Featured Research

from universities, journals, and other organizations

Universal RNA extraction protocol for land plants

Date:
December 16, 2013
Source:
American Journal of Botany
Summary:
Studies of gene expression in plants and other organisms rely on the extraction of high-quality RNA. 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. Researchers have developed a new protocol for RNA extraction that can be used across land plants, which comprise over 300,000 species.

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.

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.


Story Source:

The above story is based on materials provided by American Journal of Botany. Note: Materials may be edited for content and length.


Journal Reference:

  1. Roxana Yockteng, Ana M. R. Almeida, Stephen Yee, Thiago Andre, Colin Hill, Chelsea D. Specht. A Method for Extracting High-Quality RNA from Diverse Plants for Next-Generation Sequencing and Gene Expression Analyses. Applications in Plant Sciences, 2013; 1 (12): 1300070 DOI: 10.3732/apps.1300070

Cite This Page:

American Journal of Botany. "Universal RNA extraction protocol for land plants." ScienceDaily. ScienceDaily, 16 December 2013. <www.sciencedaily.com/releases/2013/12/131216155046.htm>.
American Journal of Botany. (2013, December 16). Universal RNA extraction protocol for land plants. ScienceDaily. Retrieved July 30, 2014 from www.sciencedaily.com/releases/2013/12/131216155046.htm
American Journal of Botany. "Universal RNA extraction protocol for land plants." ScienceDaily. www.sciencedaily.com/releases/2013/12/131216155046.htm (accessed July 30, 2014).

Share This




More Plants & Animals News

Wednesday, July 30, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Raw: Thousands Flocking to German Crop Circle

Raw: Thousands Flocking to German Crop Circle

AP (July 30, 2014) Thousands of people are trekking to a Bavarian farmer's field to check out a mysterious set of crop circles. (July 30) Video provided by AP
Powered by NewsLook.com
Concern Grows Over Worsening Ebola Crisis

Concern Grows Over Worsening Ebola Crisis

AFP (July 30, 2014) Pan-African airline ASKY has suspended all flights to and from the capitals of Liberia and Sierra Leone amid the worsening Ebola health crisis, which has so far caused 672 deaths in Guinea, Liberia and Sierra Leone. Duration: 00:43 Video provided by AFP
Powered by NewsLook.com
At Least 20 Chikungunya Cases in New Jersey

At Least 20 Chikungunya Cases in New Jersey

AP (July 30, 2014) At least 20 New Jersey residents have tested positive for chikungunya, a mosquito-borne virus that has spread through the Caribbean. (July 30) Video provided by AP
Powered by NewsLook.com
Raw: Otters Enjoy Water Slides at Japan Zoo

Raw: Otters Enjoy Water Slides at Japan Zoo

AP (July 30, 2014) River otters were hitting the water slides to beat the summer heatwave on Wednesday at Ichikawa City's Zoological and Botanical Garden. (July 30) Video provided by AP
Powered by NewsLook.com

Search ScienceDaily

Number of stories in archives: 140,361

Find with keyword(s):
Enter a keyword or phrase to search ScienceDaily for related topics and research stories.

Save/Print:
Share:

Breaking News:
from the past week

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News



Save/Print:
Share:

Free Subscriptions


Get the latest science news with ScienceDaily's free email newsletters, updated daily and weekly. Or view hourly updated newsfeeds in your RSS reader:

Get Social & Mobile


Keep up to date with the latest news from ScienceDaily via social networks and mobile apps:

Have Feedback?


Tell us what you think of ScienceDaily -- we welcome both positive and negative comments. Have any problems using the site? Questions?
Mobile: iPhone Android Web
Follow: Facebook Twitter Google+
Subscribe: RSS Feeds Email Newsletters
Latest Headlines Health & Medicine Mind & Brain Space & Time Matter & Energy Computers & Math Plants & Animals Earth & Climate Fossils & Ruins