Allele-Specific H3K79 Di- versus Trimethylation Distinguishes Opposite Parental Alleles at Imprinted Regions

ABSTRACT Imprinted gene expression corresponds to parental allele-specific DNA CpG methylation and chromatin composition. Histone tail covalent modifications have been extensively studied, but it is not known whether modifications in the histone globular domains can also discriminate between the parental alleles. Using multiplex chromatin immunoprecipitation-single nucleotide primer extension (ChIP-SNuPE) assays, we measured the allele-specific enrichment of H3K79 methylation and H4K91 acetylation along the H19/Igf2 imprinted domain. Whereas H3K79me1, H3K79me2, and H4K91ac displayed a paternal-specific enrichment at the paternally expressed Igf2 locus, H3K79me3 was paternally biased at the maternally expressed H19 locus, including the paternally methylated imprinting control region (ICR). We found that these allele-specific differences depended on CTCF binding in the maternal ICR allele. We analyzed an additional 11 differentially methylated regions (DMRs) and found that, in general, H3K79me3 was associated with the CpG-methylated alleles, whereas H3K79me1, H3K79me2, and H4K91ac enrichment was specific to the unmethylated alleles. Our data suggest that allele-specific differences in the globular histone domains may constitute a layer of the “histone code” at imprinted genes.

Download Full-text

Mouse endogenous X-linked genes do not show lineage-specific delayed inactivation during development

Genetics Research ◽

10.1017/s0016672300033292 ◽

1995 ◽

Vol 65 (3) ◽

pp. 223-227 ◽

Cited By ~ 13

Author(s):

Jeanne M. Lebon ◽

Patrick P. L. Tam ◽

Judith Singer-Sam ◽

Arthur D. Riggs ◽

Seong-Seng Tan

Keyword(s):

X Chromosome ◽

Female Mouse ◽

X Chromosome Inactivation ◽

Mouse Embryos ◽

Primer Extension ◽

Rt Pcr ◽

Single Nucleotide ◽

Allele Specific ◽

Endogenous Genes ◽

Single Nucleotide Primer Extension

SummaryX chromosome inactivation (XCI) has been assumed to be complete in all cells of female mouse embryos at about 6 d post coitum (dpc). However, a recent study on β-galactosidase expression of an X-linkedlacZtransgene suggests that XCI is probably not complete several days after this time in some lineages. To help resolve this issue, we analysed XCI in embryos which carry the T(X;16)16H (Searle's) translocation and are heterozygous at the X-linkedHprtandPgk-1genes. The quantitative RT-PCR single nucleotide primer extension (SNuPE) assay was used to measureHprtandPgk-1allele-specific transcripts in embryos 9·5 dpc. No transcripts from the normal X chromosome were found in any of the tissues tested, indicating that inactivation was complete for these endogenous genes.

Download Full-text

Successful Computational Prediction of Novel Imprinted Genes from Epigenomic Features

Molecular and Cellular Biology ◽

10.1128/mcb.01355-09 ◽

2010 ◽

Vol 30 (13) ◽

pp. 3357-3370 ◽

Cited By ~ 37

Author(s):

Chelsea M. Brideau ◽

Kirsten E. Eilertson ◽

James A. Hagarman ◽

Carlos D. Bustamante ◽

Paul D. Soloway

Keyword(s):

Single Nucleotide Polymorphism Array ◽

Computational Prediction ◽

Imprinted Genes ◽

Nucleotide Polymorphism ◽

Specific Expression ◽

Single Nucleotide ◽

Rigorous Testing ◽

Local Sequence ◽

Allele Specific ◽

Mouse Cells

ABSTRACT Approximately 100 mouse genes undergo genomic imprinting, whereby one of the two parental alleles is epigenetically silenced. Imprinted genes influence processes including development, X chromosome inactivation, obesity, schizophrenia, and diabetes, motivating the identification of all imprinted loci. Local sequence features have been used to predict candidate imprinted genes, but rigorous testing using reciprocal crosses validated only three, one of which resided in previously identified imprinting clusters. Here we show that specific epigenetic features in mouse cells correlate with imprinting status in mice, and we identify hundreds of additional genes predicted to be imprinted in the mouse. We used a multitiered approach to validate imprinted expression, including use of a custom single nucleotide polymorphism array and traditional molecular methods. Of 65 candidates subjected to molecular assays for allele-specific expression, we found 10 novel imprinted genes that were maternally expressed in the placenta.

Download Full-text

331 ABNORMAL DNA METHYLATION PATTERNS AND ALLELE-SPECIFIC EXPRESSION OF IMPRINTED GENES IN BOVINE-INDUCED PLURIPOTENT STEM CELLS

Reproduction Fertility and Development ◽

10.1071/rdv27n1ab331 ◽

2015 ◽

Vol 27 (1) ◽

pp. 254 ◽

Cited By ~ 1

Author(s):

F. F. Bressan ◽

J. Therrien ◽

F. Filion ◽

F. Perecin ◽

L. C. Smith ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Ips Cells ◽

Allelic Expression ◽

Ctcf Binding ◽

Imprinted Genes ◽

Ips Cell ◽

Biallelic Expression ◽

Allele Specific ◽

Methylation Patterns

Pluripotency reacquisition of somatic cells has been achieved through nuclear transfer (NT) to oocytes and, more recently, through induction with pluripotency-related factors (iPS cells). However, the epigenetic reprogramming process that enables the derivation of both NT-derived cloned animals and iPS cells is usually incomplete, leading to unhealthy offspring and poorly reprogrammed iPS cell lines. These unfavourable outcomes result in part from abnormal genome DNA methylation that leads to aberrant gene expression patterns. For instance, differentially methylated regions (DMR) and monoalleleic expression of imprinted genes, essential for normal cellular commitment and early development, are thought to be severely disturbed by reprogramming techniques. Indeed, H19 and SNRPN, imprinted genes, were disturbed in bovine NT-derived embryos and fetuses. Herein we investigated whether the DMR and parent-of-origin expression of the imprinted genes H19 and SNRPN are also perturbed in iPS lines. To analyse the DMR methylation patterns and allelic expression of H19 and SNRPN using parental-specific polymorphisms, we derived multiple clones of bovine iPS (biPS) cells from an interspecies (Bos indicus × Bos taurus) fetal fibroblast (bFF) using transduction with a policystronic lentivirus containing mouse Oct4, Sox2 c-Myc, and Klf-4 transcription factors. The DNA methylation patterns were evaluated by bisulfite sequencing and allelic expression by designing allele-specific PCR probes. We also quantified transcript expression by RT-PCR of H19, IGF2, SNRPN, OCT4, and NANOG by normalization with 3 housekeeping genes (GAPDH, NAT1, and ACTB). The biPS lines were characterised by a high nuclear : cytoplasmic ratio, dome-shaped colonies, positive AP activity, embryoid body formation, in vitro and in vivo (teratoma) formation, and expression of pluripotency-related genes. Compared to the bFF cells, methylation analyses of H19 showed partial hypomethylation of the paternal DMR on 1 iPS cell line and partial demethylation of the CTCF-binding region in the DMR of 2 other biPS lines, indicating abnormal demethylation of 3 out of the 4 biPS lines analysed. Methylation analyses of SNRPN revealed a partial hypomethylation in the maternal DMR and partial hypermethylation of the paternal DMR in 2 iPS lines. Gene expression analyses revealed the biallelic expression of H19 and decreased global expression of both H19 and IGF2, as well as the exclusively monoallelic paternal expression and significant increase in global expression of SNRPN. Interestingly, although OCT4 was substantially overexpressed in biPS lines, we identified a hypermethylation of the CG-rich region of the OCT4 exon 1. Endogenous NANOG expression was observed in 2 biPS clones. We conclude that imprinting errors are observed in biPS clones, suggesting that these epigenetic anomalies are related to the reprogramming process and could be directly responsible for the variable phenotypes and low success rates of both cloning and iPS derivation procedures.Financial support was from NSERC, FAPESP (13/13686-8, 11/08376-4, 57877-3/2008, 08.135-2/2013), CNPq (573754/2008-0, 482163/2013-5).

Download Full-text

APC allele-specific expression in carriers of Ashkenazi Jewish mutation I1307K

Journal of Clinical Oncology ◽

10.1200/jco.2009.27.15_suppl.e22181 ◽

2009 ◽

Vol 27 (15_suppl) ◽

pp. e22181-e22181

Author(s):

G. Capella ◽

E. Castellsague ◽

G. Rennert ◽

S. Gruber

Keyword(s):

Incomplete Penetrance ◽

Ashkenazi Jewish ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Increased Risk ◽

Allele Specific ◽

Single Nucleotide Primer Extension ◽

Rna And Dna ◽

Dna Mutant

e22181 Background: I1307K is a missense APC variant with incomplete penetrance that has been found in 6% of Jewish Ashkenazi population and confers a two-fold increased risk to develop multiple adenomas and colorectal tumours. It is believed that it creates a hypermutable region within the gene that leads to an accumulation of mutations. It remains unknown whether the presence of this mutation modifies APC expression. Our goal was to study whether allele-specific expression (ASE) of I1307K is present at the germline and tumoral level. Methods: Paired germline/carcinoma RNA and DNA was studied from eleven I1307K carriers. To analyze changes in the mutant/wt allelic ratio we used single nucleotide primer extension (SNuPE) for the I1307K and the rs2229992 APCcoding SNP. Fourteen controls were also analyzed. Results: No germline allele specific expression was found in I1307K carriers (range=0.954–1.173). Significant ASE was observed in 8 of the 10 carcinomas analyzed. In 4 cases the I1307K allele was overexpressed (range=2.51–9.51) and in 4 cases was underexpressed (range=0.09–0.28). Tumor ASE correlated with the DNA mutant/wt allelic dose. Conclusions: I1307K variant is not associated with allelic specific expression at the germline level. I1307K overexpression is not selected for during tumor progression. No significant financial relationships to disclose.

Download Full-text

Orientation of mouse H19 ICR affects imprinted H19 gene expression through promoter methylation-dependent and -independent mechanisms

Communications Biology ◽

10.1038/s42003-021-02939-9 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Hitomi Matsuzaki ◽

Yu Miyajima ◽

Akiyoshi Fukamizu ◽

Keiji Tanimoto

Keyword(s):

Gene Expression ◽

Critical Role ◽

Maternal Allele ◽

Detailed Mechanism ◽

Parental Allele ◽

Insulator Activity ◽

Allele Specific ◽

H19 Gene ◽

Imprinting Control Region ◽

Endogenous Locus

AbstractThe mouse Igf2/H19 locus is regulated by genomic imprinting, in which the paternally methylated H19 imprinting control region (ICR) plays a critical role in mono-allelic expression of the genes in the locus. Although the maternal allele-specific insulator activity of the H19 ICR in regulating imprinted Igf2 expression has been well established, the detailed mechanism by which the H19 ICR controls mono-allelic H19 gene expression has not been fully elucidated. In this study, we evaluated the effect of H19 ICR orientation on imprinting regulation in mutant mice in which the H19 ICR sequence was inverted at the endogenous locus. When the inverted-ICR allele was paternally inherited, the methylation level of the H19 promoter was decreased and the H19 gene was derepressed, suggesting that methylation of the H19 promoter is essential for complete repression of H19 gene expression. Unexpectedly, when the inverted allele was maternally inherited, the expression level of the H19 gene was lower than that of the WT allele, even though the H19 promoter remained fully hypomethylated. These observations suggested that the polarity of the H19 ICR is involved in controlling imprinted H19 gene expression on each parental allele, dependent or independent on DNA methylation of the H19 promoter.

Download Full-text

Faculty Opinions recommendation of Detection of Imprinted Genes by Single-Cell Allele-Specific Gene Expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727301661.793529626 ◽

2017 ◽

Author(s):

Hans van Bokhoven

Keyword(s):

Gene Expression ◽

Single Cell ◽

Specific Gene ◽

Imprinted Genes ◽

Specific Gene Expression ◽

Allele Specific

Download Full-text

Investigation of TAGAP gene polymorphism (rs1738074) in Turkish pediatric celiac patients

Turkish Journal of Biochemistry ◽

10.1515/tjb-2020-0419 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Melek Pehlivan ◽

Tülay K. Ayna ◽

Maşallah Baran ◽

Mustafa Soyöz ◽

Aslı Ö. Koçyiğit ◽

...

Keyword(s):

Pediatric Patients ◽

Disease Risk ◽

Polymerase Chain Reaction Method ◽

Control Group ◽

Healthy Children ◽

Single Nucleotide ◽

Significant Difference ◽

Allele Specific ◽

And Control

Abstract Objectives There are several hypotheses on the effects of the rs1738074 T/C single nucleotide polymorphism in the TAGAP gene; however, there has been no study on Turkish pediatric patients. We aimed to investigate the association of celiac disease (CD) and type 1 diabetes mellitus (T1DM) comorbidity with the polymorphism in the TAGAP gene of Turkish pediatric patients. Methods Totally, 127 pediatric CD patients and 100 healthy children were included. We determined the polymorphism by the allele-specific polymerase chain reaction method. We used IBM SPSS Statistics version 25.0 and Arlequin 3.5.2 for the statistical analyses. The authors have no conflict of interest. Results It was determined that 72% (n=154) of only CD patients had C allele, whereas 28% (n=60) had T allele. Of the patients with celiac and T1DM, 42.5% (n=17) and 57.5% (n=23) had T and C alleles, respectively. Of the individuals in control group, 67% (n=134) had C allele, whereas 33% (n=66) had T allele. Conclusions There was no significant difference in the genotype and allele frequencies between the patient and control groups (p>0.05). There was no significant association between the disease risk and the polymorphism in our study group.

Download Full-text

Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT

Scientific Reports ◽

10.1038/s41598-021-83459-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

M. Joseph Tomlinson ◽

Shawn W. Polson ◽

Jing Qiu ◽

Juniper A. Lake ◽

William Lee ◽

...

Keyword(s):

Broiler Chickens ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Specific Expression ◽

Single Nucleotide ◽

Allele Specific Expression ◽

Detection Tool ◽

Commercial Broiler ◽

Significant Phenomenon ◽

Allele Specific

AbstractDifferential abundance of allelic transcripts in a diploid organism, commonly referred to as allele specific expression (ASE), is a biologically significant phenomenon and can be examined using single nucleotide polymorphisms (SNPs) from RNA-seq. Quantifying ASE aids in our ability to identify and understand cis-regulatory mechanisms that influence gene expression, and thereby assist in identifying causal mutations. This study examines ASE in breast muscle, abdominal fat, and liver of commercial broiler chickens using variants called from a large sub-set of the samples (n = 68). ASE analysis was performed using a custom software called VCF ASE Detection Tool (VADT), which detects ASE of biallelic SNPs using a binomial test. On average ~ 174,000 SNPs in each tissue passed our filtering criteria and were considered informative, of which ~ 24,000 (~ 14%) showed ASE. Of all ASE SNPs, only 3.7% exhibited ASE in all three tissues, with ~ 83% showing ASE specific to a single tissue. When ASE genes (genes containing ASE SNPs) were compared between tissues, the overlap among all three tissues increased to 20.1%. Our results indicate that ASE genes show tissue-specific enrichment patterns, but all three tissues showed enrichment for pathways involved in translation.

Download Full-text