Featured Research

from universities, journals, and other organizations

Reading the human genome: First step-by-step look at transcription initiation

Date:
February 27, 2013
Source:
DOE/Lawrence Berkeley National Laboratory
Summary:
Researchers have achieved a major advance in understanding how genetic information is transcribed from DNA to RNA by providing the first step-by-step look at the biomolecular machinery that reads the human genome.

Berkeley Lab researchers have produced the first step-by-step snapshots of the assembly of transcription factors and RNA polymerase into a transcription pre-initiation complex.
Credit: Image courtesy of Nogales group

Researchers with the U.S. Department of Energy (DOE)'s Lawrence Berkeley National Laboratory (Berkeley Lab) have achieved a major advance in understanding how genetic information is transcribed from DNA to RNA by providing the first step-by-step look at the biomolecular machinery that reads the human genome.

"We've provided a series of snapshots that shows how the genome is read one gene at a time," says biophysicist Eva Nogales who led this research. "For the genetic code to be transcribed into messenger RNA, the DNA double helix has to be opened and the strand of gene sequences has to be properly positioned so that RNA polymerase, the enzyme that catalyzes transcription, knows where the gene starts. The electron microscopy images we produced show how this is done."

Says Paula Flicker of the National Institutes of Health's National Institute of General Medical Sciences, which partly funded the research, "The process of transcription is essential to all living things so understanding how it initiates is enormously important. This work is a beautiful example of integrating multiple approaches to reveal the structure of a large molecular complex and provide insight into the molecular basis of a fundamental cellular process."

Nogales, who holds joint appointments with Berkeley Lab, the University of California (UC) at Berkeley, and the Howard Hughes Medical Institute (HHMI), is the corresponding author of a paper describing this study in the journal Nature. The paper is titled "Structural visualization of key steps in human transcription initiation." Co-authors are Yuan He, Jie Fang and Dylan Taatjes.

The fundamental process of life by which information in the genome of a living cell is used to generate biomolecules that carry out cellular activities is the so-called "central dogma of molecular biology." It states that genetic information flows from DNA to RNA to proteins. This straightforward flow of information is initiated by an elaborate system of proteins that operate in a highly choreographed fashion with machine-like precision. Understanding how this protein machinery works in the context of passing genetic information from DNA to RNA (transcription) is a must for identifying malfunctions that can turn cells cancerous or lead to a host of other problems.

Berkeley Lab researchers have produced the first step-by-step snapshots of the assembly of transcription factors and RNA polymerase into a transcription pre-initiation complex. (Image courtesy of Nogales group)

Nogales and members of her research group used cryo-electron microscopy (cryo-EM), where protein samples are flash-frozen at liquid nitrogen temperatures to preserve their structure, to carry out in vitro studies of reconstituted and purified versions of the "transcription pre-initiation complex." This complex is a large assemblage of proteins composed of RNA polymerase II (Pol II) plus a class of proteins known as general transcription factors that includes the TATA-binding protein (TBP), TFIIA, TFIIB, TFIIF, TFIIE and TFIIH. All of the components in this complex work together to ensure the accurate loading of DNA into Pol II at the start of a gene sequence.

"There's been a lack of structural information on how the transcription pre-initiation complex complex is assembled, but with cryo-EM and our in vitro reconstituted system we've been able to provide pseudo-atomic models at various stages of transcription initiation that illuminate critical molecular interactions during this step-by-step process," Nogales says.

The in vitro reconstituted transcription pre-initiation complex was developed by Yuan He, lead author on the Nature paper and a post-doctoral student in Nogales's research group.

"This reconstituted system provided a model for the sequential assembly pathway of transcription initiation and was essential for us to get the most biochemically homogenous samples," Nogales says. "Also essential was our ability to use automated data collection and processing so that we could generate all our structures in a robust manner."

Among the new details revealed in the step-by-step cryo-EM images was how the transcription factor protein TFIIF engages Pol II and promoter DNA to stabilize both a closed DNA pre-initiation complex and an open DNA-promoter complex, and also how it regulates the selection of a transcription start-site.

"Comparing the closed versus open DNA states led us to propose a model that describes how DNA is moved during the process of promoter opening," says He. "Our studies provide insight into how THIIH uses ATP hydrolysis as a source of energy to actually open and push the DNA to the active site of Pol II."

Nogales and her colleagues plan to further investigate the process of DNA loading into Pol II, as well as to include additional transcription factors into the assembly that are required for regulation of gene expression.

"Our goal is to actually build a structural model of the entire -- more than two million daltons -- protein machinery that recognizes and regulates all human DNA promoters," Nogales says. "For now we have the structural framework that's been needed to integrate biochemical and structural data into a unified mechanistic understanding of transcription initiation."

This research was funded by the National Institute of General Medical Sciences and the National Cancer Institute under NIH grant numbers GM063072 and CA127364.


Story Source:

The above story is based on materials provided by DOE/Lawrence Berkeley National Laboratory. Note: Materials may be edited for content and length.


Journal Reference:

  1. Yuan He, Jie Fang, Dylan J. Taatjes, Eva Nogales. Structural visualization of key steps in human transcription initiation. Nature, 2013; DOI: 10.1038/nature11991

Cite This Page:

DOE/Lawrence Berkeley National Laboratory. "Reading the human genome: First step-by-step look at transcription initiation." ScienceDaily. ScienceDaily, 27 February 2013. <www.sciencedaily.com/releases/2013/02/130227151306.htm>.
DOE/Lawrence Berkeley National Laboratory. (2013, February 27). Reading the human genome: First step-by-step look at transcription initiation. ScienceDaily. Retrieved September 20, 2014 from www.sciencedaily.com/releases/2013/02/130227151306.htm
DOE/Lawrence Berkeley National Laboratory. "Reading the human genome: First step-by-step look at transcription initiation." ScienceDaily. www.sciencedaily.com/releases/2013/02/130227151306.htm (accessed September 20, 2014).

Share This



More Health & Medicine News

Saturday, September 20, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Could Grief Affect The Immune Systems Of Senior Citizens?

Could Grief Affect The Immune Systems Of Senior Citizens?

Newsy (Sep. 19, 2014) The study found elderly people are much more likely to become susceptible to infection than younger adults going though a similar situation. Video provided by Newsy
Powered by NewsLook.com
Jury Delivers Verdict in Salmonella Trial

Jury Delivers Verdict in Salmonella Trial

AP (Sep. 19, 2014) A federal jury has convicted three people in connection with an outbreak of salmonella poisoning five years ago that sickened hundreds of people and was linked to a number of deaths. (Sept. 19) Video provided by AP
Powered by NewsLook.com
How The 'Angelina Jolie Effect' Increased Cancer Screenings

How The 'Angelina Jolie Effect' Increased Cancer Screenings

Newsy (Sep. 19, 2014) Angelina's Jolie's decision to undergo a preventative mastectomy in 2013 inspired many women to seek early screenings for the disease. Video provided by Newsy
Powered by NewsLook.com
The Cost of Ebola

The Cost of Ebola

Reuters - Business Video Online (Sep. 18, 2014) As Sierra Leone prepares for a three-day "lockdown" in its latest bid to stem the spread of Ebola, Ciara Lee looks at the financial implications of fighting the largest ever outbreak of the disease. Video provided by Reuters
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