scholarly journals RSQ: a statistical method for quantification of isoform-specific structurome using transcriptome-wide structural profiling data

2016 ◽  
Author(s):  
Yunfei Wang ◽  
Xiaopeng Zhu ◽  
Ming Sun ◽  
Yong Chen ◽  
Yiwen Chen ◽  
...  
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Rna Structures ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Quantification Method ◽  
Rna Conformation ◽  
Non Coding Rnas ◽  
Potential Impact ◽  
Accurate Quantification

AbstractThe structure of RNA, which is considered to be a second layer of information alongside the genetic code, provides fundamental insights into the cellular function of both coding and non-coding RNAs. Several high-throughput technologies have been developed to profile transcriptome-wide RNA structures, i.e., the structurome. However, it is challenging to interpret the profiling data because the observed data represent an average over different RNA conformations and isoforms with different abundance. To address this challenge, we developed an RNA structurome quantification method (RSQ) to statistically model the distribution of reads over both isoforms and RNA conformations, and thus provide accurate quantification of the isoform-specific structurome. The quantified RNA structurome enables the comparison of isoform-specific conformations between different conditions, the exploration of RNA conformation variation affected by single nucleotide polymorphism (SNP),and the measurement of RNA accessibility for binding of either small RNAs in RNAi-based assays or RNA binding protein in transcriptional regulation. The model used in our method sheds new light on the potential impact of the RNA structurome on gene regulation.

scholarly journals Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

2012 ◽  
Vol 41 (1) ◽  
pp. 44-53 ◽  
Author(s):  
Raheleh Salari ◽  
Chava Kimchi-Sarfaty ◽  
Michael M. Gottesman ◽  
Teresa M. Przytycka
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Rna Conformation ◽  
Induced Changes

How to find small non-coding RNAs in bacteria

2005 ◽  
Vol 386 (12) ◽  
pp. 1219-1238 ◽  
Author(s):  
Jörg Vogel ◽  
Cynthia Mira Sharma
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Critical Role ◽  
Rna Molecules ◽  
Regulatory Circuit ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Response To Stress ◽  
Non Coding Rnas

AbstractSmall non-coding RNAs (sRNAs) have attracted considerable attention as an emerging class of gene expression regulators. In bacteria, a few regulatory RNA molecules have long been known, but the extent of their role in the cell was not fully appreciated until the recent discovery of hundreds of potential sRNA genes in the bacteriumEscherichia coli. Orthologs of theseE. colisRNA genes, as well as unrelated sRNAs, were also found in other bacteria. Here we review the disparate experimental approaches used over the years to identify sRNA molecules and their genes in prokaryotes. These include genome-wide searches based on the biocomputational prediction of non-coding RNA genes, global detection of non-coding transcripts using microarrays, and shotgun cloning of small RNAs (RNomics). Other sRNAs were found by either co-purification with RNA-binding proteins, such as Hfq or CsrA/RsmA, or classical cloning of abundant small RNAs after size fractionation in polyacrylamide gels. In addition, bacterial genetics offers powerful tools that aid in the search for sRNAs that may play a critical role in the regulatory circuit of interest, for example, the response to stress or the adaptation to a change in nutrient availability. Many of the techniques discussed here have also been successfully applied to the discovery of eukaryotic and archaeal sRNAs.

scholarly journals Emerging Functions for snoRNAs and snoRNA-Derived Fragments

2021 ◽  
Vol 22 (19) ◽  
pp. 10193
Author(s):  
Maliha Wajahat ◽  
Cameron Peter Bracken ◽  
Ayla Orang
Keyword(s):  
Small Rnas ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Biological Significance ◽  
Specific Interactions ◽  
Additional Source ◽  
Widespread Implementation ◽  
Non Coding Rna ◽  
Complex Picture ◽  
Non Coding Rnas

The widespread implementation of mass sequencing has revealed a diverse landscape of small RNAs derived from larger precursors. Whilst many of these are likely to be byproducts of degradation, there are nevertheless metabolically stable fragments derived from tRNAs, rRNAs, snoRNAs, and other non-coding RNA, with a number of examples of the production of such fragments being conserved across species. Coupled with specific interactions to RNA-binding proteins and a growing number of experimentally reported examples suggesting function, a case is emerging whereby the biological significance of small non-coding RNAs extends far beyond miRNAs and piRNAs. Related to this, a similarly complex picture is emerging of non-canonical roles for the non-coding precursors, such as for snoRNAs that are also implicated in such areas as the silencing of gene expression and the regulation of alternative splicing. This is in addition to a body of literature describing snoRNAs as an additional source of miRNA-like regulators. This review seeks to highlight emerging roles for such non-coding RNA, focusing specifically on “new” roles for snoRNAs and the small fragments derived from them.

scholarly journals PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice

2016 ◽  
Vol 113 (52) ◽  
pp. 15144-15149 ◽  
Author(s):  
Yourong Fan ◽  
Jiangyi Yang ◽  
Sandra M. Mathioni ◽  
Jinsheng Yu ◽  
Jianqiang Shen ◽  
...  
Keyword(s):  
Male Sterility ◽  
Small Rnas ◽  
Noncoding Rna ◽  
Hybrid Rice ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Long Day ◽  
Photoperiod Sensitive

Phased small-interfering RNAs (phasiRNAs) are a special class of small RNAs, which are generated in 21- or 24-nt intervals from transcripts of precursor RNAs. Although phasiRNAs have been found in a range of organisms, their biological functions in plants have yet to be uncovered. Here we show that phasiRNAs generated by the photopheriod-sensetive genic male sterility 1 (Pms1) locus were associated with photoperiod-sensitive male sterility (PSMS) in rice, a germplasm that started the two-line hybrid rice breeding. The Pms1 locus encodes a long-noncoding RNA PMS1T that was preferentially expressed in young panicles. PMS1T was targeted by miR2118 to produce 21-nt phasiRNAs that preferentially accumulated in the PSMS line under long-day conditions. A single nucleotide polymorphism in PMS1T nearby the miR2118 recognition site was critical for fertility change, likely leading to differential accumulation of the phasiRNAs. This result suggested possible roles of phasiRNAs in reproductive development of rice, demonstrating the potential importance of this RNA class as regulators in biological processes.

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