Application of reversed-phase high-performance liquid chromatography with fluorimetric detection for simultaneous assessment of global DNA and total RNA methylation in Lepidium sativum: effect of plant exposure to Cd(II) and Se(IV).

In the present work, application of the previously established reversed-phase liquid chromatography procedure based on fluorescent labeling of cytosine and methylcytosine moieties with 2-bromoacetophenone (HPLC-FLD) is presented for simultaneous evaluation of global DNA and total RNA methylation at cytosine carbon 5. The need for such analysis was comprehended from the recent advances in the field of epigenetics that highlight the importance of non-coding RNAs in DNA methylation and suggest that RNA methylation might play a similar role in the modulation of genetic information, as previously demonstrated for DNA. In order to adopt HPLC-FLD procedure for DNA and RNA methylation analysis in a single biomass extract, two extraction procedures with different selectivity toward nucleic acids were examined, and a simplified calibration was designed allowing for evaluation of methylation percentage based on the ratio of chromatographic peak areas: cytidine/5-methylcytidine for RNA and 2'-deoxycytidine/5-methyl-2'-deoxycytidine for DNA. As a proof of concept, global DNA and total RNA methylation were determined in Lepidium sativum hydroponically grown in the presence of different Cd(II) or Se(IV) concentrations, expecting that plant exposure to abiotic stress might affect not only global DNA but also total RNA methylation. The results obtained showed the increase of DNA methylation in the treated plants up to concentration levels 2 mg L(-1) Cd and 1 mg L(-1) Se in the growth medium. For higher stressors' concentration, global DNA methylation tended to decrease. Most importantly, an inverse correlation was found between DNA and RNA methylation levels (r = -0.6788, p = 0.031), calling for further studies of this particular modification of nucleic acids in epigenetic context.

RNA quality assessment: a view from plant qPCR studies.

Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) is probably the most common molecular technique used in transcriptome analyses today. The simplicity of the technology and associated protocols that generate results without the need to understand the underlying principles has made RT-qPCR the method of choice for RNA quantification. Rather than the 'gold standard technology' often used to describe it, the performance of RT-qPCR suffers from considerable pitfalls during general workflow. The inconsistency of conventional methods for the evaluation of RNA quality and its influence on qPCR performance as well as stability of reference genes is summarized and discussed here.

Preparation and quality assessment of RNA from cell-specific samples obtained by laser microdissection.

Laser microdissection is a powerful tool to obtain cell-specific isolates from complex tissue samples. This chapter outlines how to prepare plant material for microdissection and methods to extract and measure high-quality RNA suitable for a variety of different downstream applications.

Genetic distinction of radix adenophorae from its adulterants by the DNA sequence of 5S-rRNA spacer domains.

Radix Adenophorae (Shashen), a traditional Chinese medicine commonly used as an antitussive and expectorant, is derived from roots of Adenophora stricta Miq. and Adenophora tetraphylla (Thunb.) Fisch. Twelve species and varieties of Adenophora and Glehnia, however, could act as substitutes or adulterants of Radix Adenophorae on the commercial markets in South East Asia, and roots of Adenophora hunanensis Nannf. and Glihnia littoralis F. Schmidt ex Miq. are the most common examples. The authentic identification of dried roots of A. stricta and A. tetraphylla, however, is difficult on the basis of appearance and morphology. A molecular genetic approach was developed here to identify the species of Radix Adenophorae. The 5S-rRNA spacer domains (approximately 250 bp) were amplified by the polymerase chain reaction (PCR) from genomic DNAs isolated from A. stricta, A. tetraphylla, A. hunanensis and G. littoralis, and subsequently, the nucleotide sequences were determined. Diversity in DNA sequence and restriction enzyme mapping among various species were found in their 5S-rRNA spacer domains, which could serve as markers for authentic identification of Radix Adenophorae.

Assessment of the number and expression of P-type H(+)-ATPase genes in tomato.

Seven genomic fragments encoding isoforms of tomato (Lycopersicon esculentum) plasma membrane H(+)-ATPase were cloned and characterized. Genomic DNA gel-blot analysis indicated that probes corresponding to LHA1 through LHA7 hybridized to a common set of seven to nine restriction fragments at moderate stringency and to single, distinct fragments at high stringency. RNA gel-blot and polymerase chain reaction (PCR)-based RNA analyses indicated that LHA1, LHA2, and LHA4 transcripts were present in all organs examined (roots, hypocotyls, stems, immature leaves, mature leaves, green fruit, and red ripe fruit). LHA1 mRNA was present at similar abundance in all organs, LHA2 mRNA was most abundant in hypocotyls and leaves, and LHA4 mRNA was most abundant in roots and hypocotyls. RNA gel-blot and RNA-based PCR assays indicated that LHA3, LHA5, LHA6, and LHA7 mRNA was present at very low or nondetectable levels in all organs, suggesting that these genes are either expressed at very low levels or in organs not examined or that they are regulated by hormonal or environmental cues that were not tested. Indoleacetic acid (IAA) treatment of tomato hypocotyl segments resulted in modest changes in abundance of LHA1, LHA2, and LHA4 transcripts, but these changes were not correlated with the time course of IAA-induced growth. In addition, constitutively silent LHA genes were not activated by IAA. These results indicate that at least seven genomic sequences are present in tomato that may encode plasma membrane H(+)-ATPases, at least three of which are expressed relatively abundantly at the mRNA level.