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

对于不同细胞和组织类型和表型中基因表达的调节，不同的染色质结构以及DNA与蛋白质和非编码RNA（ncRNA）的相互作用是重要的。自从下一代全球RNA测序技术（RNAseq）问世以来，在人类和模型动物的转录组中发现的非编码转录本的数量迅速增加。大量研究表明，除了短的非编码RNA外，长的非编码RNA（longnoncodingRNA，lnRNA）也是参与相关分子调控过程的重要功能组分，与特定的分化和生长过程以及多种疾病的发病机制有关。基于目前的知识，在其他物种的lncRNA的功能相关性，我们假设，这些非编码转录也可能发挥调节作用，在调制复杂的代谢模式，不同的表型在牛。该项目的目的是确定lncRNA和lncRNA相关的机制，调节性状分化牛的代谢和能量分配，这可能会调节能量和饲料转化的效率以及牛不同代谢类型的不同遗传生理组成。与人类和小鼠的注释良好的转录组相比，牛的转录组仍然没有充分注释和充分鉴定。为了建立全面的转录组目录，我们将使用全球转录组测序的无假设方法来识别和注释来自乳制品类型x牛肉类型交叉群体的性状分化牛的代谢相关组织的未知和非编码转录本。本研究将筛选出部分具有潜在代谢特异性的差异表达lncRNA，并利用ChIRPseq（Chromatin Isolation by RNA Purification Sequencing）方法进行全基因组lncRNA相互作用区域的鉴定和定位，以期对牛基因组和转录组进行更深入的功能注释。此外，我们想阐明，是否以及在何种程度上lncRNA代表中央调控节点，在那里能量代谢的变化可以被感知和适应性基因表达的调制具体。表达谱和新的功能基因信息有助于阐明和提高我们对不同代谢过程调控的分子理解。此外，代谢类型特异性表达标签可用于开发用于限定表型的分子生物标志物，以便基于对相应代谢类型中的特定调控过程的了解提供用于牛的选择和管理的改进方法。

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.