Journal: bioRxiv

Article Title: Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana

doi: 10.1101/2022.09.21.507229

Figure Lengend Snippet: a) GER5-ATCOPIA78/ONSEN locus. TEs, Araport11 gene annotation, and DRS-AtRTD3 transcript isoforms are shown. * indicates isoforms examined by RT-qPCR in c. b), c) Relative expression of transcripts corresponding to GER5 protein coding sequence (CDS; AT5G13200 . 1 and AT5G13200 . 2 ) and altTE-Gi ( MSTRG . 3521 . 2, 4, 6 ) under mock and ABA stress conditions in indicated genotypes. Bars represent the means of four biological replicates ± standard error of the mean (SEM). *, p < 0.05 by t -test for comparison between Col-0 and mutants under mock conditions, and +, p < 0.05 by t -test under ABA stress conditions. d) Relative expression of transcripts corresponding to GER5 CDS ( AT5G13200 . 1 ) in the A. thaliana ecotypes with or without ATCOPIA78/ONSEN insertion in the 3′-UTR. Bars represent the means of four biological replicates ± SEM. *, p < 0.05 by t -test for comparison between Col-0 and mutants. e) Relative transcript levels of GER5 ( AT5G13200 . 2 ) at 0, 30, 60, 90, and 120 min after cordycepin treatment in Col-0, ibm2, edm2, suvh456 , and ecotypes without ATCOPIA78/ONSEN insertion (Ler-0 and Sha). Expression levels at 0 min are set as 1. Bars represent the means of four biological replicates ± SEM. *, p < 0.05 by t -test.

Article Snippet: Library preparation was performed using the Ligation Sequencing Kit (Oxford Nanopore Technologies) and sequencing was performed using MinION (device: MIN-101B, flow cell: R9.4.1) at OIST SQC.

Techniques: Quantitative RT-PCR, Expressing, Sequencing, Comparison