostly due to the higher divergence of the different mouse repeats.

Animals↗

PubMed2004

Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes.

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.

Animals↗

PubMed2003

Unbiased whole-genome amplification directly from clinical samples.

Preparation of genomic DNA from clinical samples is a bottleneck in genotyping and DNA sequencing analysis and is frequently limited by the amount of specimen available. We use Multiple Displacement Amplification (MDA) to amplify the whole genome 10,000-fold directly from small amounts of whole blood, dried blood, buccal cells, cultured cells, and buffy coats specimens, generating large amounts of DNA for genetic testing. Genomic DNA was evenly amplified with complete coverage and consistent representation of all genes. All 47 loci analyzed from 44 individuals were represented in the amplified DNA at between 0.5- and 3.0-fold of the copy number in the starting genomic DNA template. A high-fidelity DNA polymerase ensures accurate representation of the DNA sequence. The amplified DNA was indistinguishable from the original genomic DNA template in 5 SNP and 10 microsatellite DNA assays on three different clinical sample types for 20 individuals. Amplification of genomic DNA directly from cells is highly reproducible, eliminates the need for DNA template purification, and allows genetic testing from small clinical samples. The low amplification bias of MDA represents a dramatic technical improvement in the ability to amplify a whole genome compared with older, PCR-based methods.

Blood Cells↗

PubMed2005

The LINEs and SINEs of Entamoeba histolytica: comparative analysis and genomic distribution.

Autonomous non-long terminal repeat retrotransposons are commonly referred to as long interspersed elements (LINEs). Short non-autonomous elements that borrow the LINE machinery are called SINES. The Entamoeba histolytica genome contains three classes of LINEs and SINEs. Together the EhLINEs/SINEs account for about 6% of the genome. The recognizable functional domains in all three EhLINEs included reverse transcriptase and endonuclease. A novel feature was the presence of two types of members-some with a single long ORF (less frequent) and some with two ORFs (more frequent) in both EhLINE1 and 2. The two ORFs were generated by conserved changes leading to stop codon. Computational analysis of the immediate flanking sequences for each element showed that they inserted in AT-rich sequences, with a preponderance of Ts in the upstream site. The elements were very frequently located close to protein-coding genes and other EhLINEs/SINEs. The possible influence of these elements on expression of neighboring genes needs to be determined.

Amino Acid Sequence↗

PubMed2006

Sauria SINEs: Novel short interspersed retroposable elements that are widespread in reptile genomes.

SINEs are short interspersed retrotransposable elements that invade new genomic sites. Their retrotransposition depends on reverse transcriptase and endonuclease activities encoded by partner LINEs (long interspersed elements). Recent genomic research has demonstrated that retroposons account for at least 40% of the human genome. Hitherto, more than 30 families of SINEs have been characterized in mammalian genomes, comprising approximately 4600 extant species; the distribution and extent of SINEs in reptilian genomes, however, are poorly documented. With more than 7400 species of lizards and snakes, Squamata constitutes the largest and most diverse group of living reptiles. We have discovered and characterized a novel SINE family, Sauria SINEs, whose members are widely distributed among genomes of lizards, snakes, and tuataras. Sauria SINEs comprise a 5' tRNA-related region, a tRNA-unrelated region, and a 3' tail region (containing short tandem repeats) derived from LINEs. We distinguished eight Sauria SINE subfamilies in genomes of four major squamate lineages and investigated their evolutionary relationships. Our data illustrate the overall efficacy of Sauria SINEs as novel retrotransposable markers for elucidation of squamate evolutionary history. We show that all Sauria SINEs share an identical 3' sequence with Bov-B LINEs and propose that they utilize the enzymatic machinery of Bov-B LINEs for their own retrotransposition. This finding, along with the ubiquity of Bov-B LINEs previously demonstrated in squamate genomes, suggests that these LINEs have been an active partner of Sauria SINEs since this SINE family was generated more than 200 million years ago.

Animals↗

PubMed2002

V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit.

We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central conserved domain preceded by a 5'-end tRNA-related region and followed by a potentially recombinogenic (TG)(n) tract, with a 3' tail derived from the 3' untranslated region (UTR) of the corresponding partner long interspersed repetitive element (LINE) that encodes a functional reverse transcriptase. The central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be approximately 550 Myr old or older in view of the timing of divergence of the lamprey lineage from the bony fish lineage. The central conserved domain might have been subject to some form of positive selection. Although the contemporary 3' tails of V-SINEs differ from one another, it is possible that the original 3' tail might have been replaced, via recombination, by the 3' tails of more active partner LINEs, thereby retaining retropositional activity and the ability to survive for long periods on the evolutionary time scale. It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates.

Amino Acid Sequence↗

PubMed1999

Analysis of major repetitive DNA sequences in the dog (Canis familiaris) genome.

A systematic screening and analysis of repeated DNA sequences from a dog genomic library composed of small DNA inserts enabled us to characterize abundant canine repetitive DNA families. Four main families were identified: i) a group of highly repeated tRNA-derived short interspersed repetitive DNA elements (tRNA-SINEs); ii) another type of SINE-like element that was mainly found inserted into long interspersed repetitive elements (LINEs); iii) LINEs of the L1 type; and iv) satellite or satellite-like DNA. Surprisingly, no SINEs derived from 7SL RNA were found in the dog genome. These data should help in the analysis of canine DNA sequences and in the design of canine genome mapping reagents.

Animals↗

PubMed2001

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

To test whether regions undergoing genomic imprinting have unique genomic characteristics, imprinted and nonimprinted human loci were compared for nucleotide and retroelement composition. Maternally and paternally expressed subgroups of imprinted genes were found to differ in terms of guanine and cytosine, CpG, and retroelement content, indicating a segregation into distinct genomic compartments. Imprinted regions have been normally permissive to L1 long interspersed transposable element retroposition during mammalian evolution but universally and significantly lack short interspersed transposable elements (SINEs). The primate-specific Alu SINEs, as well as the more ancient mammalian-wide interspersed repeat SINEs, are found at significantly low densities in imprinted regions. The latter paleogenomic signature indicates that the sequence characteristics of currently imprinted regions existed before the mammalian radiation. Transitions from imprinted to nonimprinted genomic regions in cis are characterized by a sharp inflection in SINE content, demonstrating that this genomic characteristic can help predict the presence and extent of regions undergoing imprinting. During primate evolution, SINE accumulation in imprinted regions occurred at a decreased rate compared with control loci. The constraint on SINE accumulation in imprinted regions may be mediated by an active selection process. This selection could be because of SINEs attracting and spreading methylation, as has been found at other loci. Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival.

CpG Islands↗