Non-germ Line Restoration of Genomic Imprinting for a Small Subset of Imprinted Genes in Ubiquitin-like PHD and RING Finger Domain-Containing 1 (Uhrf1) Null Mouse Embryonic Stem Cells

Analysis of the pluripotent and germline marker gene expression, and the state of X chromosome reactivation of primordial germ cells in pig gonads

The gonadal primordial germ cells (PGCs) possess a unique state of pluripotency and X chromosome activity. However, extensive evidence indicates developmental variability in PGCs across different species. This study aims to evaluate the pluripotency status, specific gene expression patterns, and X chromosome reactivation (XCR) of pig gonadal PGCs. Single-cell RNA-seq revealed significant heterogeneity within the population of gonadal PGCs. Notably, these PGCs expressed high levels of pluripotency markers OCT4, PRDM14, and NANOG, while lacking SOX2 expression. Through the screening of marker genes and subsequent protein expression validation, we identified growth differentiation factor 3 (GDF3) as a specific surface marker for pig gonadal PGCs, facilitating their efficient purification for further study. Furthermore, analysis of gonadal PGCs demonstrated complete XCR. This was evidenced by the absence of repressive histone modifications (H3K27me3, H3K9me3, and H2AK119ub), the lack of X inactive specific transcript (XIST) RNA FISH signal, and the doubled expression of X-linked genes. Additionally, these PGCs expressed high levels of genes associated with epigenetic modification, chromatin remodeling, and XIST-associated RNA-binding. These factors likely play a crucial role in regulating pluripotency and X chromosome activity. In summary, this study reveals the heterogeneity in pig gonadal PGCs and identifies GDF3 as a specific surface marker. It also elucidates the expression patterns of pluripotency transcription factors and the events involved in XCR.

Association of UHRF1 gene polymorphisms with oligospermia in Chinese males

BACKGROUND

UHRF1 plays an important role in maintaining DNA methylation patterns during spermatogenesis. This study was performed to evaluate the association between UHRF1 gene variations and infertility in males with oligozoospermia in a Chinese population.

METHODS

In this case-control study of 735 Chinese men, single-nucleotide polymorphism (SNP) genotypes and alleles in the UHRF1 gene were assessed by direct sequencing. The effects of the mutations on UHRF1 transcription were investigated using a dual-luciferase reporter gene assay.

RESULTS

We identified 24 SNPs, including nine SNPs in the promoter region, three in the 5' untranslated region, five in introns, and seven in exons. Interestingly, the genotype frequencies of SNP rs2656927 (P = 0.014) and rs8103849 (P < 0.001) significantly differed between men with oligozoospermia in case group 1 and normozoospermic men. Moreover, four variants (three were novel) were detected only in the patient group, with two in introns and the others in the promoter region. The results of the luciferase assay showed that the -1615C>T-C and -1562A>G-A alleles increased luciferase activity compared with the -1615C>T-T and -1562A>G-G alleles.

CONCLUSIONS

We detected two SNPs in the UHRF1 gene showing a significant difference between the case and control groups. Two screened SNPs affected UHRF1 promoter activity, improving the understanding of the pathophysiology of oligozoospermia.

Imprint stability and plasticity during development

There have been a number of recent insights in the area of genomic imprinting, the phenomenon whereby one of two autosomal alleles is selected for expression based on the parent of origin. This is due in part to a proliferation of new techniques for interrogating the genome that are leading researchers working on organisms other than mouse and human, where imprinting has been most studied, to become interested in looking for potential imprinting effects. Here, we recap what is known about the importance of imprints for growth and body size, as well as the main types of locus control. Interestingly, work from a number of labs has now shown that maintenance of the imprint post implantation appears to be a more crucial step than previously appreciated. We ask whether imprints can be reprogrammed somatically, how many loci there are and how conserved imprinted regions are in other species. Finally, we survey some of the methods available for examining DNA methylation genome-wide and look to the future of this burgeoning field.

Target specificity of mammalian DNA methylation and demethylation machinery

We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.

Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling

Complex cytoplasmic nucleotide-sensing mechanisms can recognize foreign DNA based on a lack of methylation and initiate an immune response to clear the infection. Zebrafish embryos with global DNA hypomethylation caused by mutations in the ubiquitin-like with PHD and ring finger domains 1 (uhrf1) or DNA methyltransferase 1 (dnmt1) genes exhibit a robust interferon induction characteristic of the first line of defense against viral infection. We found that this interferon induction occurred in non-immune cells and examined whether intracellular viral sensing pathways in these cells were the trigger. RNA-seq analysis of uhrf1 and dnmt1 mutants revealed widespread induction of Class I retrotransposons and activation of cytoplasmic DNA viral sensors. Attenuating Sting, phosphorylated Tbk1 and, importantly, blocking reverse transcriptase activity suppressed the expression of interferon genes in uhrf1 mutants. Thus, activation of transposons in cells with global DNA hypomethylation mimics a viral infection by activating cytoplasmic DNA sensors. This suggests that antiviral pathways serve as surveillance of cells that have derepressed intragenomic parasites due to DNA hypomethylation.

Widespread recovery of methylation at gametic imprints in hypomethylated mouse stem cells following rescue with DNMT3A2

BACKGROUND

Imprinted loci are paradigms of epigenetic regulation and are associated with a number of genetic disorders in human. A key characteristic of imprints is the presence of a gametic differentially methylated region (gDMR). Previous studies have indicated that DNA methylation lost from gDMRs could not be restored by DNMT1, or the de novo enzymes DNMT3A or 3B in stem cells, indicating that imprinted regions must instead undergo passage through the germline for reprogramming. However, previous studies were non-quantitative, were unclear on the requirement for DNMT3A/B and showed some inconsistencies. In addition, new putative gDMR has recently been described, along with an improved delineation of the existing gDMR locations. We therefore aimed to re-examine the dependence of methylation at gDMRs on the activities of the methyltransferases in mouse embryonic stem cells (ESCs).

RESULTS

We examined the most complete current set of imprinted gDMRs that could be assessed using quantitative pyrosequencing assays in two types of ESCs: those lacking DNMT1 (1KO) and cells lacking a combination of DNMT3A and DNMT3B (3abKO). We further verified results using clonal analysis and combined bisulfite and restriction analysis. Our results showed that loss of methylation was approximately equivalent in both cell types. 1KO cells rescued with a cDNA-expressing DNMT1 could not restore methylation at the imprinted gDMRs, confirming some previous observations. However, nearly all gDMRs were remethylated in 3abKO cells rescued with a DNMT3A2 expression construct (3abKO + 3a2). Transcriptional activity at the H19/Igf2 locus also tracked with the methylation pattern, confirming functional reprogramming in the latter.

CONCLUSIONS

These results suggested (1) a vital role for DNMT3A/B in methylation maintenance at imprints, (2) that loss of DNMT1 and DNMT3A/B had equivalent effects, (3) that rescue with DNMT3A2 can restore imprints in these cells. This may provide a useful system in which to explore factors influencing imprint reprogramming.