Small RNAs in early mammalian development: from gametes to gastrulation

Abstract

Small non-coding RNAs, including microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), play essential roles in mammalian development. The function and timing of expression of these three classes of small RNAs differ greatly. piRNAs are expressed and play a crucial role during male gametogenesis, whereas endo-siRNAs are essential for oocyte meiosis. By contrast, miRNAs are ubiquitously expressed in somatic tissues and function throughout post-implantation development. Surprisingly, however, miRNAs are non-essential during pre-implantation embryonic development and their function is suppressed during oocyte meiosis. Here, we review the roles of small non-coding RNAs during the early stages of mammalian development, from gamete maturation through to gastrulation.

Fig. 1.

Biogenesis of microRNAs (miRNAs), endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs). (A) Canonical miRNAs are processed from long primary miRNAs (pri-miRNAs) into short hairpin precursor miRNAs (pre-miRNAs) by the microprocessor, a complex consisting of the RNA binding protein Dgcr8 and the RNase III enzyme Drosha. By contrast, non-canonical miRNAs are transcribed directly as short hairpins (shRNAs) or derive from introns that can refold into shRNAs (mirtrons). (B) Precursors of endo-siRNAs are derived from long stem-loop structures (inverted repeat), opposing strand transcription (cis endo-siRNAs), or gene-pseudogene pairs (trans endo-siRNAs). Both miRNAs and endo-siRNAs are then processed by the RNase III enzyme Dicer to produce double-stranded RNAs of ~21 nucleotides. (C) piRNAs are processed from single-stranded RNA precursors that are often encoded by intergenic repetitive elements or transposons. The mechanisms that drive piRNA biogenesis are not well understood, although a ‘ping-pong mechanism’ has been described for a subset of piRNAs. In this model, Mili cleaves the primary piRNA, which is subsequently recognized by Miwi2. Miwi2 cleaves the other strand of the precursor that can then bind to Mili, thus forming a positive amplification loop. (D) Following their processing, miRNAs and endo-siRNAs are assembled into ribonucleoprotein (RNP) complexes called RNA-induced silencing complexes (RISCs). The key components of RISCs are proteins of the Argonaute (Ago) family. In mammals, four Ago proteins (Ago 1-4) function in miRNA repression but only Ago2 functions in siRNA repression. The fate of piRNAs is unknown. On the DNA, blue represents the positive strand and red represents the negative strand.

Fig. 2.

Small RNA functions during germ cell and early embryonic development. Piwi-interacting RNAs (piRNAs) and microRNAs (miRNAs) are essential in the developing male germline, whereas endogenous small interfering RNAs (endo-siRNAs) play their most crucial role in oocyte maturation. There is a transition from endo-siRNAs or piRNAs to miRNAs during pre-implantation development. PGCs, primordial germ cells.

Fig. 3.

Small RNA functions in stem cells derived from the mouse blastocyst. By the time of implantation, the mammalian blastocyst has developed three different cell lineages: trophectoderm, primitive endoderm and epiblast (shown on left). Three distinct self-renewing cell lines can be derived from these lineages: trophoblast stem (TS) cells, extra-embryonic endoderm (XEN) cells and embryonic stem (ES) cells. Studies of stem cell lines lacking either Dgcr8 or Dicer provide insights into small RNA-mediated regulation of stem cell maintenance, proliferation and differentiation (right).

Fig. 4.

The opposing roles of ESCC and Let-7 microRNAs (miRNAs) in the switch between self-renewal and differentiation. In mouse ES cells (left panel), ESCC miRNAs (green) and stemness factors are highly expressed. ESCC miRNAs are regulated by the core ES cell transcription factors such as Oct4, Sox2, Nanog, Tcf3 and Myc. Upon differentiation (right panel), the expression of Let-7 miRNAs (red) increases and helps to repress stemness factors such as Lin28, Myc and Sall4.