Identification of clustered YY1 binding sites in imprinting control regions

Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence features derived from a tandem array of YY1 binding sites of Peg3-DMR (differentially methylated region) le...

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Bibliographic Details
Published in:Genome Research 2006-07, Vol.16 (7), p.901-911
Main Authors: Kim, Jeong Do, Hinz, Angela K, Bergmann, Anne, Huang, Jennifer M, Ovcharenko, Ivan, Stubbs, Lisa, Kim, Joomyeong
Format: Article
Language:English
Subjects:
Alleles
Animals
Binding Sites
Chromatin Immunoprecipitation
Cluster Analysis
DNA Methylation
Enhancer Elements, Genetic
Female
Genome
Genome, Human
Genomic Imprinting
Humans
Insulator Elements - genetics
Letter
Male
Mice
Promoter Regions, Genetic
Rats
Transcription Factors
YY1 Transcription Factor - genetics
YY1 Transcription Factor - metabolism
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Summary:Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence features derived from a tandem array of YY1 binding sites of Peg3-DMR (differentially methylated region) led us to identify three additional clustered YY1 binding sites, which are also localized within the DMRs of Xist, Tsix, and Nespas. These regions have been shown to play a critical role as ICRs for the regulation of surrounding genes. These ICRs have maintained a tandem array of YY1 binding sites during mammalian evolution. The in vivo binding of YY1 to these regions is allele specific and only to the unmethylated active alleles. Promoter/enhancer assays suggest that a tandem array of YY1 binding sites function as a potential orientation-dependent enhancer. Insulator assays revealed that the enhancer-blocking activity is detected only in the YY1 binding sites of Peg3-DMR but not in the YY1 binding sites of other DMRs. Overall, our identification of three additional clustered YY1 binding sites in imprinted domains suggests a significant role for YY1 in mammalian genomic imprinting.
ISSN:1088-9051
1549-5469
1549-5477
DOI:10.1101/gr.5091406