Rapid isolation of total RNA from mammalian tissues

Analysis of current and alternative phenol based RNA extraction methodologies for cyanobacteria

Background

The validity and reproducibility of gene expression studies depend on the quality of extracted RNA and the degree of genomic DNA contamination. Cyanobacteria are gram-negative prokaryotes that synthesize chlorophyll a and carry out photosynthetic water oxidation. These organisms possess an extended array of secondary metabolites that impair cell lysis, presenting particular challenges when it comes to nucleic acid isolation. Therefore, we used the NHM5 strain of Nostoc punctiforme ATCC 29133 to compare and improve existing phenol based chemistry and procedures for RNA extraction.

Results

With this work we identify and explore strategies for improved and lower cost high quality RNA isolation from cyanobacteria. All the methods studied are suitable for RNA isolation and its use for downstream applications. We analyse different Trizol based protocols, introduce procedural changes and describe an alternative RNA extraction solution.

Conclusion

It was possible to improve purity of isolated RNA by modifying protocol procedures. Further improvements, both in RNA purity and experimental cost, were achieved by using a new extraction solution, PGTX.

A method for the direct measurement of mRNA in discrete regions of mammalian brain

A rapid and nearly quantitative method for the direct analysis of steady-state mRNA levels in microgram quantities of frozen mammalian brain is described. Briefly, tissue punches 0.5-1.0 mm in diameter were sampled from 250-microns-thick cryostat sections of rat brain (approximately 50-200 micrograms tissue). The samples were homogenized in 50 microliters of a denaturing gel loading buffer and applied directly to a 2.2 M formaldehyde-agarose gel for electrophoresis and subsequent RNA blot analysis. The method is extremely rapid, results in excellent recovery of intact RNA, and allows the direct assay of mRNA levels in discrete subregions of the mammalian brain.

Structure and organization of the gene encoding rat S-adenosylmethionine decarboxylase

The gene for S-adenosylmethionine decarboxylase (AdoMetDC) was isolated from a rat genomic library using AdoMetDC cDNA as a probe. Nucleotide sequence analysis shows that the rat AdoMetDC gene consists of 8 exons which encode a protein identical to that inferred by a rat AdoMetDC cDNA sequence. The exons range in length from 43 to 1964 base pairs spanning 15672 bases of chromosomal DNA. All of the exon/intron junctions were found to conform to the consensus splice donor and acceptor sequences. Exon 8 corresponds to the 3' noncoding region of the 2 species of AdoMetDC mRNA which are formed by alternative utilization of 2 polyadenylation signals separated from each other by 1272 nucleotides. The transcription initiation site was located by S1 nuclease protection and by primer extension analysis, -325 nucleotides upstream of the translation initiation codon. The promoter region of the rat AdoMetDC gene contains a TATA box at -29 base pairs. No typical GC or CAAT boxes are located in the promoter, but six GC boxes and several putative binding sites for both tissue-specific and non-specific transcription factors are found in the proximal part of intron 1. Southern blot analyses reveal a complex hybridization pattern suggesting that there are multiple copies of the AdoMetDC gene in the rat genome.

Analytical procedures for a cryptic messenger RNA that mediates translational control of prostaglandin synthase by glucocorticoids

Expression of the enzyme prostaglandin H synthase in cultured vascular smooth muscle cells required epidermal growth factor (EGF) and type beta transforming growth factor (TGF-beta) and was inhibited by cycloheximide but not actinomycin D. Preincubation with the glucocorticoid dexamethasone (0.5 microM) blocked the EGF-induced expression of prostaglandin H (PGH) synthase. Following dexamethasone addition, levels of hybridizable mRNA for PG synthase were reduced by over 90% within 1 h. After dexamethasone was removed, PG synthase mRNA recovered within 3 h by a process that was not inhibited by actinomycin D. These observations, together with other findings, suggested that the mRNA was being converted into some nonextractable and nontranslated form, probably by binding of a glucocorticoid-induced protein to the conserved 3' untranslated region. In order to investigate further the nature of this phenomenon, seven different literature procedures were evaluated for extracting and determining the PG synthase mRNA. Five of the seven procedures failed to detect hybridizable PG synthase mRNA in glucocorticoid-treated cells. Two procedures, however, recovered mRNA in both glucocorticoid-treated and control cells. A comparison of the protocols indicated that only those methods that incorporate a cationic detergent (sodium N-lauroylsarcosine), instead of anionic detergents in the lysis or homogenization buffers, successfully extract the glucocorticoid-suppressed PG synthase mRNA. Based upon these results two procedures are described, one that optimizes the extraction and determination of the glucocorticoid-suppressed (cryptic) form of the mRNA, and another which optimizes the analysis of normal mRNA without extracting the cryptic form. The results indicate that translational control of PG synthase by glucocorticoids is regulated by converting the mRNA into a cryptic form that is more firmly tissue bound than normal mRNA.

Simultaneous isolation of total cellular RNA and DNA from tissue culture cells using phenol and lithium chloride

A rapid procedure for the isolation of intact total cellular RNA from cultured cells is described. This method combines the simultaneous disruption of cells and extraction of nucleic acids in a single step with the use of phenol and a buffer containing 100 mM LiCl. Total cellular RNA can be isolated in approximately 2 hours. The yield and quality of the RNA is comparable to the more widely employed methods requiring extensive preparatory steps such as extraction using guanidinium thiocyanate and subsequent CsCl gradient centrifugation. The RNA isolated using our procedure contains transcripts up to 10 kb in length and is suitable for Northern analysis. This procedure also yields high-molecular-weight DNA, which is a suitable substrate for restriction endonucleases.

Production of human tissue-type plasminogen activator in different mammalian cell lines using an Epstein-Barr virus vector

Human tissue-type plasminogen activator (t-PA) cDNA inserted into an Epstein-Barr virus (EBV) derived expression vector was transfected into human HeLa, 293, K-562 and hamster CHO-K1 cells and the expression of t-PA was studied. The best t-PA producing cell clones were found among CHO-K1 cells (up to 11 micrograms d-1 per 10(6) cells). However, HeLa and 293 cells were most efficiently transfected, e.g. about 70% of the selected cell clones were t-PA positive. The vector DNA copy numbers correlated with the mRNA levels and the protein levels for all cell lines analysed, with the exception for the K-562 cell line, where the production of t-PA was very low. The results obtained indicated that the highest expression levels were achieved in low density cultures.

Increases in rat striatal preproenkephalin mRNA levels following chronic treatment with the depot neuroleptic, haloperidol decanoate

Studies of the effects of chronic neuroleptic drug treatment have consistently demonstrated enhanced transcription and translation of the preproenkephalin gene in the rat striatum. However, all of these studies have used daily ip drug treatments and none have evaluated the effects of chronic depot neuroleptics. With these drug treatments, dopamine receptor blockade undergoes less variability as a result of sustained steady-state blood levels of the neuroleptic. Therefore, as a result of the increasing utilization of depot neuroleptics therapeutically, we examined the effects of haloperidol decanoate on striatal preproenkephalin mRNA levels. As with daily ip drug injections, the depot preparation was found to increase the levels of this mRNA to an apparent new steady-state level twice that of controls, by 3 days and sustaining this steady-state for the 14 day observation period. These data indicate that both continuous and fluctuating patterns of dopamine receptor blockade result in activation of the preproenkephalin gene.