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Structure of long telomeric RNA transcripts: the G-rich RNA forms a compact repeating structure containing G-quartets.

ABSTRACT: Recent studies have identified RNA transcripts arising from mammalian telomeres with the transcript of the C-rich strand (r(5'-UUAGGG-3')(n)) being much more abundant than transcripts of the G-rich strand. Here we used transmission electron microscopy, CD, and nuclease digestion to investigate the structure of approximately 640-nucleotide (nt) RNA transcripts of the C-rich and G-rich strands of mammalian telomeric DNA. The CD spectrum of the C-rich RNA in low salt (10 mm KCl) or high salt (100 mm KCl) was typical of mixed sequence RNA, whereas the CD spectrum for the G-rich RNA differed with changes characteristic of parallel G-quadruplexes at the higher salt concentration. Electron microscopy visualization of the C-rich RNA revealed relatively extended unstructured molecules 59.7 +/- 17.8 nm in length and with a width consistent with single-stranded RNA following metal coating. In contrast, the G-rich RNA was observed as round particles and short, thick rods with the rods being most prevalent in high salt conditions and absent in low salt. The rods were 22.7 +/- 4.8 nm in length and 7.6 nm in width. Digestion of the G-rich RNA with T1 RNA nuclease revealed a ladder of bands whose sizes were integral multiples of 24 nt plus a 4-nt overhang. These observations suggest a model in which G-rich telomeric RNA folds into chains of particles each consisting of four (UUAGGG) repeats stabilized by parallel G-quartets and joined by UUA linkers. These chains further condense to form short rods and round particles.

SUBMITTER: Randall A

PROVIDER: S-EPMC2682846 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

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Structure of long telomeric RNA transcripts: the G-rich RNA forms a compact repeating structure containing G-quartets.

Randall Adrian A Griffith Jack D JD

The Journal of biological chemistry 20090326 21

Recent studies have identified RNA transcripts arising from mammalian telomeres with the transcript of the C-rich strand (r(5'-UUAGGG-3')(n)) being much more abundant than transcripts of the G-rich strand. Here we used transmission electron microscopy, CD, and nuclease digestion to investigate the structure of approximately 640-nucleotide (nt) RNA transcripts of the C-rich and G-rich strands of mammalian telomeric DNA. The CD spectrum of the C-rich RNA in low salt (10 mm KCl) or high salt (100 m ...[more]

PMID: 19329435

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Project description:BackgroundEukaryotic organisms contain mitochondria, organelles capable of producing large amounts of ATP by oxidative phosphorylation. Each cell contains many mitochondria with many copies of mitochondrial DNA in each organelle. The mitochondrial DNA encodes a small but functionally critical portion of the oxidative phosphorylation machinery, a few other species-specific proteins, and the rRNA and tRNA used for the translation of these transcripts. Because the microenvironment of the mitochondrion is unique, mitochondrial genes may be subject to different selectional pressures than those affecting nuclear genes.ResultsFrom an analysis of the mitochondrial genomes of a wide range of eukaryotic species we show that there are three simple rules for the pyrimidine and purine abundances in mitochondrial DNA transcripts. Mitochondrial membrane protein transcripts are pyrimidine rich, rRNA transcripts are purine-rich and the soluble protein transcripts are purine-rich. The transitions between pyrimidine and purine-rich regions of the genomes are rapid and are easily visible on a pyrimidine-purine walk graph. These rules are followed, with few exceptions, independent of which strand encodes the gene. Despite the robustness of these rules across a diverse set of species, the magnitude of the differences between the pyrimidine and purine content is fairly small. Typically, the mitochondrial membrane protein transcripts have a pyrimidine richness of 56%, the rRNA transcripts are 55% purine, and the soluble protein transcripts are only 53% purine.ConclusionThe pyrimidine richness of mitochondrial-encoded membrane protein transcripts is partly driven by U nucleotides in the second codon position in all species, which yields hydrophobic amino acids. The purine-richness of soluble protein transcripts is mainly driven by A nucleotides in the first codon position. The purine-richness of rRNA is also due to an abundance of A nucleotides. Possible mechanisms as to how these trends are maintained in mtDNA genomes of such diverse ancestry, size and variability of A-T richness are discussed.

Dataset Information

Structure of long telomeric RNA transcripts: the G-rich RNA forms a compact repeating structure containing G-quartets.

Publications

Structure of long telomeric RNA transcripts: the G-rich RNA forms a compact repeating structure containing G-quartets.

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