Comparative and functional genomic analysis of a gene dense region at chromosome 7q22

Date

2008-04-10T06:01:39Z

Authors

Wilson, Michael Davies.

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Abstract

Genomic sequencing, comparative genomic analysis and mouse transgenics were used to investigate two regions of human chromosome 7 that are associated with chromosomal loss, duplication and disease. Williams-Beuren syndrome (WBS) is a complex neuro-developmental disorder arising from a microdeletion at chromosome band 7q11.23 that results in a hemizygous condition for a number of genes. Within this region we completely characterized 200 kilobases (kb) of genomic DNA sequence containing the genes LIMKI, WBSCRl and RFC2. The orthologous region on mouse chromosome 5 was sequenced and compared to 7q11.23. A previously unidentified gene, ( WBSCRS), was found in the region commonly deleted in WBS patients. Expression patterns and alternative splice variants of WBSCRS and WBSCRl were determined. Chromosome 7q22 has been the focus of many cytogenetic and molecular studies aimed at delineating regions commonly deleted in myeloid leukemias and myelodysplastic syndromes. We have compared a gene dense, G-C rich sub-region of 7q22 to the orthologous region on mouse chromosome 5. A physical map of 640 kb of genomic DNA from mouse chromosome 5 was derived from a series of overlapping bacterial artificial chromosomes (BAC). A 296 kb segment from the physical map, spanning from acetylcholine esterase (Ache) to transferrin receptor 2 (Tfr2), was compared to 267 kb of human sequence. A conserved linkage of twelve genes including arsenite resistance 2 (Ars2) and zonadhesin (Zan) was identified. The paired immunoglobulin-like receptor locus (PILR) at 7q22 shares homology with 7q11.23 and contains the inhibiting PILRA and activating PILRB receptors. These receptors are expressed in myeloid cells and have been established as novel regulators of innate immunity. Expression analysis of the human PILRB gene revealed it has been dramatically affected by the insertion of a segmental duplication that is paralogous to the sequence flanking the WBS critical region. Sequencing and analysis of the orthologous region in the mouse genome revealed a previously unreported paired immunoglobulin like receptor gene (Pilrb2). An evolutionary analysis of the PILR locus in six mammalian genomes revealed that this locus is dynamically evolving by means of gene duplication, insertion, mutation and conversion. Ars2 is a novel gene that is present in a diverse number of eukaryotic organisms and is essential for development in Danio rerio and Arabidopsis thaliana. To address the role of Ars2 in mammals, we characterized its expression in mouse and human tissues and implemented a gene targeting strategy to create a null allele in the mouse genome. Ars2 was found to be transcribed throughout development and was expressed ubiquitously in mouse and human tissues. The Ars2 protein localized to the nucleus. Ars2 null mice have an early embryonic lethal phenotype establishing that Ars2 is necessary for the development of diverse multi-cellular organisms. Zonadhesin (ZAN) is the only mammalian sperm protein that has been demonstrated to bind to intact zona pellucida of the egg in a species-specific manner. We investigated the in vivo role of zonadhesin by creating a mutant mouse line that lacks zonadhesin. Zonadhesin null mice show no obvious phenotype and were determined, through natural mating, to be equally as fertile as their wildtype littermates. A web-based software tool called Laj (Local alignments with java) was developed to display comparative genomic sequence data in an intuitive and informative way. All of our genomic sequence comparisons can be viewed at http:Nweb.uvic.cal-bioweb/laj.html. Laj is available at http://bio.cse.psu.edu/.

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