Enzymic and chemical structure mapping of mouse 28S ribosomal RNA-contacts in 5.8S ribosomal RNA

Walker, Thomas A.; Johnson, Kimberly D.; Olsen, Gary J.; Peters, Mary A.; Pace, Norman R.

doi:10.1021/bi00539a008

Cited by 37 publications

(35 citation statements)

References 36 publications

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“…To obtain a transcriptome-wide view of base-paired RNA (dsRNA) in unopened flower buds of Arabidopsis thaliana Col-0 ecotype (hereafter referred to as wild-type Col-0), we married classical nuclease-based structure mapping techniques [29], [30] with high-throughput sequencing technology (see Figure S1A, and Materials and Methods for details). We characterized the dsRNA component of the Arabidopsis transcriptome after one round of ribosomal RNA (rRNA)-depletion, and obtained 15,499,789 raw reads representing 4,802,974 non-redundant (NR) sequences with an average clone-abundance of 3.2 (Accession #: GSE23439).…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

et al. 2010

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The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions. This is especially evident for RNA molecules whose functionality, maturation, and regulation require formation of correct secondary structure through encoded base-pairing interactions. Unfortunately, intra- and inter-molecular base-pairing information is lacking for most RNAs. Here, we marry classical nuclease-based structure mapping techniques with high-throughput sequencing technology to interrogate all base-paired RNA in Arabidopsis thaliana and identify ∼200 new small (sm)RNA–producing substrates of RNA–DEPENDENT RNA POLYMERASE6. Our comprehensive analysis of paired RNAs reveals conserved functionality within introns and both 5′ and 3′ untranslated regions (UTRs) of mRNAs, as well as a novel population of functional RNAs, many of which are the precursors of smRNAs. Finally, we identify intra-molecular base-pairing interactions to produce a genome-wide collection of RNA secondary structure models. Although our methodology reveals the pairing status of RNA molecules in the absence of cellular proteins, previous studies have demonstrated that structural information obtained for RNAs in solution accurately reflects their structure in ribonucleoprotein complexes. Furthermore, our identification of RNA–DEPENDENT RNA POLYMERASE6 substrates and conserved functional RNA domains within introns and both 5′ and 3′ untranslated regions (UTRs) of mRNAs using this approach strongly suggests that RNA molecules are correctly folded into their secondary structure in solution. Overall, our findings highlight the importance of base-paired RNAs in eukaryotes and present an approach that should be widely applicable for the analysis of this key structural feature of RNA.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

et al. 2010

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“…2, the 5′ terminal region of the 28S rRNA was highly stable in all tested postmortem tissues up to 4 days. This exceptional stability of the domain is probably because of its secondary and tertiary structure; the domain forms tight stem-like structures by intramolecular base-pairing, and further associates with the 5.8S rRNA subunit (Houge et al, 1995; Michot et al, 1982; Walker et al, 1982). It is most plausible that such structural features confer remarkable stability to the domain during postmortem degradation.…”

Section: Discussionmentioning

confidence: 99%

Cell Death-Associated Ribosomal RNA Cleavage in Postmortem Tissues and Its Forensic Applications

Kim

Kyeong

et al. 2017

Molecules and Cells

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Estimation of postmortem interval (PMI) is a key issue in the field of forensic pathology. With the availability of quantitative analysis of RNA levels in postmortem tissues, several studies have assessed the postmortem degradation of constitutively expressed RNA species to estimate PMI. However, conventional RNA quantification as well as biochemical and physiological changes employed thus far have limitations related to standardization or normalization. The present study focuses on an interesting feature of the subdomains of certain RNA species, in which they are site-specifically cleaved during apoptotic cell death. We found that the D8 divergent domain of ribosomal RNA (rRNA) bearing cell death-related cleavage sites was rapidly removed during postmortem RNA degradation. In contrast to the fragile domain, the 5′ terminal region of 28S rRNA was remarkably stable during the postmortem period. Importantly, the differences in the degradation rates between the two domains in mammalian 28S rRNA were highly proportional to increasing PMI with a significant linear correlation observed in mice as well as human autopsy tissues. In conclusion, we demonstrate that comparison of the degradation rates between domains of a single RNA species provides quantitative information on postmortem degradation states, which can be applied for the estimation of PMI.

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“…46 This method marries classical nucleasebased structure mapping approach 48,49 with HTS technology in order to obtain base-pairing information on a transcriptomewide scale. According to the primary criteria for miRNA annotation in plants, the base-pairing between the miRNA arm and the miRNA* arm of a precursor should be extensive, with only a few mismatches and bulges allowed.…”

Section: Srna-seqmentioning

confidence: 99%

The use of high-throughput sequencing methods for plant microRNA research

Tang

Qin³

et al. 2015

RNA Biology

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Enzymic and chemical structure mapping of mouse 28S ribosomal RNA-contacts in 5.8S ribosomal RNA

Cited by 37 publications

References 36 publications

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis

Cell Death-Associated Ribosomal RNA Cleavage in Postmortem Tissues and Its Forensic Applications

The use of high-throughput sequencing methods for plant microRNA research

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