Identification, characterization and metagenome analysis of oocyte-specific genes organized in clusters in the mouse genome

Abstract

Background: Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the mouse, we have used an in silico subtraction methodology, and we have focused our attention on genes that are organized in genomic clusters.

Results: In the present work, five clusters have been studied: a cluster of thirteen genes characterized by an F-box domain localized on chromosome 9, a cluster of six genes related to T-cell leukaemia/lymphoma protein 1 (Tcl1) on chromosome 12, a cluster composed of a SPErm-associated glutamate (E)-Rich (Speer) protein expressed in the oocyte in the vicinity of four unknown genes specifically expressed in the testis on chromosome 14, a cluster composed of the oocyte secreted protein-1 (Oosp-1) gene and two Oosp-related genes on chromosome 19, all three being characterized by a partial N-terminal zona pellucida-like domain, and another small cluster of two genes on chromosome 19 as well, composed of a TWIK-Related spinal cord K+ channel encoding-gene, and an unknown gene predicted in silico to be testis-specific. The specificity of expression was confirmed by RT-PCR and in situ hybridization for eight and five of them, respectively. Finally, we showed by comparing all of the isolated and clustered oocyte-specific genes identified so far in the mouse genome, that the oocyte-specific clusters are significantly closer to telomeres than isolated oocyte-specific genes are.

Conclusion: We have studied five clusters of genes specifically expressed in female, some of them being also expressed in male germ-cells. Moreover, contrarily to non-clustered oocyte-specific genes, those that are organized in clusters tend to map near chromosome ends, suggesting that this specific near-telomere position of oocyte-clusters in rodents could constitute an evolutionary advantage. Understanding the biological benefits of such an organization as well as the mechanisms leading to a specific oocyte expression in these clusters now requires further investigation.

Figure 1

Localization of germ-cell-specific cluster in mouse chromosome 9, 12, 14 and 19 [9]. The presence of mRNAs or ESTs of these different genes in male and female germ cells was assessed by experimental (RT-PCR, Southern blot and in situ hybridization) and/or in silico methodologies as described in Methods. O stands for Ovary/Egg; T stands for Testis.

Figure 2

Alignment of Oosp protein sequence with the N-terminal part of the ZP domain (150 amino acids) of ZP3. Identities and similarities are shown with black boxes and black frames, respectively. An hypothetical disulfide bond is suspected between Cys78 and Cys98 according to experimental data obtained on the corresponding Cys61 and Cys81 of ZP3 [11].

Figure 3

Expression analysis of FBXO12B, FBXO12D, Tcl1b3, Tcl1b4, Tcl1, SpeerA, AK076711, Oosp3 and actin by RT-PCR in mouse tissues. Except for actin, total RNA from different tissues were subjected to Southern blot analysis of the RT-PCR products as described in Methods.

Figure 4

Localization of SpeerA, FBXO12B, FBXO12D, Tcl1 and Oosp3 mRNAs by in situ hybridization. Black arrows point: oocytes; gc: granulosa cells