Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy

Abstract

Background Genomic imprinting, mediated by parent-of-origin-specific epigenetic silencing, adjusts the gene expression dosage in mammals. We aimed to clarify parental allelic expression in the human placenta for 396 claimed candidate imprinted genes and to assess the evidence for the proposed enrichment of imprinted expression in the placenta. The study utilized RNA-Seq-based transcriptome and genotyping data from 54 parental-placental samples representing the three trimesters of gestation, and term cases of preeclampsia, gestational diabetes, and fetal growth disturbances. Results Almost half of the targeted genes ( n = 179; 45%) were either not transcribed or showed limited expression in the human placenta. After filtering for the presence of common exonic SNPs, adequacy of sequencing reads and informative families, 91 genes were retained (43 loci form Geneimprint database; 48 recently proposed genes). Only 11/91 genes (12.1%) showed confident signals of imprinting (binomial test, Bonferroni corrected P < 0.05; > 90% transcripts originating from one parental allele). The confirmed imprinted genes exhibit enriched placental expression ( PHLDA2 , H19 , IGF2 , MEST , ZFAT , PLAGL1 , AIM1 ) or are transcribed additionally only in the adrenal gland ( MEG3 , RTL1 , PEG10 , DLK1 ). Parental monoallelic expression showed extreme stability across gestation and in term pregnancy complications. A distinct group of additional 14 genes exhibited a statistically significant bias in parental allelic proportions defined as having 65–90% of reads from one parental allele (e.g., KLHDC10 , NLRP2 , RHOBTB3 , DNMT1 ). Molecular mechanisms behind biased parental expression are still to be clarified. However, 66 of 91 (72.5%) analyzed candidate imprinted genes showed no signals of deviation from biallelic expression. Conclusions As placental tissue is not included in The Genotype-Tissue Expression (GTEx) project, the study contributed to fill the gap in the knowledge concerning parental allelic expression. A catalog of parental allelic proportions and gene expression of analyzed loci across human gestation and in term pregnancy complications is provided as additional files. The study outcome suggested that true imprinting in the human placenta is restricted to well-characterized loci. High expression of imprinted genes during mid-pregnancy supports their critical role in developmental programming. Consistent with the data on other GTEx tissues, the number of human imprinted genes appears to be overestimated....

Targeted RNA-seq improves efficiency, resolution, and accuracy of allele specific expression for human term placentas

“…In humans, ASE analysis of RNA from many tissues was performed as part of the GTEx project 4,5 (https://gtexportal.org/home/). Placentas were not included in GTEx, but human placental tissue has been analyzed by other groups using wht-RNAseq and analyzed for ASE 18,19,50 . The goal of these studies in regard to ASE was to identify imprinted genes through a transcriptome wide approach and to categorize them by imprinting status.…”

“…These crosses permit imprinting to be distinguished from sequence dependent allelic expression bias 5,[11][12][13] . In humans, fewer SNPs are present than in crossbred animal models due to lower genetic diversity; nonetheless RNA-seq has been successfully employed in many human tissues [14][15][16][17][18][19] . Frequently, the parent's genotype is not available in human studies and ASE is determined without the parent of origin of the bias 4,5,20 .…”

Modulation of Placental Gene Expression in Small-for-Gestational-Age Infants

“…Commonly, H19 and IGF2, examples of imprinted genes, are hypomethylated (loss of methylation) in the placenta of growth-restricted infants. The H19 gene, maternally expressed (paternally imprinted), deprives the fetus of nutrients while the IGF2, paternally expressed (maternally imprinted) gene, increased the resource allocation to the infant [59]. However, these growth-related genes are not the sole pathway involved in this pathology.…”

A common 1.6 Mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans

“…The reference sample of Estonian men (n=1,134) comprised healthy young men (n=499) and subjects with proven fatherhood (n=635) ( Table 1, Table S1). The cohort of 'Estonian young men' (n=499) was to collect mother-father-placenta trios at delivery to investigate genetics of pregnancy complications (43,44). In this study, the REPROMETA fathers represented reference men with proven fertility.…”

“…b Male partners of pregnant women (3); eight men had sperm counts < 39 x 10 6 ; for four men sperm analysis was not available. c Male cohort without fatherhood data (42); 47 men had sperm counts < 39 x 10 6 ; for nine men sperm analysis was not available d REPROMETA study recruited and sampled couples after delivery of their newborn; details in (43,44). n.d., not determined a Deletion subtype analysis was carried out for cases with available sufficient quantities of DNA.…”