The transposable elements of Drosophila melanogaster – a genomics perspective.
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The transposable elements of Drosophila melanogaster – a genomics perspective.
version 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective. Brent Kronmiller2, Joseph Carlson2, Robert Svirskas2, Sandeep Patel2, Erwin Frise2, David A. wheeler5, Suzannna Lewis1, Gerald M. Rubin1*’4, Michael Ashburner6’7 and Susan E. Celniker.‘Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720,2Drosophilci Genome Pro The transposable elements of Drosophila melanogaster – a genomics perspective.ject, Lawrence Berkeley National Laboratory', Berkeley, CA 94720, ’Amersham Biosciences, 2100 East Elliot Rd., Tempe, AZ 85284, 4Howard Hughes MedicalThe transposable elements of Drosophila melanogaster – a genomics perspective.
Institute, ’Human Genome Sequencing Center and Department of Molecular and Cell Biology, Baylor College of Medicine, Houston, TX 77030, ’Department oversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective. Ashburner,Department of Genetics, Downing Street, Cambridge, England CB2 3EH. phone:+44 1223-333969fax:+ 44 1223-333992email:mall@gen.cam.ac.ukRunning Title: Transposable elements in the Drosophila euchromatin.AbstractTransposable elements are found in the genomes of nearly all eukaryotes. We have The transposable elements of Drosophila melanogaster – a genomics perspective.analyzed the Release 3 genomic sequence of Drosophila melanogasier to describe the dichromatic transposable elements in the sequenced strain of this sThe transposable elements of Drosophila melanogaster – a genomics perspective.
pecies. We identified 85 known and 8 novel families of transposable element in the Release 3 sequences; these vary in copy number between 1 and 146. Aversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective. on chromosome 4 relative to the major chromosome arms, and transposable element abundance on the X chromosome is similar to the major autosome arms. The abundance of of the three major classes of transposable elements (LTR, LINE-like, and TIR) are markedly higher in the proximal 2 Mb of each chromo The transposable elements of Drosophila melanogaster – a genomics perspective.some arm, reflecting the transition from euchromatin to heterochromatin, whereas the high abundace on chromosome 4 is due only to LINE-like and TIR elThe transposable elements of Drosophila melanogaster – a genomics perspective.
ements. More than two-thirds of the transposable elements identified in Release 3 are partial. Analysis of structural variation of elements from diffeversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.ents of the same or different classes. Transposable elements are preferentially found outside genes; only 436 of 1,573 transposable elements are contained within the 61.4 Mb of sequences which are annotated as being transcribed. The high abundance, high proportion of complete elements and low levels The transposable elements of Drosophila melanogaster – a genomics perspective. of sequence diversity in LTR families suggest that indvidual LTR elements are more likely to be recent insenions into the D. melanogaster genome, relThe transposable elements of Drosophila melanogaster – a genomics perspective.
ative to LINE-like or TIR elements. This work provides a starling point for future genomic analysis of transposable elements in Drosophila.2Introductiversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.. As d result, many biologists have an interest in the description of transposable elements in completely sequenced eukaryotic genomes, lhe evolutionary biologist wants to understand the origin of transposable elements, how they arc lost and gained by a species and the role they play in the processe The transposable elements of Drosophila melanogaster – a genomics perspective.s of genome evolution; the population geneticist wants Io know the factors that determine the frequency and distribution OÍ elements within and betweeThe transposable elements of Drosophila melanogaster – a genomics perspective.
n populations; the developmental geneticist wants to know what roles these elements may play in either normal developmental processes or in the responversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.ts and how they interact with the cellular machinery of the host, ft is for all of these reasons and more that a description of the transposable elements in the recently completed Release 3 genomic sequence of D. melanogaster is desirable.rhe contribution of Drosophila to our understanding of transp The transposable elements of Drosophila melanogaster – a genomics perspective.osable elements is long and glorious. Over 75 years ago. Milislav Demerec discovered highly mutable alleles of two genes in D. virilis, miniature andThe transposable elements of Drosophila melanogaster – a genomics perspective.
magenta (Demerec 1926; 1927; reviewed in Demerec 1935; Green 1976). Both genes were mutable in soma and germ-line and. for the miniature-3alpha alleleversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.nsposition of mobile elements; the dominant enhancers may have been particularly active elements or mutations in host genes affecting transposability (see below). There matters essentially stood until McClintock’s remarkable discovery of mutable alleles in maize and their basis -transposition of the The transposable elements of Drosophila melanogaster – a genomics perspective. Ac and Ds factors (McClintock 1950), and the discovery; some 20 years later, of insenion elements in the gal operon of Escherichia coh (see StarlingeThe transposable elements of Drosophila melanogaster – a genomics perspective.
r 1977).Green (1977) synthesized the evidence then al hand to make a strong case lor insertion as a mechanism of mutagenesis in Drosophila. Within a yversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.1978) and evidence that they were transposable was soon available (Ilyin el al. 1978; Strobel el al. 1979; Young 1979). In fact, the Hogness group had already, but unknowingly, molecularly characterized the first eukaryotic transposable element, the insertion sequences of 28S rRNA encoding genes (se The transposable elements of Drosophila melanogaster – a genomics perspective.e Glover 1977). Ihe discovery of male recombination (Hirai/.umi 1971), and two systems ol hybrid dysgenesis in D. melunogusler (see Kidwell 1979), allThe transposable elements of Drosophila melanogaster – a genomics perspective.
owed the gap, then wide, between genetic: and molec ular analyses to be bridged, rhe discovery of the causal transposable elements, tire P-element (Biversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.e publication of the Release 1 genomic sequence in Match 2000 (Adams et al. 2000) and the Release 2 genomic sequence in October 2000 encouraged several studies on the genomic distribution and abundance of transposable elements in D. me/anogaster (Berezikov, Rucheton and Busseau 2000; Jurka 2000; Bow The transposable elements of Drosophila melanogaster – a genomics perspective.en and Mc Donald 2001; Rizzon et al. 2002; Bartolomé, Maside and charlesworth 2002). Unfortunately, neither release was suitable for3rigorous analysisThe transposable elements of Drosophila melanogaster – a genomics perspective.
of its transposable elements since sequences corresponding to known transposable elements, along with other sequences known to be repetitive in the gversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective. genome assembly, an attempt was made to fill these gaps. However, comparisons of small regions sequenced by the clone-by-clone approach versus the whole genome shotgun method show that this was not a very accurate process (Myers et al. 2000; Benos et al. 2001). It was clear that any rigorous analys The transposable elements of Drosophila melanogaster – a genomics perspective.is of the transposable elements, or any other repeat, required a sequence of higher quality. This has now been achieved by the finishing efforts of thThe transposable elements of Drosophila melanogaster – a genomics perspective.
e Berkeley Drosophila Genome Project. This sequence. Release 3, is now publicly available (Celniker et al. 2002). For the first time, a reliable analyversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.ification of known and novel transposable elementsEukaryotic transposable elements are divided between those that transpose via an RNA intermediate (class 1), retrotransposons. and those that transpose by DNA excision and repair (class II), non-retrotransposons (Craig et al. 2002). Within the retrot The transposable elements of Drosophila melanogaster – a genomics perspective.ransposons, the major division is between those that possess long terminal repeats (LTR elements) (and those that do not (LINE-like elements and SINEThe transposable elements of Drosophila melanogaster – a genomics perspective.
elements (Deininger 1989)). Among the non-retrotransposons, the majority transpose via a DNA intermediate, encode their own transposase and are flankeversion 16.0: 2002-08-26: maThe transposable elements of Drosophila melanogaster - a genomics perspective.Joshua s. Kaminker1'5, Casey M. Bergman-’8, The transposable elements of Drosophila melanogaster – a genomics perspective.g after denaturation with zero-order kinetics, are quite distinct from prototypical class 1 or II elements, and have been included in our analyses (Truet et al. 1981). In addition, there are other classes of repetitive elements, such as INE-1 (Locke et al. 1999a: Locke et al. 1999b; Wilder and Hollo The transposable elements of Drosophila melanogaster – a genomics perspective.cher 2001), which are structurally distinct from all other classes of elements, have not been included in this study.While the classification of transThe transposable elements of Drosophila melanogaster – a genomics perspective.
posable elements by structural class is relatively easy, the taxonomy of transposable element families is somewhat arbitrary (Table 1). We used a critGọi ngay
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