MicroRNAs (miRNAs) are abundant, endogenous, non-coding RNAs of approximately 22 nucleotides (nt) in length (Ambros 2004; Bartel 2004; Bentwich 2005). They can bind target mRNAs and block their expression by inhibiting their translation or targeting the mRNA for degradation (Ambros 2004; Kim and Nam 2006). It is estimated that 1–5% of the genes in the genome encode for miRNAs (Lim et al. 2003), which may regulate up to 30% of all genes (Lewis et al. 2003). The first discovered miRNA was lin-4 (Lee et al. 1993), and the fact that lin-4 does not code for protein did not cause much concern. However, since the discovery of let-7 (Reinhart et al. 2000), thousands of miRNAs have been identified experimentally or computationally from a variety of species.
The pig (Sus scrofa) has tremendous biomedical importance as a model organism because it has closer phylogenic proximity to humans than mouse or other animals. Over the last few years, thousands of miRNAs from various organisms have been discovered. The majority of miRNAs are evolutionarily conserved across species and are important regulators of molecular and cellular processes, such as brain morphogenesis (Giraldez et al. 2005) and cardiomyocyte proliferation/differentiation (Zhao et al. 2005). Additional studies have shown that fat metabolism has a direct relationship with miR-14 (Xu et al. 2003), miR-143 (Esau et al. 2004) and miR-122 (Esau et al. 2006). However, little is known about the miRNA components involved in pig development.
Several research groups had applied a deep sequencing approach to successfully discover 449 new chicken miRNAs (Glazov et al. 2008) and to identify the expression levels of 212 annotated miRNAs in the porcine skeletal muscle (Nielsen et al. 2010). Similarly, a Solexa sequencing approach had been used to identify 113 amphioxus miRNAs genes (Chen et al. 2009); especially, recently researchers had successfully reported 112 conserved and 61 candidate novel porcine miRNAs from 16 different porcine tissues (Xie et al. 2011) and extended the repertoire of pig miRNAome to 867 encoding for 1004 miRNAs, of which 777 are unique (Li et al. 2010). The identification and characterization of miRNAs that are expressed at critical stages of development would provide valuable insight into the roles of miRNAs during organogenesis. Therefore, we used Solexa sequencing to systemically analyse the expression profiles of porcine embryonic miRNAs at E33 (from head and organ regions). This study will enable us to better understand the role and function of miRNAs during pig embryonic development.