Identification of germ cell-specific genes in mammalian meiotic prophase

Abstract

BackgroundMammalian 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.ResultsWe 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.ConclusionsWe 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.

Regulation of meiotic gene expression in plants

“…The pre-meiotic wave targets transposable elements. A later wave occurs in pachytene and has a less-understood function ( Li et al, 2013 ).…”

Hybrid Method Based on Information Gain and Support Vector Machine for Gene Selection in Cancer Classification

“…For instance, IG, also known as the Kullback–Leibler divergence, can analyze the correlation between attributes and classes. The wrapper methods identify a powerful gene subset according to the evaluation of a classifier, such as genetic algorithm [8] , decision tree [9] , and support vector machine (SVM) [10] . Filter methods generally run faster; however, they are unable to analyze the relationships among genes.…”

In vitromaturation alters gene expression in bovine oocytes

“…Cumulus–oocyte complexes (COCs) are dependent on adequate gene expression to initiate and to undergo oocyte maturation (meiotic progression) and embryonic development (Labrecque et al , 2013; Li et al , 2013). The mechanisms by which oocytes acquire competence to develop up to the blastocyst stage are still not fully understood.…”