Prediction of miRNA targets by learning from interaction sequences.

MicroRNAs (miRNAs) are involved in a diverse variety of biological processes through regulating the expression of target genes in the post-transcriptional level. So, it is of great importance to discover the targets of miRNAs in biological research. But, due to the short length of miRNAs and limited sequence complementarity to their gene targets in animals, it is challenging to develop algorithms to predict the targets of miRNA accurately. Here we developed a new miRNA target prediction algorithm using a multilayer convolutional neural network. Our model learned automatically the interaction patterns of the experiment-validated miRNA:target-site chimeras from the raw sequence, avoiding hand-craft selection of features by domain experts. The performance on test dataset is inspiring, indicating great generalization ability of our model. Moreover, considering the stability of miRNA:target-site duplexes, our method also showed good performance to predict the target transcripts of miRNAs

Identification and Characterization of a Cis Antisense RNA of the rpoH Gene of Salmonella enterica Serovar Typhi

Antisense RNAs from complementary strands of protein coding genes regulate the expression of genes involved in many cellular processes. Using deep sequencing analysis of the Salmonella enterica serovar Typhi (S. Typhi) transcriptome, a novel antisense RNA encoded on the strand complementary to the rpoH gene was revealed. In this study, the molecular features of this antisense RNA were assessed using northern blotting and rapid amplification of cDNA ends. The 3,508 nt sequence of RNA was identified as the antisense RNA of the rpoH gene and was named ArpH. ArpH was found to attenuate the invasion of HeLa cells by S. Typhi by regulating the expression of SPI-1 genes. In an rpoH mutant strain, the invasive capacity of S. Typhi was increased, whereas overexpression of ArpH positively regulates rpoH mRNA levels. Results of this study suggest that the cis-encoded antisense RNA ArpH is likely to affect the invasive capacity of S. Typhi by regulating the expression of rpoH

Data_Sheet_2_Identification and Characterization of a Cis Antisense RNA of the rpoH Gene of Salmonella enterica Serovar Typhi.DOCX

<p>Antisense RNAs from complementary strands of protein coding genes regulate the expression of genes involved in many cellular processes. Using deep sequencing analysis of the Salmonella enterica serovar Typhi (S. Typhi) transcriptome, a novel antisense RNA encoded on the strand complementary to the rpoH gene was revealed. In this study, the molecular features of this antisense RNA were assessed using northern blotting and rapid amplification of cDNA ends. The 3,508 nt sequence of RNA was identified as the antisense RNA of the rpoH gene and was named ArpH. ArpH was found to attenuate the invasion of HeLa cells by S. Typhi by regulating the expression of SPI-1 genes. In an rpoH mutant strain, the invasive capacity of S. Typhi was increased, whereas overexpression of ArpH positively regulates rpoH mRNA levels. Results of this study suggest that the cis-encoded antisense RNA ArpH is likely to affect the invasive capacity of S. Typhi by regulating the expression of rpoH.</p

Expression of <i>asdA</i> under different growth conditions.

<p>A. Northern blot analysis performed on total RNA isolated from <i>S.</i> Typhi cultures at different OD₆₀₀ values, as shown across the top of the blots. 5S rRNA was used as loading controls. B. Northern blot analysis of total RNA isolated from <i>S</i>. Typhi cells grown in LB to OD₆₀₀ value of 0.6 and subjected for 30 min to osmotic shock (NaCl: 0.5 M), oxidative stress (H₂O₂: 1 mM hydrogen peroxide), low iron conditions (Dp: 0.2 mM 2,2,-dipyridyl), acid stress (HCl: pH 4.5). Northern blot was performed with oligoprobe asdA-PB. C. qRT-PCR analysis of total RNA isolated from <i>S</i>. Typhi cells and subjected to the same conditions as described in B above. D. qRT-PCR analysis of RNA extracted from <i>fur</i> and <i>rpoS</i> mutant <i>S</i>. Typhi strains under iron limitation and osmotic stress respectively.</p