Biallelic transcription of the porcine IGF2R gene

Braunschweig, M

doi:10.1016/j.gene.2012.03.059

Cited by 11 publications

(7 citation statements)

References 21 publications

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“…Altered IGF2BP2 expression in C-IVF is of interest, since reduced abundance of IGF2 has been associated with lower fetal weight after in vitro culture (El Hajj and Haaf, 2013). The imprinting status of IGF2R in the pig is unclear (Killian et al, 2001; Braunschweig, 2012) but, independently of this uncertainty, our data indicated higher expression of this gene in the two in vitro groups of blastocysts, which would be in agreement with previous reports in other species and could indicate a possibility of LOS-related alterations observed in abnormal in vitro and cloned embryos (Young et al, 2001). At the same time, the reduced methylation in IGF2R specifically in the C-IVF group could suggest that this group is more likely to be susceptible to sustained deregulation of IGF2R expression and a greater probability of LOS-like syndromes.…”

Section: Discussionsupporting

confidence: 90%

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

Cánovas

Ivanova

Romar

et al. 2017

eLife

134

139

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The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first whole-genome DNA methylation datasets from single pig blastocysts showing differences between in vivo and in vitro produced embryos. Blastocysts were produced in vitro either without (C-IVF) or in the presence of natural reproductive fluids (Natur-IVF). Natur-IVF embryos were of higher quality than C-IVF in terms of cell number and hatching ability. RNA-Seq and DNA methylation analyses showed that Natur-IVF embryos have expression and methylation patterns closer to in vivo blastocysts. Genes involved in reprogramming, imprinting and development were affected by culture, with fewer aberrations in Natur-IVF embryos. Methylation analysis detected methylated changes in C-IVF, but not in Natur-IVF, at genes whose methylation could be critical, such as IGF2R and NNAT.DOI: http://dx.doi.org/10.7554/eLife.23670.001

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Section: Discussionsupporting

confidence: 90%

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

Cánovas

Ivanova

Romar

et al. 2017

eLife

134

139

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“…The human IGF2R intronic CpG island has promoter activity, and the human orthologue of Airn is present at least in Wilms’ tumours [ 35 ]. IGF2R shows imprinted expression also in sheep and dogs, but not in pigs [ 36 – 38 ]. Although the imprinted expression pattern of IGF2R is not identical in these eutherian species, the intron 2 CpG islands are maternally methylated equally.…”

Section: Introductionmentioning

confidence: 99%

Identification of a novel antisense noncoding RNA, ALID, transcribed from the putative imprinting control region of marsupial IGF2R

Suzuki

Shaw

Renfree

2018

Epigenetics & Chromatin

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BackgroundGenomic imprinting leads to maternal expression of IGF2R in both mouse and opossum. In mouse, the antisense long noncoding (lnc) RNA Airn, which is paternally expressed from the differentially methylated region (DMR) in the second intron of Igf2r, is required to silence the paternal Igf2r. In opossum, however, intriguingly, the DMR was reported to be in a different downstream intron (intron 11) and there was no antisense lncRNA detected in previous analyses. Therefore, clarifying the imprinting mechanism of marsupial IGF2R is of great relevance for understanding the origin and evolution of genomic imprinting in the IGF2R locus. Thus, the antisense lncRNA associated with the marsupial DMR can be considered as the ‘missing link’. In this study, we identified a novel antisense lncRNA, ALID, after detailed analysis of the IGF2R locus in an Australian marsupial, the tammar wallaby, Macropus eugenii, and compared it to that of the grey short-tailed opossum, Monodelphis domestica.ResultsTammar IGF2R showed maternal expression and had a maternally methylated CpG island (CGI) in intron 12 as well as a promoter CGI without differential methylation, but none in the second intron. Re-analysis of the IGF2R of opossum detected the CGI in intron 12, not intron 11, as previously reported, confirming that the DMR in intron 12 is conserved between these marsupials and so is the putative imprinting control region of marsupial IGF2R. ALID is paternally expressed from the middle of the DMR and is approximately 650 bp long with a single exon structure that is extremely short compared to Airn. Hence, the lncRNA transcriptional overlap of the IGF2R promoter, which is essential for the Igf2r silencing in the mouse, is likely absent in tammar. This suggests that fundamental differences in the lncRNA-based silencing mechanisms evolved in eutherian and marsupial IGF2R and may reflect the lack of differential methylation in the promoter CGI of marsupial IGF2R.ConclusionsOur study thus provides the best candidate factor for establishing paternal silencing of marsupial IGF2R without transcriptional overlap, which is distinct from the Igf2r silencing mechanism of Airn, but which may be analogous to the mode of action for the flanking Slc22a2 and Slc22a3 gene silencing in the mouse placenta.Electronic supplementary materialThe online version of this article (10.1186/s13072-018-0227-8) contains supplementary material, which is available to authorized users.

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“…To demonstrate the complex pattern of genomic imprinting in pigs, we showed here several examples. First, IGF2R is a known imprinted gene whose imprinting is tissue depenent 17,29 . Consistent with this knowledge, we showed that IGF2R was biallelically expressed in brain but maternally expressed in liver, muscle, and placenta in all stages.…”

Section: Resultsmentioning

confidence: 99%

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs

Quan,

Yang,

Wang

et al. 2024

Preprint

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Genetic variation in the regulation of gene expression contributes substantially to phenotypic variation. Understanding how variation in DNA sequences and epigentic modifications leads to gene expression variation remains a challenging task. In hybrid animals where cellular environments are homogeneous, differences between the expression of paternal and maternal alleles must be due to cis sequence or epigenic differences. Therefore, hybrid mapping is a powerful approach to efficiently identify and characterize genes under regulation through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we performed a comprehensive multi-omic characterization of regulatory variation across brain, liver, muscle, and placenta in four developmental stages. We produced one of the largest multi-omic datasets to date in pigs, including 16 whole genome sequenced genomes, 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We developed a novel read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We showed that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identified 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. By integrating methylation, chromatin accessibility, and gene expression data, many of these allele specific expression can be explained by allele specific methylation and/or chromatin accessibility. This study provides one of the most comprehensive characterizations of regulatory variation across multiple tissues and developmental stages in pigs and offers new opportunity of genetic improvement for this important food animal species.

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Biallelic transcription of the porcine IGF2R gene

Cited by 11 publications

References 21 publications

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

Identification of a novel antisense noncoding RNA, ALID, transcribed from the putative imprinting control region of marsupial IGF2R

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs

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