Kowalska Agata, Bozsaky Eva, Ramsauer Thomas, Rieder Dietmar, Bindea Gabriela, Lörch Thomas, Trajanoski Zlatko, Ambros Peter F
CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria.
Chromosome Res. 2007;15(3):327-39. doi: 10.1007/s10577-007-1129-y. Epub 2007 May 10.
We have tested whether a direct correlation of sequence information and staining properties of chromosomes is possible and whether this combined information can be used to precisely map any position on the chromosome. Despite huge differences of compaction between the naked DNA and the DNA packed in chromosomes we found a striking correlation when visualizing the GGCC density on both levels. Software was developed that allows one to superimpose chromosomal fluorescence intensity profiles generated by chromolysin A3 (CMA3) staining with GGCC density extracted from the Ensembl database. Thus, any position along the chromosome can be defined in megabase pairs (Mb) besides the cytoband information, enabling direct alignment of chromosomal information with the sequence data. The mapping tool was validated using 13 different BAC clones, resulting in a mean difference from Ensembl data of 2 Mb (ranging from 0.79 to 3.57 Mb). Our results indicate that the sequence density information and information gained with sequence-specific fluorochromes are superimposable. Thus, the visualized GGCC motif density along the chromosome (sequence bands) provides a unique platform for comparing different types of genomic information.
我们已经测试了染色体的序列信息与染色特性之间是否存在直接关联，以及这种组合信息是否可用于精确绘制染色体上的任何位置。尽管裸DNA与包装在染色体中的DNA在压缩程度上存在巨大差异，但我们在可视化两个层面上的GGCC密度时发现了显著的相关性。我们开发了一种软件，它能将嗜色菌素A3（CMA3）染色产生的染色体荧光强度图谱与从Ensembl数据库中提取的GGCC密度进行叠加。因此，除了细胞带信息外，染色体上的任何位置都可以用兆碱基对（Mb）来定义，从而使染色体信息能够与序列数据直接比对。使用13个不同的BAC克隆对该映射工具进行了验证，结果显示与Ensembl数据的平均差异为2 Mb（范围从0.79至3.57 Mb）。我们的结果表明，序列密度信息与通过序列特异性荧光染料获得的信息是可叠加的。因此，沿染色体可视化的GGCC基序密度（序列带）为比较不同类型的基因组信息提供了一个独特的平台。
