Sequence organization of the human Y chromosome

Three classes of DNA specific for the human Y chromosome have thus far been identified by detailed structural and functional analysis. Their properties and general chromosomal arrangement were determined by reassociation with DNA from individuals with structural alterations of the Y chromosome and by reassociation with DNA fragments of varying length. Radiolabelled XY DNA was fractionated into single copy and reiterated sequences by self reassociation to C₀t 46. Each fraction was reassociated with a vast excess of human XX DNA. The sequences failing to reassociate with XX DNA were shown to be specific for the Y chromosome. Reiterated sequences isolated during reassociation reactions requiring precise base pairing (60° in 0.12 M phosphate buffer, pH 6.8) represent about 20% of the Y chromosome. These sequences are confined to the long arm of the Y chromosome, are present in and outside the terminal fluorescent Y segment, and are interspersed at short intervals (less than 800 nucleotides) with sequences having extensive homology with other chromosomes. Under relaxed reassociation conditions (50° in 0.14 M phosphate buffer, pH 6.8) ∞ 60% of these sequences (representing ∞ 15 families with a reiteration frequency of 500) reassociated with autosomal DNA, while 40% (representing ∞ 11 families with a reiteration frequency of 350) retained their Y chromosome specificity. Single copy sequences account for ∞ 50% of the Y chromosome; these may represent otherwise unidentified structural genes. Alternatively, since the Y chromosome seems largely devoid of recognizable genes, they may represent a case where single copy sequences are not synonymous with genes for protein structure.