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United States Department of Agriculture

Agricultural Research Service


item Kabotyanski, Elena
item Le, Tanya
item Elnitski, Laura
item Miller, Webb
item Rosen, Jeffrey
item Rijnkels, Monique

Submitted to: Cold Spring Harbor Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 5/1/2005
Publication Date: 6/1/2005
Citation: Kabotyanski, E., Le, T., Elnitski, L., Miller, W., Rosen, J.M., Rijnkels, M. 2004. Identification of functional elements in a mammalian specific gene cluster [abstract]. Cold Spring Harbor Meeting. p. 51.

Interpretive Summary: Interpretive Summary not needed for this 115.

Technical Abstract: The caseins (CSN) are located in an approximately 1MB mammalian specific domain on the human genome (~700kb in mouse genome). This domain harbors about 20 genes, is AT-rich (<37% GC), and has a repeat content slightly below average (39%) [1]. The genes in the casein domain encode secreted proteins expressed in tissues with an epithelial component (predominantly in the mammary and salivary glands). Besides the nutritional function of the caseins many of these proteins have host defense properties as well as the capability to bind calcium. The CSN-region is characterized by its high evolutionary divergence. Comparative sequence analyses have shown that this domain has a conserved synteny and organization in human, chimpanzee, mouse, rat, rabbit, cow, dog, and presumably most mammals. However, comparative analysis with the chicken, fugu and zebra fish genomes indicated the absence of this whole domain. By comparing the genomic sequence of human, mouse, rat and cow we identified 13 evolutionary conserved regions (ECR's) at intergenic positions [1]. These might play a role in gene regulation based on their interspecies conservation. Preliminary analyses including more mammalian species have confirmed the conservation of a number of these ECR's. Chromatin remodeling is a hallmark of gene expression. The acetylation, methylation and phosphorylation status of the tails of the core histones H3 and H4 are markers for the chromatin conformation and remodeling. To identify functional elements in the CSN-domain we have initiated the study of chromatin remodeling in the CSN-domain. We are using Chromatin Immuno-Precipitation (ChIP) assays, to identify histone modifications at the ECR's and promoters as a function of the developmental stage and tissue/cell type. Transfection assays in tissue culture have identified an enhancer activity for the human and bovine beta-casein enhancer (BCE) and potential chromatin remodeling involvement [2,3]. We used the BCE as paradigm for the analysis of the other ECR's. Preliminary experiments in murine mammary epithelial cells (HC11) have shown a lactogenic hormone dependant acetylation of the beta-casein proximal promoter and BCE, and recruitment of Signal Transducer and Activator of Transcription (STAT) 5, a transcription factor known to be important for milk protein gene expression. We have initiated studies to investigate this region and others in lactating mouse mammary gland tissue in comparison to mouse liver. 1. Rijnkels, M., et al. Genomics, 2003. 82: p. 417-432. 2. Schmidhauser, C., et al. Mol. Biol. Cell., 1992. 3(6): p. 699-709. 3. Winklehner-Jennewein, P., et al. Gene, 1998. 217(1-2): p. 127-39.

Last Modified: 06/23/2017
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