A new platform linking chromosomal and sequence information.
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.
Kowalska
Agata
A
CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, 1090, Vienna, Austria.
Bozsaky
Eva
E
Ramsauer
Thomas
T
Rieder
Dietmar
D
Bindea
Gabriela
G
Lörch
Thomas
T
Trajanoski
Zlatko
Z
Ambros
Peter F
PF
D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial; D004396:Coloring Agents; D019295:Computational Biology / Q000379:methods*; D004247:DNA; D023281:Genomics / Q000379:methods; D012984:Software
D004396:Coloring Agents; D004247:DNA