Stenberg Per, Pettersson Fredrik, Saura Anja O, Berglund Anders, Larsson Jan
UCMP, Umeå University, Umeå, Sweden.
BMC Bioinformatics. 2005 Jun 23;6:158. doi: 10.1186/1471-2105-6-158.
All 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.
By 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.
Our 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.
所有真核生物都需要区分其每一条染色体。已经描述了一些能够识别完整、特定染色体的蛋白质复合物，例如剂量补偿复合物以及最近在果蝇中发现的常染色体特异性的四号染色体涂色（POF）蛋白。然而，尚未发现染色体特异性且分布于相应染色体全长的序列。在此，我们提出一种全新的、无偏倚的、详尽的计算方法，用于在三个果蝇基因组中探寻染色体特异性序列。
通过将基因组注释和细胞学数据与三个果蝇基因组的多变量统计相结合，我们发现了能够区分穆勒F元素（黑腹果蝇的四号染色体）与果蝇中所有其他染色体的序列特征，这些特征并非归因于核苷酸组成、简单序列重复或重复元件的差异。基于这些特征，我们鉴定出在F元素中强烈富集的复杂基序，并发现有迹象表明黑腹果蝇的基序可能参与POF与F元素的结合。此外，黑腹果蝇和雅库布果蝇的X染色体也能够与其他染色体区分开来，尽管程度较小。令人惊讶的是，F元素序列特征的保守性不仅在大约相隔5500万年的物种之间存在，而且在F元素的测序部分呈线性分布。
我们的结果表明，染色体区分特征并非性染色体所特有，在果蝇的至少一条常染色体（F元素）上也存在。
