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. 2018 Mar 6;46(6):3019–3033. doi: 10.1093/nar/gky163

Figure 1.

Figure 1.

Characterization of 5S rRNA genes and their genomic distribution in Col-0. (A) Scheme of 5S rRNA genes, comprising the 120 bp transcribed sequence (gray arrow) containing the internal promoter sequence (box A, I, C), the 380 bp long intergenic region and the Thymine-rich termination sequence (T-stretch). TSS and TTS indicate transcription start and termination sequence respectively. Positions of primers (pink arrowheads) used to determine 5S rRNA gene copy number by qPCR in (B) are indicated. (B) Mean 5S rRNA gene copy number in Col-0 determined by in silico analysis (dark gray) of the Mi-Seq dataset and two publicly available Hi-Seq datasets from the 1001 genome project and the mutation accumulation (MA) lines (28,34,35) after normalization to 18 single copy genes, and by qPCR (light grey). For the latter, mean values of 5S rDNA copy numbers from three biological replicates of Col-0 plants normalized to two single copy genes (HXK1, At4g29130 and UEV1C, At2g36060) are shown. Error bars correspond to SEM for three biological replicates. (C) Schematic representation of the predominant 5S rDNA loci in the pericentromeric regions (white) of chromosome 3 (orange), 4 (red) and 5 (green) in the Col-0 ecotype. (D) (Top) Major T-stretch signatures of each 5S rDNA locus in the Col-0 genome derived from the Mi-Seq data set. (Bottom) Relative frequencies of the predominant T-stretch signatures (colored fractions) and the T-stretches with single nucleotide polymorphisms (uncolored fractions) assigned to the three different loci by their characteristic nucleotide combinations (details in Supplemental Figure S1C) are shown in the pie chart. (E) DNA FISH on meiotic bivalents with LNA-DNA mixmer probes designed to specifically recognize the major T-stretch signatures (described in (D)) of chromosome 4 (red) and chromosome 5 (green), DNA is counterstained with DAPI (blue). The scale bar presents 10 μM. (F) Percentage of 5S rRNA gene copies carrying the T-stretch signatures characteristic of 5S rRNA genes from chromosomes 3, 4 and 5 in the Col-0 genome.