scholarly journals A Comprehensive Overview of Genomic Imprinting in Breast & Its Deregulation in Cancer

2018 ◽  
Author(s):  
Tine Goovaerts ◽  
Sandra Steyaert ◽  
Chari A Vandenbussche ◽  
Jeroen Galle ◽  
Olivier Thas ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Genomic Imprinting ◽  
Significant Loss ◽  
Dna Demethylation ◽  
Distribution Model ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Comprehensive Overview ◽  
Loss Of Imprinting ◽  
A Genome

ABSTRACTGenomic imprinting, the parent-of-origin specific monoallelic expression of genes, plays an important role in growth and development. Loss of imprinting of individual genes has been found in varying cancers, yet data-analytical challenges have impeded systematic studies so far. We developed a mixture distribution model to detect monoallelically expressed loci in a genome-wide manner without the need for genotyping data, and applied the methodology on TCGA breast tissue RNA-seq data. We identified 35 putatively imprinted genes in healthy breast. In breast cancer however, HM13 was featured by significant loss of imprinting and expression upregulation, which could be linked to DNA demethylation. Other imprinted genes (25 out of 35) demonstrated consistent expression downregulation in breast cancer, which often correlated with loss of imprinting. A breast imprinted gene network, deregulated in cancer, might hence be present. In summary, our novel methodology highlights the massive deregulation of imprinting in breast cancer.

scholarly journals Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shiran Bar ◽  
Dan Vershkov ◽  
Gal Keshet ◽  
Elyad Lezmi ◽  
Naama Meller ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Dna Demethylation ◽  
Human Embryos ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Genome Wide ◽  
A Genome ◽  
Parental Imprinting

AbstractIn mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity.

scholarly journals Evolution of viviparity in mammals: what genomic imprinting tells us about mammalian placental evolution

2019 ◽  
Vol 31 (7) ◽  
pp. 1219 ◽  
Author(s):  
Tomoko Kaneko-Ishino ◽  
Fumitoshi Ishino
Keyword(s):  
Oxygen Concentration ◽  
Genomic Imprinting ◽  
Atmospheric Oxygen ◽  
Epigenetic Mechanism ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Low Oxygen ◽  
Exogenous Dna ◽  
A Genome ◽  
Key Factor

Genomic imprinting is an epigenetic mechanism of regulating parent-of-origin-specific monoallelic expression of imprinted genes in viviparous therian mammals such as eutherians and marsupials. In this review we discuss several issues concerning the relationship between mammalian viviparity and genomic imprinting, as well as the domestication of essential placental genes: why has the genomic imprinting mechanism been so widely conserved despite the evident developmental disadvantages originating from monoallelic expression? How have genomic imprinted regions been established in the course of mammalian evolution? What drove the evolution of mammalian viviparity and how have genomic imprinting and domesticated genes contributed to this process? In considering the regulatory mechanism of imprinted genes, reciprocal expression of paternally and maternally expressed genes (PEGs and MEGs respectively) and the presence of several essential imprinted genes for placental formation and maintenance, it is likely that complementary, thereby monoallelic, expression of PEGs and MEGs is an evolutionary trade-off for survival. The innovation in novel imprinted regions was associated with the emergence of imprinting control regions, suggesting that genomic imprinting arose as a genome defence mechanism against the insertion of exogenous DNA. Mammalian viviparity emerged in the period when the atmospheric oxygen concentration was the lowest (~12%) during the last 550 million years (the Phanerozoic eon), implying this low oxygen concentration was a key factor in promoting mammalian viviparity as a response to a major evolutionary pressure. Because genomic imprinting and gene domestication from retrotransposons or retroviruses are effective measures of changing genomic function in therian mammals, they are likely to play critical roles in the emergence of viviparity for longer gestation periods.

Erasing genomic imprinting memory in mouse clone embryos produced from day 11.5 primordial germ cells

Development ◽  
2002 ◽  
Vol 129 (8) ◽  
pp. 1807-1817 ◽  
Author(s):  
Jiyoung Lee ◽  
Kimiko Inoue ◽  
Ryuichi Ono ◽  
Narumi Ogonuki ◽  
Takashi Kohda ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genomic Imprinting ◽  
Nuclear Transfer ◽  
Monoallelic Expression ◽  
Parental Origin ◽  
Imprinted Genes ◽  
Specific Expression ◽  
Male And Female ◽  
Imprinted Gene ◽  
Methylation Patterns

Genomic imprinting is an epigenetic mechanism that causes functional differences between paternal and maternal genomes, and plays an essential role in mammalian development. Stage-specific changes in the DNA methylation patterns of imprinted genes suggest that their imprints are erased some time during the primordial germ cell (PGC) stage, before their gametic patterns are re-established during gametogenesis according to the sex of individuals. To define the exact timing and pattern of the erasure process, we have analyzed parental-origin-specific expression of imprinted genes and DNA methylation patterns of differentially methylated regions (DMRs) in embryos, each derived from a single day 11.5 to day 13.5 PGC by nuclear transfer. Cloned embryos produced from day 12.5 to day 13.5 PGCs showed growth retardation and early embryonic lethality around day 9.5. Imprinted genes lost their parental-origin-specific expression patterns completely and became biallelic or silenced. We confirmed that clones derived from both male and female PGCs gave the same result, demonstrating the existence of a common default state of genomic imprinting to male and female germlines. When we produced clone embryos from day 11.5 PGCs, their development was significantly improved, allowing them to survive until at least the day 11.5 embryonic stage. Interestingly, several intermediate states of genomic imprinting between somatic cell states and the default states were seen in these embryos. Loss of the monoallelic expression of imprinted genes proceeded in a step-wise manner coordinated specifically for each imprinted gene. DNA demethylation of the DMRs of the imprinted genes in exact accordance with the loss of their imprinted monoallelic expression was also observed. Analysis of DNA methylation in day 10.5 to day 12.5 PGCs demonstrated that PGC clones represented the DNA methylation status of donor PGCs well. These findings provide strong evidence that the erasure process of genomic imprinting memory proceeds in the day 10.5 to day 11.5 PGCs, with the timing precisely controlled for each imprinted gene. The nuclear transfer technique enabled us to analyze the imprinting status of each PGC and clearly demonstrated a close relationship between expression and DNA methylation patterns and the ability of imprinted genes to support development.

scholarly journals Shared Role for Differentially Methylated Domains of Imprinted Genes

2002 ◽  
Vol 22 (7) ◽  
pp. 2089-2098 ◽  
Author(s):  
Bonnie Reinhart ◽  
Mariam Eljanne ◽  
J. Richard Chaillet
Keyword(s):  
Genomic Imprinting ◽  
Mutant Mouse ◽  
Paternal Allele ◽  
Mouse Strains ◽  
Imprinted Genes ◽  
Maternal Allele ◽  
Wild Type ◽  
Loss Of Imprinting ◽  
Intracisternal A Particle ◽  
Mouse Genomic

ABSTRACT For most imprinted genes, a difference in expression between the maternal and paternal alleles is associated with a corresponding difference in DNA methylation that is localized to a differentially methylated domain (DMD). Removal of a gene's DMD leads to a loss of imprinting. These observations suggest that DMDs have a determinative role in genomic imprinting. To examine this possibility, we introduced sequences from the DMDs of the imprinted Igf2r, H19, and Snrpn genes into a nonimprinted derivative of the normally imprinted RSVIgmyc transgene, created by excising its own DMD. Hybrid transgenes with sequences from the Igf2r DMD2 were consistently imprinted, with the maternal allele being more methylated than the paternal allele. Only the repeated sequences within DMD2 were required for imprinting these transgenes. Hybrid transgenes containing H19 and Snrpn DMD sequences and ones containing sequences from the long terminal repeat of a murine intracisternal A particle retrotransposon were not imprinted. The Igf2r hybrid transgenes are comprised entirely of mouse genomic DNA and behave as endogenous imprinted genes in inbred wild-type and mutant mouse strains. These types of hybrid transgenes can be used to elucidate the functions of DMD sequences in genomic imprinting.

scholarly journals Multiple Mechanisms Regulate Imprinting of the Mouse Distal Chromosome 7 Gene Cluster

1998 ◽  
Vol 18 (6) ◽  
pp. 3466-3474 ◽  
Author(s):  
Tamara Caspary ◽  
Michele A. Cleary ◽  
Catherine C. Baker ◽  
Xiao-Juan Guan ◽  
Shirley M. Tilghman
Keyword(s):  
Dna Methylation ◽  
Gene Cluster ◽  
Genomic Imprinting ◽  
Dna Methyltransferase ◽  
Regulatory Elements ◽  
Chromosome 7 ◽  
Imprinted Genes ◽  
Global Regulator ◽  
Loss Of Imprinting ◽  
Distal Chromosome

ABSTRACT Genomic imprinting is an epigenetic process that results in the preferential silencing of one of the two parental copies of a gene. Although the precise mechanisms by which genomic imprinting occurs are unknown, the tendency of imprinted genes to exist in chromosomal clusters suggests long-range regulation through shared regulatory elements. We characterize a 800-kb region on the distal end of mouse chromosome 7 that contains a cluster of four maternally expressed genes, H19, Mash2, Kvlqt1, andp57Kip2 , as well as two paternally expressed genes, Igf2 and Ins2, and assess the expression and imprinting of Mash2, Kvlqt1, andp57Kip2 during development in embryonic and extraembryonic tissues. Unlike Igf2 and Ins2, which depend on H19 for their imprinting,Mash2, p57Kip2 , andKvlqt1 are unaffected by a deletion of the H19gene region, suggesting that these more telomeric genes are not regulated by the mechanism that controls H19,Igf2, and Ins2. Mutations in humanp57Kip2 have been implicated in Beckwith-Wiedemann syndrome, a disease that has also been associated with loss of imprinting of IGF2. We find, however, that a deletion of the gene has no effect on imprinting within the cluster. Surprisingly, the three maternally expressed genes are regulated very differently by DNA methylation; p57Kip2 is activated, Kvlqt1 is silenced, and Mash2 is unaffected in mice lacking DNA methyltransferase. We conclude thatH19 is not a global regulator of imprinting on distal chromosome 7 and that the telomeric genes are imprinted by a separate mechanism(s).

scholarly journals Characterization of imprinted genes in rice reveals post-fertilization regulation and conservation at some loci of imprinting in plant species

2017 ◽  
Author(s):  
Chen Chen ◽  
Tingting Li ◽  
Shan Zhu ◽  
Zehou Liu ◽  
Zhenyuan Shi ◽  
...  
Keyword(s):  
Plant Species ◽  
Genomic Imprinting ◽  
Biological Significance ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Dependent Manner ◽  
Cultivated Rice ◽  
Parental Allele ◽  
Intraspecific Variations ◽  
High Level

AbstractGenomic imprinting is an epigenetic phenomenon by which certain genes display monoallelic expression in a parent-of-origin-dependent manner. Hundreds of imprinted genes have been identified from several plant species. Here we identified, with a high level of confidence, 208 imprinted candidates from rice. Imprinted genes of rice showed limited association to the transposable elements, which is contrast to the findings inArabidopsis. Generally, imprinting of rice is conserved within species, but intraspecific variations were confirmed here. Imprinting between cultivated rice and wild rice are likely similar. The imprinted genes of rice do not show significant selective signatures overall, which suggests that domestication imposes limited evolutionary effects on genomic imprinting of rice. Though the conservation of imprinting in plants is limited, here we prove that some loci tend to be imprinted in different species. In addition, our results suggest that differential epigenetic regulation between parental alleles can be established either prior to or post-fertilization. The imprinted 24-nt small RNAs, but not the 21-nt ones, likely involve the regulation of imprinting in an opposite parental-allele targeting manner. Together, our findings suggest that regulation of imprinting can be very diverse, and genomic imprinting as well as imprinted genes have essential evolutionary and biological significance.

scholarly journals Genomic imprinting and the social brain

2006 ◽  
Vol 361 (1476) ◽  
pp. 2229-2237 ◽  
Author(s):  
Anthony R Isles ◽  
William Davies ◽  
Lawrence S Wilkinson
Keyword(s):  
Genomic Imprinting ◽  
Parental Investment ◽  
Social Groups ◽  
Monoallelic Expression ◽  
Imprinted Genes ◽  
Epigenetic Mark ◽  
Parental Allele ◽  
Intragenomic Conflict ◽  
Starting Point ◽  
The Social

Genomic imprinting refers to the parent-of-origin-specific epigenetic marking of a number of genes. This epigenetic mark leads to a bias in expression between maternally and paternally inherited imprinted genes, that in some cases results in monoallelic expression from one parental allele. Genomic imprinting is often thought to have evolved as a consequence of the intragenomic conflict between the parental alleles that occurs whenever there is an asymmetry of relatedness. The two main examples of asymmetry of relatedness are when there is partiality of parental investment in offspring (as is the case for placental mammals, where there is also the possibility of extended postnatal care by one parent), and in social groups where there is a sex-biased dispersal. From this evolutionary starting point, it is predicted that, at the behavioural level, imprinted genes will influence what can broadly be termed bonding and social behaviour. We examine the animal and human literature for examples of imprinted genes mediating these behaviours, and divide them into two general classes. Firstly, mother–offspring interactions (suckling, attachment and maternal behaviours) that are predicted to occur when partiality in parental investment in early postnatal offspring occurs; and secondly, adult social interactions, when there is an asymmetry of relatedness in social groups. Finally, we return to the evolutionary theory and examine whether there is a pattern of behavioural functions mediated by imprinted genes emerging from the limited data, and also whether any tangible predictions can be made with regards to the direction of action of genes of maternal or paternal origin.

scholarly journals Genetically Raised Circulating Bilirubin Levels and Risk of Ten Cancers: A Mendelian Randomization Study

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 394
Author(s):  
Nazlisadat Seyed Seyed Khoei ◽  
Robert Carreras-Torres ◽  
Neil Murphy ◽  
Marc J. Gunter ◽  
Paul Brennan ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Lung Cancer ◽  
Squamous Cell ◽  
Cell Lung Cancer ◽  
Hodgkin’S Lymphoma ◽  
Mendelian Randomization ◽  
Hodgkin's Lymphoma ◽  
Squamous Cell Lung Cancer ◽  
Phenotypic Variance ◽  
A Genome

Bilirubin, an endogenous antioxidant, may play a protective role in cancer development. We applied two-sample Mendelian randomization to investigate whether genetically raised bilirubin levels are causally associated with the risk of ten cancers (pancreas, kidney, endometrium, ovary, breast, prostate, lung, Hodgkin’s lymphoma, melanoma, and neuroblastoma). The number of cases and their matched controls of European descent ranged from 122,977 and 105,974 for breast cancer to 1200 and 6417 for Hodgkin’s lymphoma, respectively. A total of 115 single-nucleotide polymorphisms (SNPs) associated (p < 5 × 10−8) with circulating total bilirubin, extracted from a genome-wide association study in the UK Biobank, were used as instrumental variables. One SNP (rs6431625) in the promoter region of the uridine-diphosphoglucuronate glucuronosyltransferase1A1 (UGT1A1) gene explained 16.9% and the remaining 114 SNPs (non-UGT1A1 SNPs) explained 3.1% of phenotypic variance in circulating bilirubin levels. A one-standarddeviation increment in circulating bilirubin (≈ 4.4 µmol/L), predicted by non-UGT1A1 SNPs, was inversely associated with risk of squamous cell lung cancer and Hodgkin’s lymphoma (odds ratio (OR) 0.85, 95% confidence interval (CI) 0.73–0.99, P 0.04 and OR 0.64, 95% CI 0.42–0.99, p 0.04, respectively), which was confirmed after removing potential pleiotropic SNPs. In contrast, a positive association was observed with the risk of breast cancer after removing potential pleiotropic SNPs (OR 1.12, 95% CI 1.04–1.20, p 0.002). There was little evidence for robust associations with the other seven cancers investigated. Genetically raised bilirubin levels were inversely associated with risk of squamous cell lung cancer as well as Hodgkin’s lymphoma and positively associated with risk of breast cancer. Further studies are required to investigate the utility of bilirubin as a low-cost clinical marker to improve risk prediction for certain cancers.

scholarly journals Pterostilbene Changes Epigenetic Marks at Enhancer Regions of Oncogenes in Breast Cancer Cells

Antioxidants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1232
Author(s):  
Sadaf Harandi-Zadeh ◽  
Cayla Boycott ◽  
Megan Beetch ◽  
Tony Yang ◽  
Benjamin J. E. Martin ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Cancer Cells ◽  
Breast Cancer Cells ◽  
Dna Methyltransferase ◽  
Epigenetic Marks ◽  
Chip Sequencing ◽  
Dietary Polyphenols ◽  
A Genome ◽  
Epigenetic Patterns

Epigenetic aberrations are linked to sporadic breast cancer. Interestingly, certain dietary polyphenols with anti-cancer effects, such as pterostilbene (PTS), have been shown to regulate gene expression by altering epigenetic patterns. Our group has proposed the involvement of DNA methylation and DNA methyltransferase 3B (DNMT3B) as vital players in PTS-mediated suppression of candidate oncogenes and suggested a role of enhancers as target regions. In the present study, we assess a genome-wide impact of PTS on epigenetic marks at enhancers in highly invasive MCF10CA1a breast cancer cells. Following chromatin immunoprecipitation (ChIP)-sequencing in MCF10CA1a cells treated with 7 μM PTS for 9 days, we discovered that PTS leads to increased binding of DNMT3B at enhancers of 77 genes, and 17 of those genes display an overlapping decrease in the occupancy of trimethylation at lysine 36 of histone 3 (H3K36me3), a mark of active enhancers. We selected two genes, PITPNC1 and LINC00910, and found that their enhancers are hypermethylated in response to PTS. These changes coincided with the downregulation of gene expression. Of importance, we showed that 6 out of 17 target enhancers, including PITPNC1 and LINC00910, are bound by an oncogenic transcription factor OCT1 in MCF10CA1a cells. Indeed, the six enhancers corresponded to genes with established or putative cancer-driving functions. PTS led to a decrease in OCT1 binding at those enhancers, and OCT1 depletion resulted in PITPNC1 and LINC00910 downregulation, further demonstrating a role for OCT1 in transcriptional regulation. Our findings provide novel evidence for the epigenetic regulation of enhancer regions by dietary polyphenols in breast cancer cells.

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