A rapid TRIzol-based two-step method for DNA-free RNA extraction from Arabidopsis siliques and dry seeds

Extraction of high-quality RNA from Arabidopsis seeds has been a challenge. Here we report a two-step TRIzol-based procedure for RNA extraction from Arabidopsis siliques and dry seeds. This procedure employs a modified, high pH (pH 9.5) extraction buffer. High pH plus the addition of either DTT or β-mercaptoethanol in the extraction buffer effectively inhibits RNase activity during the extraction, and removes most polysaccharides, polyphenols and other insoluble material. TRIzol reagent was subsequently used to purify the RNA. Using this procedure we isolated high-quality DNA-free RNA samples without DNase I treatment from Arabidopsis seeds or siliques in less than 3 h.     

Ensuring recovery of intact RNA from rat pancreas

The isolation of intact RNA from rat pancreas is compromised by autolysis and by the presence of endogenous ribonucleases. In order to ameliorate recovery we systematically investigated available RNA extraction methods and paid particular attention to the influence of frozen storage and ribonuclease inhibition strategies on overall yield and quality of RNA. Modifications to the basic procedure of Chomczynski and Sacchi (1987) are described which allow, reproducibly, to obtain rat pancreatic RNA suitable for Northern blot hybridization, RT-PCR, and differential display analysis.     

莲藕组织总RNA的快速提取方法

莲藕组织富含多糖、脂质、酚类等物质,用一般的方法较难提取高质量的RNA。在改进前人方法的基础上,建立了一种高效、简单的CTAB-LiCl提取法,能快速提取高质量的莲藕组织总RNA,并且产率高、完整性好、纯度高,能进一步满足RT-PCR等分子生物学实验的需要。此外,该方法也适用于其它富含多糖、脂质、酚类等物质的植物组织总RNA的提取。     

The Escherichia coli major exoribonuclease RNase II is a component of the RNA degradosome

Multiprotein complexes that carry out RNA degradation and processing functions are found in cells from all domains of life. In Escherichia coli, the RNA degradosome, a four-protein complex, is required for normal RNA degradation and processing. In addition to the degradosome complex, the cell contains other ribonucleases that also play important roles in RNA processing and/or degradation. Whether the other ribonucleases are associated with the degradosome or function independently is not known. In the present work, IP (immunoprecipitation) studies from cell extracts showed that the major hydrolytic exoribonuclease RNase II is associated with the known degradosome components RNaseE (endoribonuclease E), RhlB (RNA helicase B), PNPase (polynucleotide phosphorylase) and Eno (enolase). Further evidence for the RNase II-degradosome association came from the binding of RNase II to purified RNaseE in far western affinity blot experiments. Formation of the RNase II–degradosome complex required the degradosomal proteins RhlB and PNPase as well as a C-terminal domain of RNaseE that contains binding sites for the other degradosomal proteins. This shows that the RNase II is a component of the RNA degradosome complex, a previously unrecognized association that is likely to play a role in coupling and coordinating the multiple elements of the RNA degradation pathways.     

一种高效经济的高质量植物RNA提取方法

建立了一种高效经济的植物RNA提取方法.在提取缓冲液中加入蔗糖、氯化钾和镁离子以提供对RNA分子的保护.破碎后的细胞于提取缓冲液中裂解后,用酚/氯仿变性并去除内源RNA酶和其他蛋白质,而后用pH 5.6 的NaAc沉淀RNA.用该方法提取RNA的得率较高,经电泳检测,RNA的完整性很好.RNA印迹分析和RT-PCR也都得到很好的结果.该方法还使实验成本大大降低.     

A New Method for Rapid Extraction of High Quality RNA from Recalcitrant Tissues of Grapevine

A quick, inexpensive, and reliable protocol for the extraction of RNA from grapevine berry skins containing large quantities of polyphenols, procyanidins, and polysaccharides is described. The method involves an extraction step in the presence of ribonuclease inhibitors and compounds that compete with vacuolar contaminants for binding to RNA. After extraction with organic solvents, RNA is bound to a fibrous cellulose matrix and processed to eliminate the remaining contaminants and ribonucleases. Following this method, highly stable RNA, sufficiently pure for northern hybridizations and enzymatic processing, may be obtained from as little as 200 mg of starting amounts of fresh material and without multiple, time consuming precipitations or ultracentrifugation steps. This procedure may also prove useful for extracting RNA from recalcitrant tissues of other plant species. Abbreviations: ATA, aurintricarboxylic acid; CF11, cellulose fibrous medium (type 11); PVPP, polyvinylpolypyrrolidone; RT room temperature; VRC, vanadyl ribonucleoside complex.     

Modifications of the guanidine hydrochloride procedure for the extraction of RNA: isolation from a variety of tissues and adherent/nonadherent cell types.

In a previous report dealing with the guanidine hydrochloride protocol for the extraction of RNA from mouse peritoneal macrophages, we identified a major source of RNA-degrading activity and showed that its removal early in the extraction procedure resulted in a more dependable method for the recovery of high-quality RNA. This report extends these findings and demonstrates the general applicability of the technique to a variety of fresh or frozen adherent cell types, cell suspensions and tissues, further highlighting stages at which degradation is most likely to occur and how to avoid a variety of pitfalls associated with the extraction procedure.     

Optimization of RNA Isolation from Brittle Leaf Disease Affected Date Palm Leaves and Construction of a Subtractive cDNA Library

A simple and efficient method was described here for the isolation of high-quality RNA from date palm leaves affected with Brittle Leaf Disease (BLD) and containing high amount of phenolic compounds. The procedure was based on the use of a non-ionic detergent Nonidet-P40 (NP-40), Polyvinylpyrrolidone (PVP), and beta-mercaptoethanol in the extraction buffer in order to isolate cytoplasmic RNA and to prevent the oxidation of phenolic compounds. This method allowed the isolation of intact RNA, suitable for cDNA synthesis and library construction. Differential screening of the subtractive cDNA library from affected leaf RNA led to the identification of some BLD-induced genes.     

Extraction of High-Quality RNA from Rubber Tree Leaves

A specific technique capable of producing high-quality RNA for rapid amplification of cDNA ends (RACE) was established for challenging tissues: leaves of the rubber tree. Total RNA was extracted by cetyltrimethylammonium bromide (CTAB)-LiCl combined with TRIzol reagent. The isolated RNA was highly intact. With RNA as template, full-length cDNA was obtained (NCBI, AY461413) by RACE.     

胰腺癌及癌旁组织中提取RNA样品的方法优化及鉴定

摘要 目的：优化胰腺癌及癌旁组织总RNA的提取方法,为胰腺相关疾病的发病机制研究提供高质量的实验样本。方法：采用组织块分离剪碎、RNase清洗及抑制等方法对胰腺癌及癌旁组织进行预处理,液氮研磨及trizol-氯仿抽提的方法提取组织RNA。通过琼脂糖凝胶电泳及生物分析仪鉴定RNA的完整性。使用等量RNA作为逆转录模板,以oligo dT引物对信使RNA（message RNA, mRNA）进行逆转录;以茎环结构引物对微小RNA（microRNA, miRNA）进行逆转录。通过定量PCR的方法检测mRNA及miRNA的表达水平。结果：相较于常规方法,优化方法提取的RNA样品降解程度低,完整性较高。相对于胰腺癌组织,癌旁组织RNA更易降解,mRNA的表达水平出现降低趋势;但miRNA的表达在胰腺癌及癌旁组织中无明显差异。结论：胰腺癌及癌旁组织的预处理可降低RNA降低程度,可为RNA的表达检测提供高质量的实验样本,增加实验准确度。     

Isolation of high-quality RNA from white spruce tissue using a three-stage purification method and subsequent cloning of a transcript from the PR-10 gene family

Isolation of PinmIII cDNA homologues from white spruce tissues required a rigorous RNA extraction protocol developed following assessment of three previously reported conifer RNA extraction protocols. Total RNA was extracted via several purification steps designed to minimize binding of phenolics to nucleic acids and was then subjected to caesium chloride ultra-centrifugation. This procedure produced consistently high-quality, intact RNA from both needles and roots with spectrophotometric ratios of approximately 2.0 for both 260/280 nm and 260/230 nm. Total RNA was obtained from the roots of cold-hardened white spruce seedlings for cDNA library construction. More than 2 million recombinant phage particles were generated from 5 microg of a poly(A)+RNA fraction, and ca. 1.3 million cDNA particles were amplified for storage. Approximately 500,000 primary recombinant clones were screened with an heterologous PinmIII cDNA sequence yielding a unique clone, picgl, that was very similar to members of the PR10 gene family.     

Techniques for RNA extraction from cells cultured in starPEG–heparin hydrogels

Three-dimensional (3D) cell culture models that provide a biologically relevant microenvironment are imperative to investigate cell–cell and cell–matrix interactions in vitro. Semi-synthetic star-shaped poly(ethylene glycol) (starPEG)–heparin hydrogels are widely used for 3D cell culture due to their highly tuneable biochemical and biomechanical properties. Changes in gene expression levels are commonly used as a measure of cellular responses. However, the isolation of high-quality RNA presents a challenge as contamination of the RNA with hydrogel residue, such as polymer or glycosaminoglycan fragments, can impact template quality and quantity, limiting effective gene expression analyses. Here, we compare two protocols for the extraction of high-quality RNA from starPEG–heparin hydrogels and assess three subsequent purification techniques. Removal of hydrogel residue by centrifugation was found to be essential for obtaining high-quality RNA in both isolation methods. However, purification of the RNA did not result in further improvements in RNA quality. Furthermore, we show the suitability of the extracted RNA for cDNA synthesis of three endogenous control genes confirmed via quantitative polymerase chain reaction (qPCR). The methods and techniques shown can be tailored for other hydrogel models based on natural or semi-synthetic materials to provide robust templates for all gene expression analyses.     

RNA Isolation from Mouse Pancreas: A Ribonuclease-rich Tissue

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge. As a primary function of the pancreas is to aid in digestion, mouse pancreas may contain as much a 75 mg of ribonuclease. We report modifications of standard phenol/guanidine thiocyanate lysis reagent protocols to isolate RNA from mouse pancreas. Guanidine thiocyanate is a strong protein denaturant and will effectively disrupt the activity of ribonuclease under most conditions. However, critical modifications to standard protocols are necessary to successfully isolate RNA from ribonuclease-rich tissues. Key steps include a high lysis reagent to tissue ratio, removal of undigested tissue prior to phase separation and inclusion of a ribonuclease inhibitor to the RNA solution. Using these and other modifications, we routinely isolate RNA with RNA Integrity Number (RIN) greater than 7. The isolated RNA is of suitable quality for routine gene expression analysis. Adaptation of this protocol to isolate RNA from ribonuclease rich tissues besides the pancreas should be readily achievable.     

Isolation of functional RNA from small amounts of different grape and apple tissues

An efficient, simple, and small-scale procedure for isolating functional ribonucleic acid (RNA) was successfully applied to many different tissues of grape and apple. These woody plants are rich in polyphenolic compounds and polysaccharides that could impair the RNA extraction. The method chosen is based on the use of hot borate buffer at alkaline pH supplemented with several adjuvants and followed by selective precipitations. Starting with only 0.4 g of fresh tissue and working with small tubes (2 mL), we were able to obtain good yields of high-quality RNA suitable for further applications. The procedure can be proposed for many applications, and it is particularly highly recommended when isolating RNA from a large number of samples.