Projects / Programmes
Effect of RNA variants on phenotypic variability in animal models
| Code |
Science |
Field |
Subfield |
| 4.06.03 |
Biotechnical sciences |
Biotechnology |
Animal biotechnology |
| Code |
Science |
Field |
| 4.04 |
Agricultural and Veterinary Sciences |
Agricultural biotechnology |
alternative promoter usage, alternative polyadenylation (APA), animal models, mouse model, obesity, phenotypic variability, WTSS-seq, WTTS-seq
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 - 2023 |
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 |
0 |
| 5. |
25435 |
PhD Janez Konc |
Computer intensive methods and applications |
Researcher |
2020 - 2023 |
233 |
| 6. |
16361 |
PhD Tanja Kunej |
Animal production |
Head |
2020 - 2023 |
913 |
| 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)
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
