SnoRNA U21 is also intron‐encoded in <i>Drosophila melanogaster</i> but in a different host‐gene as compared to warm‐blooded vertebrates

Renalier, Marie-Hélène; Nicoloso, Monique; Qu, Liang‐Hu; Bachellerie, Jean‐Pierre

doi:10.1016/0014-5793(95)01511-6

Cited by 14 publications

(3 citation statements)

References 31 publications

(70 reference statements)

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“…The snoRNA complement of fruit flies has been studied extensively in the past [ 12 , 13 ]. Earlier studies, in particular, used computationally predicted candidates derived from known targets [ 14 , 15 , 16 , 17 ]. Many of the fruit fly snoRNAs appear in clusters, more precisely in different introns of a single host gene [ 10 , 18 ], albeit in sometimes unusual arrangements.…”

Section: Introductionmentioning

confidence: 99%

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster

Agrisani

Tafer

Stadler

et al. 2015

ncRNA

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A computational screen for novel small nucleolar RNAs in Drosophila melanogaster uncovered 15 novel snoRNAs and snoRNA-like long non-coding RNAs. In contrast to earlier surverys, the novel sequences are mostly poorly conserved and originate from unusual genomic locations. The majority derive from precurors antisense to well-known protein-coding genes, and four of the candidates are produced from exon-coding regions. Only a minority of the new sequences appears to have canonical target sites in ribosomal or small nuclear RNAs. Taken together, these evolutionary young, poorly conserved, and genomically atypical sequences point at a class of snoRNA-like transcripts with predominantly regulatory functions in the fruit fly genome.

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Section: Introductionmentioning

confidence: 99%

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster

Agrisani

Tafer

Stadler

et al. 2015

ncRNA

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“…One of these is U17 , which is encoded within an intron of the ribosomal protein rpS7 in gene in Xenopus laevis (C ecconi et al 1995) and Takifugu rubripes (C ecconi et al 1996), but in the non‐protein coding gene h U17HG in human (P addison et al 2002). Other examples are U18, which is located in the rpL1 gene in vertebrates and in elongation factor EF‐1β gene in S. cerevisiae (M axwell and F ournier 1995), U24 , which is located intronically in RpL7 in D. melanogaster , but in an unknown gene in S. cerevisiae (Q u et al 1995), and finally U21 , which have changed location from an intron in the ARF‐1 (ADP ribosylation factor) gene in D. melanogaster to an RpL5 intron in mammals and chicken (R enalier et al 1996).…”

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confidence: 99%

Evolutionary profiling of the U49 snoRNA gene

et al. 2003

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Small nucleolar RNAs (snoRNAs) are involved in precursor ribosomal RNA (pre-rRNA) processing and rRNA base modifications (2'-O-ribose methylation and pseudouridylation). Their genomic organization show great flexibility: some are individually or polycistronically transcribed, while others are encoded within introns of other genes. Here, we present an evolutionary analysis of the U49 gene in seven species. In all species analyzed, U49 contains the typical hallmarks of C and D box motifs, and a conserved 12-15 nt sequence complementary to rRNA that define them as homologs. In mouse, human, and Drosophila U49 is found encoded within introns of different genes, and in plants it is transcribed polycistronically from four different locations. In addition, U49 has two copies in two different introns of the RpL14 gene in Drosophila. The results indicate a substantial degree of duplication and translocation of the U49 gene in evolution. In light of its variable organization we discuss which of the two proposed mechanisms of rearrangement has acted upon the U49 snoRNA gene: chromosomal duplication or transposition through an RNA intermediate.

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“…It could also be caused by an RNA structure-dependent drop-off of the reverse transcriptase (47) or by preferential amplification of some of the short cDNA sequences during library generation. However, such cases cannot be distinguished based on the sole analysis of cDNA sequences.…”

Section: Discussionmentioning

confidence: 99%

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

Żywicki

Bąkowska-Żywicka

Polacek

2012

Nucleic Acids Research

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The exploration of the non-protein-coding RNA (ncRNA) transcriptome is currently focused on profiling of microRNA expression and detection of novel ncRNA transcription units. However, recent studies suggest that RNA processing can be a multi-layer process leading to the generation of ncRNAs of diverse functions from a single primary transcript. Up to date no methodology has been presented to distinguish stable functional RNA species from rapidly degraded side products of nucleases. Thus the correct assessment of widespread RNA processing events is one of the major obstacles in transcriptome research. Here, we present a novel automated computational pipeline, named APART, providing a complete workflow for the reliable detection of RNA processing products from next-generation-sequencing data. The major features include efficient handling of non-unique reads, detection of novel stable ncRNA transcripts and processing products and annotation of known transcripts based on multiple sources of information. To disclose the potential of APART, we have analyzed a cDNA library derived from small ribosome-associated RNAs in Saccharomyces cerevisiae. By employing the APART pipeline, we were able to detect and confirm by independent experimental methods multiple novel stable RNA molecules differentially processed from well known ncRNAs, like rRNAs, tRNAs or snoRNAs, in a stress-dependent manner.

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SnoRNA U21 is also intron‐encoded in Drosophila melanogaster but in a different host‐gene as compared to warm‐blooded vertebrates

Abstract: U21 is an intron-encoded snoRNA in vertebrates which contains a 13-nt tract of complementarity to an invariant sequence in eukaryotic 28S rRNA. Here, we report the character-

Cited by 14 publications

References 31 publications

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster

Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster

Evolutionary profiling of the U49 snoRNA gene

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis

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