A boundary of long-range G + C% mosaic domains in the human MHC locus: pseudoautosomal boundary-like sequence exists near the boundary.
The human genome is composed of long-range G+C% (GC%) mosaic structures related to chromosome bands. We found the human MHC locus to be an example of megabase-level GC% mosaic structures and predicted a possible boundary of the megabase-level domains within an undercharacterized 450-kb region harboring the junction of MHC classes II and III. Chromosome walking of the 450-kb region and base-compositional analysis precisely located the boundary of the mosaic domains, disclosing a sharp GC% transition. Near the transition point there was a 20-kb dense Alu cluster, a 30-kb dense LINE-1 cluster, and a sequence highly homologous with the pseudoautosomal boundary of the short arms of human sex chromosomes (PAB1X and PAB1Y); PAB1X and PAB1Y are the interface between sex-specific and pseudoautosomal regions. Many PAB1XY-like sequences (PABLs) were detected by hybridization against genomic DNA, and the new sequences defined the complete form of PABLs to be about 650 nt.
Fukagawa
T
T
Department of Evolutionary Genetics, National Institute of Genetics, Shizuoka-ken, Japan.
Sugaya
K
K
Matsumoto
K
K
Okumura
K
K
Ando
A
A
Inoko
H
H
Ikemura
T
T
D001482:Base Composition; D001483:Base Sequence; D002874:Chromosome Mapping; D018244:Chromosomes, Artificial, Yeast; D003001:Cloning, Molecular; D003360:Cosmids; D003596:Cytosine / Q000032:analysis; D004247:DNA / Q000737:chemistry / Q000235:genetics; D005802:Genes, MHC Class II; D015894:Genome, Human; D006147:Guanine / Q000032:analysis; D006801:Humans; D008285:Major Histocompatibility Complex; D008969:Molecular Sequence Data; D009030:Mosaicism; D012091:Repetitive Sequences, Nucleic Acid; D012689:Sequence Homology, Nucleic Acid; D014960:X Chromosome; D014998:Y Chromosome
D006147:Guanine; D003596:Cytosine; D004247:DNA