Rediscovering hypoxia though RNA regulation

Hypoxia is a common stress condition for living cells and organisms, and is linked to
many diseases such as cancer. During hypoxia, cells compensate for the lack of
oxygen, by activating a series of adaptive responses to satisfy the metabolic,
bioenergetic and redox demands. These responses are multifaceted requiring precise
regulation of gene expression and involving several cellular pathways. Transcriptional
mechanisms like unfolded protein response (UPR), mammalian target of rapamycin
(mTOR) signalling, and gene regulation by hypoxia inducible factor (HIF) have been
extensively studied. However gene expression during hypoxia is also highly affected
post-transcriptionally and RNA binding proteins (RBPs) are critical in controlling these
processes (e.g. mRNA stability and translation efficiency). Moreover recent data have
proposed the intriguing and novel idea that enzymes can also function as RNA binding
proteins, and that RNA binding would modulate their activity probably in an allosteric
fashion; however very little is known about the mechanistic details, or whether this
happens during hypoxia. The aims of this project are: Aim 1. To reveal changes in RNA
binding activity of RBPs in response to hypoxia through an unbiased proteomics
approach with quantitative mass spectrometry analysis. (Year 2 - Note Year 1 is for
rotation projects). Aim 2. To define the link between changes in RNA binding of
metabolic enzymes and their metabolic activity through metabolomics approaches.
(Year 2). Aim 3. The information on RBPs and hypoxia metabolism from aim 1 and 2
will reveal which RPB candidates to focus on for mechanistic analysis, including
canonical RBPs and enzymes that bind RNA during hypoxia. These will be explored
using cellular, biochemical, biophysical and structural approaches to understand the
precise mechanisms of RNA regulation.( Year 3-4). For this we will employ a combined
structural, biophysical, and cellular biology approach, in conjugation with...