Comparison of dot chromosome sequences from D-melanogaster and D-virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains
Comparison of dot chromosome sequences from D-melanogaster and D-virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains
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DOI：
10.1186/gb-2006-7-2-r15
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发表时间：
2006-01-01
期刊：
影响因子：
12.3
通讯作者：
Elgin, SCR
中科院分区：
文献类型：
--
作者：
Slawson, EE;Shaffer, CD;Elgin, SCR
背景：果蝇的第四染色体，即斑点染色体，通过异染色质蛋白1(HP1)和组蛋白H3K9me抗体的免疫荧光染色显示，在很大程度上是异染色质。相反，在华支睾吸虫的点染色体上没有HP1和H3K9me，这表明该区域是常染的。结果：完成了11个与马尾藻斑点染色体杂交的融合体(372,650个碱基对)和7个来自主要常着色质染色体臂的融合体(273,110个碱基对)的测序和分析。黑腹盘藻斑点染色体上的大部分基因仍然存在于黑腹盘藻的斑点染色体上，但也出现了许多倒位现象。两个物种的点染色体在基因密度和编码密度上都与主要染色体臂相似，但两个物种的点染色体基因都有较大的内含子。马尾藻的点染色体融合体具有较高的重复密度(22.8%)，与马尾藻的同源区(26.5%)相似。然而，在重复元素的表示上有很大的差异。DNA转座子残基仅占马尾藻斑点染色体的6.3%，但其同源区域的18.4%；Dine-1和1360元素在马尾藻中尤为丰富。结论：结合RNAi的最新研究结果，我们认为特定的重复元件和密度在决定高阶染色质包装中起着重要作用。
Background: Chromosome four of Drosophila melanogaster, known as the dot chromosome, is largely heterochromatic, as shown by immunofluorescent staining with antibodies to heterochromatin protein 1 (HP1) and histone H3K9me. In contrast, the absence of HP1 and H3K9me from the dot chromosome in D. virilis suggests that this region is euchromatic. D. virilis diverged from D. melanogaster 40 to 60 million years ago.Results: Here we describe finished sequencing and analysis of 11 fosmids hybridizing to the dot chromosome of D. virilis (372,650 base-pairs) and seven fosmids from major euchromatic chromosome arms ( 273,110 base-pairs). Most genes from the dot chromosome of D. melanogaster remain on the dot chromosome in D. virilis, but many inversions have occurred. The dot chromosomes of both species are similar to the major chromosome arms in gene density and coding density, but the dot chromosome genes of both species have larger introns. The D. virilis dot chromosome fosmids have a high repeat density (22.8%), similar to homologous regions of D. melanogaster (26.5%). There are, however, major differences in the representation of repetitive elements. Remnants of DNA transposons make up only 6.3% of the D. virilis dot chromosome fosmids, but 18.4% of the homologous regions from D. melanogaster; DINE-1 and 1360 elements are particularly enriched in D. melanogaster. Euchromatic domains on the major chromosomes in both species have very few DNA transposons (less than 0.4%).Conclusion: Combining these results with recent findings about RNAi, we suggest that specific repetitive elements, as well as density, play a role in determining higher-order chromatin packaging.