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Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. Here, we undertake joint profiling of the transcriptome and DNA methylome of individual oocytes from reproductively young and old mice undergoing natural ovulation. We find reduced complexity as well as increased variance in the transcriptome of oocytes from aged females. This transcriptome heterogeneity is reflected in the identification of discrete sub‐populations. Oocytes with a transcriptome characteristic of immature chromatin configuration (NSN) clustered into two groups: one with reduced developmental competence, as indicated by lower expression of maternal effect genes, and one with a young‐like transcriptome. Oocytes from older females had on average reduced CpG methylation, but the characteristic bimodal methylation landscape of the oocyte was preserved. Germline differentially methylated regions of imprinted genes were appropriately methylated irrespective of age. For the majority of differentially expressed transcripts, the absence of correlated methylation changes suggests a post‐transcriptional basis for most age‐related effects on the transcriptome. However, we did find differences in gene body methylation at which there were corresponding changes in gene expression, indicating age‐related effects on transcription that translate into methylation differences. Interestingly, oocytes varied in expression and methylation of these genes, which could contribute to variable competence of oocytes or penetrance of maternal age‐related phenotypes in offspring., Early embryo development is heavily supported by maternal transcripts and epigenetic states produced in the oocyte. To investigate the effects of age, we compare the transcriptome and methylome of germinal vesicle oocytes from young and old mice using parallel single‐cell RNA sequencing and whole‐genome bisulphite sequencing. We find increased variance in the transcriptome of oocytes from aged females, altered expression of maternal effect genes and differences in gene body methylation at which there were corresponding changes in gene expression.

The GNAS locus on chromosome 20q13.11 is the archetypal complex imprinted locus. It comprises a bewildering array of alternative transcripts determined by differentially imprinted promoters which encode distinct proteins. It also provides the classic example of tissue-specific imprinted gene expression, in which the canonical GNAS transcript coding for Gsalpha is expressed predominantly from the maternal allele in a set of seemingly unrelated tissues. Functionally, this rather obscure imprinting is nevertheless of considerable clinical significance, as it dictates the nature of the disease caused by inactivating mutations in Gsalpha, with end organ hormone resistance specifically on maternal transmission (pseudohypoparathyroidism type 1a, PHP1a). In addition, there is a bona fide imprinting disorder, PHP1b, which is caused specifically by DNA methylation defects in the differentially methylated regions (DMRs) that determine tissue-specific monoallelic expression of GNAS. Although the genetic defect in PHP1a and the disrupted imprinting in PHP1b both essentially result in profound reduction of Gsalpha activity in tissues with monoallelic GNAS expression, and despite a growing awareness of the overlap in these two conditions, there are important pathophysiological differences between the two whose basis is not fully understood. PHP1b is one of the only imprinted gene syndromes in which cis-acting mutations have been discovered that disrupt methylation of germline-derived imprint marks; such imprinting mutations in GNAS are helping to provide important new insights into the mechanisms of imprinting establishment generally.

DNA methylation can be considered a component of epigenetic memory with a critical role during embryo development, and which undergoes dramatic reprogramming after fertilization. Though it has been a focus of research for many years, the reprogramming mechanism is still not fully understood. Recent results suggest that absence of maintenance at DNA replication is a major factor, and that there is an unexpected role for TET3-mediated oxidation of 5mC to 5hmC in guarding against de novo methylation. Base-resolution and genome-wide profiling methods are enabling more comprehensive assessments of the extent to which ART might impair DNA methylation reprogramming, and which sequence elements are most vulnerable. Indeed, as we also review here, studies showing the effect of culture media, ovarian stimulation or embryo transfer on the methylation pattern of embryos emphasize the need to face ART-associated defects and search for strategies to mitigate adverse effects on the health of ART-derived children.

Hepatocyte nuclear factor 4 (HNF-4) is a member of the nuclear-receptor gene superfamily. HNF-4 binds to response elements of several liver-enriched genes and exhibits a restricted pattern of expression, suggesting an important role for HNF-4 in tissue-specific gene regulation. Here, we report the generation of three mutated forms of the HNF-4 protein, their effects on the ability of the protein to transactivate through HNF-4-response elements, and their ability to suppress transactivation by the wild-type protein. Two mutated forms of the HNF-4 protein, one in which the DNA-binding domain has been deleted and another in which the HNF-4 proximal box has been replaced by that of the glucocorticoid receptor, behaved as inhibitors of the wild-type protein. The properties of a carboxy-terminal-deletion mutant allow us to propose a region of HNF-4 involved in transactivation.

A subset of genes in mammals, known as imprinted genes, show a conditional expression strategy in which transcription depends on an allele’s parental origin. Several explanations have been advanced to explain this phenomenon and these, with varying levels of success, predict the functions of imprinted genes. After outlining these explanations, we summarize what is known about human genetic disorders involving abnormal expression of imprinted genes and ask what this can tell us about the evolution of imprinting.