Navigation Links
A universal RNA extraction protocol for land plants
Date:12/16/2013

RNA, a nucleic acid involved in protein synthesis, is widely used in genetic research to study patterns of gene expression in different organisms. The types and quantities of RNA present in an organism indicate which genes are expressed, providing insight on the genes responsible for particular phenotypes.

Many tools, such as next-generation sequencing and quantitative PCR, are available for studying gene expression. However, these tools rely on the extraction of high-quality RNA from the organism of interest, and this can be a challenging task. Compared to genomic DNA, RNA is more delicate and prone to degradation. Additionally, many plant tissues are infused with starch, fibers, or secondary compounds that inhibit the isolation of RNA of sufficient quality and/or quantity.

Although numerous protocols for RNA extraction have been developed, most of these are plant-specific, with many tailored for particular crop plants or model organisms (e.g., Arabidopsis), making their utility for non-model plant species, which constitute the vast bulk of plant diversity, somewhat limited.

Researchers at the University of California, Berkeley, have developed a new protocol for RNA extraction that can be used across land plants, which comprise over 300,000 species. The protocol is available for free viewing in the December issue of Applications in Plant Sciences (http://www.bioone.org/doi/pdf/10.3732/apps.1300070).

According to Chelsea Specht, associate professor in the Department of Plant and Microbial Biology at UC Berkeley and senior author of the study, this protocol will greatly facilitate RNA-based studies of non-model plant species.

"Using this protocol, we can successfully extract high yields and high-quality RNA from tissues of any type from plants across the diversity of land plants, including tissues that are mechanically difficult to grind, rich in starch, or laden with secondary compounds."

Lead author Roxana Yockteng, Specht, and their colleagues tested the protocol on a wide variety of land plant species (one moss species, three gymnosperm species, and numerous angiosperm species) as well as different tissue types (e.g., leaves, flowers, and cones). They were able to consistently recover large quantities of high-quality RNA from the samples tested, demonstrating the broad utility of the protocol.

Specht says the efficacy of the protocol lies in its flexibility; there are numerous steps in the protocol that can be readily modified to accommodate variations in plant chemistry and structure.

"You can micromanage your RNA extraction and make small changes that work for you, regardless of what lab you're in or what plant you are working with."

The protocol also includes an optional cleanup step at the end, which permits the acquisition of clean, high-quality RNA from problematic samples (e.g., those rich in lignin and/or secondary metabolites) without a significant loss in RNA quantity. This step is a modification of a similar method designed for cleaning DNA.

According to Specht, the new protocol will have numerous applications in plant genetic research. Studies of gene expression involving reverse transcriptase PCR, quantitative PCR, or RNA-sequencing (transcriptome profiling) can use this protocol to extract the requisite high-quality RNA. Additionally, researchers can use transcriptomes generated from next-generation sequencing to develop probes for targeted sequence capture for phylogenetic and phylogeographic studies.

The ability to use this protocol on an array of plants and tissue types will also facilitate comparative analyses of transcriptomes across diverse lineages, says Specht, permitting researchers to investigate a variety of interesting evolutionary questions. This was challenging before, as existing protocols are generally too taxon- or tissue-specific for use across numerous phylogenetically divergent species.


'/>"/>

Contact: Beth Parada
apps@botany.org
American Journal of Botany
Source:Eurekalert

Related biology news :

1. Victory stance may be a universal gesture of triumph -- not pride -- study suggests
2. Flu antibody’s one-handed grab may boost effort toward universal vaccine, new therapies
3. Universal rules discovered that allow anticipation of critical transitions
4. One law to rule them all -- sizes within a species appear to follow a universal distribution
5. Specialised germanium surface as universal protein adapter
6. Chimpanzees have 5 universal personality dimensions
7. Cost-effective: Universal HIV testing in India
8. U of T-led study cracks universal RNA code, suggests a new cause for autism
9. Scientists closer to universal flu vaccine after pandemic natural experiment
10. China Botanic Receives Patent on its Schisandra Lignin Extraction Method
11. Tailored methane measurement services are to be developed for shale gas extraction, municipal waste
Post Your Comments:
*Name:
*Comment:
*Email:
(Date:6/27/2016)... June 27, 2016 Research and Markets has ... 2016-2020" report to their offering. ... America to grow at a CAGR of 12.28% during ... based on an in-depth market analysis with inputs from industry experts. ... the coming years. The report also includes a discussion of the ...
(Date:6/22/2016)... , June 22, 2016  The American College of ... Trade Show Executive Magazine as one of the fastest-growing ... May 25-27 at the Bellagio in Las Vegas ... the highest percentage of growth in each of the following ... exhibiting companies and number of attendees. The 2015 ACMG Annual ...
(Date:6/22/2016)... June 22, 2016   Acuant , ... verification solutions, has partnered with RightCrowd ® ... for Visitor Management, Self-Service Kiosks and Continuous ... that add functional enhancements to existing physical ... and venues with an automated ID verification ...
Breaking Biology News(10 mins):
(Date:6/23/2016)... 23, 2016   EpiBiome , a precision microbiome ... in debt financing from Silicon Valley Bank (SVB). The ... to advance its drug development efforts, as well as ... "SVB has been an incredible strategic partner to ... traditional bank would provide," said Dr. Aeron Tynes ...
(Date:6/23/2016)... ... June 23, 2016 , ... In a new case ... Denmark detail how a patient who developed lymphedema after being treated for breast cancer ... could change the paradigm for dealing with this debilitating, frequent side effect of cancer ...
(Date:6/23/2016)... 23, 2016 Andrew ... http://doi.org/10.17925/OHR.2016.12.01.22 Published recently in ... journal from touchONCOLOGY, Andrew D Zelenetz , ... cancer care is placing an increasing burden on ... biologic therapies. With the patents on many biologics ...
(Date:6/23/2016)... (PRWEB) , ... June 23, 2016 , ... ... on quality, regulatory and technical consulting, provides a free webinar on ... on July 13, 2016 at 12pm CT at no charge. , Incomplete investigations ...
Breaking Biology Technology: