Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana

Abstract

Approximately seven hundred 45S rRNA genes (rDNA) in the Arabidopsis thaliana genome are organised in two 4 Mbp-long arrays of tandem repeats arranged in head-to-tail fashion separated by an intergenic spacer (IGS). These arrays make up 5 % of the A. thaliana genome. IGS are rapidly evolving sequences and frequent rearrangements inside the rDNA loci have generated considerable interspecific and even intra-individual variability which allows to distinguish among otherwise highly conserved rRNA genes. The IGS has not been comprehensively described despite its potential importance in regulation of rDNA transcription and replication. Here we describe the detailed sequence variation in the complete IGS of A. thaliana WT plants and provide the reference/consensus IGS sequence, as well as genomic DNA analysis. We further investigate mutants dysfunctional in chromatin assembly factor-1 (CAF-1) (fas1 and fas2 mutants), which are known to have a reduced number of rDNA copies, and plant lines with restored CAF-1 function (segregated from a fas1xfas2 genetic background) showing major rDNA rearrangements. The systematic rDNA loss in CAF-1 mutants leads to the decreased variability of the IGS and to the occurrence of distinct IGS variants. We present for the first time a comprehensive and representative set of complete IGS sequences, obtained by conventional cloning and by Pacific Biosciences sequencing. Our data expands the knowledge of the A. thaliana IGS sequence arrangement and variability, which has not been available in full and in detail until now. This is also the first study combining IGS sequencing data with RFLP analysis of genomic DNA.

Higher-order organisation of extremely amplified, potentially functional and massively methylated 5S rDNA in European pikes (Esox sp.)

“…In contrast, major spacer length variants tend to form independent arrays (Additional file 7: Table S3). Interestingly, in Arabidopsis where 5S loci are located on three chromosomes, a similar block-like structures composed of homo- and heterogenous arrays were detected in BAC libraries [60] and recent PacBio sequencing revealed substantial spacer polymorphisms in the 45S rDNA intergenic spacers located on two chromosomes [61]. These results suggest that the higher-order repeat structure may be evolutionary conserved.…”

Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors

“…Nonetheless, some rDNA VAR3 copies map to NOR2 (Chandrasekhara et al, 2016), while the low-abundance rDNA variant VAR4 also maps near the centromere of chromosome 3 (Abou-Ellail et al, 2011). A fifth rRNA gene variant (VAR5) was reported by Havlová et al (2016). The rDNA VAR5 was described as a VAR3 subtype based on the rDNA sequence length measured from the end of the 25S to the first SalI restriction site in the 39ETS ( Figure 2B).…”

Roles of RAD51 and RTEL1 in telomere and rDNA stability in Physcomitrella patens

“…In addition to telomeres, other genomic loci are not only essential for cell survival, but are also very sensitive markers of genome instability such as the loci coding for 5S and 45S ribosomal RNA genes (rDNA). In A. thaliana , 45S rDNA loci showed changes in the dosage and expression pattern of rRNA gene variants, as well as in their distribution to nucleolar organizer regions 2 and 4, in response to dysfunction of a number of chromatin‐associated proteins as for example histone methyltransferases, factors involved in DNA repair or histone chaperones (Mozgova et al ., ; Pontvianne et al ., , , , ; Durut et al ., ; Muchova et al ., ; Havlová et al ., ; Pavlistova et al ., ). Therefore, to elucidate the role of RAD51 and RTEL1 in P. patens genome stability, we primarily examined the sensitivity of corresponding mutants to DNA damage, the maintenance of their telomeres and rDNA, and repair of DSBs induced by genotoxins with various modes of action.…”