Small noncoding RNAs (ncRNAs) are regulatory elements of gene expression in all cell types and tissues. An ever-increasing number of studies have implicated ncRNAs in differentiation and developmental processes. In mammals, as a consequence of fertilization, the content of ncRNAs in the zygote is mostly the result of the maternal material included on oocytes and the potential sperm-borne paternal contributions. The genetic identity program of any individual is the reprogramming of each parental contribution to the zygotic genome activation. In mouse, this activation occurs at 2-cell stage. In this program of early development the small ncRNAs can play important roles. Here, we describe protocols for collection of oocytes, spermatozoa, and zygotes in mouse, followed by RNA purification to analyze the different types of small ncRNA by next-generation sequencing approaches (NGS). Bioinformatics protocols also describe the methodology able to characterize microRNAs (miRNAs) as the most well-known and widespread regulatory small ncRNA. The comparative analysis allows identifying the changes and background previous to zygotic genome activation.
Keywords: NGS; Oocyte; Small noncoding RNAs; Spermatozoa; Zygote; miRNAs.