DNA was converted (me5C to T) using the
EpiTect Plus Bisulfite Conversion Kit (Qiagen). The target region was then amplified by PCR using the
Ex Taq DNA Polymerase, Hot Start Version Kit (TaKaRa Bio Inc.) and oligo primers
o112/o113 and
o124/o125 (
Supplementary Table S1) to amplify promoter/5ʹETS and 3ʹETS, respectively. 3ʹETS PCR products were run on an agarose gel, sliced from the gel, and purified using a
GeneClean® Turbo Kit (MP Biomedicals). PCR products were cloned into a
pGEM®-T easy vector (Promega), transformed into
Escherichia coli DH5α, and sequenced using T7 and SP6 primers. The sequences obtained were mapped to a reference sequence and the alignment was sent to CyMATE to analyse methylation sites in the sequence. The results were analysed using the prop.test function in R software to verify significant differences with R software (Pontvianne
et al., 2012 (
link)).
Montacié C., Riondet C., Wei L., Darrière T., Weiss A., Pontvianne F., Escande M.L., de Bures A., Jobet E., Barbarossa A., Carpentier M.C., Aarts M.G., Attina A., Hirtz C., David A., Marchand V., Motorin Y., Curie C., Mari S., Reichheld J.P, & Sáez-Vásquez J. (2023). NICOTIANAMINE SYNTHASE activity affects nucleolar iron accumulation and impacts rDNA silencing and RNA methylation in Arabidopsis. Journal of Experimental Botany, 74(15), 4384-4400.