Glossary of Fiber-seq terms
Fiber-seq protocol
A treatment of DNA chromatin fibers with the Hia5 enzyme which preferentially methylates accessible adenosines. The fibers are then sequenced using a long-read platform that can detect the m6A modifications.
Fiber-seq read or fiber
A DNA fiber that has been sequenced using the Fiber-seq protocol and has m6A modifications called.
m6A
N6-methyladenosine: A DNA modification made during the Fiber-seq protocol on accessible adenosines. Native m6A sites are exceedingly rare or non-existent in eukaryotic DNA.
Inferred nucleosome
A nucleosome inferred from the Fiber-seq data. The nucleosome position along the DNA is inferred by the ft add-nucleosomes algorithm using the m6A modifications (not a direct observation of a nucleosome).
MSP
Methyltransferase sensitive patch: A stretch of a Fiber-seq read that has a high density of m6A sites. Specifically it is defined as a region that is inferred to not be occluded by a nucleosome.
FIRE
Fiber-seq Inferred Regulatory Element: A MSP that is inferred to be a regulatory element based on features of the MSP including m6A density.