PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots

We uncovered the diversity of non-canonical splice sites at the human transcriptome using deep transcriptome profiling. We mapped a total of 3.7 billion human RNA-seq reads and developed a set of stringent filters to avoid false non-canonical splice site detections. We identified 184 splice sites with non-canonical dinucleotides and U2/U12-like consensus sequences. We selected 10 of the herein identified U2/U12-like non-canonical splice site events and successfully validated 9 of them via reverse transcriptase-polymerase chain reaction and Sanger sequencing. Analyses of the 184 U2/U12-like non-canonical splice sites indicate that 51% of them are not annotated in GENCODE. In addition, 28% of them are conserved in mouse and 76% are involved in alternative splicing events, some of them with tissue-specific alternative splicing patterns. Interestingly, our analysis identified some U2/U12-like non-canonical splice sites that are converted into canonical splice sites by RNA A-to-I editing. Moreover, the U2/U12-like non-canonical splice sites have a differential distribution of splicing regulatory sequences, which may contribute to their recognition and regulation. Our analysis provides a high-confidence group of U2/U12-like non-canonical splice sites, which exhibit distinctive features among the total human splice sites.

show abstract

“…The visualization of the RNA structures was obtained using PseudoViewer3 (33) and edited with Adobe Illustrator.…”

Section: Methodsmentioning

confidence: 99%

A comprehensive survey of non-canonical splice sites in the human transcriptome

Parada

Munita

Cerda

et al. 2014

Nucleic Acids Research

110

View full text Add to dashboard Cite

show abstract

“…The analyses involved 18 nucleotide sequences. The secondary structures of ITS2 sequences for the new species and its most related species were predicted using the ITS2 Database III (Koetschan et al 2010) and illustrated with PseudoViewer3 (Byun & Han 2009). …”

Section: Methodsmentioning

confidence: 99%

A new species in the lichen genus Peltigera from northern China based on morphology and DNA sequence data

2015

View full text Add to dashboard Cite

“…The program was set to search the H. pylori 26695_uid57787 DNA sequence within the intergenic regions of the plus (default) and minus DNA strands. The STAR program (26) was used to fold the untranslated sequences, and PseudoViewer (27) was used to visualize the secondary structure.…”

Section: Methodsmentioning

confidence: 99%

Aconitase Functions as a Pleiotropic Posttranscriptional Regulator in Helicobacter pylori

2015

View full text Add to dashboard Cite

Posttranscriptional regulation in bacteria has increasingly become recognized as playing a major role in response to environmental stimuli. Aconitase is a bifunctional protein that not only acts enzymatically but also can be a posttranscriptional regulator. To investigate protein expression regulated by Helicobacter pylori AcnB in response to oxidative stress, a global proteomics study was conducted wherein the ⌬acnB strain was compared to the parent strain when both strains were O 2 stressed. Many proteins, including some involved in urease activity, in combating oxidative stress, and in motility, were expressed at a significantly lower level in the ⌬acnB strain. A bioinformatics prediction tool was used to identify putative targets for aconitase-mediated regulation, and electrophoretic mobility shift assays demonstrated that apo-AcnB is able to bind to RNA transcripts of hpn (encoding a nickel-sequestering protein), ahpC (encoding alkyl hydroperoxide reductase), and flgR (encoding flagellum response regulator). Compared to the wild type (WT), the ⌬acnB strain had decreased activities of the nickel-containing enzymes urease and hydrogenase, and this could be correlated with lower total nickel levels within ⌬acnB cells. Binding of apo-AcnB to the hpn 5= untranslated region (UTR) may inhibit the expression of Hpn. In agreement with the finding that AcnB regulates the expression of antioxidant proteins such as AhpC, ⌬acnB cells displayed oxidative-stress-sensitive phenotypes. The ⌬acnB strain has a lesser motility ability than the WT strain, which can likely be explained by the functions of AcnB on the FlgRS-RpoN-FlgE regulatory cascade. Collectively, our results suggest a global role for aconitase as a posttranscriptional regulator in this gastric pathogen. IMPORTANCEBacterial survival depends on the ability of the cell to sense and respond to a variety of environmental changes. For Helicobacter pylori, responding to environmental stimuli within the gastric niche is essential for persistence and host colonization. However, there is much to be learned about the regulatory mechanisms that H. pylori employs to orchestrate its response to different stimuli. In this study, we explore the role of aconitase, a bifunctional protein that has been found to act as a posttranscriptional regulator in several other bacteria. Our results shed light on the magnitude of aconitase-mediated regulation in H. pylori, and we propose that aconitase acts as a global regulator of key genes involved in virulence.

show abstract

PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots

Abstract: The new version of PseudoViewer, PseudoViewer3, is available at (http://pseudoviewer.inha.ac.kr).

Cited by 150 publications

References 7 publications

A comprehensive survey of non-canonical splice sites in the human transcriptome

A comprehensive survey of non-canonical splice sites in the human transcriptome

A new species in the lichen genus Peltigera from northern China based on morphology and DNA sequence data

Aconitase Functions as a Pleiotropic Posttranscriptional Regulator in Helicobacter pylori

Contact Info

Product

Resources

About