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Epitranscriptome analysis is our Method of the Year for 2016 for its crucial role in understanding RNA modifications on the transcriptome scale. Featured is a stylized image of an RNA with modified bases. Cover design by E. Dewalt.
This Review describes the latest methods for profiling common epitranscriptomic marks, their scale, resolution and ability to quantify. It also discusses remaining challenges.
Three-dimensional localization microscopy can yield important biological insights. A photometric approach is described that allows users to gain 3D information from existing 2D images and to improve axial resolution obtained with existing biplane setups.
A new method, R-scape, tests whether observed sequence covariation supports a conserved secondary structure in RNA. The program finds no evidence for previously proposed conserved secondary structures in several lncRNAs.
Membrane proteins can be stabilized in a native-like setting using lipid-bilayer-based nanodiscs encircled by a membrane scaffold protein. Covalently circularized nanodiscs now offer enhanced stability and control over nanodisc diameter size, improving the quality of structural data.
An extremely bright, truly monomeric RFP, mScarlet, is described that outperforms existing RFPs in diverse labeling applications, especially in FRET with ratiometric imaging.
The authors present a computational framework for false-discovery-rate-controlled metabolite annotation from high-resolution imaging mass spectrometry data.
InWeb_InBioMap (InWeb_IM for short) is a scored, integrated human protein–protein interaction network resource aggregated from public, experimentally determined protein–protein interactions. The resource enables functional interpretation of large-scale genomics data.
DMS-MaPseq enables genome-wide and target-specific RNA secondary structure probing of even rare or heterogeneously structured RNAs in vivo and was used to study structure involved in translation regulation as well as nascent transcripts.
BUM-HMM is a statistically robust modeling pipeline for interpreting high-throughput RNA structure probing data, including that from transcriptome-wide experiments.
An instrumental setup for atmospheric pressure MALDI-based mass spectrometry imaging with improved lateral resolution enables subcellular-level details to be resolved.