“Breakthrough Article” in Nucleic Acids Research: Powerful FDF-PAGE Technique Reveals Previously Undetected Small RNAs Hidden by Complementary Transcripts

Investigators working in the Plant Sciences Department of Cambridge University and the School of Biological Sciences, Edinburgh University, led by Dr. David Baulcombe, have identified shortcomings in current methods for detecting small RNAs (between 18 nucleotides and 30 nucleotides in length) and have used a new approach to identify small RNAs that might be under the control of competing endogenous RNAs (ceRNAS). This new work has been awarded the status of “Breakthrough Article” by the Nucleic Acids Research (NAR) journal and was published online in the open-access NAR on June 13, 2015. The article is titled “FDF-PAGE: A Powerful Technique Revealing Previously Undetected Small RNAs Sequestered by Complementary Transcripts.” FDF-PAGE is the abbreviation for “fully denaturing formaldehyde-polyacrylamide gel electrophoresis.” Small RNA sequencing is a powerful approach for investigating the regulation of gene expression inside cells. Millions of sequence “reads” can be obtained, providing clues to the control of thousands of genes. The data, however, are limited by the quality of the RNA used as the raw material for sequencing. Dr. Baulcombe and coworkers show that it is likely that some small RNAs will hybridize to complementary sequences and that this binding will reduce their detection. To overcome this problem, the authors add a procedure for separating complementary strands to the protocol for RNA preparation prior to sequencing. This method provides a more robust and accurate profile of cellular RNAs and is likely to find wide application in the sequencing of small RNAs. Reviewers and editors at NAR who have examined this new study describe its results as an important advance for understanding small RNAs and reducing biases that lead to incorrect hypotheses. One reviewer noted “This is the next step.
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