Technical reviews
Articles for RNA modification work in four directions: what each route reports and where two methods for the same mark differ, how a result is read once it comes back, how a project is put together when several marks or readouts are involved, and how a modification result is set against the biology around it.
01Choosing a method
Method choice rather than biology: what each route reports and where its limits are.
Choosing between single-base, RIP and array routes
The three lines resolve different things. This review covers the question each one answers and how to pick by the resolution the conclusion needs.
REVIEWWhat antibody-based profiling can and cannot resolve
Enrichment reports where signal accumulates across a transcript. Here is what that means for interpretation, and when a site-level method has to take over.
REVIEWWhat LC-MS adds to a sequencing result
Sequencing reports positions, mass spectrometry reports composition. What the two answer, and where an independent measurement is worth having.
02Method comparisons
Where two methods read the same mark, what actually separates them.
Two ways to read m6A at base resolution: CAM-seq and GLORI2-seq
Both convert unmodified adenosine and leave m6A intact. The difference is the chemistry around that conversion, and it changes which samples suit each route.
REVIEWPseudouridine: BID-seq and BACS-seq
Two bisulfite-based routes that read the same mark through different signals — a deletion signature in one, a conversion signature in the other.
03Reading the result
How to interpret what comes back from a modification experiment.
Reading a modification ratio
What the ratio at a site actually represents, why it is a per-site quantity, and why it cannot be read as an average across a transcript.
REVIEWReading the cap end: m6Am and cap-proximal methylation
The same methyl mark one nucleotide behind the cap and inside the transcript are two different observations. What separates them, and what a profile at the cap can claim.
04Modification biology
Where a mark meets the rest of the cell: what a modification means for the transcript that carries it, and how a modification result is set against structure, damage and translation.
How modifications shape transcript fate
Splicing, nuclear export, translation and stability: what each level requires on the modification side, and why a position needs a single-base readout.
REVIEWRNA modifications, R-loops and the DNA damage response
A modification, a DNA–RNA hybrid and a repair signal are three different measurements. What can be claimed when they are read together.
REVIEWEmerging RNA modifications: 2'-O-Me, D and m3C
Three marks outside the usual set: the chemistry behind each, how each is read today, and what a first study can hold.
REVIEWPairing modification and translation readouts
Why a modification map alone does not finish the argument, and what the design has to do so that the two halves align.
REVIEWReading modifications on tRNA and the fragments derived from it
A position on a tRNA, the abundance of that tRNA and the fragments processed from it are three measurements. Where each one is the right readout, and where they are confused.
REVIEWHow modified RNA is read by innate immune machinery
Cap identity, ribose methylation and uridine isomerisation all change how a transcript is recognized. What has been reported, and what the two sides of such a study measure.
05Study design
How a project is put together when more than one mark, or more than one kind of readout, is involved.
06GlycoRNA
Glycosylated RNA is read differently from a base-level modification.
07How to use these articles
Each article answers a question rather than describing a service. The method articles work through what a route reports; the biology articles set a modification result against the transcript and the cell around it. For the service itself — the chemistry, the workflow and the deliverables — follow the link in the article to the method page.
Single-Base RNA Modification Sequencing
The methods behind the resolution-and-position articles above.
14 methodssite-level RIPRNA Modification RIP-Sequencing
The enrichment line the antibody-profiling article discusses.
9 methodstranscript-level CITEDPublications cited on this site
The primary papers behind each method, with DOI taken from Crossref.
Reference31 papers08FAQ
Are these articles about the methods or about the biology?
There are two groups. The method articles work through what a technology reports and where its limits sit, so a method choice can be made on the readout rather than on a general impression. The biology articles take the readout as given and work out how it relates to transcript fate, genome structure and translation.
Can I read the article for a mark I am interested in?
The list covers method choice, method comparisons, how to read a result, study design, GlycoRNA and modification biology. The full set of marks with their methods, and the resolution each method reports, is on the modification types page. The articles explain a readout; the service detail sits on the method pages.
Where do the references live?
The primary papers behind each method are collected on the publications page, with journal, year and DOI taken from Crossref rather than retyped. The articles link back to that page, so a reference can be checked at source rather than taken second-hand.