Figure 3

DRB2 is able to bind TE transcripts. (a) RNA Immunoprecipitation (RIP) from mixed floral tissues of SINE transcripts in DRB2-FlagHA x ddm1 plants and ddm1 plants included as a negative control. Total RNA is extracted following the IP, DNase treated and reverse transcribed. PCR amplification is performed with primers specific to one element, and a second set of primers specific to the putative co-transcript. Each time, a control reaction is performed with water instead of matrix cDNA (H₂O), and each time, absence of contaminant genomic DNA is assessed by performing the same amplification with the non-reverse transcribed material (−RT). (b) Same RIP experiment performed on a diverse set of TEs, one Copia, two Gypsies and one CACTA. Primer sets used to amplify the Athila family are designed on a consensus sequence and can therefore amplify numerous genomic copies, both in the LTR and in the internal sequence. Evadé, GP3 are locus specific primers while CAC1/2/3 primers detect three different loci. The same control reactions are performed.