A Survey of Imprinted Gene Expression in Mouse Trophoblast Stem Cells

Abstract

Several hundred mammalian genes are expressed preferentially from one parental allele as the result of a process called genomic imprinting. Genomic imprinting is prevalent in extra-embryonic tissue, where it plays an essential role during development. Here, we profiled imprinted gene expression via RNA-Seq in a panel of six mouse trophoblast stem lines, which are ex vivo derivatives of a progenitor population that gives rise to the placental tissue of the mouse. We found evidence of imprinted expression for 48 genes, 31 of which had been described previously as imprinted and 17 of which we suggest as candidate imprinted genes. An equal number of maternally and paternally biased genes were detected. On average, candidate imprinted genes were more lowly expressed and had weaker parent-of-origin biases than known imprinted genes. Several known and candidate imprinted genes showed variability in parent-of-origin expression bias between the six trophoblast stem cell lines. Sixteen of the 48 known and candidate imprinted genes were previously or newly annotated noncoding RNAs and six encoded for a total of 60 annotated microRNAs. Pyrosequencing across our panel of trophoblast stem cell lines returned levels of imprinted expression that were concordant with RNA-Seq measurements for all eight genes examined. Our results solidify trophoblast stem cells as a cell culture-based experimental model to study genomic imprinting, and provide a quantitative foundation upon which to delineate mechanisms by which the process is maintained in the mouse.

Canine MAS1: monoallelic expression is suggestive of an imprinted gene

“…More recently, Calabrese et al . () suggested that Mas1 was a candidate imprinted gene, following detection of parent‐of‐origin biased expression (maternal allele) in trophoblastic stem cells.…”

Using long-read sequencing to detect imprinted DNA methylation

“…Among the 135 genes, 53 corresponded to well-characterised imprinted genes in classic databases (33)(34)(35)(36). A further 17 of these genes, including Fkbp6, Smoc1/2, Gzmc/d/e/f/g, Zdhhc14 and Arid1b have been identified as imprinted in one or several recent studies (12)(13)(14)(15). The remaining 65 genes constitute novel candidate genes with parent-biased expression in mouse placenta.…”

“…Other novel secondary DMRs overlapped introns rather than transcriptional start sites. Park2, a recently identified maternally-biased gene (13), had seven intronic DMRs, all displaying hypermethylation of the maternal allele. Rian displayed a DMR that had not been previously reported in mice, although its human ortholog also presents an intronic imprinted DMR (45 Imprinted genes are much more frequently located within 100-100,000 bp of an imprinted DMR.…”

“…We thus conduct a survey of differential methylation and expression in murine embryonic placenta. Recent studies have increased the number of genes identified as subject to imprinting in mouse to about 200 (10)(11)(12)(13)(14)(15). The cause of the differential expression between paternal and maternal alleles is only known for a subset of these genes; maternal histone marks can play a role (14), and in other cases it involves the differential methylation of adjacent regions (5).…”

A piggyBac-based toolkit for inducible genome editing in mammalian cells

“…We next examined whether we could use CRISPR-Bac to activate and repress transcription of a lncRNA using dCas9-VP160 and dCas9-KRAB, respectively. We chose to target a lncRNA called Airn in two cell types: mouse ESCs, where Airn is naturally expressed at low levels, and mouse trophoblast stem cells (TSCs), where Airn is expressed and active ( (Andergassen et al, 2017;Calabrese et al, 2015;Latos et al, 2009); Figure 5A). In ESCs, we were able to activate Airn ~12-fold above its levels in non-targeting sgRNA control cells ( Figure 5B), but we were not able to repress Airn, likely due to its low endogenous expression (not shown; (Latos et al, 2009)).…”