Multiple MSP pseudogenes in a local repeat cluster on 1p36.2: An expandinggenomic graveyard?

Chromosomal region 1p36.2 harbors an intriguing gene cluster of about 1 Rib . In addition to normal high-copy-number repeats, this cluster consists ent irely of locally repeated sequences among which there are tRNA and small nu clear RNA (snRNA) genes. In 23 PACs and YACs from the 1p36.2 cluster, we id entified eight different copies of a sequence with about 97% homology to th e macrophage stimulating protein (MSP) gene located on chromosomal band 3p2 1. These MSP-like (MSPL) sequences on 1p36.2 are scattered over the repeat region. Nucleotide substitutions and single nucleotide deletions in exons o f all identified MSPL genes on 1p36.2 mark them as pseudogenes. We construc ted a phylogenetic tree of these sequences with their most likely order of origin in evolution. MSP from 3p21 could be identified as the ancestral seq uence, a copy of which was captured into the cluster of tRNA and snRNA gene s on 1p36.2 about 6 million years (MY) ago. MSP subsequently coamplified wi th the other sequences in the cluster. Analysis of the DNA of 18 individual s shows that the MSPL copy number is polymorphic, with a range of four to s even or more copies per haploid genome. Analysis of corresponding clusters in macaque chromosomes indicated an age for the tRNA/snRNA cluster of at le ast 30 MY. The MSPL sequence thus functions as a probe for the more recent primate evolution of this cluster and suggests a continuation of its unusua l activity over the last 6 Rn. (C) 1999 Academic Press.