Monthly Archives: February 2013

Feb. 27, 2013 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."

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

A genome sequencing platform to help physicians screen patients for the most appropriate drugs for their conditions such as for cancer treatments is one component of a new company thats a spinout from a collaboration between Philadelphia-area Coriell Institute for Medical Research and its technology partner IBM.

Coriell Institute CEO Michael Christman and Scott Megill, Coriells chief information officer, who is leading the spinout, told MedCity News in a phone interview how the startup will work and explained its timeline.

Coriell Life Sciences in Camden, New Jersey,will be at the center of a genome ecosystem transmitting queries from physicians to genomic-sequencing interpreters. It will also provide cloud-based storage for each patients genomic sequence. It sees itself as something of an Amazon.com for genomic sequencing. It does not own the content, but through the ecosystem it is setting up, it is facilitating the interaction between physicians, researchers and the interpreters of that data. The company is making it easier to order, store and interpret genome sequence data for physicians.

Heres how it works: A physician would order a test that requires genomic sequencing the same way he or she would order a diagnostic test. Coriell sends the sequencing order to a network of third-party interpreters it is in the process of assembling. The results will be transmitted to the patients medical records and the genome would be stored in its cloud-based vault. Physicians could use it to order follow-up tests or researchers could utilize the de-identified data.

Megill said he expects Coriell Life Sciences genome vault will be ready by early summer and its genomic exchange product is expected to be ready sometime this fall.

Christman said the startups programs would provide a huge economic benefit by helping the right patients get the right care at the right time. We are at a special time [for genomic sequencing] where doctors want to use this tool.For example, it would be able to identify patients who wont respond well to Plavix an anticlotting drug thats ineffective for about 25 percent of the patients for whom it is prescribed. Instead, they could be prescribed U.S. Food and Drug Administration-approved alternative drugs and save a lot of money. Thats just the tip of the iceberg, Christman said. He also pointed out that genomic sequencing is increasingly being done in utero through the mothers blood and negates a potentially more risky approach using amniocentesis.

IBM has been helping to build the technology platform for the spinout that will transmit the information gathered from the genomic sequencing data back to the patients medical records. It will also provide a secure way to store the cloud-based data.

The partnership with IBM dates back to 2011, when the company provided monitoring software to instantly alert Coriell researchers before any mechanical failure occurs and in turn, protect the integrity of its biological samples.

[Photo from Flickr user andylepp]

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Cloud-based genome sequencing exchange could make personalized medicine easier for physicians