Featured Research

from universities, journals, and other organizations

Importance of transcription in animals has been underestimated by system-wide analyses

Date:
February 27, 2014
Source:
PeerJ
Summary:
Over the last decade, a number of studies have suggested that, in animal cells, translation and protein turnover play a larger role in determining the different levels at which proteins are expressed than transcription. A new study suggests that the major reason why protein and mRNA abundance measurements are poorly correlated is because of various types of measurement error in the protein and mRNA abundance, rather than transcription having minimal impact on protein expression levels.

Over the last ten years, a number of studies have suggested that, in animal cells, translation and protein turnover play a larger role in determining the different levels at which proteins are expressed than transcription. The major evidence supporting these claims is a weak correlation between system-wide protein and mRNA abundance measurements.

A highly cited Nature article by Schwanhausser et al. in 2011 provides the most comprehensive example of such analyses. A new study just published in PeerJ by Li et al., however, questions the conclusions of these papers. This new study suggests that the major reason why protein and mRNA abundance measurements are poorly correlated is because of various types of measurement error in the protein and mRNA abundance, rather than transcription having minimal impact on protein expression levels.

Li et al. first show that Schwanhausser et al.'s protein abundances have a non linear error that leads to a dramatic underestimation of low abundance proteins, a result that has been independently supported by a separate benchmarking study by Ahrne et al. Li et al. rescale Schwanhausser et al.'s protein abundance estimates using data for housekeeping proteins and show that the rescaled data show a higher correlation with mRNA abundances than the uncorrected protein data. In addition, they estimate the impact of other sources of error on the mRNA and protein abundance measurements using direct experimental data, and they find that, when error is explicitly measured and modeled, an even greater correlation between mRNA and protein is expected. Li et al. use a second, independent strategy to determine the contribution of mRNA levels to protein expression: they show that the variance in translation rates directly measured by ribosome profiling is dramatically lower than that inferred by Schwanhausser et al., and that the measured and inferred translation rates correlate poorly. Incorporating protein and mRNA turnover data in this analysis, the results from Li et al. suggest that mRNA levels explain ~81% of the variance in protein levels, transcription 71%, RNA degradation 10%; translation 11%; and protein degradation 8%. This conclusion differs dramatically from the previous estimates of differences in mRNA levels explaining 10-40% of the differences in protein levels in the current literature.

Li et al.'s analysis provides an accurate framework for quantifying gene expression and protein abundance levels by explicitly considering sources of error. This work highlights the importance of appropriate statistical analyses of the large quantitative data sets that are increasingly being produced by experimentalists and are being used to study fundamental cellular mechanisms.


Story Source:

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


Journal Reference:

  1. Jingyi Jessica Li, Peter J Bickel, Mark D Biggin. System wide analyses have underestimated protein abundances and the importance of transcription in mammals. PeerJ, 2014; 2: e270 DOI: 10.7717/peerj.270

Cite This Page:

PeerJ. "Importance of transcription in animals has been underestimated by system-wide analyses." ScienceDaily. ScienceDaily, 27 February 2014. <www.sciencedaily.com/releases/2014/02/140227092143.htm>.
PeerJ. (2014, February 27). Importance of transcription in animals has been underestimated by system-wide analyses. ScienceDaily. Retrieved July 29, 2014 from www.sciencedaily.com/releases/2014/02/140227092143.htm
PeerJ. "Importance of transcription in animals has been underestimated by system-wide analyses." ScienceDaily. www.sciencedaily.com/releases/2014/02/140227092143.htm (accessed July 29, 2014).

Share This




More Plants & Animals News

Tuesday, July 29, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Deadly Ebola Virus Threatens West Africa

Deadly Ebola Virus Threatens West Africa

AP (July 28, 2014) West African nations and international health organizations are working to contain the largest Ebola outbreak in history. It's one of the deadliest diseases known to man, but the CDC says it's unlikely to spread in the U.S. (July 28) Video provided by AP
Powered by NewsLook.com
Traditional African Dishes Teach Healthy Eating

Traditional African Dishes Teach Healthy Eating

AP (July 28, 2014) Classes are being offered nationwide to encourage African Americans to learn about cooking fresh foods based on traditional African cuisine. The program is trying to combat obesity, heart disease and other ailments often linked to diet. (July 28) Video provided by AP
Powered by NewsLook.com
Asteroid's Timing Was 'Colossal Bad Luck' For The Dinosaurs

Asteroid's Timing Was 'Colossal Bad Luck' For The Dinosaurs

Newsy (July 28, 2014) The asteroid that killed the dinosaurs struck at the worst time for them. A new study says that if it hit earlier or later, they might've survived. Video provided by Newsy
Powered by NewsLook.com
Raw: Sea Turtle Hatchlings Emerge from Nest

Raw: Sea Turtle Hatchlings Emerge from Nest

AP (July 27, 2014) A live-streaming webcam catches loggerhead sea turtle hatchlings emerging from a nest in the Florida Keys. (July 27) 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