Pseudogenes populate the mammalian genome as remnants of artefactual incorporation of coding messenger RNAs into transposon pathways 1 . Here we show that a subset of pseudogenes generates endogenous small interfering RNAs (endo-siRNAs) in mouse oocytes. These endo-siRNAs are often processed from double-stranded RNAs formed by hybridization of spliced transcripts from proteincoding genes to antisense transcripts from homologous pseudogenes. An inverted repeat pseudogene can also generate abundant small RNAs directly. A second class of endo-siRNAs may enforce repression of mobile genetic elements, acting together with Piwi-interacting RNAs. Loss of Dicer, a protein integral to small RNA production, increases expression of endo-siRNA targets, demonstrating their regulatory activity. Our findings indicate a function for pseudogenes in regulating gene expression by means of the RNA interference pathway and may, in part, explain the evolutionary pressure to conserve argonaute-mediated catalysis in mammals.Small-RNA-directed gene silencing pathways have been adapted to accept numerous inputs and to act on many types of downstream targets. In few places is this more apparent than in animal germ lines where two classes of small RNAs-microRNAs (miRNAs) and Piwiinteracting RNAs (piRNAs)-with distinct biogenesis mechanisms and biological functions have been reported. Although miRNAs, as a group, are ubiquitously expressed, piRNAs have thus far been found only in germ cells and in a few gonadal somatic cells types 2 . piRNAs repress the activity of mobile genetic elements, forming a small RNA-based, innate immune system with both genetically encoded and adaptive components2 -9.In mice, a homozygous mutation in any single Piwi family member causes male sterility accompanied by gonadal hypotrophy 5 , 10 , 11. In Mili and Miwi2 mutants, meiosis is not completed and germ cells are progressively lost5. This correlates with an activation of transposons, particularly the non-long terminal repeat (LTR) retrotransposon, L1 (refs 5 , 12).

Transcription of endogenous genes in preimplantation 1- and 2-cell mouse embryos was determined by monitoring the incorporation of BrUTP by plasma membrane-permeabilized embryos. Incorporation is observed starting by mid-S phase in the 1-cell embryo and increases progressively; the amount of incorporation by the 1-cell embryo in G2 is about 20% that of the 2-cell embryo in G2. Incorporation by the male pronucleus is always about four to five times greater than that of the female pronucleus. Nevertheless, the amount of incorporation by the female pronucleus present in parthogenetically activated eggs is similar to the total amount of incorporation in inseminated eggs, i.e., the transcriptional capacity of the female pronucleus is not inherently less than that of the male pronucleus. Inhibiting the first round of DNA replication does not prevent the initiation of transcription in the 1-cell embryo, but does inhibit the extent of BrUTP incorporation by 35%. The transcriptional machinery of the 1-cell embryo appears to be rate-limiting, since the total amount of BrUTP incorporation by parthenogenetically activated and dispermic eggs is similar to that in monospermic eggs; trispermic eggs incorporate BrUTP to only about 60% the level of monospermic eggs. A transcriptionally repressive state may start to develop in the 2-cell embryo, since inhibiting the second round of DNA replication results in an 50% increase in BrUTP incorporation. Trapoxin treatment, which induces histone hyperacetylation, enhances incorporation by 2-cell embryos 1.8-fold and suggests that histone hyperacetylation can relieve this repression.

Dicer is an essential component of RNA interference (RNAi) pathways, which have broad functions in gene regulation and genome organization. Probing the consequences of tissue-restricted Dicer loss in mice indicates a critical role for Dicer during meiosis in the female germline. Mouse oocytes lacking Dicer arrest in meiosis I with multiple disorganized spindles and severe chromosome congression defects. Oogenesis and early development are times of significant post-transcriptional regulation, with controlled mRNA storage, translation, and degradation. Our results suggest that Dicer is essential for turnover of a substantial subset of maternal transcripts that are normally lost during oocyte maturation. Furthermore, we find evidence that transposon-derived sequence elements may contribute to the metabolism of maternal transcripts through a Dicer-dependent pathway. Our studies identify Dicer as central to a regulatory network that controls oocyte gene expression programs and that promotes genomic integrity in a cell type notoriously susceptible to aneuploidy.

Summary Aneuploidy arising early in development is the leading genetic cause of birth defects and developmental disabilities in humans. Most errors in chromosome number originate from the egg, and maternal age is well established as the key risk factor. Although the importance of this problem for reproductive health is widely recognized, the underlying molecular basis for age-related aneuploidy in female meiosis is unknown. Here we show that weakened chromosome cohesion is a leading cause of aneuploidy in oocytes in a natural aging mouse model. We find that sister kinetochores are farther apart at both Metaphase I and II, indicating reduced centromere cohesion. Moreover, levels of the meiotic cohesin protein REC8 are severely reduced on chromosomes in oocytes from old mice. To test whether cohesion defects lead to the observed aneuploidies, we monitored chromosome segregation dynamics at Anaphase I in live oocytes and counted chromosomes in the resulting Metaphase II eggs. About 90% of age-related aneuploidies are best explained by weakened centromere cohesion. Together, these results demonstrate that the maternal age-associated increase in aneuploidy is often due to a failure to effectively replace cohesin proteins that are lost from chromosomes during aging.

The H19 gene is imprinted with preferential expression from the maternal allele. The putative imprinting control region for this locus is hypermethylated on the repressed paternal allele. Although maternal-specific expression of H19 is observed in mouse blastocysts that develop in vivo, biallelic expression has been documented in embryos and embryonic stem cells experimentally manipulated by in vitro culture conditions. In this study the effect of culture on imprinted H19 expression and methylation was determined. After culture of 2-cell embryos to the blastocyst stage in Whitten's medium, the normally silent paternal H19 allele was aberrantly expressed, whereas little paternal expression was observed following culture in KSOM containing amino acids (KSOM+AA). Analysis of the methylation status of a CpG dinucleotide located in the upstream imprinting control region revealed a loss in methylation in embryos cultured in Whitten's medium but not in embryos cultured in KSOM+AA. Thus, H19 expression and methylation were adversely affected by culture in Whitten's medium, while the response of H19 to culture in KSOM+AA approximated more closely the in vivo situation. It is unlikely that biallelic expression of H19 following culture in Whitten's medium is a generalized effect of lower methylation levels, since the amount of DNA methyltransferase activity and the spatial distribution of Dnmt1 protein were similar in in vivo-derived and cultured embryos. Moreover, imprinted expression of Snrpn was maintained following culture in either medium, indicating that not all imprinted genes are under the same stringent imprinting controls. The finding that culture conditions can dramatically, but selectively, affect the expression of imprinted genes provides a model system for further study of the linkage between DNA methylation and gene expression.