Chromatin modification of the human imprinted NDN (necdin) gene detected by in vivo footprinting

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Abstract
Allele‐specific transcription is a characteristic feature of imprinted genes. Many imprinted genes are also transcribed in a tissue‐ or cell type‐specific manner. Overlapping epigenetic signals must, therefore, modulate allele‐specific and tissue‐specific expression at imprinted loci. In addition, long‐range interactions with an Imprinting Center (IC) may influence transcription, in an allele‐specific or cell‐type specific manner. The IC on human chromosome 15q11 controls parent‐of‐origin specific allelic identity of a set of genes located in cis configuration within 2 Mb. We have now examined the chromatin accessibility of the promoter region of one of the Imprinting Centre‐controlled genes, NDN encoding necdin, using in vivo DNA footprinting to identify sites of DNA–protein interaction and altered chromatin configuration. We identified sites of modified chromatin that mark the parental alleles in NDN‐expressing cells, and in cells in which NDN is not expressed. Our results suggest that long‐lasting allele‐specific marks and more labile tissue‐specific marks layer epigenetic information that can be discriminated using DNA footprinting methodologies. Sites of modified chromatin mark the parental alleles in NDN‐expressing cells, and in cells in which NDN is not expressed. Our results suggest that a layering of epigenetic information controls allele‐ and tissue‐specific gene expression of this imprinted gene. J. Cell. Biochem. 94: 1046–1057, 2005.