PhD Project

Preventing Noncoding Transcription in Budding Yeast

I am currently a PhD student in the Cell Fate and Gene Regulation Laboratory at the Francis Crick Institute in London, working with Dr. Folkert van Werven

I'm interested in studying the mechanisms of gene expression in budding yeast through molecular and cellular biology, and bioinformatics.

Specifically, I'm exploring how noncoding transcription is regulated by transcription factors, the chromatin environment, and mechanisms that control gene expression.

Noncoding RNAs (ncRNAs) can have specific functional roles in regulating gene expression, or may represent transcriptional noise from the "leakiness" of the transcription machinery. Transcription can be stochastic, and the mechanisms by which cells robustly limit the extent of non-coding transcription is an area of active research. I would like to address this by identifying and characterising the molecular mechanisms controlling non-coding transcription.

Recently, we found that a sequence-specific transcription factor called Rap1 prevents expression of divergent noncoding transcripts at gene promoters. 

A bit more detail:

The budding yeast S. cerevisiae is an ideal model system to study the fundamental and conserved principles of transcriptional regulation. Regulation of gene expression is essential for cells to respond to environmental changes, and is fundamental to eukaryotic complexity. In most eukaryotes, a larger fraction of the genome is transcribed than actually codes for protein; this phenomenon is known as pervasive transcription.  For example, in human cells - only about 2% of the genetic information is coding, but up to 70-80% of the genome is transcribed in different cell types. 

Non-coding transcription by RNA polymerase can produce a broad class of non-protein coding RNAs (ncRNAs), often from cryptic or hidden promoters. Non-coding transcription events can be long or short, sense or anti-sense (relative to the coding gene direction), overlap a gene itself or be completely outside, or in the case of divergent promoters, generate a non-coding RNA initiating in the opposite direction as the functional mRNA - from the same promoter.

These ncRNAs can have diverse regulatory functions throughout the steps of gene expression, for example, by recruiting transcription factors or chromatin remodellers, acting as molecular scaffolds to influence local chromatin architecture, or even competing for regulatory factors. In addition, local transcription through a gene promoter can co-transcriptionally remodel chromatin through histone methyltransferases (HMTs) and histone de-acetylases (HDACs), establishing a chromatin structure repressive to transcription in the wake of nucleosome displacement by RNA polymerase.

However, non-coding RNAs may also represent transcriptional noise from the "leakiness" of the transcription machinery. Some non-coding transcription has very specific roles in gene regulation. However, other non-coding RNAs may be products of spurious transcription initiation events, and are easier to detect in various genetic backgrounds (for example cells defective in ncRNA degradation).

As non-coding transcription can perturb gene expression and transcriptional fidelity, cells must have various systems in place to prevent inappropriate non-coding transcription. The degradation of ncRNAs, which affects their lifespan and molecular function in the cell, has been better characterised in yeast and mammalian cells. However, it is not well understood how sequence-specific transcription factors and the local chromatin environment prevent aberrant non-coding transcription, and the extent to which they do so.

Understanding how aberrant non-coding transcription is controlled will expand our understanding of gene regulation in complex programmes of development and in response to environmental cues, and how these processes can go wrong in disease.