ArticleBMC bioinformatics2005
Sequence signature analysis of chromosome identity in three Drosophila species.
Article in BMC bioinformatics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 (The Journal of biological chemistry · 2018Article
- Variable Rates of Simple Satellite Gains across the Drosophila Phylogeny.Molecular biology and evolution · 2018Article
- Increased expression of X-linked genes in mammals is associated with a higher stability of transcripts and an increased ribosome density.Genome biology and evolution · 2015Article
- A method for processing multivariate data in medical studies.Statistics in medicine · 2013Article
- POF regulates the expression of genes on the fourth chromosome in Drosophila melanogaster by binding to nascent RNA.Molecular and cellular biology · 2012Article
- Sequence signatures involved in targeting the Male-Specific Lethal complex to X-chromosomal genes in Drosophila melanogaster.BMC genomics · 2012Article
- HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster.PLoS genetics · 2012Article
- Buffering and the evolution of chromosome-wide gene regulation.Chromosoma · 2011Review
- Drosophila dosage compensation: a complex voyage to the X chromosome.Development (Cambridge, England) · 2009Review
- Article
- Fast comparison of DNA sequences by oligonucleotide profiling.BMC research notes · 2008Article
- Global patterns of sequence evolution in Drosophila.BMC genomics · 2007Article
- POF and HP1 bind expressed exons, suggesting a balancing mechanism for gene regulation.PLoS genetics · 2007Article
- Species-specific positive selection of the male-specific lethal complex that participates in dosage compensation in Drosophila.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Painting of fourth and chromosome-wide regulation of the 4th chromosome in Drosophila melanogaster.The EMBO journal · 2007Article
- Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex.Genes & development · 2006Article
- Dosage compensation, the origin and the afterlife of sex chromosomes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2006Review
- The dot chromosome of Drosophila: insights into chromatin states and their change over evolutionary time.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2006Review
- Review
- A surrogate approach to study the evolution of noncoding DNA elements that organize eukaryotic genomes.The Journal of heredityReview
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAll eukaryotic organisms need to distinguish each of their chromosomes. A few protein complexes have been described that recognise entire, specific chromosomes, for instance dosage compensation complexes and the recently discovered autosome-specific Painting of Fourth (POF) protein in Drosophila. However, no sequences have been found that are chromosome-specific and distributed over the entire length of the respective chromosome. Here, we present a new, unbiased, exhaustive computational method that was used to probe three Drosophila genomes for chromosome-specific sequences.
resultsBy combining genome annotations and cytological data with multivariate statistics related to three Drosophila genomes we found sequence signatures that distinguish Muller's F-elements (chromosome 4 in D. melanogaster) from all other chromosomes in Drosophila that are not attributable to differences in nucleotide composition, simple sequence repeats or repeated elements. Based on these signatures we identified complex motifs that are strongly overrepresented in the F-elements and found indications that the D. melanogaster motif may be involved in POF-binding to the F-element. In addition, the X-chromosomes of D. melanogaster and D. yakuba can be distinguished from the other chromosomes, albeit to a lesser extent. Surprisingly, the conservation of the F-element sequence signatures extends not only between species separated by approximately 55 Myr, but also linearly along the sequenced part of the F-elements.
conclusionOur results suggest that chromosome-distinguishing features are not exclusive to the sex chromosomes, but are also present on at least one autosome (the F-element) in Drosophila.
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