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Projects / Programmes source: ARIS

Effect of RNA variants on phenotypic variability in animal models

Research activity

Code Science Field Subfield
4.06.03  Biotechnical sciences  Biotechnology  Animal biotechnology 

Code Science Field
4.04  Agricultural and Veterinary Sciences  Agricultural biotechnology 
Keywords
alternative promoter usage, alternative polyadenylation (APA), animal models, mouse model, obesity, phenotypic variability, WTSS-seq, WTTS-seq
Evaluation (rules)
source: COBISS
Researchers (9)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  33148  PhD Maša Čater  Biotechnology  Technical associate  2022  109 
2.  05098  PhD Peter Dovč  Biotechnology  Researcher  2020 - 2023  935 
3.  10412  PhD Simon Horvat  Biotechnical sciences  Researcher  2020 - 2023  561 
4.  56162  Vito Jurić    Technical associate  2021 - 2022 
5.  25435  PhD Janez Konc  Computer intensive methods and applications  Researcher  2020 - 2023  236 
6.  16361  PhD Tanja Kunej  Animal production  Head  2020 - 2023  919 
7.  53633  Špela Mikec  Biotechnology  Junior researcher  2020 - 2023  32 
8.  38858  Katja Skulj    Technical associate  2020 - 2021  14 
9.  55504  Martin Šimon    Technical associate  2021 - 2023  39 
Organisations (2)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0481  University of Ljubljana, Biotechnical Faculty  Ljubljana  1626914  66,832 
2.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,278 
Abstract
Background: Human organism develops from one cell type into more than 250 types and from one fertilized egg into 1012 - 1016 cells. During these processes, the nuclear genome remains mostly unchanged in somatic cells. However, the phenome, such as body form evolves and progresses. A finite genome produces an infinite phenome during a life span. However, a large part of genetic causes for phenotypic variability and complex traits such as obesity is still unknown; termed “missing heritability”. It was hypothesized that alternative transcripts, or RNA variants are key to facilitate information transfer from genome to phenome in response to various environments. In order to determine transcriptome diversity, whole transcriptome start site sequencing (WTSS-seq) and whole transcriptome termini site sequencing (WTTS-seq) were developed to profile 5’- and 3’-ends of transcripts. WTTS-seq and WTSS-seq have shown a potential to identify novel associations between genome and phenome and have demonstrated advantages in comparison to the conventional RNA-seq to study RNA variants. Aim of the study: The aim of this proposal is to use WTSS-seq and WTTS-seq methods to analyze to what extent alternative promoter use and alternative polyadenylation drive divergent fat deposition in a mouse model. Unique Fat and Lean lines developed by 60 generations of divergent selection on fatness will be employed. These two models present globally unique animal models suitable for the identification of genes and mechanisms of healthy leanness and obesity in human. The main objective will be to examine how long term divergent selection in high and low body fat changed the genome-wide mechanisms and architecture of alternative promoter use or alternative polyadenylation site regulation. Materials and Methods: Mouse lines selected for fatness for more than 60 generations will be used and divided into four groups: 1. fat content (fat/lean), 2. diet (high/low fat), 3. age (young/adult), and 4. sex. RNA will be extracted from white fat. Alternative 5’ transcriptional start site and poly(A) site usages will be analyzed using WTSS-seq and WTTS-seq methods followed by validation using in silico / dry (genomics database) and wet lab (qPCR) methods. Sequencing will be performed on Ion Torrent Personal Genome Machine. Update of the Obesity gene atlas in mouse will be performed using available databases and bioinformatics tools. Associations between genetic variants, RNA variants, gain/loss of miRNA binding sites and gain/loss of protein interactions using synthesis of multi-omics data. Complementarity of the research group: Researchers at WSU have developed WTSS-seq and WTTS-seq methods and applied them in investigation of genetic information flows from genome to phenome in different species. Researchers at the UL are the only in the world to have selection lines F (Fat) and L (Lean), which differ in fat content by more than 4 times. Researchers at the UL also have rich expertise in bioinformatics, database development and multi-omics studies, which will enable inclusion of novel data to a systems; integromics view of the genotype-phenotype associations. Expected results and future plans: We expect to identify novel candidate loci via RNA variants associated with fat content in mouse polygenic model. We plan to introduce WTSS-seq and WTTS-seq to the laboratory at UL to study other traits in other animal models, for example coat color in goats and milk protein content. New candidate loci will then be combined with other, previously reported genomics loci associated with analyzed traits to enable multi-omics view of molecular mechanisms responsible for phenotype variability. Results could contribute to identification of genes and mechanisms of healthy leanness and obesity and novel targets for therapy. Feasibility of the project: The project is feasible since both WTSS-seq and WTTS-seq are well optimized and studied using different animal models published in established j
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