Comparison of dot chromosome sequences from D. melanogaster and D. virilisreveals an enrichment of DNA transposon sequences in heterochromatic domains

Slawson, Elizabeth E.; Shaffer, C.; Malone, Colin D.; Leung, Wilson; Kellmann, Elmer; Shevchek, Rachel B; Craig, Charles P.; Bloom, Seth M.; Bogenpohl, James W.; Dee, James; Morimoto, Emiko; Myoung, Jenny; Nett, Andrew; Ozsolak, Fatih; Tittiger, Mindy; Zeug, A.; Pardue, Mary Lou; Buhler, Jeremy; Mardis, Elaine R.; Elgin, Sarah C. R.

doi:10.1186/gb-2006-7-2-r15

Cited by 50 publications

(36 citation statements)

References 72 publications

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“…In the bat and maize genome, distantly related Helitrons are also found in close proximity to other Helitron insertions sometimes directly next to one another (Thomas et al in revision GBE), [47]. A similar pattern might be seen with Helentron mediated transposition events and might account for the clustering of related insertions [5,16,21,22,55]. Similarly, missed termination sequences or composite transposition between neighboring Helitrons can lead to the capture of host sequence (gene transduction).…”

Section: Discussionmentioning

confidence: 93%

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DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

2014

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BackgroundThe Drosophila INterspersed Elements-1 (DINE-1/INE1) transposable elements (TEs) are the most abundant component of the Drosophila melanogaster genome and have been associated with functional gene duplications. DINE-1 TEs do not encode any proteins (non-autonomous) thus are moved by autonomous partners. The identity of the autonomous partners has been a mystery. They have been allied to Helitrons (rolling-circle transposons), MITEs (DNA transposons), and non-LTR retrotransposons by different authors.ResultsWe report multiple lines of bioinformatic evidence that illustrate the relationship of DINE-1 like TEs to endonuclease-encoding rolling-circle TEs (Helentrons). The structural features of Helentrons are described, which resemble the organization of the non-autonomous partners, but differ significantly from canonical Helitrons. In addition to the presence of an endonuclease domain fused to the Rep/Helicase protein, Helentrons have distinct structural features. Evidence is presented that illustrates that Helentrons are widely distributed in invertebrate, fish, and fungal genomes. We describe an intermediate family from the Phytophthora infestans genome that phylogenetically groups with Helentrons but that displays Helitron structure. In addition, evidence is presented that Helentrons can capture gene fragments in a pattern reminiscent of canonical Helitrons.ConclusionsWe illustrate the relationship of DINE-1 and related TE families to autonomous partners, the Helentrons. These findings will allow their proper classification and enable a more accurate understanding of the contribution of rolling-circle transposition to the birth of new genes, gene networks, and genome composition.

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Section: Discussionmentioning

confidence: 93%

“…DINE-1 like elements are most abundant in the centromeres and heterochromatic regions of the chromosomes of drosophilids [5,6,10,16,21]. In D. serido they also predominate the heterochromatic regions of the sex chromosomes [16].…”

Section: Introductionmentioning

confidence: 99%

DINE-1, the highest copy number repeats in Drosophila melanogaster are non-autonomous endonuclease-encoding rolling-circle transposable elements (Helentrons)

2014

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“…In that case, DmSETDB1 function would depend on partners or DNA sequences specific for Chromosome 4, such as for instance the Chromosome 4-specific factor POF [60,61], or the Hoppel element, also known as 1360, which is over-represented on the D. melanogaster Chromosome 4 [62], and which could be an initiation site for heterochromatin formation [21]. …”

Section: Discussionmentioning

confidence: 99%

Drosophila SETDB1 Is Required for Chromosome 4 Silencing

et al. 2007

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Histone H3 lysine 9 (H3K9) methylation is associated with gene repression and heterochromatin formation. In Drosophila, SU(VAR)3–9 is responsible for H3K9 methylation mainly at pericentric heterochromatin. However, the histone methyltransferases responsible for H3K9 methylation at euchromatic sites, telomeres, and at the peculiar Chromosome 4 have not yet been identified. Here, we show that DmSETDB1 is involved in nonpericentric H3K9 methylation. Analysis of two DmSetdb1 alleles generated by homologous recombination, a deletion, and an allele where the 3HA tag is fused to the endogenous DmSetdb1, reveals that this gene is essential for fly viability and that DmSETDB1 localizes mainly at Chromosome 4. It also shows that DmSETDB1 is responsible for some of the H3K9 mono- and dimethyl marks in euchromatin and for H3K9 dimethylation on Chromosome 4. Moreover, DmSETDB1 is required for variegated repression of transgenes inserted on Chromosome 4. This study defines DmSETDB1 as a H3K9 methyltransferase that specifically targets euchromatin and the autosomal Chromosome 4 and shows that it is an essential factor for Chromosome 4 silencing.

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“…Sequence data are submitted to Genbank, and annotation results to FlyBase. One scientific paper has been published based on the student work (9); contributing students are co-authors. We anticipate an accumulation of publications and database contributions with time.…”

Section: Assessment and Sustainabilitymentioning

confidence: 99%