Location: Children's Nutrition Research CenterTitle: Characterization of "cis"-regulatory elements ("c"RE) associated with mammary gland function) Author
Submitted to: Meeting Abstract
Publication Type: Abstract only
Publication Acceptance Date: 9/18/2013
Publication Date: 10/1/2013
Citation: Rijnkels, M., Molenaar, A., Singh, K., Dobson, J., Oden, K., Jeyasankar, C., Freeman-Zadrowski, C., Lemay, D. 2013. Characterization of "cis"-regulatory elements ("c"RE) associated with mammary gland function [abstract]. Procedings of the 10th International Symposium on Milk Genomics and Human Health, October 1-3, 2013, Davis, California. Interpretive Summary:
Technical Abstract: The Bos taurus genome assembly has propelled dairy science into a new era; still, most of the information encoded in the genome has not yet been decoded. The human Encyclopedia of DNA Elements (ENCODE) project has spearheaded the identification and annotation of functional genomic elements in the human genome. This has shown that a genome sequence assembly is just the first step on the path of connecting the genetic code to molecular mechanisms for a full understanding of biology. The same can be expected of cattle. In this project we plan to identify cRE relevant to bovine lactation. An improved understanding and knowledge of gene regulatory networks and cRE in the mammary gland of cattle would allow for direct genetic selection of traits, particularly those that are expensive to select based on phenotype or low heritability. It would also lead to a more complete understanding of mammary gland biology, enabling novel strategies to improve the quality, efficiency, and sustainability of milk production. The objectives are: (1) Identify cRE in the non-lactating and lactating bovine mammary gland genome-wide by DNase-seq., (2) Identify the non-lactating and lactating mammary gland transcriptomes by whole RNA-seq., (3) Annotate and characterize mammary gland cRE by computational analysis, identifying high-resolution genome-wide in-vivo footprints of DNA-binding factors, and overlapping SNPs. To date we have harvested non-lactating mammary gland samples from 22 approximately 15-month-old heifers before insemination and the same animals at peak lactation, and isolated mammary epithelial organoids. Using these organoids we optimized and are preforming DNaseI experiments for DNase-seq, and isolated RNA and small-RNA for RNA-seq. Tissue sections were processed for histology and blood sample were also collected.