Genomic imprinting is closely associated with human genetic disorders due to its functional hemizygosity. The Peg3 domain on human chromosome 19q13.4/proximal mouse chromosome 7 is also associated with several imprinting-related genetic disorders, including frequent loss of human PEG3 expression in the patients of glioma, breast and ovarian cancers. Thus, the long-term objective of this project is to understand the mechanisms controlling the imprinting of the Peg3 domain. In the previous funding cycle, we predicted that the Peg3 domain is likely controlled by one potential ICR (Imprinting Control Region), the Peg3-DMR (Differentially Methylated Region). We subsequently demonstrated that deletion of the Peg3-DMR has a global impact on the transcription of the Peg3 domain. Paternal and maternal transmission of this targeted deletion also resulted in decreased and increased growth rates of the mouse, respectively, an imprinting phenotype associated with proximal mouse chromosome 7. We also discovered that this potential ICR has a very unusual tandem array of YY1 binding sites, and that reducing the in vivo levels of YY1 protein during oogenesis resulted in target-specific DNA hypomethylation on the Peg3-DMR. Based on these observations, we hypothesize 1) that the imprinting of the Peg3 domain is controlled by the Peg3-DMR and 2) that this control requires YY1 as a main trans factor for targeting de novo DNA methylation during oogenesis. In the current proposal, we will test these hypotheses with the following three aims.
Aim1 will further characterize the ICR roles played by the Peg3-DMR using the mutant mice lacking the Peg3-DMR.
Aim2 will dissect the exact contributions of YY1 to the observed ICR roles of the Peg3-DMR by generating another KO allele with mutated YY1 sites.
Aim3 will investigate potential mechanisms by which YY1 establishes and maintains the allele-specific DNA methylation of the Peg3-DMR. The results from these experiments will provide valuable insights regarding previously unnoticed roles for YY1 in genomic imprinting as well as human genetic disorders linked to the Peg3 domain.

Public Health Relevance

A small number of mammalian genes (less than 200) are not functionally equal between the two parental alleles due to an unusual dosage control mechanism, genomic imprinting. The current proposal is aiming to characterize regulatory mechanisms of genomic imprinting.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Louisiana State University A&M Col Baton Rouge
Schools of Arts and Sciences
Baton Rouge
United States
Zip Code
Lee, Suman; Kim, Joomyeong (2016) NGS-based deep bisulfite sequencing. MethodsX 3:1-7
He, Hongzhi; Ye, An; Kim, Hana et al. (2016) PEG3 Interacts with KAP1 through KRAB-A. PLoS One 11:e0167541
Bakshi, Arundhati; Herke, Scott W; Batzer, Mark A et al. (2016) DNA methylation variation of human-specific Alu repeats. Epigenetics 11:163-73
Perera, Bambarendage P U; Kim, Joomyeong (2016) Next-generation sequencing-based 5' rapid amplification of cDNA ends for alternative promoters. Anal Biochem 494:82-4
He, Hongzhi; Ye, An; Kim, Joomyeong (2016) Transcriptional Truncation of the Long Coding Imprinted Gene Usp29. PLoS One 11:e0158004
He, Hongzhi; Perera, Bambarendage P U; Ye, An et al. (2016) Parental and sexual conflicts over the Peg3 imprinted domain. Sci Rep 6:38136
Perera, Bambarendage P U; Kim, Joomyeong (2016) Alternative promoters of Peg3 with maternal specificity. Sci Rep 6:24438
Perera, Bambarendage P U; Kim, Joomyeong (2016) Sex and Tissue Specificity of Peg3 Promoters. PLoS One 11:e0164158
Kim, Hana; Ekram, Muhammad B; Bakshi, Arundhati et al. (2015) AEBP2 as a transcriptional activator and its role in cell migration. Genomics 105:108-15
Frey, Wesley D; Kim, Joomyeong (2015) Tissue-Specific Contributions of Paternally Expressed Gene 3 in Lactation and Maternal Care of Mus musculus. PLoS One 10:e0144459

Showing the most recent 10 out of 54 publications