2'-O-methylation of the wobble residue of elongator pre-tRNA<sup>Met</sup>in<i>Haloferax volcanii</i>is guided by a box C/D RNA containing unique features

Joardar, Archi; Malliahgari, Srinivas Reddy; Skariah, Geena; Gupta, Ramesh C.

doi:10.4161/rna.8.5.16015

Cited by 16 publications

(13 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S4). Finally, in archaeal and vertebrate elongator tRNAs Met(CAT), the wobble cytidine is 2 ′ -O-methylated, and, in Archaea, this methyltranfer reaction is catalyzed by box C/D RNPs (Joardar et al 2011;Boccaletto et al 2018).…”

Section: Snord97 and Scarna97 Are Predicted To Direct 2 ′ -O-methylatmentioning

confidence: 99%

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Vitali

Kiss

2019

Genes Dev.

View full text Add to dashboard Cite

Site-specific 2′-O-ribose methylation of mammalian rRNAs and RNA polymerase II-synthesized spliceosomal small nuclear RNAs (snRNAs) is mediated by small nucleolar and small Cajal body (CB)-specific box C/D ribonucleoprotein particles (RNPs) in the nucleolus and the nucleoplasmic CBs, respectively. Here, we demonstrate that 2′-O-methylation of the C34 wobble cytidine of human elongator tRNAMet(CAT) is achieved by collaboration of a nucleolar and a CB-specific box C/D RNP carrying the SNORD97 and SCARNA97 box C/D 2′-O-methylation guide RNAs. Methylation of C34 prevents site-specific cleavage of tRNAMet(CAT) by the stress-induced endoribonuclease angiogenin, implicating box C/D guide RNPs in controlling stress-responsive production of putative regulatory tRNA fragments.

show abstract

Section: Snord97 and Scarna97 Are Predicted To Direct 2 ′ -O-methylatmentioning

confidence: 99%

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Vitali

Kiss

2019

Genes Dev.

View full text Add to dashboard Cite

show abstract

“…Although a portion of methylation sites are widely conserved, many are conserved only between closely related species or within phyla [40]. Recent discoveries that stretch the possibilities of functional H/ACA and C/D box RNA structure [46,94,95] illustrate the need for computational programs that are specialized by clades (Table 2). Th e recent availability of high-throughput sequencing data strengthens computational searches by narrowing 'search space' and confi rming predictions with transcriptional data.…”

Section: Figure 3 Types Of Genomic Organization Of Snorna Genes Withmentioning

confidence: 99%

Small nucleolar RNAs and RNA-guided post-transcriptional modification

Lui

Lowe

2013

Essays in Biochemistry

View full text Add to dashboard Cite

snoRNAs (small nucleolar RNAs) constitute one of the largest and best-studied classes of non-coding RNAs that confer enzymatic specificity. With associated proteins, these snoRNAs form ribonucleoprotein complexes that can direct 2'-O-methylation or pseudouridylation of target non-coding RNAs. Aided by computational methods and high-throughput sequencing, new studies have expanded the diversity of known snoRNA functions. Complexes incorporating snoRNAs have dynamic specificity, and include diverse roles in RNA silencing, telomerase maintenance and regulation of alternative splicing. Evidence that dysregulation of snoRNAs can cause human disease, including cancer, indicates that the full scope of snoRNA roles remains an unfinished story. The diversity in structure, genomic origin and function between snoRNAs found in different complexes and among different phyla illustrates the surprising plasticity of snoRNAs in evolution. The ability of snoRNAs to direct highly specific interactions with other RNAs is a consistent thread in their newly discovered functions. Because they are ubiquitous throughout Eukarya and Archaea, it is likely they were a feature of the last common ancestor of these two domains, placing their origin over two billion years ago. In the present chapter, we focus on recent advances in our understanding of these ancient, but functionally dynamic RNA-processing machines.

show abstract

“…In contrast to Eubacteria, the methylation of the wobble residue C34 of Haloferax volcanii elongator tRNA Met is guided by a box C/D RNA targeting the tRNA intron-containing precursor [29]. 2′- O -methylation of both nucleotides C34 and U39 in H. volcanii pre-tRNA Trp also requires the box C/D ribonucleoprotein (RNP) machinery.…”

Section: Introductionmentioning

confidence: 99%

Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation

et al. 2017

View full text Add to dashboard Cite

Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2′-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth conditions. However, until now, RiboMethSeq was only employed for rRNA, and the whole sequencing and analysis pipeline was only adapted to this long and rather conserved RNA species. A deep understanding of RNA modification functions requires large and global analysis datasets for other important RNA species, namely for transfer RNAs (tRNAs), which are well known to contain a great variety of functionally-important modified residues. Here, we evaluated the application of the RiboMethSeq protocol for the analysis of tRNA 2′-O-methylation in Escherichia coli and in Saccharomyces cerevisiae. After a careful optimization of the bioinformatic pipeline, RiboMethSeq proved to be suitable for relative quantification of methylation rates for known modified positions in different tRNA species.

show abstract

2'-O-methylation of the wobble residue of elongator pre-tRNA^MetinHaloferax volcaniiis guided by a box C/D RNA containing unique features

Cited by 16 publications

References 62 publications

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Small nucleolar RNAs and RNA-guided post-transcriptional modification

Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation

Contact Info

Product

Resources

About

2'-O-methylation of the wobble residue of elongator pre-tRNAMetinHaloferax volcaniiis guided by a box C/D RNA containing unique features

Cited by 16 publications

References 62 publications

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNAMet(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNAMet(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Small nucleolar RNAs and RNA-guided post-transcriptional modification

Next‐Generation Sequencing‐Based RiboMethSeq Protocol for Analysis of tRNA 2′‐O‐Methylation

Contact Info

Product

Resources

About

2'-O-methylation of the wobble residue of elongator pre-tRNA^MetinHaloferax volcaniiis guided by a box C/D RNA containing unique features

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP

Cooperative 2′-O-methylation of the wobble cytidine of human elongator tRNA^Met(CAT) by a nucleolar and a Cajal body-specific box C/D RNP