Skip to main content

Role of ncRNAs in Chromatin and Transcription

Final Report Summary - CRIPTON (Role of ncRNAs in Chromatin and Transcription)

The majority of our DNA is converted to another type of related molecule called RNA. A small proportion of this RNA comes from our genes and this gives rise to proteins. The rest of the RNA (termed non-coding RNA or ncRNA) is much less understood in terms of its role in the cell. The overall objective of our project was to explore the functions of ncRNAs. In particular, we focussed on how they are involved in regulating gene expression, and how this is related to the control of pluripotency and to diseased states such as cancer.

Our research has made a number of important contributions towards the understanding of these ncRNAs. The first involves an ncRNA called 7SK. We have found that 7SK is able to negatively control a specific set of genes in embryonic stem cells, which are cells that are “naïve” and can become any type of different cell type. By controlling these genes, 7SK could allow cells to stay unspecified. We also made the unexpected discovery of 7SK regulation of anti-sense transcription and transcriptional termination genome-wide. Furthermore, in collaboration with Prof. Austin Smith's group, we characterised the function of a novel ncRNA (Ephemeron) in mouse embryonic stem cell pluripotency and differentiation.

The second finding involves identification of a new family of ncRNAs that we call tapRNAs (Topological Anchor Point RNAs), which are present in mice and humans. We find that tapRNAs have common functions in that they can positively influence genes that are close to them, helping to turn them on. TapRNAs are found to be positioned in very specific areas of our genome and therefore may play key roles in defining the 3-dimentional structure of the genome. We have also shown that tapRNAs have a role to play in cancer, since they are often mis-expressed in primary human tumours and they can alter phenotypic properties associated with cancer cells in vitro.

Recently, it has become evident that many (if not all) RNAs, including ncRNAs, are co- or post-transcriptionally modified. We searched for RNA modifying enzymes whose activity is essential for growth of cancer cells. This approach identified METTL3, an enzyme that catalyses m6A RNA modification, as an essential factor for growth of acute myeloid leukaemia cells. Importantly, this activity requires METTL3 enzymatic activity to be intact. Furthermore, METTL3 was required to be bound to the promoters of a subset of genes where it modified its substrate RNAs co-transcriptionally. This work revealed a new paradigm for RNA target selection, namely stable recruitment of RNA modifying enzymes to specific genes. Moreover, our findings identify a new pathway necessary for AML growth and define the METTL3 m6A methyltransferase as a new candidate target for the treatment of AML.