ERISdb: A Database of Plant Splice Sites and Splicing Signals

Szcześniak, Michał Wojciech; Kabza, Michał; Pokrzywa, Rafał; Gudyś, Adam; Makałowska, Izabela

doi:10.1093/pcp/pct001

Cited by 46 publications

(58 citation statements)

References 58 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…36 We analyzed the splice sites of 2,806 rice circRNAs identified in this study. The full-length sequences of some circRNAs could not be exactly mapped to a certain genome position showing several bases shuffling.…”

Section: Alternative Circularization Of Circrnas In Ricementioning

confidence: 99%

See 1 more Smart Citation

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

et al. 2016

View full text Add to dashboard Cite

Circular RNAs (circRNAs) have been identified in diverse eukaryotic species and are characterized by RNA backsplicing events. Current available methods for circRNA identification are able to determine the start and end locations of circRNAs in the genome but not their full-length sequences. In this study, we developed a method to assemble the full-length sequences of circRNAs using the backsplicing RNA-Seq reads and their corresponding paired-end reads. By applying the method to an rRNA-depleted/RNase R-treated RNA-Seq dataset, we for the first time identified full-length sequences of nearly 3,000 circRNAs in rice. We further showed that alternative circularization of circRNA is a common feature in rice and, surprisingly, found that the junction sites of a large number of rice circRNAs are flanked by diverse non-GT/AG splicing signals while most human exonic circRNAs are flanked by canonical GT/AG splicing signals. Our study provides a method for genome-wide identification of full-length circRNAs and expands our understanding of splicing signals of circRNAs.

show abstract

Section: Alternative Circularization Of Circrnas In Ricementioning

confidence: 99%

“…36 Szabo et al (2015) first found a small portion of U12-dependent circRNAs in humans. 30 Besides backsplicing reads, our method predicts circRNAs mainly depending on full-length sequence acquisition rather than filtration by the GT/AG splicing signals.…”

mentioning

confidence: 99%

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

et al. 2016

View full text Add to dashboard Cite

show abstract

“…The repeated sequence may contribute to conformational changes, making the promoter more accessible for transcription factors and RNA polymerase II [62], or facilitating the interaction of splicing factors with upstream transcription factors [27]. Alternatively, the repeated sequence possibly contained regulatory sequences involved in IME; however, we were not able to identify any candidate intron regulatory sequences using ERISdb [63], possibly due to the limited knowledge of intron regulatory elements in plants. Nevertheless, we found that the repeated sequence was T-rich, with T-nucleotides accounting for more than 40% of the whole sequence.…”

Section: Discussionmentioning

confidence: 99%

A Leader Intron of a Soybean Elongation Factor 1A (eEF1A) Gene Interacts with Proximal Promoter Elements to Regulate Gene Expression in Synthetic Promoters

2016

View full text Add to dashboard Cite

Introns, especially the first intron in the 5’ untranslated region (5’UTR), can significantly impact gene expression via intron-mediated enhancement (IME). In this study, we demonstrate the leader intron of a soybean elongation factor 1A (eEF1A) gene (GmScreamM8) was essential for the high activity of the native promoter. Furthermore, the interaction of the GmScreamM8 leader intron with regulatory element sequences from several soybean eEF1A promoters was studied using synthetic promoters, which consisted of element tetramers upstream of a core promoter used to regulate a green fluorescent protein (gfp) reporter gene. Element tetramers, placed upstream of a GmScreamM8 core promoter, showed very high activity using both transient expression in lima bean cotyledons and stable expression in soybean hairy roots, only if the native leader intron was included, suggesting an interaction between intronic sequences and promoter elements. Partial deletions of the leader intron showed that a 222 bp intronic sequence significantly contributed to very high levels of GFP expression. Generation of synthetic intron variants with a monomeric or trimeric repeat of the 222 bp intronic sequence, yielded almost two-fold higher expression compared to the original intron, while partial deletion of the 222 bp intronic repeated sequence significantly decreased gene expression, indicating that this intronic sequence was essential for the intron-element interaction enhancement.

show abstract

“…The predicted branch point sequences for both Arabidopsis thaliana and Oryza sativa (brach_ download.gz) were downloaded from Database of Plant Splice Sites and Splicing Signals (http://lemur.amu.edu.pl/share/ERISdb/ home.html) (Szcześniak et al 2013). NCBI BLASTN was used to search for sequences complementary to the 24-nt sutr-siRNAs smRNA sequences.…”

Section: Isolation and Analysis Of Sutr-sirna Targetsmentioning

confidence: 99%

Stress-induced endogenous siRNAs targeting regulatory intron sequences in Brachypodium

Wang

Dinwiddie

Lee

et al. 2014

RNA

View full text Add to dashboard Cite

Exposure to abiotic stresses triggers global changes in the expression of thousands of eukaryotic genes at the transcriptional and post-transcriptional levels. Small RNA (smRNA) pathways and splicing both function as crucial mechanisms regulating stress-responsive gene expression. However, examples of smRNAs regulating gene expression remain largely limited to effects on mRNA stability, translation, and epigenetic regulation. Also, our understanding of the networks controlling plant gene expression in response to environmental changes, and examples of these regulatory pathways intersecting, remains limited. Here, to investigate the role of smRNAs in stress responses we examined smRNA transcriptomes of Brachypodium distachyon plants subjected to various abiotic stresses. We found that exposure to different abiotic stresses specifically induced a group of novel, endogenous small interfering RNAs (stress-induced, UTR-derived siRNAs, or sutr-siRNAs) that originate from the 3 ′ UTRs of a subset of coding genes. Our bioinformatics analyses predicted that sutr-siRNAs have potential regulatory functions and that over 90% of sutr-siRNAs target intronic regions of many mRNAs in trans. Importantly, a subgroup of these sutrsiRNAs target the important intron regulatory regions, such as branch point sequences, that could affect splicing. Our study indicates that in Brachypodium, sutr-siRNAs may affect splicing by masking or changing accessibility of specific cis-elements through base-pairing interactions to mediate gene expression in response to stresses. We hypothesize that this mode of regulation of gene expression may also serve as a general mechanism for regulation of gene expression in plants and potentially in other eukaryotes.

show abstract

ERISdb: A Database of Plant Splice Sites and Splicing Signals

Cited by 46 publications

References 58 publications

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice

A Leader Intron of a Soybean Elongation Factor 1A (eEF1A) Gene Interacts with Proximal Promoter Elements to Regulate Gene Expression in Synthetic Promoters

Stress-induced endogenous siRNAs targeting regulatory intron sequences in Brachypodium

Contact Info

Product

Resources

About