Post-transcriptional regulation of Gene Expression

The flow of genetic information from DNA to RNA to protein involves complex mechanisms of regulation acting downstream of the process of transcription, which produces RNA molecules from a DNA template. Pre-mRNA splicing is the process by which non-coding intervening sequences (introns) are excised from precursor RNAs and coding sequences (exons) are joined to form the mature messenger RNA. A further level of complexity is added by alternative splicing, where a series of different mRNA molecules can be produced by the differential use of splice sites within a pre-mRNA, enabling a single gene to increase its coding capacity. We will study the regulation of Alternative splicing, in particular related to its coupling to the process of transcription. We are investigating a cellular process that controls the quality of RNA produced by cells, termed Nonsense-mediated decay (NMD), which degrades RNAs that encode harmful proteins for the cell. We will focus on a specialised NMD machinery that is localised to the endoplasmic reticulum (ER) and has a role during cellular stress. Finally, we will study the mechanism by which short non-coding RNAs (termed microRNAs) are produced from longer intricately folded precursors and regulate the expression of cellular mRNAs. Our research programme is at the basic end of the spectrum. We expect to contribute to a greater understanding on how the production of cellular RNAs is tightly controlled and how its dysregulation can contribute to human disease. We rely on a variety of experimental systems, including mammalian cell lines in culture, nematodes (C. elegans) and mouse models and we use cell biological, biochemical and single-molecule approaches.

Gene expression is extensively regulated at the post-transcriptional level. RNAs associate with RNA-binding proteins (RBPs) to form ribonucleoprotein (RNP) complexes. There is a great variety of RBPs, each with unique RNA-binding activity that have a profound impact on gene expression networks, affecting processes as diverse as transcription, RNA splicing, microRNA (miRNA) biogenesis and function and mRNA translation.

The major aim of this programme is to study the mechanisms of post-transcriptional regulation of gene expression. We will address important questions concerning the role of RNA-binding proteins (RBPs) in Gene Expression at different levels during the RNA processing cascade from splicing in the nucleus to translation in the cytoplasm. This proposal will illustrate how alterations in RBP-mediated gene regulation can contribute to human disease.

We will study different aspects of RNA processing, including

- The Nonsense-mediated decay (NMD) pathway is a surveillance mechanism that selectively degrades mRNAs harbouring premature termination codons (PTCs), preventing the synthesis of truncated proteins. This pathway also controls the expression of naturally occurring transcripts and acts to modulate the phenotypic outcome of many inherited genetic disorders that arise as consequence of a frameshift or mutations that generate PTCs. Most studies to date have focused on cytoplasmic NMD; however, it is largely unknown how this mechanism operates on transcripts encoding secreted or ER-resident proteins. We have uncovered evidence that suggests the existence of an NMD pathway dedicated to Endoplasmic Reticulum (ER)-localised mRNAs, which involves two NMD factors that localize to the ER, NBAS and SEC13. We will focus on the functional characterisation of the ER-NMD pathway. We will use a variety of cells in culture, and will rely in cell biological, single molecule and biochemical approaches.

- Alternative splicing (AS) is a major contributor to protein isoform diversity. We will study the regulation of AS, in particular related to its coupling to transcription. We will focus on the role of RNA Polymerase II elongation rate in the regulation of Gene Expression and Alternative splicing in development and during differentiation. We will use mouse models and mouse embryonic stem cells (ESCs), both in an undifferentiated state and during neuronal differentiation.

- Due to the central role of miRNAs in the regulation of gene expression, their levels must be tightly controlled, since dysregulated miRNA expression can result in grossly aberrant gene expression and lead to human disease. We will investigate how RBPs influence miRNA biogenesis and will focus on the role of genetic variation in the production of miRNAs in human populations.