Department of Biochemistry University of Oxford Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU

Tel: +44 (0)1865 613200
Fax: +44 (0)1865 613201
Image showing the global movement of lipids in a model planar membrane
Matthieu Chavent, Sansom lab
Anaphase bridges in fission yeast cells
Whitby lab
Lactose permease represented using bending cylinders in Bendix software
Caroline Dahl, Sansom lab
Epithelial cells in C. elegans showing a seam cell that failed to undergo cytokinesis
Serena Ding, Woollard lab
Collage of Drosophila third instar larva optic lobe
Lu Yang, Davis lab
First year Biochemistry students at a practical class
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Lidia Vasilieva
Regulation of gene expression in eukaryotes

Co-workers:  Katie Duckett, Dong-Hyuk Heo, Tea Kecman, Cornelia Kilchert, Dogukan Ulgen, Sina Wittmann, and Beth Watts 

RNAs are involved in many key cellular processes, and even minor alterations in RNA level are often detrimental and could lead to diseases in human. Our research is aimed to understand how chromatin modifiers, transcription factors and the exosome complex, a major RNA processing/degradation machinery orchestrate different aspects of RNA metabolism: transcription, RNA processing and RNA quality control. Our laboratory is using biochemical approaches combined with genome-wide functional analyses including RNA-seq and ChIP-seq to uncover molecular mechanisms regulating levels of individual transcripts in eukaryotes.

Recent studies have revealed that eukaryotic genomes store more information than previously thought, producing a variety of previously un-annotated non-coding RNAs, highlighting the importance of gene regulation at the post-transcriptional level.

Interestingly, we discovered that the exosome interacts with the transcription factor Nrd1 involved in RNA release and termination of RNA polymerase II (Pol II) transcription machinery (Vasiljeva and Buratowski, 2006; Vasiljeva et al., 2008). This allows the exosome to degrade non-coding RNAs in the nucleus and to produce mature 3' ends of sn/snoRNAs by 3'-5' exonucleolytic trimming. One of our current goals is to gain further insight into how fate of protein-coding and non-coding transcripts is determined.  We address this important problem by identifying new RNA-binding proteins involved in transcriptional and post-transcriptional regulation of RNAs levels and study their function within the cell.

Publications

  1. Kilchert C, Wittmann S, Vasiljeva L.(2016) The regulation and functions of the nuclear RNA exosome complex. Nature Rev Mol Cell Biol. 17, 227-39. 
  2. Kilchert C, Wittmann S, Passoni M, Shah S, Granneman S, Vasiljeva L.(2015)Regulation of mRNA Levels by Decay-Promoting Introns that Recruit the Exosome Specificity Factor Mmi1. Cell Report. 22;13, 2504-15.
  3. Shah, S., Kilchert, C., Wittmann, S., and Vasiljeva, L. (2014) ‘lncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast’ Genes and Development 28, 231-244.
  4. Volanakis, A., Passoni, M., Hector, R., Kilchert, C., Shah, S., Granneman, S., and Vasiljeva, L. (2013) Spliceosome-Mediated-Decay (SMD) regulates expression of non-intronic genes in budding yeast. Genes and Development  27, 2025-38. 
More Publications...

Research Images

Figure 1: Model of the exosome complex based on structural data (Liu et al., 2006) and current view on the various functions of the exosome in the cell. The six-subunit RNAse PH-like ring (Rrp41, Rrp45, Rrp42, Mtr3, Rrp43, and Rrp46) assembles with three cap proteins (Csl4, Rrp4, and Rrp40) containing S1/KH domains into a nine-subunit core. Catalytic subunits Rrp44 (Dis3) (shown in yellow) and Rrp6 associate with the core
 

Figure 2: Exosome regulates heterochromatic silencing.Deletion of a non-essential subunit of the exosome, Rrp6, resulted in de-repression of the ADE2 reporter inserted near the right telomere of ChrV. Expression of the ADE2 gene correlates with the loss of red sectored colonies (Vasiljeva et al., 2008)
 

Figure 3: Purification of the Nrd1 complex and analysis of associated proteins by SDS- PAGE Silver staining (Vasiljeva and Buratowski, 2006)


Contact:lidia.vasilieva@bioch.ox.ac.uk
Graduate Student and Postdoctoral Positions: Enquiries with CV welcome