How DNA methylation patterns are shaped during development - how methylation and demethylation are targeted to specific loci at specific times - is not known. Germ cells establish methylation imprints depending on the sex of the gonad after erasing the male and female -specific marks inherited from the previous generation. Our main hypothesis is that DNA cytosine 5-hydroxymethylation and chromatin composition are important components of the imprint cycle, being involved in the erasure and establishment phases in germ cells and in the maintenance phase in the soma. To demonstrate this, we will analyze DNA methylation, DNA cytosine hydroxymethylation and chromatin globally and at specific imprinted genes in germ cells and somatic cells. To test the role of specific epigenetic modifiers in the cycle of imprinting, we will genetically perturb these functions during the erasure, establishment and maintenance phases of the imprinting cycle. These results collectively will help understand how DNA methylation, DNA hydroxymethylation and chromatin marks collaborate in the epigenetic remodeling of germ cells and in erasing, establishing and maintaining genomic imprints. Correct global epigenetic remodeling and imprint reseting during embryonic-fetal germ cell development is essential for the health of the next generation and for future generations.

Public Health Relevance

We propose to test the role of DNA cytosine hydroxymethylation and chromatin in the erasure, establishment and maintenance of genomic imprints. Experiments using genome-wide mapping methods, novel allele- specific assays and mouse genetic tools will collectively help understand how DNA methylation, DNA hydroxymethylation and chromatin marks collaborate in the global epigenetic remodeling of germ cells and in erasing, establishing and maintaining genomic imprints. Correct global epigenetic remodeling and imprint resetting during embryonic-fetal germ cell development is essential for the health of the next generation and for future generations.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM064378-09A1
Application #
8291937
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2002-04-01
Project End
2016-04-30
Budget Start
2012-05-01
Budget End
2013-04-30
Support Year
9
Fiscal Year
2012
Total Cost
$349,440
Indirect Cost
$141,440
Name
City of Hope/Beckman Research Institute
Department
Type
DUNS #
027176833
City
Duarte
State
CA
Country
United States
Zip Code
91010
Hahn, Maria A; Szabó, Piroska E; Pfeifer, Gerd P (2014) 5-Hydroxymethylcytosine: a stable or transient DNA modification? Genomics 104:314-23
Tran, Diana A; Bai, Angela Y; Singh, Purnima et al. (2014) Characterization of the imprinting signature of mouse embryo fibroblasts by RNA deep sequencing. Nucleic Acids Res 42:1772-83
Singh, Purnima; Li, Arthur X; Tran, Diana A et al. (2013) De novo DNA methylation in the male germ line occurs by default but is excluded at sites of H3K4 methylation. Cell Rep 4:205-19
Lee, Dong-Hoon; Tran, Diana A; Singh, Purnima et al. (2011) MIRA-SNuPE, a quantitative, multiplex method for measuring allele-specific DNA methylation. Epigenetics 6:212-23
Abe, Masanobu; Tsai, Shirley Y; Jin, Seung-Gi et al. (2011) Sex-specific dynamics of global chromatin changes in fetal mouse germ cells. PLoS One 6:e23848
Iqbal, Khursheed; Jin, Seung-Gi; Pfeifer, Gerd P et al. (2011) Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine. Proc Natl Acad Sci U S A 108:3642-7
Singh, Purnima; Wu, Xiwei; Lee, Dong-Hoon et al. (2011) Chromosome-wide analysis of parental allele-specific chromatin and DNA methylation. Mol Cell Biol 31:1757-70
Singh, Purnima; Cho, Janice; Tsai, Shirley Y et al. (2010) Coordinated allele-specific histone acetylation at the differentially methylated regions of imprinted genes. Nucleic Acids Res 38:7974-90
Singh, Purnima; Han, Li; Rivas, Guillermo E et al. (2010) Allele-specific H3K79 Di- versus trimethylation distinguishes opposite parental alleles at imprinted regions. Mol Cell Biol 30:2693-707
Lee, Dong-Hoon; Singh, Purnima; Tsark, Walter M K et al. (2010) Complete biallelic insulation at the H19/Igf2 imprinting control region position results in fetal growth retardation and perinatal lethality. PLoS One 5:e12630

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