Researchers are increasingly exploring the biological effects of several different kinds of chemical modifications made to RNA molecules in cells. A chemical tweak that creates a base known as pseudouridine (Ψ) is among the most common of these modifications. Its biological function has, however, not been extensively studied, in large part due to the lack of sufficiently sensitive tools for its detection. This is no longer a problem. Researchers led by Ludwig Oxford’s Chunxiao Song reported in Nature Methods in September a method for the highly sensitive sequencing of Ψ. The technique—2-bromoacrylamide-assisted cyclization sequencing (BACS)—is based on new bromoacrylamide cyclization chemistry that induces Ψ-to-C mutation signatures for the quantification of Ψ stoichiometry and its sequencing at single-base resolution. BACS overcomes key limitations of existing methods for Ψ sequencing to generate a far more sensitive and accurate readout of the modification across RNA species. The researchers applied BACS to detect all pseudouridine sites in human ribosomal RNA. They also used their new method to generate, among other things, the first quantitative pseudouridine map of human small nucleolar RNA and transfer RNA, identify the sequence motifs and targets of three enzymes that generate the modification and an abundant pseudouridine site in Epstein–Barr virus-encoded small RNA EBER2. Chunxiao and his team expect BACS will be swiftly and widely adopted in the field for the study of pseudouridine biology.
Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome
Nature Methods, 2024 September 30