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The Estrogen receptor alpha cistrome defined by DamIP

ABSTRACT: We have developed a new method to study DNA-protein interaction in vivo called DamIP, which is based on fusing a protein of interest to a mutant form of DNA adenine methylatransferase (Dam) from E. coli. We showed previously that DamIP can efficiently identify in vivo binding sites of Dam-tethered human estrogen receptor alpha (hERα). In current study, we present the cistrome of hERα determined by DamIP and high throughput sequencing (DamIP-seq). The DamIP-seq defined hERα cistrome overlaps significantly with those determined by ChIP-chip or ChIP-seq, but identifies many new binding regions. As shown by conventional ChIP assay, many DamIP-seq unique hERα binding regions show relatively stable hERα binding, whereas DamIP-seq misses some regions with very transient hERα binding. The methyl-adenine modifications introduced by Dam are stable and do not decrease over 12 days. In summary, the current study provides both an alternate view of the hERα cistrome to further understand the mechanism of hERα mediated transcription, and a new tool to explore other transcriptional factors and cofactors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE33804 | GEO | 2011/11/19

SECONDARY ACCESSION(S): PRJNA148121

REPOSITORIES: GEO

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Project description:Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem-cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila Kc cells. We found that Pc associates with large genomic regions of up to ~150kb in size, hereafter referred to as âPc-domainsâ. Sce and esc accompany Pc in most of these domains. PcG-bound chromatin is trimethylated at histone H3 lysine 27 and in general transcriptionally silent. Furthermore, PcG proteins preferentially bind to developmental genes. Many of these encode transcriptional regulators and key components of signal transduction pathways, including Wingless, Hedgehog, Notch and Delta. We also identify several new putative functions of PcG proteins, such as in steroid hormone biosynthesis. These results highlight the extensive involvement of PcG proteins in the coordination of development through the formation of large repressive chromatin domains. Keywords: DamID, Chromatin immunoprecipitation, ChIP-chip To study PcG binding profiles we used DamID, which is based on the ability of a chromatin protein fused to E.coli DNA adenine methyltransferase (Dam) to methylate the native binding site of the chromatin protein. Dam-fusion proteins are expressed at very low levels to avoid mistargeting. Subsequently, methylated DNA fragments are isolated, labeled and hybridized to a microarray. Methylated DNA fragments from cells transfected with Dam alone served as reference. Genomic binding sites of the protein can then be identified based on the targeted methylation pattern. For detailed background information on DamID, see: van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat Genet 27, 304-8 (2001); van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat Biotechnol 18, 424-8 (2000).

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The Estrogen receptor alpha cistrome defined by DamIP

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