Identification and characterization of the role of noncoding RNA for gene regulation of metabolic processes in cattle

• Applicants: Professorin Dr. Christa Kühn; Dr. Rosemarie Weikard
• Subject Area: Animal Breeding, Animal Nutrition, Animal Husbandry
• Term: from 2015 to 2021
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 283644157

For the regulation of gene expression in different cell and tissue types and phenotypes different chromatin architecture as well as DNA interactions with proteins and noncoding RNAs (ncRNA) are important. Since the global RNA sequencing technology of the next generation (RNAseq) has been introduced the number of noncoding transcripts discovered in the transcriptomes of human and model animals is rapidly increasing. Numerous studies showed that besides the short noncoding RNAs, the long noncoding RNAs (lnRNAs) are also an important functional component involved in relevant molecular regulatory processes and associated with specific differentiation and growth processes and with the pathogenesis of a variety of diseases. Based on current knowledge regarding functional relevance of lncRNAs in other species we postulate that these noncoding transcripts may also play a regulatory role in the modulation of complex metabolic pattern characterizing different phenotypes in cattle. The aim of this project is to identify lncRNAs and lncRNAs-associated mechanisms that regulate metabolism and energy partitioning of trait-differentiated cattle, which may modulate efficiency of energy and feed transformation and the different genetic-physiological make-up of divergent metabolic types in cattle. Compared to the well annotated transcriptomes of human and mouse the bovine transcriptome is still inadequately annotated and insufficiently identified. To establish comprehensive transcriptome catalogs we will use the hypothesis-free approach of global transcriptome sequencing to identify and annotate yet unknown and noncoding transcripts from metabolically relevant tissues of trait-differentiated cattle from a dairy type x beef type cross population. Some of the differentially expressed lncRNAs, which are potentially specific for metabolic types, will be selected for genomewide identifying and mapping of lncRNA-interacting DNA-regions using the method of ChIRPseq (Chromatin Isolation by RNA Purification Sequencing).As a result of the study we expect a deeper functional annotation of the bovine genome and transcriptome. Moreover, we want to elucidate, whether and to what extent lncRNAs represent central regulatory nodes, where changes in energy metabolism can be sensed and adaptive gene expression is modulated specifically. The expression profiles and novel functional gene information can contribute to clarify and improve our molecular understanding regarding the regulation of divergent metabolic processes. In addition, metabolic type-specific expression signatures can be used to develop molecular biomarkers for defined phenotypes in order to provide improved methods for selection and management of cattle based on knowledge of specific regulatory processes in the respective metabolic type.

• DFG Programme: Research Grants