The expanding snoRNA world

Bachellerie, Jean Pierre; Cavaillé, Jérôme; Hüttenhofer, Alexander

doi:10.1016/s0300-9084(02)01402-5

Cited by 597 publications

(496 citation statements)

References 143 publications

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“…These conserved small RNA regulators modify alternative splicing of many transcripts (Bachellerie et al, 2002). In this study, the identification of hypomethylation and enhanced expression of the three snoRNAs suggest a potential relationship between cancer and dysregulation of snoRNAs.…”

Section: Discussionmentioning

confidence: 63%

Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer

et al. 2010

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BACKGROUND: Testicular germ cell tumour (TGCT) is the most common malignant tumour in young males. Although aberrant DNA methylation is implicated in the pathophysiology of many cancers, only a limited number of genes are known to be epigenetically changed in TGCT. This report documents the genome-wide analysis of differential methylation in an in vitro model culture system. Interesting genes were validated in TGCT patient samples. METHODS: In this study, we used methylated DNA immunoprecipitation (MeDIP) and whole-genome tiling arrays to identify differentially methylated regions (DMRs). RESULTS: We identified 35 208 DMRs. However, only a small number of DMRs mapped to promoters. A genome-wide analysis of gene expression revealed a group of differentially expressed genes that were regulated by DNA methylation. We identified several candidate genes, including APOLD1, PCDH10 and RGAG1, which were dysregulated in TGCT patient samples. Surprisingly, APOLD1 had previously been mapped to the TGCT susceptibility locus at 12p13.1, suggesting that it may be important in TGCT pathogenesis. We also observed aberrant methylation in the loci of some non-coding RNAs (ncRNAs). One of the ncRNAs, hsa-mir-199a, was downregulated in TGCT patient samples, and also in our in vitro model culture system. CONCLUSION: This report is the first application of MeDIP-chip for identifying epigenetically regulated genes and ncRNAs in TGCT. We also demonstrated the function of intergenic and intronic DMRs in the regulation of ncRNAs.

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Section: Discussionmentioning

confidence: 63%

Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer

et al. 2010

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“…[1][2][3][4][5] Two types of modifications of nucleotides in precursor rRNAs have been discovered: 6,7 (1) the conversion of specific uridines to pseudouridines (C); and (2) the addition of methyl groups to specific nucleotides, mostly to O2 0 of ribose (Nm). 2 0 -O-methylation is catalyzed by a conserved class of snoRNPs which contains a box C/D RNA and several protein components.…”

Section: Introductionmentioning

confidence: 99%

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

Wei¹,

Yang²,

Yu³

et al. 2013

Phys. Chem. Chem. Phys.

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“…Moreover, the 23 newly identified H/ACA RNAs from the T. brucei genome also carry a single hairpin and an AGA box at the 3Ј end, 2 suggesting that this is the prototype of the trypanosomatid H/ACA RNA. Another organism possessing single hairpin pseudouridine guides is archaea (36,37), whereas all eukaryotic H/ACA snoRNAs carry two hairpins connected by the hinge region. Interestingly, archaea were also shown to possess H/ACA-like RNA that carry multiple hairpins.…”

Section: Discussionmentioning

confidence: 99%

Small Nucleolar RNA Clusters in Trypanosomatid Leptomonas collosoma

Liang

Ochaion

et al. 2004

Journal of Biological Chemistry

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Trypanosomatid small nucleolar RNA (snoRNA) genes are clustered in the genome. snoRNAs are transcribed polycistronically and processed into mature RNAs. In this study, we characterized four snoRNA clusters in Leptomonas collosoma. All of the clusters analyzed carry both C/D and H/ACA RNAs. The H/ACA RNAs are composed of a single hairpin, a structure typical to trypanosome and archaea guide RNAs. Using deletion and mutational analysis of a tagged C/D snoRNA situated within the snoRNA cluster, we identified 10-nucleotide flanking sequences that are essential for processing snoRNA from its precursor. Chromosome walk was performed on a snoRNA cluster, and a sequence of 700 bp was identified between the first repeat and the upstream open reading frame. Cloning of this sequence in an episome vector enhanced the expression of a tagged snoRNA gene in an orientation-dependent manner. However, continuous transcript spanning of this region was detected in steady-state RNA, suggesting that snoRNA transcription also originates from an upstreamlong polycistronic transcriptional unit. The 700-bp fragment may therefore represent an example of many more elements to be discovered that enhance transcription along the chromosome, especially when transcription from the upstream gene is reduced or when enhanced transcription is needed.In eukaryotes, pre-rRNA transcript undergoes numerous site-specific modifications before cleavage. Two prevalent modifications, 2Ј-O-methylation and conversion of uridine to pseudouridine, are guided by C/D box and H/ACA box small nucleolar RNAs (snoRNAs), 1 respectively (1-3). The C/D snoRNAs carry short conserved motives, as do the C box (RUG-AUGA) and D box (CUGA), near the 5Ј and 3Ј ends, respectively, as well as the internal DЈ and CЈ boxes. Sequences (Ͼ10 nt) upstream from the D and/or DЈ box can interact with the target RNA by perfect base pairing. The 5th nt on the target RNA upstream from the D or DЈ box in the duplex is methylated, which is known as the "ϩ5 rule" (1). The H/ACA snoRNAs that guide pseudouridylation carry two hairpin structures linked by the H box (AnAnnA) in the hinge region and an ACA box 3 nt upstream from the 3Ј end. The internal loop interacts with the target RNA to form the pseudouridylation pocket. The uridine on the target RNA to be isomerized is located usually 14 -16 nts upstream from the ACA and/or H box (2, 3).In vertebrates, all guide snoRNAs are intronic (4, 5). Most yeast snoRNAs are encoded by independent genes, some of which are found in clusters. However, seven intronic genes were also described (6). In plants, most snoRNAs are clustered and are independently transcribed, but intronic snoRNA gene clusters also exist (7-9). The intronic snoRNA genes are transcribed from the promoter of host genes by RNA polymerase II (10, 11). The polycistronic snoRNAs in yeast are transcribed by polymerase II from their own promoters carrying the TATA box and the binding site of Rap1p, a transcription factor involved in ribosomal protein expression (6). In plants, promoters exp...

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The expanding snoRNA world

Cited by 597 publications

References 143 publications

Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer

Genome-wide DNA methylation profiling reveals novel epigenetically regulated genes and non-coding RNAs in human testicular cancer

Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations

Small Nucleolar RNA Clusters in Trypanosomatid Leptomonas collosoma

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