Sequencing-based methods called Dart

Some years ago James Hadfield at Enseqlopedia made a spreadsheet of acronyms for sequencing-based methods with some 50 rows. I can only imagine how long it would be today.

The overloading of acronyms is becoming a bit ridiculous. I recently saw a paper about DART-seq, a method for detecting N6-methyladenosine in RNA (Meyer 2019), and thought, ”wait a minute, isn’t DART-seq a reduced representation genotyping method?” It is, only stylised as DArTseq (seriously). Apparently, it’s also a droplet RNA-sequencing method (Saikia et al. 2018).

What are these methods doing?

  • DArT, diversity array technology, is a way to enrich for a part of a genome. It was originally developed with array technology in mind (Jaccoud et al. 2001). They take some DNA, cut it with restriction enzymes, add adapters and amplify regions close to the cut. Then they clone the resulting DNA, and then attach it to a slide, and that gives a custom microarray of anonymous fragments from the genome. For the Dart-seq version, it seems they make a sequencing library instead of going on to cloning (Ren et al. 2015). It falls in the same family as GBS and RAD-seq methods.
  • DART-seq, droplet-assisted RNA targeting, builds on Drop-seq, where they put single cells and beads that carry primers into the same oil droplet. As cells lyse, the RNA sticks to the primer. The beads also have a barcode so they can be identified in sequencing. Then they break the emulsion, reverse transcribe the RNA attached to beads, amplify and sequence. That is cool. However, because they capture the RNA with oligo-dT primers, they sequence from the 3′ end of the RNA. The Dart method adds primers to the beads, so they can target some specific RNAs and amplify more of them. It’s the super-high-tech version of gene-specific primers for reverse transcription..
  • DART-seq, deamination adjacent to RNA modification targets, uses a synthetic fusion protein that combines APOBEC1, which deaminates cytidines, with a protein domain from YTHDF2 which binds N6-methyladenosine. If an RNA has N6-methyladenosine, cytidines that are close to it, as is usually the case with this base modification, will be deaminated to uracil. After RNA-sequencing, this will look like Cs next to As turning into Ts. Neat! It’s a little bit like bisulfite sequencing of methylated DNA, but with RNA.

On the one hand: Don’t people search the internet before they name their methods, or do they not care? On the other hand, realistically, the genotyping method Dart and the single cell RNA-seq method Dart are unlikely to show up in the same work. If you can call your groups ”treatment” and ”control” for the purpose of a paper, maybe you can call your method ”Dart”, and no-one gets too confused.