PARIS: detecting RNA structure in living cells

An international team of scientists, including Garvan’s Professor John Mattick and Dr Martin Smith, has shed new light on the complex ways in which the nucleic acid RNA folds and binds to itself within our cells.
20 May 2016

An international team of scientists, including Professor John Mattick and Dr Martin Smith of the Garvan Institute of Medical Research, has shed new light on the complex ways in which the nucleic acid RNA folds and binds to itself within our cells. Their work has been published this week in the leading journal Cell.

The team, which was led by Professor Howard Chang at Stanford University, developed an innovative technique called PARIS (Psoralen Analysis of RNA Interaction and Structure) to ‘read’ RNA structures within cells. Their work has uncovered, for the first time, a complete picture of how RNA can be organised within cells – information that will be invaluable in understanding cellular processes in health and disease.

RNAs (or ribonucleic acids) are molecules that are transcribed from DNA. Once thought simply to encode the information to specify protein production, RNAs are now known to have a much broader role. Research by Professor Mattick and colleagues, with other groups, over the past 20 years has uncovered a vast number of regulatory RNAs that transmit other information to guide cellular differentiation and development.

Like DNA, RNA contains long sequences that contain four types of ‘base’ (A, C, G and U in the case of RNA) – but, unlike DNA, RNA is a single-stranded molecule. This means that RNA can bind to itself, forming complex assortments of double-stranded regions and, often, three-dimensional structures. 

In the video abstract that accompanies the publication, the research team explain why an understanding of the structure of RNA, not just its base sequence, is important. “Structured RNAs play important roles in all types of cellular processes,” they explain. “For example, the catalytic centre of the ribosome [which is the site of protein production] is entirely made up of RNA structures. Therefore, we need to study the structures to understand the function of RNA.”

The team points out that it has been very challenging to define how RNA is structured in living cells, in part because conventional methods have required RNA to be removed from cells and purified – a process that is likely to disrupt and alter some RNA-RNA interactions and that cannot detect changes in RNA structure.

However, the PARIS method overcomes these limitations by detecting double-stranded RNA structures in living cells (three human and mouse cell lines were used in the research). It can detect structures with high resolution and gives a global readout of RNA structures and interactions within the cell.

Dr Smith says, “In developing PARIS, our collaborators at Stanford have made a significant advance in ‘reading’ RNA structure and interaction in living cells, across the whole set of RNA species in the cell (the transcriptome).

“The research has identified numerous long-range interactions at single base resolution between both individual and distinct RNA sequences, as well as highlighting that a large proportion of all RNA structures can exist in alternative conformations.

“Garvan’s contribution to the research has been to develop a bioinformatic strategy to confirm which of the double-stranded RNA structures detected by PARIS are evolutionarily conserved and likely to be important. We compared RNA sequences with their equivalents in other mammalian genomes to substantiate the PARIS results, adding an additional layer of support to the study’s findings.”

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