Mapping of 5-methylcytosine residues in Nicotiana tabacum 5S rRNA genes by genomic sequencing

Fulneček, Jaroslav; Matyášek, Roman; Kovařı́k, Aleš; Bezděk, M.

doi:10.1007/s004380050798

Cited by 65 publications

(33 citation statements)

References 25 publications

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“…After washing under high-stringency conditions, the hybridisation bands were visualized with a PhosphorImager (Storm, Molecular Dynamics, Sunnyvale, CA), and the data were processed by ImageQuant software (Molecular Dynamics). The probes were a 220-bp PCR product derived from the 3' end of the 26S rRNA gene of tobacco [23] and a cloned ~120 bp of the 5S genic region, also from tobacco [24]. …”

Section: Methodsmentioning

confidence: 99%

“…The positions of the PCR primers are depicted in Figure 1. The primers were: 5SLf (5'-CCTGGGAATTCCTCGTGTT-3'), 5SLr (5'-TGCGTTAAAGCTTGTATGATCGCAT-3') from [24], and 26Sf (5'-GAATTCACCCAAGTGTTGGGAT-3'), originally called P1 in [23]. The PCR profile used for amplification was: initial denaturation at 94°C for 3 min followed by 35 cycles of 20 s at 94°C, 30 s at 57°C and 30 s at 72°C; and a final extension step at 72°C, 10 min.…”

Section: Methodsmentioning

confidence: 99%

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Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

et al. 2010

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BackgroundIn flowering plants and animals the most common ribosomal RNA genes (rDNA) organisation is that in which 35S (encoding 18S-5.8S-26S rRNA) and 5S genes are physically separated occupying different chromosomal loci. However, recent observations established that both genes have been unified to a single 35S-5S unit in the genus Artemisia (Asteraceae), a genomic arrangement typical of primitive eukaryotes such as yeast, among others. Here we aim to reveal the origin, distribution and mechanisms leading to the linked organisation of rDNA in the Asteraceae by analysing unit structure (PCR, Southern blot, sequencing), gene copy number (quantitative PCR) and chromosomal position (FISH) of 5S and 35S rRNA genes in ~200 species representing the family diversity and other closely related groups.ResultsDominant linked rDNA genotype was found within three large groups in subfamily Asteroideae: tribe Anthemideae (93% of the studied cases), tribe Gnaphalieae (100%) and in the "Heliantheae alliance" (23%). The remaining five tribes of the Asteroideae displayed canonical non linked arrangement of rDNA, as did the other groups in the Asteraceae. Nevertheless, low copy linked genes were identified among several species that amplified unlinked units. The conserved position of functional 5S insertions downstream from the 26S gene suggests a unique, perhaps retrotransposon-mediated integration event at the base of subfamily Asteroideae. Further evolution likely involved divergence of 26S-5S intergenic spacers, amplification and homogenisation of units across the chromosomes and concomitant elimination of unlinked arrays. However, the opposite trend, from linked towards unlinked arrangement was also surmised in few species indicating possible reversibility of these processes.ConclusionsOur results indicate that nearly 25% of Asteraceae species may have evolved unusual linked arrangement of rRNA genes. Thus, in plants, fundamental changes in intrinsic structure of rDNA units, their copy number and chromosomal organisation may occur within relatively short evolutionary time. We hypothesize that the 5S gene integration within the 35S unit might have repeatedly occurred during plant evolution, and probably once in Asteraceae.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

et al. 2010

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“…The endogenous family of 5S rRNA genes was immunoprecipited with anti H3K9me2 but not H3K4me3 ( Fig. S3C ) consistent with their heterochromatic nature 50 and heavy DNA methylation 51 . Actin genes showed intermediate signals with both euchromatic and heterochromatic signals, whereas in Arabidopsis, actin genes were strictly euchromatic 52 .…”

Section: Resultsmentioning

confidence: 76%

Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture

2013

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In plants, silencing is usually accompanied by DNA methylation and heterochromatic histone marks. We studied these epigenetic modifications in different epialleles of 35S promoter (P35S)-driven tobacco transgenes. In locus 1, the T-DNA was organized as an inverted repeat, and the residing neomycin phosphotransferase II reporter gene (P35S-nptII) was silenced at the posttranscriptional (PTGS) level. Transcriptionally silenced (TGS) epialleles were generated by trans-acting RNA signals in hybrids or in a callus culture. PTGS to TGS conversion in callus culture was accompanied by loss of the euchromatic H3K4me3 mark in the transcribed region of locus 1, but this change was not transmitted to the regenerated plants from these calli. In contrast, cytosine methylation that spread from the transcribed region into the promoter was maintained in regenerants. Also, the TGS epialleles generated by trans-acting siRNAs did not change their active histone modifications. Thus, both TGS and PTGS epialleles exhibit euchromatic (H3K4me3 and H3K9ac) histone modifications despite heavy DNA methylation in the promoter and transcribed region, respectively. However, in the TGS locus (271), abundant heterochromatic H3K9me2 marks and DNA methylation were present on P35S. Heterochromatic histone modifications are not automatically installed on transcriptionally silenced loci in tobacco, suggesting that repressive histone marks and cytosine methylation may be uncoupled. However, transient loss of euchromatic modifications may guide de novo DNA methylation leading to formation of stable repressed epialleles with recovered eukaryotic marks. Compilation of available data on epigenetic modification of inactivated P35S in different systems is provided.

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“…The NTS units seem to have been subject to rapid evolution. In the natural tobacco allotetraploids, Nicotiana tabacum [19] and Nicotiana rustica [20], two 5S rDNA families were identified that differed in the length of the NTS sequence. Similar differences in the NTS units have been described in 5S rDNAs from fishes such as Oreochromis niloticus , Oncorhynchus mykiss , Coregonus [21], Merluccius [10], and Rhizoprionodon sharks [22].…”

Section: Discussionmentioning

confidence: 99%

Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp

Chun

Tang

et al. 2017

BMC Genet

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BackgroundThe allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. The 5S rDNAs of paternal common carp were made up of a coding sequence (CDS) and a non-transcribed spacer (NTS) unit, and while the 5S rDNAs of maternal red crucian carp contained a CDS and a NTS unit, they also contained a variable number of interposed regions (IPRs). The CDSs of the 5S rDNAs in both parental fishes were conserved, while their NTS units seemed to have been subjected to rapid evolution.ResultsThe diploid hybrid 2nF1 inherited all the types of 5S rDNAs in both progenitors and there were no signs of homeologous recombination in the 5S rDNAs of 2nF1 by sequencing of PCR products. We obtained two segments of 5S rDNA with a total length of 16,457 bp from allotetraploid offspring 4nAT through bacterial artificial chromosome (BAC) sequencing. Using this sequence together with the 5S rDNA sequences amplified from the genomic DNA of 4nAT, we deduced that the 5S rDNAs of 4nAT might be inherited from the maternal progenitor red crucian carp. Additionally, the IPRs in the 5S rDNAs of 4nAT contained A-repeats and TA-repeats, which was not the case for the IPRs in the 5S rDNAs of 2nF1. We also detected two signals of a 200-bp fragment of 5S rDNA in the chromosomes of parental progenitors and hybrid progenies by fluorescence in situ hybridization (FISH).ConclusionsWe deduced that during the evolution of 5S rDNAs in different ploidy hybrid fishes, interlocus gene conversion events and tandem repeat insertion events might occurred in the process of polyploidization. This study provided new insights into the relationship among the evolution of 5S rDNAs, hybridization and polyploidization, which were significant in clarifying the genome evolution of polyploid fish.

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Mapping of 5-methylcytosine residues in Nicotiana tabacum 5S rRNA genes by genomic sequencing

Cited by 65 publications

References 25 publications

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

Repeated reunions and splits feature the highly dynamic evolution of 5S and 35S ribosomal RNA genes (rDNA) in the Asteraceae family

Epigenetic switches of tobacco transgenes associate with transient redistribution of histone marks in callus culture

Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp

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