Large-Scale Identification of Mirtrons in Arabidopsis and Rice

A new catalog of microRNA (miRNA) species called mirtrons has been discovered in animals recently, which originate from spliced introns of the gene transcripts. However, only one putative mirtron, osa-MIR1429, has been identified in rice (Oryza sativa). We employed a high-throughput sequencing (HTS) data- and structure-based approach to do a genome-wide search for the mirtron candidate in both Arabidopsis (Arabidopsis thaliana) and rice. Five and eighteen candidates were discovered in the two plants respectively. To investigate their biological roles, the targets of these mirtrons were predicted and validated based on degradome sequencing data. The result indicates that the mirtrons could guide target cleavages to exert their regulatory roles post-transcriptionally, which needs further experimental validation

Degradome sequencing data-based identification of the targets of the mature mirtrons in <i>Arabidopsis</i> and rice.

<p>For all the sub-figures (A to D), the first panels depict the degradome signals all along the target transcripts, and the other panels provide detailed views of the cleavage signals within the regions surrounding the target recognition sites (denoted by gray horizontal lines). The transcript IDs are shown in the first panels, and the mirtron IDs are listed in the other panels (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s007" target="_blank">Table S3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s008" target="_blank">S4</a> for the sequence information corresponding to the mirtron IDs). The <i>x</i> axes measure the positions of the signals along the transcripts, and the <i>y</i> axes measure the signal intensities based on normalized counts (in RPM, reads per million), allowing cross-library comparison. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s006" target="_blank">Table S2</a> for the degradome data sets used in this analysis.</p

High-throughput sequencing (HTS) data- and structure-based identification of mirtrons in <i>Arabidopsis</i> and rice.

<p>(A) A “match 5′ end” mirtron resided within the 15^th intron of AT3G60950.1. (B) A “match 3′ end” mirtron resided within the second intron of AT1G76680.1. (C) A “match both ends” mirtron resided within the first intron of AT4G27410.1. (D) A “match 5′ end” mirtron resided within the 5^th intron of LOC_Os04g09380.1. (E) A “match 3′ end” mirtron resided within the 13^th intron of LOC_Os09g04260.1. (F) A “match both ends” mirtron resided within the first intron of LOC_Os03g57750.2. For all the panels, the short reads perfectly mapped to the mirtron precursors along with their normalized read counts in RPM (reads per million) are shown (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163.s005" target="_blank">Table S1</a> for the small RNA HTS data sources and see “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#s3" target="_blank">Materials and Methods</a>” for read count normalization). The mature mirtrons with significantly higher expression levels compared to the coordinates on the other arms were highlighted in red color, and the coordinates were in blue. For the mirtron precursors generating mirtrons with indistinguishable expression levels on both arms, their mature mirtrons were highlighted in green color. The mature mirtrons and their coordinates were also indicated in the stem-loop structures of their precursors. The parenthesis-dot formed secondary structure expression along with the free energy, and the stem-loop structures were all predicted and generated by RNAshapes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031163#pone.0031163-Steffen1" target="_blank">[17]</a>.</p

Geological Significance of Rare Earth Elements in Marine Shale of the Upper Permian Dalong Formation in the Lower Yangtze Region, South China

The rare earth elements (REEs) provide significant geological information and serve as a reliable indicator for predicting the paleoclimate, paleoenvironment, and paleotectonic evolution of sedimentary rocks. The REEs, major elements, and trace elements of 75 marine shale samples collected from the Late Permian Dalong Formation at the Fantiansi (FTS) and Putaoling (PTL) sections in the Lower Yangtze region were analyzed. The results revealed that the major elements Al2O3, K2O, and TiO2 were primarily influenced by clay minerals associated with terrigenous detrital, whereas SiO2 and Na2O were not affected by clay minerals. The ΣREE values obtained from the Late Permian Dalong Formation at the Fantiansi (FTS) and Putaoling (PTL) sections in the Lower Yangtze region were found to be lower than those of the Post-Archean Average Shale (PAAS) (184.8 μg/g). The study of REE indicators related to the source, redox conditions, and tectonic settings led to the following conclusions: (a) ΣREE showed strong positive correlations with TiO2, Al2O3, K2O, and Na2O, but exhibited relatively weak correlations with Fe2O3 and P2O5, suggesting that REEs were mainly associated with clay minerals, but were also influenced by pyrite, phosphates, and other minerals; (b) The high values of Ce/Ce*, MoEF, UEF, and Corg/P were mainly concentrated in Stages I, II, III and V of the Dalong Formation at the FTS and PTL sections, and the corresponding strong anoxic environment was more conducive to the preservation of organic matter; (c) The diagram between La/Yb and ΣREE, Al2O3-TiO2, TiO2-Zr, and La/Th-Hf bivariate diagrams indicated that the provenance of the rocks from the Dalong formations was primarily felsic igneous rocks; (d) Discriminant-function diagrams and La-Th-Sc, Th-Sc-Zr/10 and Th-Co-Zr/10 triangular diagrams show that the clastic sediments of the Dalong formations were derived most likely from continental island arcs. This study corresponds to the background of the transition from continental margin to continental collision structure in South China during the Late Permian

Examples of paired PASR (promoter-associated small RNA) and TASR (terminus-associated small RNA) peaks potentially mediating site-specific DNA methylation, and analysis of their biogenesis and action pathways.

<p>Examples of paired PASR (promoter-associated small RNA) and TASR (terminus-associated small RNA) peaks potentially mediating site-specific DNA methylation, and analysis of their biogenesis and action pathways.</p