Oncogenic potential of yin yang 1 mediated through control of imprinted genes

The transcription factor Yin Yang (YY) 1 is one of the most evolutionarily well-conserved DNA binding proteins that is ubiquitously expressed among different tissue types. YY1 functions as a critical regulator for a diverse set of genes, making its role in the cancerous environment elusive. Recent studies have demonstrated that clusters of YY1 binding sites are overrepresented in imprinted gene loci. These clustered binding sites may function as a molecular rheostat with respect to YY1 protein levels. YY1 levels were documented to be altered in various tumor tissues in conjunction with the transcriptional levels of the imprinted genes it regulates. This review highlights the unexplored mechanism through which fluctuations in YY1 protein levels alter the transcriptional status of imprinted genes containing clustered YY1 binding sites, which potentially could affect cancer development and/or progression. © 2011 by Begell House, Inc

DNA-binding motif and target genes of the imprinted transcription factor PEG3

The Peg3 gene is expressed only from the paternally inherited allele located on proximal mouse chromosome 7. The PEG3 protein encoded by this imprinted gene is predicted to bind DNA based on its multiple zinc finger motifs and nuclear localization. In the current study, we demonstrated PEG3\u27s DNA-binding ability by characterizing its binding motif and target genes. We successfully identified target regions bound by PEG3 from mouse brain extracts using chromatin immunoprecipitation analysis. PEG3 was demonstrated to bind these candidate regions through the consensus DNA-binding motif AGTnnCnnnTGGCT. In vitro promoter assays established that PEG3 controls the expression of a given gene through this motif. Consistent with these observations, the transcriptional levels of a subset of the target genes are also affected in a mutant mouse model with reduced levels of PEG3 protein. Overall, these results confirm PEG3 as a DNA-binding protein controlling specific target genes that are involved in distinct cellular functions. © 2012

Identification of PBX1 Target Genes in Cancer Cells by Global Mapping of PBX1 Binding Sites

PBX1 is a TALE homeodomain transcription factor involved in organogenesis and tumorigenesis. Although it has been shown that ovarian, breast, and melanoma cancer cells depend on PBX1 for cell growth and survival, the molecular mechanism of how PBX1 promotes tumorigenesis remains unclear. Here, we applied an integrated approach by overlapping PBX1 ChIP-chip targets with the PBX1-regulated transcriptome in ovarian cancer cells to identify genes whose transcription was directly regulated by PBX1. We further determined if PBX1 target genes identified in ovarian cancer cells were co-overexpressed with PBX1 in carcinoma tissues. By analyzing TCGA gene expression microarray datasets from ovarian serous carcinomas, we found co-upregulation of PBX1 and a significant number of its direct target genes. Among the PBX1 target genes, a homeodomain protein MEOX1 whose DNA binding motif was enriched in PBX1-immunoprecipicated DNA sequences was selected for functional analysis. We demonstrated that MEOX1 protein interacts with PBX1 protein and inhibition of MEOX1 yields a similar growth inhibitory phenotype as PBX1 suppression. Furthermore, ectopically expressed MEOX1 functionally rescued the PBX1-withdrawn effect, suggesting MEOX1 mediates the cellular growth signal of PBX1. These results demonstrate that MEOX1 is a critical target gene and cofactor of PBX1 in ovarian cancers

Oncogenic Potential of Yin Yang 1 Mediated Through Control of Imprinted Genes

The transcription factor Yin Yang (YY) 1 is one of the most evolutionarily well-conserved DNA binding proteins that is ubiquitously expressed among different tissue types. YY1 functions as a critical regulator for a diverse set of genes, making its role in the cancerous environment elusive. Recent studies have demonstrated that clusters of YY1 binding sites are overrepresented in imprinted gene loci. These clustered binding sites may function as a molecular rheostat with respect to YY1 protein levels. YY1 levels were documented to be altered in various tumor tissues in conjunction with the transcriptional levels of the imprinted genes it regulates. This review highlights the unexplored mechanism through which fluctuations in YY1 protein levels alter the transcriptional status of imprinted genes containing clustered YY1 binding sites, which potentially could affect cancer development and/or progression

Identification of an Evolutionarily Conserved Cis-Regulatory Element Controlling the Peg3 Imprinted Domain

<div><p>The mammalian Peg3 domain harbors more than 20 evolutionarily conserved regions (ECRs) that are spread over the 250-kb genomic interval. The majority of these ECRs are marked with two histone modifications, H3K4me1 and H3K27ac, suggesting potential roles as distant regulatory elements for the transcription of the nearby imprinted genes. In the current study, the chromatin conformation capture (3C) method was utilized to detect potential interactions of these ECRs with the imprinted genes. According to the results, one region, ECR18, located 200-kb upstream of Peg3 interacts with the two promoter regions of Peg3 and Zim2. The observed interaction is most prominent in brain, but was also detected in testis. Histone modification and DNA methylation on ECR18 show no allele bias, implying that this region is likely functional on both alleles. In vitro assays also reveal ECR18 as a potential enhancer or repressor for the promoter of Peg3. Overall, these results indicate that the promoters of several imprinted genes in the Peg3 domain interact with one evolutionarily conserved region, ECR18, and further suggest that ECR18 may play key roles in the transcription and imprinting control of the Peg3 domain as a distant regulatory element.</p> </div

Interaction of the promoter of Peg3/Usp29 with ECRs.

<p>Potential long-range interaction of the Peg3 promoter was tested using the +1 oligonucleotide as a base primer along with a set of oligonucleotides that are derived from multiple regions of the Peg3 domain. The initial survey was performed with a fixed number of cycles (36 cycles) using the three libraries derived from neonatal brain, testis and liver, and these results are shown on bottom. Quantitative PCR analyses were also performed. The results are summarized with graphs on top. For this series of analyses, the Ct (threshold cycle) value for each primer set was first calculated from the control library with ligation, and subsequently used as an internal control for the normalization of the Ct values derived from the three tissue libraries.</p

ECR18 as a shared enhancer for the Peg3 domain.

<p>(<b>A</b>) The diagram represents the paternal allele of the Peg3 domain with each gene being indicated with a horizontal arrow. The transcriptional level of each gene is also indicated with a vertical arrow: the thicker or thinner arrow indicates higher or lower expression levels for a given gene. Potential interaction between ECR18 and the promoter of each gene is indicated by a dotted line. (<b>B</b>) The diagram represents the paternal allele of Peg3 domain in the mutant animals that have a deletion in the Peg3-DMR, an ICR for the Peg3 domain. (<b>C</b>) The diagram represents the maternal allele of the Peg3 domain in the wild-type animals. The maternal allele in the mutant animals is not shown since the mutational effects are very minimal.</p

Epigenetic modifications and evolutionary conservation of ECR18.

<p>(<b>A</b>) Immunoprecipitated DNA with anti-H3K27ac antibodies was first amplified with PCR, and the subsequent PCR products were digested with an enzyme to differentiate parental alleles for a given locus. The promoter regions of imprinted genes show mono-allelic or one allele-biased patterns whereas ECR18 shows a bi-allelic pattern similar to those seen the input DNA. (<b>B</b>) DNA mthylation analysis on ECR18. The bisulfite-converted DNA from male and female neonates were used for PCR amplification. The amplified PCR products were digested with <i>Taq</i>I, and the digestion by this enzyme indicates methylation on the original DNA. (<b>C</b>) The panel represents a snapshot of UCSC Genome Browser showing the peaks of the two histone modifications, H3K27ac and H3K4me1, detected in the human PEG3 domain.</p

3C strategy for the Peg3 domain.

<p>The upper diagram details the genomic region covered by the two BAC clones (178C5 and 117K9) that have been used for preparing two control libraries, the relative positions of 18 ECRs, the relative positions of oligonucleotides that have been used for 3C experiments. Each oligonucleotide has been named with a numeric value to indicate its relative position to the transcription start site of Peg3. The gel images on the bottom panel show the results derived from the two sets of control experiments testing the efficiency and compatibility of each primer set. For both control experiments, the +1 oligonucleotide was used as a base primer, which intends to detect long-range interaction between the Peg3 promoter and other regions.</p