Identification of germ cell-specific genes in mammalian meiotic prophase.

BMC Bioinformatics 2013 Feb 27;14:72. Epub 2013 Feb 27.

School of Molecular Biosciences, Washington State University, PO Box 647520, Pullman, WA 99164, USA.

Background: Mammalian germ cells undergo meiosis to produce sperm or eggs, haploid cells that are primed to meet and propagate life. Meiosis is initiated by retinoic acid and meiotic prophase is the first and most complex stage of meiosis when homologous chromosomes pair to exchange genetic information. Errors in meiosis can lead to infertility and birth defects. However, despite the importance of this process, germ cell-specific gene expression patterns during meiosis remain undefined due to difficulty in obtaining pure germ cell samples, especially in females, where prophase occurs in the embryonic ovary. Indeed, mixed signals from both germ cells and somatic cells complicate gonadal transcriptome studies.

Results: We developed a machine-learning method for identifying germ cell-specific patterns of gene expression in microarray data from mammalian gonads, specifically during meiotic initiation and prophase. At 10% recall, the method detected spermatocyte genes and oocyte genes with 90% and 94% precision, respectively. Our method outperformed gonadal expression levels and gonadal expression correlations in predicting germ cell-specific expression. Top-predicted spermatocyte and oocyte genes were both preferentially localized to the X chromosome and significantly enriched for essential genes. Also identified were transcription factors and microRNAs that might regulate germ cell-specific expression. Finally, we experimentally validated Rps6ka3, a top-predicted X-linked spermatocyte gene. Protein localization studies in the mouse testis revealed germ cell-specific expression of RPS6KA3, mainly detected in the cytoplasm of spermatogonia and prophase spermatocytes.

Conclusions: We have demonstrated that, through the use of machine-learning methods, it is possible to detect germ cell-specific expression from gonadal microarray data. Results from this study improve our understanding of the transition from germ cells to meiocytes in the mammalian gonad. Further, this approach is applicable to other tissues for which isolating cell populations remains difficult.

Download full-text PDF

Source
http://dx.doi.org/10.1186/1471-2105-14-72DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3599307PMC
February 2013
15 Reads

Publication Analysis

Top Keywords

germ cell-specific
28
cell-specific expression
16
germ cells
12
germ
10
expression
8
oocyte genes
8
gonadal expression
8
meiotic prophase
8
gene expression
8
microarray data
8
cell-specific
7
meiosis
5
prophase
5
cells
5
genes
5
cell-specific patterns
4
patterns gene
4
expression microarray
4
data mammalian
4
identifying germ
4

Similar Publications