Research progress on non-coding small RNA in oral submucosal fibrosis / 口腔疾病防治

@#Oral submucous fibrosis (OSF) is one of the most common precancerous lesions of the oral mucosa, and its pathogenesis has not been fully elucidated. Small noncoding RNAs (SncRNAs), a class of RNA molecules that do not code for proteins, have been widely reported to be involved in the regulation of a variety of human diseases. An increasing number of studies have shown that a variety of SncRNAs play important roles in the pathogenesis of OSF. Current studies have shown that microRNAs (miRNAs) are involved in OSF disease progression by regulating the expression of related transcription factors and genes or epithelial mesenchymal transformation to regulate the activation of fibroblasts (FBs). Long noncoding RNAs (lncRNAs) that transform growth factor-β/suppressor of mothers against decapentaplegic (TGF-β/Smad) signaling pathways or interact with miRNAs are involved in the development of OSF. Circular RNAs (circRNAs) play a role in OSF by interacting with miRNAs. tRNA-derived small RNAs (tsRNAs) are involved in the progression of various fibrotic diseases, but their specific mechanism of action in OSF still needs to be further explored. In the future, it is still necessary to focus on the targets of SncRNAs mediating OSF progression and explore their function and molecular mechanism in OSF to provide new ideas for the diagnosis and treatment of OSF.

Accurate quantification of 3'-terminal 2'-O-methylated small RNAs by utilizing oxidative deep sequencing and stem-loop RT-qPCR / 医学前沿

The continuing discoveries of novel classes of RNA modifications in various organisms have raised the need for improving sensitive, convenient, and reliable methods for quantifying RNA modifications. In particular, a subset of small RNAs, including microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), are modified at their 3'-terminal nucleotides via 2'-O-methylation. However, quantifying the levels of these small RNAs is difficult because 2'-O-methylation at the RNA 3'-terminus inhibits the activity of polyadenylate polymerase and T4 RNA ligase. These two enzymes are indispensable for RNA labeling or ligation in conventional miRNA quantification assays. In this study, we profiled 3'-terminal 2'-O-methyl plant miRNAs in the livers of rice-fed mice by oxidative deep sequencing and detected increasing amounts of plant miRNAs with prolonged oxidation treatment. We further compared the efficiency of stem-loop and poly(A)-tailed RT-qPCR in quantifying plant miRNAs in animal tissues and identified stem-loop RT-qPCR as the only suitable approach. Likewise, stem-loop RT-qPCR was superior to poly(A)-tailed RT-qPCR in quantifying 3'-terminal 2'-O-methyl piRNAs in human seminal plasma. In summary, this study established a standard procedure for quantifying the levels of 3'-terminal 2'-O-methyl miRNAs in plants and piRNAs. Accurate measurement of the 3'-terminal 2'-O-methylation of small RNAs has profound implications for understanding their pathophysiologic roles in biological systems.

Computational prediction and characterisation of miRNAs and their pathway genes in human schistosomiasis caused by Schistosoma haematobium

BACKGROUND Key genes control the infectivity of the Schistosoma haematobium causing schistosomiasis. A method for understanding the regulation of these genes might help in developing new disease strategies to control schistosomiasis, such as the silencing mediated by microRNAs (miRNAs). The miRNAs have been studied in schistosome species and they play important roles in the post-transcriptional regulation of genes, and in parasite-host interactions. However, genome-wide identification and characterisation of novel miRNAs and their pathway genes and their gene expression have not been explored deeply in the genome and transcriptome of S. haematobium. OBJECTIVES Identify and characterise mature and precursor miRNAs and their pathway genes in the S. haematobium genome. METHODS Computational prediction and characterisation of miRNAs and genes involved in miRNA pathway from S. haematobium genome on SchistoDB. Conserved domain analysis was performed using PFAM and CDD databases. A robust algorithm was applied to identify mature miRNAs and their precursors. The characterisation of the precursor miRNAs was performed using RNAfold, RNAalifold and Perl scripts. FINDINGS We identified and characterised 14 putative proteins involved in miRNA pathway including ARGONAUTE and DICER in S. haematobium. Besides that, 149 mature miRNAs and 131 precursor miRNAs were identified in the genome including novel miRNAs. MAIN CONCLUSIONS miRNA pathway occurs in the S. haematobium, including endogenous miRNAs and miRNA pathway components, suggesting a role of this type of non-coding RNAs in gene regulation in the parasite. The results found in this work will open up a new avenue for studying miRNAs in the S. haematobium biology in helping to understand the mechanism of gene silencing in the human parasite Schistosome.

Research progress in the role of small RNA fragments derived from tRNA in malignant tumors / 医学研究生学报

Noncoding small RNAs are the important regulators of vital processes. Through the high-throughput sequencing and analyses of small RNA fragments, a new class of non-coding small RNAs has been presented, which can be matched to the known tRNA gene. The different sources of tRFs are classified into various types depending on where they match on the parental tRNA. The tRFs can be expressed in a variety of organisms. Recent studies have found that the tRFs have a variety of biological functions in the regulation of gene expression, epigenetics，tumor suppression, neurodegeneration and so on. As a regulatory RNA, the tRFs play an important role in development and progression of tumors, and are known to play regulatory roles in the proliferation and metastasis of tumor cells. This article reviews the research progress on the classification，biological function and role of tRFs in malignant tumors.

Buscando agujaseen un pajar: viajes de rnas pequeños in silico e in vitro / Finding for a Neadle in a Haystack: Trips of Small RNAs from in silico to in vitro

Lo que se conoce tradicionalmente como análisis del transcriptoma comprende la caracterización y cuantificación del conjunto de RNAs transcritos en la célula. En los primeros años, los estudios del transcriptoma se enfocaron principalmente a RNA mensajeros o RNA codificantes. Más recientemente, debido a avances en la tecnología de secuenciammiento de última generación, los estudios del transcriptoma se han extendido a RNAs no codificantes. Estas moléculas presentan gran variedad de funciones en la regulación celular. Una caracterización completa del conjunto de ncRNAs no es alcanzable con las aproximaciones disponibles. Hoy en día la identificación de RNAs no codificantes y de sus RNA pequeños derivados, es un tema de vital importancia en el análisis genético. Uno de los avances recientes en el estudio del transcriptoma por ejemplo, se enfoca en la biología de RNA de interferencia y su aplicación clínica. Durante los últimos años se han desarrollado continuamente la capacidad de cómputo, eficiencia y capacidad de almacenamiento para modelar y procesar grandes volúmenes de información producto de secuenciamiento de última generación. Como consecuencia, esta revisión presenta el análisis del transcriptoma desde una perspectiva histórica unida a la modelación computacional de RNA no codificantes de datos de bibliotecas de RNAs pequeños.

What is commonly known about transcriptome studies encompass the characterization and quantification of the complete set of RNA transcripts produced by a cell. In its early days these analysis mainly focused on examination of messenger RNAs or coding RNAs. More recently, due to advances in next-generation sequencing technologies, transcriptome analysis has expanded to non-conding RNAs (ncRNAs). These molecules exhibit high variety of functions in cell regulation. Through characterization of complete sets of ncRNAs is not attainable with current approaches. At present de novo identification of ncRNAs and ncRNA-derived small RNAs is a major issue in genetic analysis. One of the most important recent advances of transcriptome analysis focuses, for example, on RNA interference (RNAi) biology and its clinical application. High-performance computing, storage capability and computational modeling have been continuously developed during last years to process and model large amounts of products of next generation sequencing methods. As consequence this review describes transcriptome sequencing analysis from a historical perspective to its link to computational approaches to model ncRNAs from small RNA library data.

A RNA Isolation Method Suitable for a Wide Range of Materials / 生物化学与生物物理进展

High levels of RNase,polysaccharides and polyphenol compounds make isolation of high quality RNA difficult. Thus it is presented an effective RNA extraction method based on the nuclease adsorbent macaloid,poly vinyl pyrrolidone,and high concentration of KAc and ethylene glycol monobutyl ether,which has successfully extracted high-quality RNA from many materials difficult to RNA isolation,such as RNase-rich rabbit liver,plant and microbial tissues rich in polysaccharides,lipids and polyphenol compounds. This method was found to be better than the ones in common use-Trizol and Guanidinium isothiocyanate,the yield of which was at least three time higher. Furtherly,small RNA was enriched from total RNA sample from rice seedling through by repeat deposit which deals with high concentration of LiCl,PEG8000 and NaCl. The small RNA gained was confirmed to be used for following molecular biological research by RT-PCR with the primers designed on osa-mir-156 sequence from rice miRNA.