CpG islands of chicken are concentrated on microchromosomes

The chicken karyotype comprises 39 chromosome pairs of which at least 29 are 'microchromosomes'. Microchromosomes account for about 25% of the genomic DNA, but they are cytologically indistinguishable from one another. Due to technical limitations there is a strong bias of mapped genes within the chicken genome database ChickGBASE towards macrochromosomes 1-6 and Z, with specific assignments to only one microchromosome. Several genes have, however, been assigned to the microchromosome group as a whole, demonstrating that these tiny chromosomes do not represent genetically inert DNA. To determine the overall chromosomal distribution of genes, as well as to provide a mapping resource, we prepared a CpG island library from chicken using differential binding to a methyl-CpG binding column before and after de novo methylation. Surprisingly, we found that chicken CpG islands are highly concentrated on the microchromosomes, whereas macrochromosomes 1-6 are comparatively gene-poor by this assay. Our results raise the possibility that gene density on chicken microchromosomes approaches the maximum value known for vertebrates.