Triphosphate residues at the 5' ends of rRNA precursor and 5S RNA from Dictyostelium discoideum.

Batts-Young, Bambi; Lodish, Harvey F.

doi:10.1073/pnas.75.2.740

Cited by 28 publications

(8 citation statements)

References 38 publications

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“…These predictions hold true for actin and tubulin (ACT2 and TUB8) mRNA controls, transcribed by Pol II, which were significantly more depleted by Treatment A than by Treatments B or C, consistent with these mRNAs bearing 7-methylG caps (Figure 2D). By contrast, a Pol I-transcribed control transcript, 45S pre-rRNA, which is expected to have a 5’ triphosphate (Batts-Young and Lodish 1978), was equally depleted by Treatments A and B, as expected for RNAs with triphosphate groups at their 5’ ends, and was less depleted by Treatment C (Figure 2D). Pol V transcribed RNAs respond similar to the Pol I 45S pre-rRNA control, being equally depleted by Treatments A and B, and less depleted by Treatment C (Figure 2D).…”

Section: P4r2 and Pol V Transcript Characteristicsmentioning

confidence: 66%

The RNAs of RNA-directed DNA methylation

Wendte

Pikaard

2017

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

134

112

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Summary RNA-directed chromatin modification that includes cytosine methylation silences transposable elements in both plants and mammals, contributing to genome defense and stability. In Arabidopsis thaliana, most RNA-directed DNA methylation (RdDM) is guided by small RNAs derived from double-stranded precursors synthesized at cytosine-methylated loci by nuclear multisubunit RNA Polymerase IV (Pol IV), in close partnership with the RNA-dependent RNA polymerase, RDR2. These small RNAs help keep transposons transcriptionally inactive. However, if transposons escape silencing, and are transcribed by multisubunit RNA polymerase II (Pol II), their mRNAs can be recognized and degraded, generating small RNAs that can also guide initial DNA methylation, thereby enabling subsequent Pol IV-RDR2 recruitment. In both pathways, the small RNAs find their target sites by interacting with longer noncoding RNAs synthesized by multisubunit RNA Polymerase V (Pol V). Despite a decade of progress, numerous questions remain concerning the initiation, synthesis, processing, size and features of the RNAs that drive RdDM. Here, we review recent insights, questions and controversies concerning RNAs produced by Pols IV and V, and their functions in RdDM. We also provide new data concerning Pol V transcript 5’ and 3’ ends.

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Section: P4r2 and Pol V Transcript Characteristicsmentioning

confidence: 66%

The RNAs of RNA-directed DNA methylation

Wendte

Pikaard

2017

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanism

134

112

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“…To confirm the assignment of pppA-Up to product X we applied digestion with endonuclease P 1,We expect as digestion products pppA, pU 1* and P. and indeed all three products are found after electrophoresis on Analysis of the oligonucleotide corresponding to spot X in Fig. 1 coelectrophoresed as well and the spot close to the origin has an electrophoretic mobility, which may be expected for pppAp (1). This set of data shows that product X has the sequence pppA-Up.…”

Section: Analysis Of the 5' Terminus Of 37s Rnamentioning

confidence: 76%

The primary transcript of the ribosomal repeating unit in yeast

1979

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Endgroup analysis of 37S ribosomal precursor RNA from Saccharomyces carlsbergensis has revealed that the major 5' endgroup is ppA-Up, with a molar yield of 0.8. This shows that most, if not all, 37S RNA molecules have preserved a transcriptional initiation sequence. Analysis of the 3' terminus of 37S RNA has shown the presence of a uridine rich oligonucleotide, tentatively identified as U6-8-A-NOH. This long stretch of uridines at the 3' end of 37S RNA may represent a transcriptional termination site. The two sets of data on the terminal sequences suggest that 37S ribosomal precursor RNA, if not already spliced, is a primary transcription product. Since the 3' terminus of 26S rRNA, U-U-U-G-UOH., appears to be clearly different from the 3' end of 37S RNA, we conclude that 37S ribosomal precursor RNA contains additional nucleotides 3'-distal to the 26S rRNA sequence.

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“…In higher eukaryotes, 5S and 45S rDNAs usually have separate chromosomal loci (Castilho & Heslop‐Harrison, 1995; Benabdelmouna & Abirached‐Darmency, 1997; D'Hont et al ., 1998; Benabdelmouna, Abirached‐Darmency & Darmency, 2001), and are transcribed by the RNA polymerases III and I, respectively (Srivastava & Schlessinger, 1991). The localization of 5S and 45S rDNAs within the same repeat occurs only rarely in eukaryotes, and seems to be confined to ‘lower’ eukaryote groups, such as some protozoa, ‘fungi’, and cryptophytes (Srivastava & Schlessinger, 1991; Belkhiri, Buchko & Klassen, 1992); however, 5S and 45S rDNAs are seemingly not transcribed together in these organisms (Batts‐Young & Lodish, 1978). The most striking exception in eukaryotes is the liverwort Marchantia polymorpha , in which the 18S, 5.8S, 26S, and 5S rDNAs are located within the same repeat according to DNA sequence analyses (Sone et al ., 1999), but the mechanism of transcription is not known.…”

Section: Introductionmentioning

confidence: 99%

Disposition of ribosomal DNAs in the chromosomes of perennial oats (Poaceae: Aveneae)

Winterfeld

Röser

2007

Botanical Journal of the Linnean Society

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The chromosomal loci of 5S and 45S ribosomal DNAs (rDNAs) and the activity of nucleolar-organizing regions (NORs) were analysed in perennial oats of the genera Ammophila, Amphibromus, Arrhenatherum, Avena, Deschampsia, and Helictotrichon s.l. (Poaceae: Aveneae) using fluorescence in situ hybridization, staining with chromomycin/4′,6-diamidino-2-phenylindole (DAPI), and silver impregnation. All chromosomes with a secondary constriction were nucleolar active. In chromosomes without a secondary constriction, NORs corresponded exclusively to broad bands of 45S rDNA with chromomycin-positive, DAPI-negative, and silver-positive stainability. Additional minor bands of 45S rDNA showed no nucleolar activity. 5S rDNA was localized mostly in loci different from the nucleolar-active 45S rDNA. If both rDNAs occurred within the same chromosome, they were at largely corresponding distances from the centromere, irrespective of their particular localization in either the same chromosome arm or in opposite arms. In the latter case, 5S rDNA was never more distal to the centromere than 45S rDNA. A new model was devised to explain this non-random distribution of both rDNAs in nucleolar-organizing chromosomes, which identified the Rabl orientation of chromosomes as ensuring a spatial proximity of 5S to 45S rDNA in interphase nuclei, even if they were localized in opposite arms. The possible role of the Rabl orientation in determining the spread and accumulation of 5S rDNA sequences in further chromosomes of the genome was discussed. B chromosomes were devoid of 5S rDNA, but most contained 45S rDNA and were nucleolar active. In some large groups of species, the number and arrangement of 5S and 45S rDNA sites in the chromosomes were remarkably uniform, especially in Helictotrichon subgenus Helictotrichon and Helictotrichon subgenus Pratavenastrum. Such distribution patterns have survived many speciation processes and have also remained widely unchanged in polyploids.

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Triphosphate residues at the 5' ends of rRNA precursor and 5S RNA from Dictyostelium discoideum.

Cited by 28 publications

References 38 publications

The RNAs of RNA-directed DNA methylation

The RNAs of RNA-directed DNA methylation

The primary transcript of the ribosomal repeating unit in yeast

Disposition of ribosomal DNAs in the chromosomes of perennial oats (Poaceae: Aveneae)

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