Wednesday, July 30, 2008

Gene families and spermatogenesis

I completed my PhD project at the Department of Growth and Reproduction, Righospitalet, which was lead by Professor Niels Erik Skakkebaek. Senior Scientist Henrik Leffers was my everyday supervisor, however, since Henrik was a molecular biologist, computational sparring was introduced in the form of Niels Larsen, who at the time was Software Development Leader at Integrated Genomics in Chicago. I visited Niels in Chicago for three months, where I learned to write production quality code. For computational sparring back in Denmark, Professor Soeren Brunak from Denmarks Technical University was affilated as my co-supervisor.

The title of my Ph.D. thesis was "Bioinformatic Analysis of Gene Families in Mouse and Human Spermatogenesis". Initially we determined gene expression profiles during the development of spermatogenesis in newborn mice. I wrote a data integration system to incorporate data from differnt sources including Differential Display, DNA array, and in situ hybridization data. We were able to show that the first wave of spermatogenesis was constituted of three major clusters of expression originating from Sertoli cells, Pachytene germ cells, and spermatids - and that all genes expressed could be associated to one or more of these clusters. This made it possible to determine the germ cell composition of the growing testis from total RNA and work is still ongoing to utilize this to located disrupted germ cell populations that may be caused by hormone like agents such as phthalates, parabenes, and pesticides - leading to impaired testicular function.

During this process we came across a novel gene family, where the Human orthologs showed a distinct genomic location pattern: the members of the gene family was positioned in the arms of direct and inverted segmental duplications. A sensitive psiBLAST-like approach revealed that these genes via their promoter sequence were in fact related to four known human gene families with similar genomic location patterns. Thus, all these genes could be involved in infertility since inverted segmental duplications are subject to non-homologous recombination with consequent gene loss - as described for the well studied AZF gene family. Also, the complex genomic patterns might lead to overexpression of these genes resulting in cancer. Below is a dotplot and a line plot showing a 150Kbp inverted segmental duplications - or palindrome - that harbors the VCY genes.

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