A new platform linking chromosomal and sequence information

Abstract

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.

The meaning of DAPI bands observed after C-banding and FISH procedures

“…Hou et al ( 2004 ) demonstrated that chromomycin binds specifi cally to the minor groove of the DNA double helix containing the sequence GGCC. Kowalska et al ( 2007 ) found that the distribution of R bands observed with CMA on human chromosomes corresponds to the GGCC densities of published DNA sequences of human genome for each chromosome arm.…”

The hierarchically organized splitting of chromosomal bands for all human chromosomes

“…As noted by Kowalska and coworkers (2007) [ 20 ] sub-band information provided in different human genome sequence databases are not identical. This might be partially due to the different initial sources of G-banded ideogram used and leads to discrepancies in gene mapping in different databases.…”

Chromosomal variation among populations of a fungus-farming ant: implications for karyotype evolution and potential restriction to gene flow

“…The difference in karyotype length appears to be related to the evolution of longer centromeres, as evidenced by the long negative blocks of DAPI staining along the centromeric region. Additional evidence for centromere differences comes from the intensity variation of the CMA 3 + blocks, which directly reflects differences in the richness of CG nucleotides [ 27 ] and may point to marked changes in the nucleotide composition of the centromeric satellite DNA of T. holmgreni .…”