James Parker
Structural and molecular biology of RNA silencing
Co-workers: Muhan Wang
The small RNA – 18 to 30 nucleotides – is a new player in cell biology. Over the last few years many diverse mechanisms in plants, animals and yeast have been identified that incorporate small RNAs for the regulation of gene expression. These include RNA interference (RNAi), microRNA-mediated gene regulation and defence against transposons in germ cells mediated by Piwi-interacting RNAs, or piRNAs. Central to all these mechanisms is the Argonaute protein, which provides the core scaffold for the operation of the small ‘guide’ RNA strand and the ‘slicer’ activity which cleaves target mRNAs.
We study the molecular mechanisms of small RNAs. We use structural biology, molecular biology and biophysical methods to understand how the components of these pathways interact together and function. Examples of relevant complexes include RISC (RNA-induced silencing complex) - the effector complex of RNAi and microRNA-mediated silencing, RITS (RNA-induced initiation of transcriptional gene silencing) - a complex that mediates remodelling of heterochromatin via siRNAs, and Microprocessor, the Drosha/DGCR8 complex responsible for the processing of microRNAs. Understanding the molecular principles underlying these pathways will lead to insights into disease resistance, stem cell biology and oncogenesis.
Publications
- Parker JS (2010) How to slice: snapshots of Argonaute in action. Silence 1:3
- Parker JS, Parizotto EA, Wang M, Roe SM and Barford D (2009) Enhancement of the seed-target recognition step in RNA silencing by a PIWI/MID domain protein. Molecular Cell 33, 204-14
- Parker JS, Roe SM and Barford D (2006) Molecular mechanism of target RNA transcript recognition by Argonaute-guide complexes. Cold Spring Harb Symp Quant Biol. 71, 45-50
- Parker JS, Roe SM and Barford D (2005) Structural insights into mRNA recognition from a PIWI domain-siRNA guide complex. Nature 434, 663-6
- Parker JS, Roe SM and Barford D (2004) Crystal structure of a PIWI protein suggests mechanisms for siRNA recognition and slicer activity. EMBO Journal 23, 4727-37
More Publications...
Research Images
Figure 1: Structure of a PIWI domain - guide RNA (green) - mRNA (yellow) complex. The location of the slicer catalytic site in PIWI and the scissile phosphate in the mRNA are shown in red. The metal ion that anchors the 5' end of the guide RNA is shown as a red sphere
Figure 2: Crystals of apo-AfPiwi (left) and AfPiwi-RNA complex (right)
Figure 3: Electrophoretic mobility shift assay demonstrating the formation of a distinct complex between AfPiwi and an siRNA-like duplex
Figure 4: Structure of the 5'-end recognition pocket in AfPiwi
Contact:james.parker@bioch.ox.ac.uk
Graduate Student and Postdoctoral Positions: Enquiries with CV welcome