Molecular cloning, mRNA expression and imprinting status of PEG3, NAP1L5 and PPP1R9A genes in pig

Cognitive Skills and DNA Methylation Are Correlating in Healthy and Novice College Students Practicing Preksha Dhyāna Meditation

The impact of different meditation protocols on human health is explored at the cognitive and cellular levels. Preksha Dhyana meditation has been observed to seemingly affect the cognitive performance, transcriptome, and methylome of healthy and novice participant practitioners. In this study, we performed correlation analyses to investigate the presence of any relationships in the changes in cognitive performance and DNA methylation in a group of college students practicing Preksha Dhyāna (N = 34). Nine factors of cognitive performance were assessed at baseline and 8 weeks postintervention timepoints in the participants. Statistically significant improvements were observed in six of the nine assessments, which were predominantly relating to memory and affect. Using Illumina 850 K microarray technology, 470 differentially methylated sites (DMS) were identified between the two timepoints (baseline and 8 weeks), using a threshold of p-value < 0.05 and methylation levels beyond -3% to 3% at every site. Correlation analysis between the changes in performance on each of the nine assessments and every DMS unveiled statistically significant positive and negative relationships at several of these sites. The identified DMS were in proximity of essential genes involved in signaling and other important metabolic processes. Interestingly, we identified a set of sites that can be considered as biomarkers for Preksha meditation improvements at the genome level.

Identification of imprinted genes in the skeletal muscle of newborn piglets by high-throughput sequencing

Imprinted genes - exhibiting parent-specific transcription - play essential roles in the process of mammalian development and growth. Skeletal muscle growth is crucial for meat production. To further understand the role of imprinted genes during the porcine skeletal muscle growth, DNA-seq and RNA-seq were used to explore the characteristics of imprinted genes from porcine reciprocal crosses. A total of 584 545 single-nucleotide variations were discovered in the DNA-seq data of F0 parents, heterozygous in two pig breeds (Yorkshire and Min pigs) but homozygous in each breed. These single-nucleotide variations were used to determine the allelic-specific expression in F1 individuals. Finally, eight paternal expression sites and three maternal expression sites were detected, whereas two paternally expressed imprinted genes (NDN and IGF2) and one maternally expressed imprinted gene (H1-3) were validated by Sanger sequencing. DNA methylation regulates the expression of imprinted genes, and all of the identified imprinted genes in this study were predicted to possess CpG islands. PBX1 and YY1 binding motifs were discovered in the promoter regions of all three imprinted genes, which were candidate elements regulating the transcription of imprinted genes. For these identified imprinted genes, IGF2 and NDN promoted muscle growth whereas H1-3 inhibited cell proliferation, corroborating the 'parental conflict' theory that paternally expressed imprinted genes assisted descendants' growth whereas maternally expressed imprinted genes inhibited it. This study discovered porcine imprinted genes in skeletal muscle and was the first to reveal that H1-3 was expressed by the maternal allele to our knowledge. Our findings provided valuable resources for the potential utilization of imprinted genes in pig breeding.

Reproductive fluids, used for the in vitro production of pig embryos, result in healthy offspring and avoid aberrant placental expression of PEG3 and LUM

Background

In vitro embryo production (IVP) and embryo transfer (ET) are two very common assisted reproductive technologies (ART) in human and cattle. However, in pig, the combination of either procedures, or even their use separately, is still considered suboptimal due to the low efficiency of IVP plus the difficulty of performing ET in the long and contorted uterus of the sow. In addition, the potential impact of these two ART on the health of the offspring is unknown. We investigated here if the use of a modified IVP system, with natural reproductive fluids (RF) as supplements to the culture media, combined with a minimally invasive surgery to perform ET, affects the output of the own IVP system as well as the reproductive performance of the mother and placental molecular traits.

Results

The blastocyst rates obtained by both in vitro systems, conventional (C-IVP) and modified (RF-IVP), were similar. Pregnancy and farrowing rates were also similar. However, when compared to in vivo control (artificial insemination, AI), litter sizes of both IVP groups were lower, while placental efficiency was higher in AI than in RF-IVP. Gene expression studies revealed aberrant expression levels for PEG3 and LUM in placental tissue for C-IVP group when compared to AI, but not for RF-IVP group.

Conclusions

The use of reproductive fluids as additives for the culture media in pig IVP does not improve reproductive performance of recipient mothers but could mitigate the impact of artificial procedures in the offspring.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-020-00544-0.

The Landscape of Genomic Imprinting at the Porcine SGCE/PEG10 Locus from Methylome and Transcriptome of Parthenogenetic Embryos

In mammals, imprinted genes often exist in the form of clusters in specific chromosome regions. However, in pigs, genomic imprinting of a relatively few genes and clusters has been identified, and genes within or adjacent to putative imprinted clusters need to be investigated including those at the SGCE/PEG10 locus. The objective of this study was to, using porcine parthenogenetic embryos, investigate imprinting status of genes within the genomic region spans between the COL1A2 and ASB4 genes in chromosome 9. Whole-genome bisulfite sequencing (WGBS) and RNA sequencing (RNA-seq) were conducted with normal and parthenogenetic embryos, and methylome and transcriptome were analyzed. As a result, differentially methylated regions (DMRs) between the embryos were identified, and parental allele-specific expressions of the SGCE and PEG10 genes were verified. The pig imprinted interval was limited between SGCE and PEG10, since both the COL1A2 and CASD1 genes at the centromere-proximal region and the genes between PPP1R9A and ASB4 toward the telomere were non-imprinted and biallelically expressed. Consequently, our combining analyses of methylome, transcriptome, and informative polymorphisms revealed the boundary of imprinting cluster at the SGCE/PEG10 locus in pig chromosome 9 and consolidated the landscape of genomic imprinting in pigs.

Conservation of imprinting of MKRN3 and NAP1L5 in rabbits

Maternally imprinted genes of makorin ring finger protein 3 (MKRN3) and nucleosome assembly protein 1-like 5 (NAP1L5) have been identified in many species but have not yet been investigated in rabbits. In this study, a polymorphism-based approach and bisulfite-sequencing PCR (BSP) were used to determine the imprinting status of MKRN3 and NAP1L5 in rabbits. The single nucleotide polymorphism (SNP)-based sequencing results demonstrated that MKRN3 and NAP1L5 were expressed preferentially from the paternal allele. Furthermore, the BSP results showed the gamete-specific methylation patterns and hemimethylation in brain and full methylation in liver were observed in MKRN3 and NAP1L5 respectively. Thus, we provide the first evidence that MKRN3 and NAP1L5 are paternally expressed genes and that the CpG islands located in the promoter region may be the putative differentially methylated region of these two genes in rabbits.

Conservation of genomic imprinting at the NDN, MAGEL2 and MEST loci in pigs

Imprinted genes have important effects on the regulation of fetal growth, development, and postnatal behavior. However, the study of imprinted genes has been limited in mammalian species other than human and mouse. Therefore, the study of porcine imprinted genes is useful for defining the extent of conservation of genomic imprinting among different species. In this study, the imprinting status of porcine NDN, MAGEL2 and MEST genes was determined by direct sequencing of the cDNAs and detection of single nucleotide polymorphisms (SNPs) identified in individuals from reciprocal crosses between Meishan and Large White pigs for allele discrimination. The analysis was carried out in 13 different tissues (skeletal muscle, fat, pituitary gland, heart, lung, liver, kidney, spleen, stomach, small intestine, uterus, ovary and testis) from 12 two-month-old piglets. Imprinting analysis showed that NDN and MAGEL2 were paternally expressed in all tissues where the genes were expressed as in human and mouse. Interestingly, MEST showed tissue-specific imprinting, being paternally expressed in skeletal muscle, fat, pituitary gland, heart, kidney, lung, stomach and uterus, and maternally expressed in spleen and liver.