From Sequence to Chromosome: The Tip of the
            <i>X</i>
            Chromosome of
            <i>D. melanogaster</i>

Benos, Panayiotis V.; Gatt, Melanie K.; Ashburner, Michael; Murphy, Lee; Harris, David J.; Barrell, Bart; Ferraz, Concepción; Vidal, Sophie; Brun, Catherine; Demailles, Jacques; Cadieu, Édouard; Dreano, Stéphane; Gloux, Stéphanie; Lelaure, Valérie; Mottier, Stéphanie; Galibert, Francis; Borkova, Dana; Miñana, Belén; Kafatos, Fotis C.; Louis, Christos; Sidén‐Kiamos, Inga; Bolshakov, Slava; Papagiannakis, George; Spanos, Lefteris; Cox, Sarah; Madueño, Encarnación; Pablos, Beatriz de; Modolell, Juan; Peter, Annette; Schöttler, Petra; Werner, Meike; Mourkioti, Foteini; Beinert, Nicole; Dowe, G. H. C.; Schäfer, Ulrich; Jäckle, Herbert; Bucheton, Alain; Callister, Deborah M.; Campbell, Louise; Darlamitsou, Areti; Henderson, Nadine S.; McMillan, Paul J.; Salles, Cathy; Tait, Evelyn; Valenti, Phillipe; Robert, D C; Saunders,; Glover, David M.

doi:10.1126/science.287.5461.2220

Cited by 29 publications

(19 citation statements)

References 26 publications

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“…Primers for the most distal of the amplicons (numbered 1-4) were designed using the X chromosome sequence from Canton-S, originally part of the Drosophila Sequencing Project (accession no. AL031884) and sequenced by the European Drosophila Genome Project (Benos et al 2000). As mentioned above, Canton-S possesses a structurally distinct X subtelomere from the reference strain, y; cn bw sp, in that it includes a repetitive region of the subtelomere containing the canonical X TAS, characterized by Karpen and Spradling (1992;see Figure 2).…”

Section: Methodsmentioning

confidence: 99%

Molecular Population Genetics of Drosophila Subtelomeric DNA

2008

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DNA sequence surveys in yeast and humans suggest that the forces shaping telomeric polymorphism and divergence are distinctly more dynamic than those in the euchromatic, gene-rich regions of the chromosomes. However, the generality of this pattern across outbreeding, multicellular eukaryotes has not been determined. To characterize the structure and evolution of Drosophila telomeres, we collected and analyzed molecular population genetics data from the X chromosome subtelomere in 58 lines of North American Drosophila melanogaster and 29 lines of African D. melanogaster. We found that Drosophila subtelomeres exhibit high levels of both structural and substitutional polymorphism relative to linked euchromatic regions. We also observed strikingly different patterns of variation in the North American and African samples. Moreover, our analyses of the polymorphism data identify a localized hotspot of recombination in the most-distal portion of the X subtelomere. While the levels of polymorphism decline sharply and in parallel with rates of crossing over per physical length over the distal first euchromatic megabase pairs of the X chromosome, our data suggest that they rise again sharply in the subtelomeric region (%80 kbp). These patterns of historical recombination and geographic differentiation indicate that, similar to yeast and humans, Drosophila subtelomeric DNA is evolving very differently from euchromatic DNA. P OPULATION geneticists aspire to understand the evolutionary forces shaping patterns of molecular polymorphism and divergence. The recent increase in the quantity of DNA sequence data from proteincoding regions has led to considerable advances in our understanding of the forces governing the evolution of such regions. For example, genomic surveys have revealed functional variants as well as classes of genes enriched for the signature of natural selection (e.g., Bustamante et al. 2005;Nielsen et al. 2005;Begun et al. 2007). In contrast, regions of the genome containing fewer genes but an increased density of repetitive sequences have been less amenable to population and molecular evolutionary analysis. These regions, typically found adjacent to telomeres and centromeres, are collectively referred to as the heterochromatin. Because heterochromatic DNA is difficult to clone, sequence, and assemble, much less is known about the structure of these regions. Thus, there is almost no foundation for effective population or comparative genomic analyses. Indeed, only recently have researchers begun to identify the sparsely distributed protein-coding sequences embedded in heterochromatin (reviewed in Yasuhara and Wakimoto 2006).Most population and molecular evolutionary surveys from telomeric regions come from yeast and primates (but see recent work on Arabidopsis in Kuo et al. 2006). These studies show that telomeric DNA is evolving very differently from the gene-rich euchromatin. For example, the telomeric regions of several human chromosomes are dramatically different from the corresponding regions in c...

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Section: Methodsmentioning

confidence: 99%

Molecular Population Genetics of Drosophila Subtelomeric DNA

2008

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“…The BAC clones (Benos et al 2000) and cosmids clones (Siden-Kiamos et al 1990) are available from http://www.geneservice.co.uk. Cosmid and BAC 96-well IDs and accession numbers are as follows: 30B7 (AL021107), 137E7 (AL021108), 131F2 (AL024456), 63B12 (AL021106), 86E4 (AL021086), 39E1 (AL009191), BACH0.26e3 (AL035245).…”

Section: Clonesmentioning

confidence: 99%

“…Cosmid and BAC clones used by the European Drosophila Genome Project (Benos et al 2000) were obtained from the participant laboratories or from the Human Genome Mapping Project (HGMP) resource center. The BAC clones (Benos et al 2000) and cosmids clones (Siden-Kiamos et al 1990) are available from http://www.geneservice.co.uk.…”

Section: Clonesmentioning

confidence: 99%

The Drosophila MSL complex activates the transcription of target genes

Straub¹,

Gilfillan²,

Maier³

et al. 2005

Genes Dev.

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The mechanism through which gene expression originating from the single male or the two female X chromosomes in Drosophila is adjusted to autosomal gene expression has remained controversial. According to the prevalent model, transcription of the male X is increased twofold by the male-specific-lethal (MSL) complex. However, a significant body of data supports an alternative model, whereby compensation involves a global repression of autosomal gene expression in males by sequestration and neutralization of an activator onto the X chromosome. In order to rigorously discriminate between these models we identified direct target genes for the MSL complex and quantified transcription in absolute terms after knockdown of MSL2. The results unequivocally document an approximate twofold activation of target genes by the MSL complex. In Drosophila, male cells contain only a single copy of the X chromosome, whereas female cells harbor two X chromosomes. The different dosage of X-linked genes in males versus females necessitates a compensatory adjustment of gene expression. The mechanism through which dosage compensation is achieved is still a matter of debate. As proposed by the prevailing model, a malespecific regulatory complex of proteins and noncoding RNA, the male-specific-lethal (MSL) complex, functions as an activator that doubles the transcription of X-linked target genes in males (for review see, Gorman and Baker 1994;Lucchesi 1998;Straub et al. 2005a). The strongest argument for this model, which we refer to as the "activation model" was the finding that all components of the complex (MSL1-3, MLE, the histone acetyl transferase MOF (males absent on the first), the noncoding RNAs roX1, and roX2) and the acetylation of Lys 16 of histone H4 (H4K16ac) are specifically enriched on the male X (Kuroda et al. 1991;Palmer et al. 1993;Bashaw and Baker 1995;Gorman et al. 1995;Zhou et al. 1995;Gu et al. 1998;Franke and Baker 1999). In selected cases, the MSL complex has been mapped to the coding regions of active genes (Sass et al. 2003). Furthermore, acetylation of K16 on histone H4 can lead to strong de-repression of transcription (Akhtar and Becker 2000). Thus, it has been proposed that the twofold increase in transcription is directly due to a change of chromatin structure caused by local or domain-wide histone hyperacetylation. However, it has never been demonstrated unequivocally in vivo that binding of the complex to a specific gene is directly related to its hyperactivation.To the contrary, the activation model has been challenged over the years, most prominently by Birchler et al. (for review, see Birchler et al. 2003;Straub et al. 2005a). They argue that due to a phenomenon called the "inverse dosage effect," the X-chromosomal monosomy in males leads to global activation of all chromosomes. According to their model, which we shall term the "inverse model," the MSL complex evolved to counteract the inverse dosage effect on autosomal gene expression. The inverse dosage effect summarizes a multitude of observations i...

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“…Amino acid sequences of the genes in divisions 1-3 of chromosome X of D. melanogaster can be obtained by anonymous FTP from ftp://ftp.ebi.ac.uk/pub/databases/edgp/misc/ ashburner/EG_genes.991229.pep.fa.gz (Benos et al 2000(Benos et al , 2001, whereas amino acid sequences of the genes identified in the Adh region are found in http://www.fruit fly.org/ sequences/aa_Adh.dros (Ashburner et al 1999). Amino acid sequences of all genes identified through the whole genome sequence (release 1.0) are available at http://www.fruitfly.org/ sequence/dlMfasta.html (Adams et al 2000).…”

Section: Source Of Sequence Datamentioning

confidence: 99%

A Comparative Genomic Analysis of Two Distant Diptera, the Fruit Fly, Drosophila melanogaster, and the Malaria Mosquito, Anopheles gambiae

Большаков

Topalis²,

Blass³

et al. 2002

Genome Res.

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Genome evolution entails changes in the DNA sequence of genes and intergenic regions, changes in gene numbers, and also changes in gene order along the chromosomes. Genes are reshuffled by chromosomal rearrangements such as deletions/insertions, inversions, translocations, and transpositions. Here we report a comparative study of genome organization in the main African malaria vector, Anopheles gambiae, relative to the recently determined sequence of the Drosophila melanogaster genome. The ancestral lines of these two dipteran insects are thought to have separated ∼250 Myr, a long period that makes this genome comparison especially interesting. Sequence comparisons have identified 113 pairs of putative orthologs of the two species. Chromosomal mapping of orthologous genes reveals that each polytene chromosome arm has a homolog in the other species. Between 41% and 73% of the known orthologous genes remain linked in the respective homologous chromosomal arms, with the remainder translocated to various nonhomologous arms. Within homologous arms, gene order is extensively reshuffled, but a limited degree of conserved local synteny (microsynteny) can be recognized.

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From Sequence to Chromosome: The Tip of the X Chromosome of D. melanogaster

Cited by 29 publications

References 26 publications

Molecular Population Genetics of Drosophila Subtelomeric DNA

Molecular Population Genetics of Drosophila Subtelomeric DNA

The Drosophila MSL complex activates the transcription of target genes

A Comparative Genomic Analysis of Two Distant Diptera, the Fruit Fly, Drosophila melanogaster, and the Malaria Mosquito, Anopheles gambiae

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