scholarly journals Mouse U2af1-rs1 is a neomorphic imprinted gene.

1997 ◽  
Vol 17 (2) ◽  
pp. 789-798 ◽  
Author(s):  
A Nabetani ◽  
I Hatada ◽  
H Morisaki ◽  
M Oshimura ◽  
T Mukai
Keyword(s):  
Genomic Imprinting ◽  
Genome Structure ◽  
Proximal Region ◽  
Paternal Allele ◽  
Chromosome 2 ◽  
Chromosome 11 ◽  
Imprinted Gene ◽  
Genome Region ◽  
Allele Specific ◽  
Allele Specific Methylation

The mouse U2af1-rs1 gene is an endogenous imprinted gene on the proximal region of chromosome 11. This gene is transcribed exclusively from the unmethylated paternal allele, while the methylated maternal allele is silent. An analysis of genome structure of this gene revealed that the whole gene is located in an intron of the Murr1 gene. Although none of the three human U2af1-related genes have been mapped to chromosome 2, the human homolog of Murr1 is assigned to chromosome 2. The mouse Murr1 gene is transcribed biallelically, and therefore it is not imprinted in neonatal mice. Allele-specific methylation is limited to a region around U2af1-rs1 in an intron of Murr1. These results suggest that in chromosomal homology and genomic imprinting, the U2af1-rs1 gene is distinct from the genome region surrounding it. We have proposed the neomorphic origin of the U2af1-rs1 gene by retrotransposition and the particular mechanism of genomic imprinting of ectopic genes.

scholarly journals Genomic Imprinting of Dopa decarboxylase in Heart and Reciprocal Allelic Expression with Neighboring Grb10

2007 ◽  
Vol 28 (1) ◽  
pp. 386-396 ◽  
Author(s):  
Trevelyan R. Menheniott ◽  
Kathryn Woodfine ◽  
Reiner Schulz ◽  
Andrew J. Wood ◽  
David Monk ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Promoter Region ◽  
Germ Line ◽  
Differential Methylation ◽  
Dopa Decarboxylase ◽  
Imprinted Genes ◽  
Chromosome 11 ◽  
Imprinted Gene ◽  
Line Methylation ◽  
Intron 1

ABSTRACT By combining a tissue-specific microarray screen with mouse uniparental duplications, we have identified a novel imprinted gene, Dopa decarboxylase (Ddc), on chromosome 11. Ddc_exon1a is a 2-kb transcript variant that initiates from an alternative first exon in intron 1 of the canonical Ddc transcript and is paternally expressed in trabecular cardiomyocytes of the embryonic and neonatal heart. Ddc displays tight conserved linkage with the maternally expressed and methylated Grb10 gene, suggesting that these reciprocally imprinted genes may be coordinately regulated. In Dnmt3L mutant embryos that lack maternal germ line methylation imprints, we show that Ddc is overexpressed and Grb10 is silenced. Their imprinting is therefore dependent on maternal germ line methylation, but the mechanism at Ddc does not appear to involve differential methylation of the Ddc_exon1a promoter region and may instead be provided by the oocyte mark at Grb10. Our analysis of Ddc redefines the imprinted Grb10 domain on mouse proximal chromosome 11 and identifies Ddc_exon1a as the first example of a heart-specific imprinted gene.

scholarly journals DNA demethylase ROS1 negatively regulates the imprinting of DOGL4 and seed dormancy in Arabidopsis thaliana

2018 ◽  
Vol 115 (42) ◽  
pp. E9962-E9970 ◽  
Author(s):  
Haifeng Zhu ◽  
Wenxiang Xie ◽  
Dachao Xu ◽  
Daisuke Miki ◽  
Kai Tang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Seed Dormancy ◽  
Genomic Imprinting ◽  
Dna Demethylation ◽  
Paternal Allele ◽  
Maternal Allele ◽  
Imprinted Gene ◽  
Differential Gene ◽  
Parent Of Origin ◽  
Dna Demethylase

Genomic imprinting is a form of epigenetic regulation resulting in differential gene expression that reflects the parent of origin. In plants, imprinted gene expression predominantly occurs in the seed endosperm. Maternal-specific DNA demethylation by the DNA demethylase DME frequently underlies genomic imprinting in endosperm. Whether other more ubiquitously expressed DNA demethylases regulate imprinting is unknown. Here, we found that the DNA demethylase ROS1 regulates the imprinting of DOGL4. DOGL4 is expressed from the maternal allele in endosperm and displays preferential methylation and suppression of the paternal allele. We found that ROS1 negatively regulates imprinting by demethylating the paternal allele, preventing its hypermethylation and complete silencing. Furthermore, we found that DOGL4 negatively affects seed dormancy and response to the phytohormone abscisic acid and that ROS1 controls these processes by regulating DOGL4. Our results reveal roles for ROS1 in mitigating imprinted gene expression and regulating seed dormancy.

ANALYSIS OF PATERNAL ALLELE-SPECIFIC METHYLATION AT MOUSE Gtl2 DURING EARLY EMBRYOGENESIS

2007 ◽  
Vol 77 (Suppl_1) ◽  
pp. 165-165
Author(s):  
Kamila Nowak ◽  
Geneva Stein ◽  
Lu Mei He ◽  
Elizabeth Powell ◽  
Tamara Davis
Keyword(s):  
Early Embryogenesis ◽  
Paternal Allele ◽  
Allele Specific ◽  
Allele Specific Methylation

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

2020 ◽  
Vol 10 (11) ◽  
pp. 4037-4047
Author(s):  
Jinsoo Ahn ◽  
In-Sul Hwang ◽  
Mi-Ryung Park ◽  
In-Cheol Cho ◽  
Seongsoo Hwang ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Genomic Region ◽  
Proximal Region ◽  
Chromosome 9 ◽  
Rna Seq ◽  
Parental Allele ◽  
Genome Bisulfite Sequencing ◽  
Allele Specific ◽  
Chromosome Regions ◽  
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.

Inactive Allele-Specific Methylation and Chromatin Structure of the Imprinted GeneU2af1-rs1on Mouse Chromosome 11

Genomics ◽  
1996 ◽  
Vol 35 (1) ◽  
pp. 248-252 ◽  
Author(s):  
Hideo Shibata ◽  
Kiyoshi Yoshino ◽  
Shoichi Sunahara ◽  
Yoichi Gondo ◽  
Motoya Katsuki ◽  
...  
Keyword(s):  
Mouse Chromosome ◽  
Chromatin Structure ◽  
Chromosome 11 ◽  
Allele Specific ◽  
Allele Specific Methylation ◽  
Mouse Chromosome 11

scholarly journals Association of allele-specific methylation of the ASNS gene with asparaginase sensitivity and prognosis in T-ALL

2021 ◽  
Author(s):  
Koshi Akahane ◽  
Shunsuke Kimura ◽  
Kunio Miyake ◽  
Atsushi Watanabe ◽  
Keiko Kagami ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Cell Lines ◽  
Cpg Island ◽  
Lymphoblastic Leukemia ◽  
Methylation Status ◽  
Aberrant Methylation ◽  
Imprinted Gene ◽  
Allele Specific ◽  
Allele Specific Methylation

Asparaginase therapy is a key component of chemotherapy for T-cell acute lymphoblastic leukemia (T-ALL) patients. Asparaginase depletes serum asparagine by deamination into aspartic acid. Normal hematopoietic cells can survive due to asparagine synthetase (ASNS) activity, while leukemia cells are supposed to undergo apoptosis due to silencing of the ASNS gene. Since the ASNS gene has a typical CpG island in its promoter, its methylation status in T-ALL cells may be associated with asparaginase sensitivity. Thus, we investigated the significance of ASNS methylation status in asparaginase sensitivity of T-ALL cell lines and prognosis of childhood T-ALL. Sequencing of bisulfite PCR products using next-generation sequencing technology in 22 T-ALL cell lines revealed a stepwise allele-specific methylation of the ASNS gene, in association with an aberrant methylation of a 7q21 imprinted gene cluster. T-ALL cell lines with ASNS hypermethylation status showed significantly higher in vitro l-asparaginase sensitivity in association with insufficient asparaginase-induced upregulation of ASNS gene expression and lower basal ASNS protein expression. A comprehensive analysis of diagnostic samples from childhood T-ALL patients in Japanese cohorts (n = 77) revealed that methylation of the ASNS gene was associated with an aberrant methylation of the 7q21 imprinted gene cluster. In childhood T-ALL patients in Japanese cohorts (n = 75), ASNS hypomethylation status was significantly associated with poor therapeutic outcome, and all cases with poor prognostic SPI1 fusion exclusively showed ASNS hypomethylation status. These observations demonstrate that ASNS hypomethylation status is associated with asparaginase resistance and is a poor prognostic biomarker in childhood T-ALL.

scholarly journals Genomic Imprinting Controls Matrix Attachment Regionsin the Igf2Gene

2003 ◽  
Vol 23 (24) ◽  
pp. 8953-8959 ◽  
Author(s):  
Michaël Weber ◽  
Hélène Hagège ◽  
Adele Murrell ◽  
Claude Brunel ◽  
Wolf Reik ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Dna Sequences ◽  
Nuclear Matrix ◽  
Regulatory Elements ◽  
Paternal Allele ◽  
Matrix Attachment Regions ◽  
Binding Assays ◽  
Allele Specific ◽  
Imprinting Control Region ◽  
Matrix Fraction

ABSTRACT Genomic imprinting at the Igf2/H19 locus originates from allele-specific DNA methylation, which modifies the affinity of some proteins for their target sequences. Here, we show that AT-rich DNA sequences located in the vicinity of previously characterized differentially methylated regions (DMRs) of the imprinted Igf2 gene are conserved between mouse and human. These sequences have all the characteristics of matrix attachment regions (MARs), which are known as versatile regulatory elements involved in chromatin structure and gene expression. Combining allele-specific nuclear matrix binding assays and real-time PCR quantification, we show that retention of two of these Igf2 MARs (MAR0 and MAR2) in the nuclear matrix fraction depends on the tissue and is specific to the paternal allele. Furthermore, on this allele, the Igf2 MAR2 is functionally linked to the neighboring DMR2 while, on the maternal allele, it is controlled by the imprinting-control region. Our work clearly demonstrates that genomic imprinting controls matrix attachment regions in the Igf2 gene.

Transient establishment of imprinted DNA methylation of transgenic human IC1 sequence in mouse during the pre-implantation period

2020 ◽  
Author(s):  
Katsuhiko Hirakawa ◽  
Hitomi Matsuzaki ◽  
Keiji Tanimoto
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Blastocyst Stage ◽  
Paternal Allele ◽  
Human Sequence ◽  
Allele Specific ◽  
Imprinting Control Region ◽  
Equivalent Sequence ◽  
Allele Specific Methylation ◽  
Implantation Period

Abstract Monoallelic gene expression at the Igf2/H19 locus is controlled by paternal allele-specific DNA methylation of the imprinting control region (H19 ICR) that is established during spermatogenesis. We demonstrated that the H19 ICR fragment in transgenic mice acquires allele-specific methylation only after fertilization, which is essential for maintaining its allelic methylation during early embryogenesis. We identified a DNA element required for establishing post-fertilization methylation within a 118 bp (m118) region. A previously generated knock-in mouse whose endogenous H19 ICR was substituted with the human H19 ICR (hIC1; 4.8 kb) sequence revealed that the hIC1 sequence was partially methylated in sperm, although this methylation was lost by the blastocyst stage, which we assume is due to a lack of an m118-equivalent sequence in the hIC1 transgene. To identify a cis sequence involved in post-fertilization methylation within the hIC1 region, we generated three transgenic mouse lines (TgM): one carrying an 8.8 kb hIC1 sequence joined to m118 (hIC1+m118), one with the 8.8 kb hIC1, and one with the 5.8 kb hIC1 sequence joined to m118 (hIC1–3′+m118). We found that the hIC1–3′ region was resistant to de novo DNA methylation throughout development. In contrast, the 5′ portion of the hIC1 (hIC1–5′) in both hIC1+m118 and hIC1 TgM were preferentially methylated on the paternal allele only during preimplantation. As DNA methylation levels were higher in hIC1+m118, the m118 sequence could also induce imprinted methylation of the human sequence. Most importantly, the hIC1–5′ sequence appears to possess an activity equivalent to that of m118.

scholarly journals Paternal allele-specific methylation at Rasgrf1 is present in monoalleleic and biallelic tissues

2008 ◽  
Vol 319 (2) ◽  
pp. 571
Author(s):  
Tamara L. Davis ◽  
Lauren Dockery ◽  
Rachel Horton ◽  
Christina Harview ◽  
Nelly Khaselev
Keyword(s):  
Paternal Allele ◽  
Allele Specific ◽  
Allele Specific Methylation

Localization of mouse imprinted gene U2af1-rs1 to A3.2-4 band of Chromosome 11 by FISH

1994 ◽  
Vol 5 (10) ◽  
pp. 655-655 ◽  
Author(s):  
M. Tada ◽  
T. Tada ◽  
N. Takagi ◽  
Y. Hayashizaki ◽  
H. Shibata ◽  
...  
Keyword(s):  
Chromosome 11 ◽  
Imprinted Gene
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