DNA sequences homologous to long double-stranded RNA. Transcription of intracisternal A-particle genes and major long repeat of the mouse genome

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

How a more plastic chromatin state is maintained and reversed during development is unknown. Heterochromatin-mediated silencing of repetitive elements occurs in differentiated cells. Here, we used repetitive elements, including retrotransposons, as model loci to address how and when heterochromatin forms during development. RNA sequencing throughout early mouse embryogenesis revealed that repetitive-element expression is dynamic and stage specific, with most repetitive elements becoming repressed before implantation. We show that LINE-1 and IAP retrotransposons become reactivated from both parental genomes after fertilization. Chromatin immunoprecipitation for H3K4me3 and H3K9me3 in 2- and 8-cell embryos indicates that their developmental silencing follows loss of activating marks rather than acquisition of conventional heterochromatic marks. Furthermore, short LINE-1 RNAs regulate LINE-1 transcription in vivo. Our data indicate that reprogramming after mammalian fertilization comprises a robust transcriptional activation of retrotransposons and that repetitive elements are initially regulated through RNA.

The potential regulation of L1 mobility by RNA interference

The hypothesis that RNA interference constrains L1 mobility seems inherently reasonable: L1 mobility can be dangerous and L1 RNA, the presumed target of RNAi, serves as a critical retrotransposition intermediate. Despite its plausibility, proof for this hypothesis has been difficult to obtain. Studies attempting to link the L1 retrotransposition frequency to alterations in RNAi activity have been hampered by the long times required to measure retrotransposition frequency, the pleiotropic and toxic effects of altering RNAi over similar time periods, and the possibility that other cellular machinery may contribute to the regulation of L1s. Another problem is that the commonly used L1 reporter cassette may serve as a substrate for RNAi. Here we review the L1-RNAi hypothesis and describe a genetic assay with a modified reporter cassette that detects approximately 4 times more L1 insertions than the conventional retrotransposition assay.

RNA silencing in mammalian oocytes and early embryos

RNA silencing is a common term for homology-dependent silencing phenomena found in the majority of eukaryotic species. RNA silencing pathways share several conserved components. The common denominator of these pathways is the presence of specific, short (21-25 nt) RNA molecules generated from different double-stranded RNA substrates by a specific RNase III activity. Short RNA molecules serve as a template for sequence-specific effects including transcriptional silencing, mRNA degradation, and inhibition of translation. This review will discuss possible roles of RNA silencing pathways in mouse oocytes and early embryos as well as the use of RNA silencing for experimental inhibition of gene expression in this model system.

Abundant transcripts from retrotransposons are unstable in fully grown mouse oocytes

One physiological function proposed for RNA interference (RNAi) is to constrain expression of repetitive elements and thereby reduce the incidence of retrotransposition. Consistent with this model is that inhibiting the RNAi pathway results in an increase in expression of repetitive elements in preimplantation mouse embryos. Mouse oocytes are essentially transcriptionally quiescent providing a unique opportunity to assess the stability of repetitive element-derived transcripts in these cells. We compared the transcriptome of freshly isolated fully grown germinal vesicle (GV)-intact oocytes to that of oocytes in which meiotic maturation in vitro was inhibited for 48 h by milrinone. Consistent with the aforementioned function for RNAi is that the abundance of only a relatively small number of transcripts decreased in the cultured oocytes, when compared to changes that occur during maturation or following fertilization, and of those, several belonged to mobile elements.

Lack of homologous sequence-specific DNA methylation in response to stable dsRNA expression in mouse oocytes

Double-stranded RNA (dsRNA) induces sequence-specific mRNA degradation in most eukaryotic organisms via a conserved pathway known as RNA interference (RNAi). Post-transcriptional gene silencing by RNAi is also connected with transcriptional silencing of cognate sequences. In plants, this transcriptional silencing is associated with sequence-specific DNA methylation. To address whether this mechanism operates in mammalian cells, we used bisulfite sequencing to analyze DNA in mouse oocytes constitutively expressing long dsRNA against the Mos gene. Our data show that long dsRNA induces efficient Mos mRNA knockdown but not CpG and non-CpG DNA methylation of the endogenous Mos sequence in oocytes and early embryos. These data demonstrate that dsRNA does not directly induce DNA methylation in the trans form of this sequence in these mammalian cells.

RNAi and expression of retrotransposons MuERV-L and IAP in preimplantation mouse embryos

Both murine endogenous retrovirus-L (MuERV-L) and intracisternal A particle (IAP), two autonomous long terminal repeat (LTR) retrotransposons, are activated during genome activation in the preimplantation mouse embryo, and both sense and antisense transcripts are detected in 2-cell and 8-cell stage embryos. Because RNA interference (RNAi) functions in the preimplantation mouse embryo, we analyzed the relationship between RNAi and MuERV-L and IAP expression by inhibiting RNAi and measuring relative changes of the levels of these transcripts. We inhibited the initial step in the RNAi pathway by injecting 1-cell embryos with mDicer siRNA or long mDicer dsRNA and analyzed MuERV-L and IAP expression at the 8-cell stage. This approach resulted in the targeted destruction of mDicer mRNA, but not Hdac1 mRNA, inhibited the RNAi pathway, and resulted in a 50% increase in IAP and MuERV-L transcript abundance. These results suggest that RNAi constrains expression of repetitive parasitic sequences in preimplantation embryos, and thereby contributes to preserving genomic integrity at a stage of development when the organism consists of only a few cells.

Transgenic RNAi in mouse oocytes: a simple and fast approach to study gene function

Double-strand RNA (dsRNA)-mediated posttranscriptional gene silencing, also known as RNA interference (RNAi), is a powerful tool to inhibit gene expression in several experimental model systems, including Arabidopsis, Caenorhabditis, and Drosophila. We previously described that the microinjection of Mos dsRNA into fully grown mouse oocytes results in the specific degradation of Mos mRNA in a time- and concentration-dependent manner. We report here a transgenic RNAi approach that is suitable to study gene function during mouse oocyte development and differentiation. The oocyte-specific Zp3 promoter was used to drive the expression of a long hairpin dsRNA ( approximately 500 bp) targeting Mos mRNA. Transgenic founder animals appeared healthy, but while males were fertile, females were not, in accordance with the known Mos null phenotype. The amount of Mos mRNA in the transgenic F(1) females was reduced by >90%, whereas there was no decrease in the nontargeted tissue plasminogen activator (Plat) mRNA. Moreover, the maturation-associated increase in mitogen-activated protein (MAP) kinase activity was not observed, and the metaphase II eggs underwent spontaneous parthenogenetic activation, thus recapitulating the Mos null phenotype. This approach provides a powerful method to study the functions of any oocyte-synthesized gene during oocyte development and early embryogenesis.

The most abundant nascent poly(A) + RNAs are transcribed by RNA polymerase III in murine tumor cells

Twelve to twenty percent of newly synthesized poly(A) + RNA is transcribed by RNA polymerase III in Ehrlich ascites carcinoma and P3O1 plasmocytoma mouse tumors. Most of this RNA designated as pol IIIpoly(A) + RNA has a size of 160 to 800 nucleotides with a maximum of distribution of ca. 300 nucleotides. Pol IIIpoly(A) + RNA fraction consists of two major classes of molecules corresponding to previously described B1 RNA and B2 RNA with the ratio of 1:4 to 2:3. All B2 RNAs present in poly(A) + fraction contain a long poly(A) segments at the 3' ends. Thus, RNA polymerase III transcripts can be polyadenylated. Several transcripts that hybridize with B2 probe were also observed in poly(A)- RNA. The major components consist of 180, 160, 120 and 95 nucleotides. The 180-nucleotide B2 RNA seems to be a primary transcript from B2 repeat. We suggest that other B2 RNAs are transcribed from truncated copies of B2 element.