Computational prediction and experimental verification of miRNAs in Panicum miliaceum L.

Abstract

MicroRNAs (miRNAs) are a class of non-coding RNAs that play critical roles in post-transcriptional regulation. Their target genes are involved in a variety of biological processes such as development, metabolism, and stress response. Panicum miliaceum L. (Panicum) is an important grain crop, but, until now, no miRNAs have been identified in this plant. Using a homology search based on expressed sequence tag (EST) analysis and miRNA precursor secondary structure, a total of 43 new miRNAs were identified. The miRNAs were found to be unevenly distributed among 11 miRNA families. Target analysis using the plant small RNA target analysis server psRNATarget showed that the newly identified miRNAs can potentially regulate 68 target genes. Ten of the 11 miRNA families were annotated as involved in RNA regulation, suggesting they may play an essential role in post-transcriptional regulation in Panicum. Selected miRNAs representing eight of the families were verified by northern blotting, indicating that the prediction method that we used to identify the miRNAs was effective.

Proteomics Identification and Validation of Desmocollin‐1 and Catechol‐O‐Methyltransferase as Proteins Associated with Breast Cancer Cell Migration and Metastasis

“…[39] Moreover, Wu and co-workers showed COMT up-regulation in pancreatic cancer cell lines and in a pancreatic cancer tissue compared to normal tissue at both transcript and protein levels. [40] A role of COMT in an estrogen-induced carcinogenesis was studied mainly in terms of its polymorphisms, where a higher risk of BC was related to Val-158-Met polymorphism in meta-analysis of Chinese population, [41] while other meta-analysis showed lower BC risk related to the same polymorphism (and lower COMT activity) specifically in Caucasian population. [42] Weisz and co-workers described COMT as an enzyme responsible for degradation of catecholestrogens, which might protect breast cells against the carcinogenesis.…”

Proso Millet (Panicum miliaceum L.) and Its Potential for Cultivation in the Pacific Northwest, U.S.: A Review

“…Wu et al (2012) have done preliminary work in characterizing proso millet microRNAs (miRNAs), which are non-coding RNAs important in post-transciptional regulation. Since there are limited proso millet genome sequences, Wu et al (2012) used ESTs to predict miRNAs instead of using genomic survey sequence analysis as has been done in other crops.…”

“…Since there are limited proso millet genome sequences, Wu et al (2012) used ESTs to predict miRNAs instead of using genomic survey sequence analysis as has been done in other crops. Wu et al (2012) identified 43 potential miRNAs and their gene targets involved in biological processes such as development, metabolism and stress response. They selected 12 miRNAs to validate and eight were verified by Northern blot hybridizations.…”

Genetic diversity and genomic resources available for the small millet crops to accelerate a New Green Revolution

“…In the latter study, a hybrid genotype outperformed local varieties, validating the potential in breeding highly WUE proso millet. Preliminary work in characterizing proso miRNAs has been accomplished with the goal of understanding mechanisms responsible for the cereal's impressive drought resistance (Wu et al, 2012 ). Despite its drought tolerance, proso is best adapted to temperate latitudes unlike other small millets.…”