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PubMed2006

Recently integrated Alu retrotransposons are essentially neutral residents of the human genome.

Alu elements represent the largest family of human mobile elements in copy number. A controversial issue with implications for both Alu biology and human genome evolution is whether selective pressures are affecting Alu elements on a large scale. To address this issue, we analyzed the genomic distribution of the three youngest known human Alu subfamilies (Ya5a2, Ya8 and Yb9) in conjunction with their insertion polymorphism status in the human population, since selection can only act on polymorphic elements. Our results indicate that: (i) polymorphic and fixed recently integrated Alu elements are found in genomic regions whose GC contents are statistically indistinguishable, and (ii) recently integrated Alu elements are inserted randomly, regardless of the GC content of the surrounding genomic DNA. These results provide strong evidence that recently integrated "young" Alu elements are not subject to positive or negative selection on a large scale. Therefore, young Alu elements can be regarded as essentially neutral residents of the human genome. These results also imply that selective processes specifically targeting Alu elements can be ruled out as explanations for the accumulation of Alu elements in GC-rich regions of the human genome.

Alu Elements↗
PubMed1999

Genomic and evolutionary analysis of Feilai, a diverse family of highly reiterated SINEs in the yellow fever mosquito, Aedes aegypti.

Five short interspersed repetitive elements (SINEs) were found fortuitously in the introns of a steroid hormone receptor AaHR3-2 gene of the yellow fever mosquito, Aedes aegypti, constituting a novel family of tRNA-related SINEs named Feilai. In addition, nine other Feilai elements were found in currently available sequences in Ae. aegypti, six of which were also near genes. Approximately 5.9 x 10(4) copies of Feilai were present in Ae. aegypti, equivalent to 2% of the entire genome. An additional 35 Feilai elements were isolated from a genomic library. Of the total 49 Feilai elements, 20 were full-length. Sequence comparisons and phylogenetic analyses of the full-length elements strongly suggest that there are at least two subfamilies within the Feilai family. There is a high degree of conservation within the two subfamilies. However, sequence divergence between the subfamilies, along with the presence of highly degenerate Feilai elements, suggests that Feilai is likely a diverse family of SINEs that has existed in Ae. aegypti for a long time. Many Feilai elements were closely associated with other transposons, especially with fragments of non-LTR retrotransposons and miniature inverted-repeat transposable elements. The 500-bp sequences immediately flanking a Feilai element were highly A + T-rich, which is consistent with the fact that no Feilai has been found in the coding regions of genes. It is likely that the highly reiterated and interspersed Feilai elements are partially responsible for the pattern of short-period interspersion of the Ae. aegypti genome. The evolutionary relationship between Feilai and the Ae. aegypti genome is likely complex.

Aedes↗
PubMed2003

A novel class of SINE elements derived from 5S rRNA.

Eukaryotic genomes are colonized by different retroposons, including short interspersed repetitive elements (SINEs). All currently known SINEs are derived from tRNA and 7SL RNA genes and exploit their type 2 internal pol III promoters. We report here a novel class of SINE elements, called SINE3, derived from 5S rRNA. SINE3s are transcribed from the type 1 internal pol III promoter. Approximately 10,000 copies of SINE3 elements are present in the zebrafish genome, they constitute approximately 0.4% of the genomic DNA. Some elements are as little as 1% diverged from each other, indicating that the retrotransposition of SINE3 in zebrafish is an ongoing process. The 3'-tail of SINE3 is significantly similar to that of CR1-like non-LTR retrotransposons, represented by numerous subfamilies in the zebrafish genome. Analogously to CR1-like elements, SINE3 copies are not flanked by target site duplications, and their 3' termini are composed of (ACATT)n and (ATT)n microsatellites, specific for different subfamilies of SINE3. Given the common structural features, it is highly likely that the enzymatic machinery encoded by CR1-like elements powers proliferation of SINE3.

Animals↗
PubMedDate not supplied

[Repetitive sequences of the tree shrew genome (Mammalia, Scandentia)].

Copies of two repetitive elements of the genome of common tree shrew (Tupaia glis) were cloned and sequenced. The first element, Tu III, is a approximately 260 bp long short interspersed element (SINE) with the 5'-end derived from glycine RNA. Tu III carries long polypurine- and polypyrimidine-rich tracts, which may contribute to the specific secondary structure of Tu III RNA. This SINE was also found in the genome of smooth-tailed tree shrew of another genus (Dendrogale). Tu III seems to be confined to the order Scandentia (tree shrews) since it was not found in DNA of other tested mammals. The second element Tu-SAT1 is a tandem repeat with a monomer length of 365 bp. Some properties of its nucleotide sequence suggest that Tu-SAT1 is a centromeric satellite.

Animals↗
PubMed2003

Potential for retroposition by old Alu subfamilies.

Alu elements sharing sequence characteristics of the "old" subfamilies are thought to currently be retrotranspositionally inactive. We analyzed one of these old subfamilies of Alu elements, Sx, for sequence conservation relative to the consensus and the length of the "A-tail" as parameters to define the presence of potential Alu Sx source genes in the human genome. Sequence identity to the left half or the right half of the Alu Sx consensus sequence was evaluated for 4424 complete elements obtained from the human genome draft sequence. A small subset of Alu Sx left halves were found to be more conserved than any of the Alu Sx right halves. Selection for promoter function in active elements may explain the slightly higher conservation of the left half. In order to determine whether this sequence identity was the result of recent activity, or simply sequence conservation for older elements, PCR amplification of some of the loci containing Sx elements with conserved left/right halves from different primate genomes was carried out. Several of these Sx Alus were found to have amplified at a later evolutionary period (<35 mya) than expected based on previous studies of Sx elements. Analysis of "A-tail" length, a feature correlated with current retroposition activity, varied between Alu Sx element loci in different primates, where the length increased in specific Alu elements in the human genome. The presence of few conserved Alu Sx elements and the dynamic expansion/contraction of the A-tail suggests that some of these older subfamilies may still be active at very low levels or in a few individuals.

Alu Elements↗
PubMed2002

Distribution and characterization of regulatory elements in the human genome.

The regulation of transcription and subsequent gene splicing are crucial to correct gene expression. Although a number of regulatory sequences involved in both processes are known, it is not clear how general their functions are in the genomic context, nor how the regulatory regions are distributed throughout the genome. Here we study the distribution of known mutagenic elements within human introns and exons to deduce the properties of regions essential for splicing and transcription. We show that intronic splicing regulators are generally found close to the splice sites, but may be found as far as 200 nucleotides away from the splice junctions. Similarly, sequences important for splicing may be located as far as 125 nucleotides away from the junctions, within exons. We characterize several types of simple repetitive sequences and low-complexity regions that are overrepresented close to both intron ends and are likely to play important roles in the splicing process. We show that the first introns within most genes play a particularly important regulatory role that is most likely, however, to be involved in transcription control. We also study the distribution of two known regulatory motifs, the GGG trinucleotide and the CpG dinucleotide, and deduce their respective importance to splicing and transcription regulation.

Base Composition↗
PubMed2000

The short interspersed repetitive element of Trypanosoma cruzi, SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons.

The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was first detected when comparing the sequences of loci that encode the TcP2beta genes. It is present in about 1,500-3,000 copies per genome, depending on the strain, and it is distributed in all chromosomes. An initial analysis of SIRE sequences from 21 genomic fragments allowed us to derive a consensus nucleotide sequence and structure for the element, consisting of three regions (I, II, and III) each harboring distinctive features. Analysis of 158 transcribed SIREs demonstrates that the consensus is highly conserved. The sequences of 51 cDNAs show that SIRE is included in the 3' end of several mRNAs, always transcribed from the sense strand, contributing the polyadenylation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroelement. VIPER's 5' end is formed by the first 182 bp of SIRE, whereas its 3' end is formed by the last 220 bp of the element. Both SIRE moieties are connected by a 1,924-bp-long fragment that carries a unique ORF encoding a complete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids derive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptase-RNase H shares significant homology to that of long terminal repeat retrotransposons. The fact that SIRE and VIPER sequences are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan parasite.

Amino Acid Sequence↗
PubMed2001

Analysis of the SINE S1 Pol III promoter from Brassica; impact of methylation and influence of external sequences.

Transcription is an important control point in the transposable element mobilization process. To better understand the regulation of the plant SINE (Short Interspersed Elements) S1, its promoter sequence was studied using an in vitro pol III transcription system derived from tobacco cells. We show that the internal S1 promoter can be functional although upstream external sequences were found to enhance this basal level of transcription. For one putative 'master' locus (na7), three CAA triplets (in positions -12, -7 and -2) and two overlapping TATA motifs (in positions -54 to -43) were important to stimulate transcription. For this locus, two transcription initiation regions were characterized, one centered on position + 1 (first nucleotide of the S1 element) and one centered on position - 19 independently of the internal motifs. The CAA triplets only influence transcription in + 1 and work in association with the internal motifs. We show that methylation can inhibit transcription at the na7 locus. We also observe that S1 RNA is cleaved in a smaller Poly (A) minus product by a process analogous to the maturation of mammalian SINEs.

Base Sequence↗
PubMed2005

Identification of a short interspersed repeat in the Reticulitermes lucifugus (Isoptera Rhinotermitidae) genome.

A SINE element (called Talua) has been isolated from Reticulitermes lucifugus genome, by means of sequence comparison between clones obtained through genomic restriction and aspecific PCR amplification. It posses all the structural features commonly found in short interspersed elements: (i) a RNA polymerase III internal promoter, (ii) flanking short direct repeats and (iii) a poly (A) tail. BLAST search reveals significant homology with other previously described SINEs and tRNAs. The repeats are G+C-rich, but they are located in A+T-rich regions. This biased genomic distribution results from the analysis of adjacent regions. A Talua element was also found in a microsatellite-containing clone from Cryptotermes secundus. The presence of the SINE also in the Kalotermitidae family, suggests the usefulness of Talua as a taxonomic marker at the family level. The importance of this element on termite genome evolution is discussed.

Animals↗
PubMed2001

Transposable B2 SINE elements can provide mobile RNA polymerase II promoters.

Short interspersed elements (SINEs) are highly abundant components of mammalian genomes that are propagated by retrotransposition. SINEs are recognized as a causal agent of human disease and must also have had a profound influence in shaping eukaryotic genomes. The B2 SINE family constitutes approximately 0.7% of total mouse genomic DNA (ref. 2) and is also found at low abundance in humans. It resembles the Alu family in several respects, such as its mechanism of propagation. B2 SINEs are derived from tRNA and are transcribed by RNA polymerase (pol) III to generate short transcripts that are not translated. We find here, however, that one B2 SINE also carries an active pol II promoter located outside the tRNA region. Indeed, a B2 element is responsible for the production of a mouse Lama3 transcript. The B2 pol II promoters can be bound and stimulated by the transcription factor USF (for upstream stimulatory factor), as shown by transient transfection experiments. Moreover, this pol II activity does not preclude the pol III transcription necessary for retrotransposition. Dispersal of B2 SINEs by retrotransposition may therefore have provided numerous opportunities for creating regulated pol II transcription at novel genomic sites. This mechanism may have allowed the evolution of new transcription units and new genes.

Animals↗
PubMed1999

CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs.

A 65-bp "core" sequence is dispersed in hundreds of thousands copies in the human genome. This sequence was found to constitute the central segment of a group of short interspersed elements (SINEs), referred to as mammalian-wide interspersed repeats, that proliferated before the radiation of placental mammals. Here, we propose that the core identifies an ancient tRNA-like SINE element, which survived in different lineages such as mammals, reptiles, birds, and fish, as well as mollusks, presumably for >550 million years. This element gave rise to a number of sequence families (CORE-SINEs), including mammalian-wide interspersed repeats, whose distinct 3' ends are shared with different families of long interspersed elements (LINEs). The evolutionary success of the generic CORE-SINE element can be related to the recruitment of the internal promoter from highly transcribed host RNA as well as to its capacity to adapt to changing retropositional opportunities by sequence exchange with actively amplifying LINEs. It reinforces the notion that the very existence of SINEs depends on the cohabitation with both LINEs and the host genome.

Animals↗
PubMed2006

Mobile element-based forensic genomics.

Mobile elements are commonly referred to as selfish repetitive DNA sequences. However, mobile elements represent a unique and underutilized group of molecular markers. Several of their characteristics make them ideally suited for use as tools in forensic genomic applications. These include their nature as essentially homoplasy-free characters, they are identical by descent, the ancestral state of any insertion is known to be the absence of the element, and many mobile element insertions are lineage specific. In this review, we provide an overview of mobile element biology and describe the application of certain mobile elements, especially the SINEs and other retrotransposons, to forensic genomics. These tools include quantitative species-specific DNA detection, analysis of complex biomaterials, and the inference of geographic origin of human DNA samples.

Alu Elements↗
PubMed1998

Recent B2 element insertions in the mouse genome.

B2 elements are a family of short interspersed repeats that have amplified within rodent genomes. Recent mobility of only two individual B2 elements has been reported to date. We identified an additional recent B2 insertion occurring within intron 4 of the murine beta-glucuronidase gene (Gus-s) of the BalbC strain of mouse by analyzing orthologous loci of a nonrandomly selected B2 element. The basis of selection for the B2 element was its high level of sequence identity to the B2 consensus. The selected B2 element was amplified by the polymerase chain reaction (PCR) using primers to the unique flanking sequences from genomic DNA of several species and laboratory strains of mice. Our results demonstrated the presence of the selected B2 element only in the genome of Mus musculus BalbC strain. Cloning and sequencing of a representative sample of the products obtained confirmed the absence of the B2 element within this intron in addition to other variations in the sequence. The detection of the B2 element only in the BalbC strain suggests that the element recently inserted within this mouse population when the initial laboratory colony was formed. Sequence comparison of the two previously identified recent B2 inserts also shows a low divergence in relation to the B2 type II consensus. The data presented confirms that recently inserted B2 elements closely match their consensus sequence, potentially allowing for their identification.

Animals↗
PubMed2001

Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales.

Short interspersed repetitive elements (SINEs) are a kind of retroposons dispersed among the eukaryotic genomes. Previously, we isolated and characterized a new SINE family, named CHR-2, members of which are distributed in the genomes of cetaceans, hippopotamuses, and ruminants. We analyzed systematically more than a hundred members of the CHR-2 SINEs, which were isolated from the genomes of cetaceans and cow, together with the additional data available in the DNA databases, and showed that these SINEs are divided into at least five distinct subfamilies that share diagnostic nucleotides and/or deletions. A hybridization analysis clearly demonstrated that, among these five subfamilies, two subfamilies, named CD and CDO, are specific to cetaceans and toothed whales, respectively. We reconstruct the evolutionary history of the CHR-2 SINEs during evolution of cetartiodactyl genomes.

Animals↗
PubMed2004

First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea.

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.

Amino Acid Sequence↗
PubMed2007

SINEs of progress: Mobile element applications to molecular ecology.

Mobile elements represent a unique and under-utilized set of tools for molecular ecologists. They are essentially homoplasy-free characters with the ability to be genotyped in a simple and efficient manner. Interpretation of the data generated using mobile elements can be simple compared to other genetic markers. They exist in a wide variety of taxa and are useful over a wide selection of temporal ranges within those taxa. Furthermore, their mode of evolution instills them with another advantage over other types of multilocus genotype data: the ability to determine loci applicable to a range of time spans in the history of a taxon. In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology.

Classification↗