Effect of transcription on folding of the <i>Tetrahymena</i> ribozyme

Heilman-Miller, Susan L.; Woodson, Sarah A.

doi:10.1261/rna.5200903

Cited by 101 publications

(90 citation statements)

References 41 publications

(54 reference statements)

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“…This is consistent with the abundant evidence for physical and functional links between transcription and RNA splicing, polyadenylation, decay, processing, and nuclear export (Neugebauer 2002;Bentley 2005). For ribozymes and certain regulatory RNAs, the order in which RNA sequences are transcribed and the rate of elongation can determine the type of folding intermediates that are formed (e.g., Poot et al 1997;Pan et al 1999b;Diegelman-Parente and Bevilacqua 2002;Heilman-Miller and Woodson 2003;Granneman and Baserga 2005;Mahen et al 2005;Wickiser et al 2005). Therefore, one effect of transcription is to directly influence the folding pathway of the RNA.…”

Section: Cotranscriptional Foldingsupporting

confidence: 82%

Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast

Jackson¹,

Koduvayur²,

Woodson³

2006

RNA

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Stable RNAs must form specific three-dimensional structures, yet many RNAs become kinetically trapped in misfolded conformations. To understand the factors that control the accuracy of RNA folding in the cell, the self-splicing activity of the Tetrahymena group I intron was compared in different genetic contexts in budding yeast. The extent of splicing was 98% when the intron was placed in its natural rDNA context, but only 3% when the intron was expressed in an exogenous pre-mRNA. Further experiments showed that the probability of forming the active intron structure depends on local sequence context and transcription by Pol I. Pre-rRNAs decayed at similar rates, whether the intron was wild type or inactivated by an internal deletion, suggesting that most of the unreacted pre-rRNA is incompetent to splice. Northern blots and complementation assays showed that mutations that destabilize the intron tertiary structure inhibited self-splicing and processing of internal transcribed spacer 2. The data are consistent with partitioning of pre-rRNAs into active and inactive populations. The misfolded RNAs are sequestered and degraded without refolding to a significant extent. Thus, the initial fidelity of folding can dictate the intracellular fate of transcripts containing this group I intron.

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Section: Cotranscriptional Foldingsupporting

confidence: 82%

Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast

Jackson¹,

Koduvayur²,

Woodson³

2006

RNA

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“…Normally, 1 H, 19 F, 45 and 31 P 91 are the feasible nuclei due to their high natural abundance (99.9885%, 100%, 100%, respectively) and their high sensitivity (2.79, 2.62, 1.13, relative value of z-component of nuclear magnetic moment in units of nuclear magneton, respectively). However, despite the high sensitivity, the spectral resolution of the 1D method is limited.…”

Section: Nmr Detectionmentioning

confidence: 99%

“…19,20 Biophysical Methods to Study RNA Folding RNA folding occurs over a wide range of timescales and therefore also a wide range of methods have to be applied in order to study these processes ( Figure 5). For the initiation of the folding reaction mainly three methods are applied: changes in pH, 21 in temperature 22,23 or in ionic strength.…”

mentioning

confidence: 99%

Time‐resolved NMR studies of RNA folding

et al. 2007

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The application of real‐time NMR experiments to the study of RNA folding, as reviewed in this article, is relatively new. For many RNA folding events, current investigations suggest that the time scales are in the second to minute regime. In addition, the initial investigations suggest that different folding rates are observed for one structural transition may be due to the hierarchical folding units of RNA. Many of the experiments developed in the field of NMR of protein folding cannot directly be transferred to RNA: hydrogen exchange experiments outside the spectrometer cannot be applied since the intrinsic exchange rates are too fast in RNA, relaxation dispersion experiments on the other require faster structural transitions than those observed in RNA. On the other hand, information derived from time‐resolved NMR experiments, namely the acquisition of native chemical shifts, can be readily interpreted in light of formation of a single long‐range hydrogen bonding interaction. Together with mutational data that can readily be obtained for RNA and new ligation technologies that enhance site resolution even further, time‐resolved NMR may become a powerful tool to decipher RNA folding. Such understanding will be of importance to understand the functions of coding and non‐coding RNAs in cells. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 360–383, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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“…In living cells, RNA folding is coupled with the transcription process (referred to as ''co-transcriptional folding''), i.e., each RNA chain starts to fold once it emerges from the polymerase, which is markedly different from ''refolding'' starting from a full-length RNA molecule. Interestingly, coupling of folding with in vitro transcription accelerates the native folding of the Tetrahymena ribozyme and an RNase P ribozyme about onefold (Pan et al 1999;Heilman-Miller and Woodson 2003b).…”

Section: Introductionmentioning

confidence: 99%

Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron

Zhang¹,

Bao²,

Leibowitz³

et al. 2009

RNA

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Pseudoknots play critical roles in packing the active structure of various functional RNAs. The importance of the P3-P7 pseudoknot in refolding of group I intron ribozymes has been recently appreciated, while little is known about the pseudoknot function in co-transcriptional folding. Here we used the Candida group I intron as a model to address the question. We show that co-transcriptional folding of the active self-splicing intron is twice as fast as refolding. The P3-P7 pseudoknot folds slowly during co-transcriptional folding at a rate constant similar to the folding of the active ribozyme, and folding of both P3-P7 and P1-P10 pseudoknots are inhibited by antisense oligonucleotides. We conclude that when RNA folding is coupled with transcription, formation of pseudoknot structures dominates the productive folding pathway and serves as a rate-limiting step in producing the self-splicing competent Candida intron.

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Effect of transcription on folding of the Tetrahymena ribozyme

Cited by 101 publications

References 41 publications

Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast

Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast

Time‐resolved NMR studies of RNA folding

Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron

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