The role of small open reading frames in myocardial fibrosis and genetic disease
File(s)
Author(s)
Quaife, Nicholas
Type
Thesis
Abstract
Regions of RNA, previously annotated as noncoding, are increasingly proving to be actively translated. These can hold functional importance when they are translated, either through their production of bioactive micropeptides, or modifying ribosome dynamics during the translation of downstream coding sequences.
In this thesis, I will first explore the potential of long noncoding RNAs to produce micropeptides that are functionally relevant in myocardial fibrosis. By analysis of the transcriptome and translatome of activated cardiac fibroblasts, several lncRNAs, differentially expressed in the fibrotic response, were identified as harbouring translated regions. I will use a combination of approaches including knockdown and overexpression to show that LINC01013 is associated with fibroblast activation by TGFB1, is profibrotic, and encodes a novel profibrotic micropeptide.
Secondly, I will characterise upstream open reading frames (uORFs) that were similarly identified as having evidence of translation, within the 5’ ‘untranslated’ region (UTR) of genes known to be involved in fibrosis. Specifically, I will show that uORFs of interleukin-11 and platelet-derived growth factor-D are regulatory of translation of the canonical coding sequence.
Lastly, I will leverage genomic analysis to functionally characterise genetic variants identified in the 5’ UTR of patients with genetic disease, but with normal candidate coding sequences. In particular, I will investigate variants in myocyte enhancer factor-2C and neurofibromin-2 which create or modify uORFs in the 5’ UTR. I will demonstrate that these have a negative effect on translation of the main coding sequence, thereby providing a novel mechanistic explanation for haploinsufficiency in these patients.
Overall, this thesis underscores the emerging importance of translation of regions previously annotated as noncoding, in both health and disease.
In this thesis, I will first explore the potential of long noncoding RNAs to produce micropeptides that are functionally relevant in myocardial fibrosis. By analysis of the transcriptome and translatome of activated cardiac fibroblasts, several lncRNAs, differentially expressed in the fibrotic response, were identified as harbouring translated regions. I will use a combination of approaches including knockdown and overexpression to show that LINC01013 is associated with fibroblast activation by TGFB1, is profibrotic, and encodes a novel profibrotic micropeptide.
Secondly, I will characterise upstream open reading frames (uORFs) that were similarly identified as having evidence of translation, within the 5’ ‘untranslated’ region (UTR) of genes known to be involved in fibrosis. Specifically, I will show that uORFs of interleukin-11 and platelet-derived growth factor-D are regulatory of translation of the canonical coding sequence.
Lastly, I will leverage genomic analysis to functionally characterise genetic variants identified in the 5’ UTR of patients with genetic disease, but with normal candidate coding sequences. In particular, I will investigate variants in myocyte enhancer factor-2C and neurofibromin-2 which create or modify uORFs in the 5’ UTR. I will demonstrate that these have a negative effect on translation of the main coding sequence, thereby providing a novel mechanistic explanation for haploinsufficiency in these patients.
Overall, this thesis underscores the emerging importance of translation of regions previously annotated as noncoding, in both health and disease.
Version
Open Access
Date Issued
2022-08
Date Awarded
2022-05
Copyright Statement
Creative Commons Attribution NonCommercial Licence
License URL
Advisor
Cook, Stuart
Barton, Paul
Sponsor
Imperial College London
Grant Number
WHCC_F26198
Publisher Department
National Heart & Lung Institute
Publisher Institution
Imperial College London
Qualification Level
Doctoral
Qualification Name
Doctor of Philosophy (PhD)