Analysis of C/D box snoRNA genes in vertebrates: The number of copies decreases in placental mammals

Makarova, J. A.; Крамеров, Д. А.

doi:10.1016/j.ygeno.2009.02.003

Cited by 21 publications

(28 citation statements)

References 63 publications

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“…Of the 12 clock genes examined, PolII levels decreased towards background levels at one or more time points in three cases (Per2, Dbp and Npas2), whereas H3K4me3 levels remained above background across the day in all cases. We then examined the chromatin signature of three snoRNA known to be independently transcribed, namely, Rnu3a (U3), Snord13 and Snord118 [23,31], and found a distinctive peak in PolII at the gene start in all three cases (figure 6 and electronic supplementary material, figure S12). A considerable temporal variation in this signal was also apparent.…”

Section: Resultsmentioning

confidence: 99%

The circadian dynamics of small nucleolar RNA in the mouse liver

Aitken¹,

Semple²

2017

J. R. Soc. Interface.

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The circadian regulation of gene expression allows plants and animals to anticipate predictable environmental changes. While the influence of the circadian clock has recently been shown to extend to ribosome biogenesis, the dynamics and regulation of the many small nucleolar RNA that are required in pre-ribosomal RNA folding and modification are unknown. Using a novel computational method, we show that 18S and 28S pre-rRNA are subject to circadian regulation in a nuclear RNA sequencing time course. A population of snoRNA with circadian expression is identified that is functionally associated with rRNA modification. More generally, we find the abundance of snoRNA known to modify 18S and 28S to be inversely correlated with the abundance of their target. Cyclic patterns in the expression of a number of snoRNA indicate a coordination with rRNA maturation, potentially through an upregulation in their biogenesis, or their release from mature rRNA at the end of the previous cycle of rRNA maturation, in antiphase with the diurnal peak in pre-rRNA. Few cyclic snoRNA have cyclic host genes, indicating the action of regulatory mechanisms in addition to transcriptional activation of the host gene. For highly expressed independently transcribed snoRNA, we find a characteristic RNA polymerase II and H3K4me3 signature that correlates with mean snoRNA expression over the day.

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Section: Resultsmentioning

confidence: 99%

The circadian dynamics of small nucleolar RNA in the mouse liver

Aitken¹,

Semple²

2017

J. R. Soc. Interface.

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“…Other well-studied examples of deeply conserved snoRNA host genes include UHG (SNHG1) (Fig. 7) and U87HG (Makarova and Kramerov 2009).…”

Section: Hundreds Of Lncrnas Are Conserved Throughout the Vertebratesmentioning

confidence: 99%

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

Nitsche¹,

Rose²,

Fasold³

et al. 2015

RNA

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Large-scale RNA sequencing has revealed a large number of long mRNA-like transcripts (lncRNAs) that do not code for proteins. The evolutionary history of these lncRNAs has been notoriously hard to study systematically due to their low level of sequence conservation that precludes comprehensive homology-based surveys and makes them nearly impossible to align. An increasing number of special cases, however, has been shown to be at least as old as the vertebrate lineage. Here we use the conservation of splice sites to trace the evolution of lncRNAs. We show that >85% of the human GENCODE lncRNAs were already present at the divergence of placental mammals and many hundreds of these RNAs date back even further. Nevertheless, we observe a fast turnover of intron/exon structures. We conclude that lncRNA genes are evolutionary ancient components of vertebrate genomes that show an unexpected and unprecedented evolutionary plasticity. We offer a public web service (http://splicemap.bioinf.unileipzig.de) that allows to retrieve sets of orthologous splice sites and to produce overview maps of evolutionarily conserved splice sites for visualization and further analysis. An electronic supplement containing the ncRNA data sets used in this study is available at

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“…The introns of some ribosome-associated genes were found to host snoRNAs that guide rRNA modifications (Maxwell and Fournier, 1995), but it is generally not the rule that snoRNAs are related to the regulation of their host genes. Strikingly, the sole function of some genes seems to be harboring snoRNAs in their introns, and their mRNA does not look as if it has a protein-coding potential (Tycowski et al, 1996; Bachellerie et al, 2002; Makarova and Kramerov, 2009). …”

Section: Functions Associated With Excised Intronsmentioning

confidence: 99%

The Function of Introns

Chorev¹,

Carmel²

2012

Front. Gene.

298

252

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The intron–exon architecture of many eukaryotic genes raises the intriguing question of whether this unique organization serves any function, or is it simply a result of the spread of functionless introns in eukaryotic genomes. In this review, we show that introns in contemporary species fulfill a broad spectrum of functions, and are involved in virtually every step of mRNA processing. We propose that this great diversity of intronic functions supports the notion that introns were indeed selfish elements in early eukaryotes, but then independently gained numerous functions in different eukaryotic lineages. We suggest a novel criterion of evolutionary conservation, dubbed intron positional conservation, which can identify functional introns.

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Analysis of C/D box snoRNA genes in vertebrates: The number of copies decreases in placental mammals

Cited by 21 publications

References 63 publications

The circadian dynamics of small nucleolar RNA in the mouse liver

The circadian dynamics of small nucleolar RNA in the mouse liver

Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved

The Function of Introns

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