One of the biggest surprises of human genomic sequencing was the finding that only ~2% of the genome codes for proteins. With the advent of sequencing technology, it has become clearer that that the majority of the genome is transcribed into non-coding RNAs (ncRNAs). Although we still do not understand the functions of these ncRNAs, it is becoming clear that a number of them act as novel regulators of cell identity and tissue homeostasis. Also, several ncRNAs are implicated in pathways relevant to stemness and ageing e.g. genomic stability, imprinting, epigenetic regulation, cell cycle control, splicing, and cell differentiation. These non-coding RNAs thus represent unexploited therapeutic targets for reprogramming applications and aging‐related diseases.
We, as a part of Institute of Translational Medicine and Centre for Drug Safety Science, aim to understand how these non-coding RNAs, in response to diseases and drugs, regulate gene expression chromatin landscape through their interactions with the epigenetic machinery (Genome Res, under review; EMBO 2018; Nature Comm 2012; Mol Cell 2010).
Aim 1: Understanding the interaction of the ncRNA with the genome.
This project focuses on ncRNAs that are nuclear and bound to chromatin. In their absence, genomic DNA undergoes striking alterations. The PhD candidate will employ cutting-edge next generation sequencing techniques such as ChIRP-seq and RAP-seq combined with mass-spectrometry to identify three-way interactions between ncRNA, the genome and proteins.
Aim 2: Understanding the effect on cell cycle and cell senescence
We are experienced in knocking these ncRNAs out using cutting edge technologies such as those involving CRISPR/Cas9. These knockout cells will be used to study effects on chromatin modification, transcriptome and cell cycle. However, a systematic analysis of cell cycle regulation by the ncRNAs needs to be carried out to understand exact functional mechanism behind this effect.
Aim 3: Finding the functional domain of the ncRNA and other similar ncRNAs
We have shown that these ncRNAs interact with chromatin modification machinery. We will use a combination of EMSA and CRISPR-Cas9 manipulations PhD student will identify exact functional domain of these ncRNAs. We will employ CLIP-seq for genome-wide identification of other ncRNAs which utilise similar functional mechanism.
We will use our expertise in next-generation sequencing methods, systems biology and bioinformatics to address these aims. The candidate will be benefitted by gaining experience in number of leading topics.
To apply for this opportunity please send your CV to Dr A Kanhere [email protected]