Regassa et al. BMC Genomics 2011, 12:57 http://www.biomedcentral.com/1471-2164/12/57 Background The bi-directional communications between the oocyte and its companion cumulus cells (CCs) is crucial for the development and functions of both cell types [1-3]. This dialogue is vital for the oocyte to acquire meiotic and developmental competence and for proliferation and dif- ferentiation of CCs [1,3-9]. The oocyte regulates prolif- eration [2,10-13], apoptosis [14], luteinization [13,15], metabolism [16] and expansion [17,18] of CCs through oocyte secreted factors (OSFs) such as growth and dif- ferentiation factor 9 (GDF9), bone morphogenetic pro- tein 15 (BMP15) and possibly others. Competent oocytes also influence the expression of cumulus specific biochemical markers that might be crucial for cumulus expansion and thereby achieve maturation and success- ful development [17-19]. CCs play an important role in the utilization of energy substrates by oocyte [20], pre- vent the oocyte from oxidative stress induced apoptosis [21,22] and stimulate glutathione synthesis [23,24] dur- ing in vitro maturation. The ability of the oocyte to form male pronuclei after fertilization strongly depends on the presence of CCs during maturation [25-27] and fertilization [28-30]. Fertilization and development to a healthy blastocyst is limited by the oocyte quality [31] and CCs play a critical role in determining oocyte devel- opmental potential both before and after ovulation [32]. The interaction between cumulus-granulosa cell derived factors such as kit ligand and oocyte secreted GDF9 is essential for oocyte growth [33,34]. This dialogue between the oocyte and CCs is accomplished mainly through the gap junction type of intercellular communication [35] and the presence of this junction supports oocyte competence in vitro [36]. For instance, complete removal of CCs before in vitro maturation or blockage of gap junction inhibits oocyte maturation [37]. Similarly, inhibition of these func- tional coupling using gap junction inhibitors significantly reduces developmental competence [38]. Developmentally competent oocytes are selected based on the number and compactness of the surrounding CCs layers [39,40] as oocytes that fail to expand their CCs can’t ovulate and/or are infertile [41-44]. There is notable species level difference regarding the source and identity of cumulus expansion enabling factor (CEEF). While OSFs, like GDF9 and BMP15 are believed to be CEEF in rat [45], their presence is not mandatory for bovine [46] and porcine [47] CCs expansion in vitro as oocytectomised complexes (CC - OO) expands as equally as the intact ones. High expression of hyaluronan synthase 2 (HAS2), inhibin beta A (INHbA), epidermal growth factor recep- tor (EGFR), geremlin (GREM1), beta cellulin (BTC), cell cycle division 44 (CD44), tumor necrosis alpha induced protein 6 (TNFAIP6) and prostaglandin synthase 2 (PTGS2) have been associated with developmental Page 2 of 20 competence of oocytes and suggested as predictors of embryo quality in women [40] and cow [48]. On the contrary, higher expressions of cysteine proteinases cathepsin B, S, K and Z have been associated with incompetent bovine oocytes [49]. Although studies were conducted to identify molecular biomarkers for developmentally competent bovine oocytes, large scale expression data on oocyte or CCs specific transcripts is still lacking. Removal of oocyte- CCs communication axis during in vitro maturation reduces CCs expansion and thereby affects oocyte devel- opmental competence but the effect of removing this communication axis on their gene expression is poorly understood. Furthermore, genes differentially expressed between germinal vesicle (GV) and metaphase II (MII) stage CCs are not identified and functional changes associated with those differentially expressed genes are not characterized. Identification of transcripts that are exclusively and commonly expressed between the oocyte and its companion CCs and those that are affected when the oocyte and its companion CCs mature in the presence or absence of one or the other would enhance our understanding of the molecules and biological pro- cesses that are involved in oocyte-CCs dialogue and oocyte maturation. Therefore, this study was conducted to 1. Identify transcripts that are co and exclusively expressed between the oocyte and CCs, 2. Enumerate those which are significantly affected when the two cell types mature with or without the other and 3. Identify significantly changed biological processes during the transition of CCs from GV to MII stage. Methods Sample collection Bovine ovaries were collected from local abattoirs and transported to the laboratory within 2-3 hours (hrs) in a thermo flask containing 0.9% physiological saline solu- tion at 39°C. Before aspiration of COCs, the ovaries were washed twice in 70% ethanol. COCs were aspirated from antral follicles having 2-8 mm diameter using 5 ml syringe attached to 18 gauge needle. The aspirated folli- cular fluid was collected in 50 ml sterilized tube at 35°C and allowed to precipitate for 15 min. COCs with evenly granulated cytoplasm surrounded by multiple layers of CCs were picked using glass-pipette and washed three times in drops of modified parker medium (MPM) sup- plemented with 12% estrus cow serum (OCS). In order to increase the homogeneity of the experi- mental samples, COCs were further screened for devel- opmental competence using brilliant cresyl blue (BCB) + staining as described in [50-52]. BCB positive (BCB ) COCs were assigned randomly into the following four experiments. Each experiment had three pools of