Evolution of Vault RNAs

Stadler, Peter F.; Chen, Julian J.‐L.; Hackermüller, Jörg; Hoffmann, Steve; Horn, Friedemann; Khaitovich, Phillip; Kretzschmar, A.; Mosig, Axel; Prohaska, Sonja J.; Qi, Xiaodong; Schütt, Katharina; Ullmann, Kerstin

doi:10.1093/molbev/msp112

Cited by 136 publications

(192 citation statements)

References 65 publications

Supporting

Mentioning

180

Contrasting

Order By: Relevance

“…All these features are shared by pre-miR-886, and for this reason it was recently proposed to be renamed as vtRNA2-1. 40,41 VtRNAs are components of the vault complex, a hollow, barrel-shaped ribonucleoprotein complex that is thought to play a role in cellular resistance to cancer therapeutic (for a review see ref. 42).…”

Section: Discussionmentioning

confidence: 99%

Upregulation of a small vault RNA (svtRNA2-1a) is an early event in Parkinson disease and induces neuronal dysfunction

et al. 2013

View full text Add to dashboard Cite

Section: Discussionmentioning

confidence: 99%

Upregulation of a small vault RNA (svtRNA2-1a) is an early event in Parkinson disease and induces neuronal dysfunction

et al. 2013

View full text Add to dashboard Cite

“…vault distal elements comprise the shown sequences and two distinct additional further distal sequence blocks for each gene. 139,140 PSe and STAF-binding sites in the human TRNAU1, RN7SL1 and 2, as well as the BCYRN1 gene were delineated by sequence homology with PSe and STAF-binding site consensus sequences (Fig. 2).…”

Section: Rnap III Genes With Promoters Within the Transcribed Sequencementioning

confidence: 99%

“…TATA-like elements were proposed for the vTRNA1-1, -2, -3, the 7SL1 and 2 genes, eBeR genes (eTAB) 138 and the mouse analog of the BCYRN1 gene. 121,122,140 Sequences at similar positions in vTRNA2-1 and TRNAU1 genes are shown. A stimulatory influence of a SP1 binding site on in vitro transcription of the eBeR2 gene was shown.…”

Section: Rnap III Genes With Promoters Within the Transcribed Sequencementioning

confidence: 99%

Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

et al. 2014

View full text Add to dashboard Cite

The discovery of constituents of eukaryotic transcription systems was enabled by the development of in vivo and in vitro methods for their study. Depending on the organism to be studied, the relative importance of each of these two general approaches has been different. Our knowledge about transcription of human genes would be considerably smaller without the results that were obtained by employing in vitro methods. Here, we will mainly focus on in vitro studies of gene expression that contributed to discoveries in the human RNA polymerase (RNAP) III transcription system.In contrast to unicellular yeast, it has until today been and will most likely remain for a many more years impossible to study human RNAP III transcription in cells that have been grown under conditions resembling at least approximately to an in vivo situation in a human being. For that reason, it has hitherto been difficult to address questions concerning the physiological regulation of human RNAP III transcription in its natural environment. However, the identification of the basal components of the RNAP III transcription system could be achieved without directly resorting to a human "in vivo model system." Yet, the identification of human RNAP III subunits and of accessory transcription factors repeatedly took advantage of in vivo systems that were established in other species. Many discoveries of components of the human RNAP III transcription system were fostered by work performed in unicellular (for example, S. cerevisiae and S. pombe) and multicellular eukaryotes (among others, X. laevis or D. melanogaster). Often, results obtained in these model systems helped researchers identify proteins of the human RNAP III transcription system. For instance, the amino acid sequences of transcription factors that were identified and cloned by employing in vivo and in vitro methods in these organisms served as guide for comparing and identifying orthologous transcription factors in human cells (e.g., TFIIIA, TFIIIB [BDP1], TFIIIC35 [GTF3C6]). However, several of the human RNAP III transcription factors were not cloned by homology, but due to extensive purification from human cells (TFIIIB [BRF2], PTF/SNAPc, TFIIIC [GTF3C1-5]). Purification of these factors by employing biochemical methods was only possible, because functional assays were developed that allowed detecting their specific activities. These assays included in vitro transcription, electrophoretic mobility shift assays (EMSA) and footprinting techniques (descriptions of these techniques are found in 1-3 ). Two techniques were essential for the biochemical purification and functional analysis of human transcription factors: (i) the elaboration of protocols that allowed deriving protein extracts from human cells and (ii) the development of cell-free in vitro transcription assays. [4][5][6] Template DNA for in vitro transcription was provided by genes cloned into plasmid DNA. In the case of RNAP III transcription, usually complete and generally short transcribed sequences were included into the...

show abstract

“…Recently, efficient gene silencing has been demonstrated for 11 small RNAs derived from box C/D sno-miRNA [5]. Similar short RNAs, in a few cases with validated functions in gene silencing, are also produced from most other well-known structured RNAs including Y RNA [4,7], vault RNAs [8][9][10], snRNAs [4], and tRNAs [11][12][13][14]. Recent work [15], furthermore, cast doubt on the microRNA nature of several short RNA products that likely originate from the 3'-end of matured tRNAs since they include the post-transcriptionally append CCA tail.…”

Section: Introductionmentioning

confidence: 99%

MicroRNA or Not MicroRNA?

Langenberger

Bartschat²,

Hertel

et al. 2011

Advances in Bioinformatics and Computational Biology

View full text Add to dashboard Cite

Abstract. The avalanche of next generation sequencing data has led to a rapid increase of annotated microRNAs in the last few years. Many of them are specific to individual species or rather narrow clades. A closer inspection of the current version of miRBase shows that dozens of entries conflict with other ncRNAs, in particular snoRNAs. With few exceptions, these cases show little similarities to canonical microRNAs, however, and thus they should be considered as mis-annotations.

show abstract

Evolution of Vault RNAs

Cited by 136 publications

References 65 publications

Upregulation of a small vault RNA (svtRNA2-1a) is an early event in Parkinson disease and induces neuronal dysfunction

Upregulation of a small vault RNA (svtRNA2-1a) is an early event in Parkinson disease and induces neuronal dysfunction

Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

MicroRNA or Not MicroRNA?

Contact Info

Product

Resources

About