Navigation Links
Is the shape of a genome as important as its content?
Date:10/29/2010

If there is one thing that recent advances in genomics have revealed, it is that our genes are interrelated, "chattering" to each other across separate chromosomes and vast stretches of DNA. According to researchers at The Wistar Institute, many of these complex associations may be explained in part by the three-dimensional structure of the entire genome. A given cell's DNA spends most of its active lifetime in a tangled clump of chromosomes, which positions groups of related genes near to each other and exposes them to the cell's gene-controlling machinery. This structure, the researchers say, is not merely the shape of the genome, but also a key to how it works.

Their study, published online as a featured article in the journal Nucleic Acids Research, is the first to combine microscopy with advanced genomic sequencing techniques, enabling researchers to literally see gene interactions. It is also the first to determine the three-dimensional structure of the fission yeast genome, S. pombe. Applying this technique to the human genome may provide both scientists and physicians a whole new framework from which to better understand genes and disease, the researchers say.

"People are familiar with the X-shapes our chromosomes form during cell division, but what they may not realize is that DNA only spends a relatively small amount of time in that conformation," said Ken-ichi Noma, Ph.D., an assistant professor in Wistar's Gene Expression and Regulation program and senior author of the study. "Chromosomes spend the majority of their time clumped together in these large, non-random structures, and I believe these shapes reflect various nuclear processes such as transcription."

To map both individual genes and the overall structure of the genome, Noma and his colleagues combined next generation DNA sequencing with a technique called chromosome conformation capture (3C). They then used fluorescent probes to pinpoint the exact location of specific genes through a microscope. With these data, the researchers were able to create detailed three-dimensional computer models of the yeast genome.

Using this novel approach, the researchers can view genes as they interact with each other. Noma and his colleagues can view where highly active genes are located, or see if genes that are turned on and off together also reside near each other in the three-dimensional structure of the genome. In total, the Wistar researchers also studied 465 so-called gene ontology groups groups of genes that share a related purpose in the cell, such as structure or metabolism.

"When the chromosomes come together, they fold into positions that bring genes from different chromosomes near each other," Noma said. "This positioning allows the processes that dictate how and when genes are read to operate efficiently on multiple genes at once."

This structure is not merely an accident of chemical attractions within and among the chromosomes although that is certainly a part of the larger whole but an arrangement guided by other molecules in the cell to create a mega-structure that dictates genetic function, Noma says. He envisions a scenario where accessory molecules, such as gene-promoting transcription factors, bind to DNA and contribute to the ultimate structure of the genome as the chromosomes fold together.

"I believe we are looking at a new way to visualize both the genome itself and the movements of all the various molecules that act on the genome," Noma said.

According to the Wistar scientists, their techniques are scalable to the human genome, even though fission yeast only has three chromosomes. In fact, the researchers found signs of "transcription factories" clusters of related genes that are read, or "transcribed," at discrete sites which have been proposed to exist in mammals.


'/>"/>

Contact: Greg Lester
glester@wistar.org
215-898-3943
The Wistar Institute
Source:Eurekalert  

Related biology news :

1. Penn scientists discover cells reorganize shape to fit the situation
2. Wistar scientists find key to keeping killer T cells in prime shape for fighting infection, cancer
3. Apple or pear shape is not main culprit to heart woes -- its liver fat
4. Ancient magma superpiles may have shaped the continents
5. Root system architecture arises from coupling cell shape to auxin transport
6. Shape changes in aroma-producing molecules determine the fragrances we detect
7. Root system architecture arises from coupling cell shape to auxin transport
8. As super-predators, humans reshape their prey at super-natural speeds
9. Grape shapes
10. Caltech and UCSD researchers shed light on how proteins find their shapes
11. RNA research strategy for Europe takes shape
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
Is the shape of a genome as important as its content?
(Date:6/2/2016)... --  The Weather Company , an IBM Business (NYSE: ... in which consumers will be able to interact with IBM ... voice or text and receive relevant information about the product ... have long sought an advertising solution that can create a ... and valuable; and can scale across millions of interactions and ...
(Date:5/16/2016)... , May 16, 2016   EyeLock LLC , ... announced the opening of an IoT Center of Excellence ... and expand the development of embedded iris biometric applications. ... level of convenience and security with unmatched biometric accuracy, ... identity aside from DNA. EyeLock,s platform uses video technology ...
(Date:4/28/2016)... Sweden , April 28, 2016 First ... M (139.9), up 966% compared with the first quarter of 2015 ... profit totaled SEK 589.1 M (loss: 18.8) and the operating margin ... 7.12 (loss: 0.32) Cash flow from operations was SEK ... The 2016 revenue guidance is unchanged, SEK 7,000-8,500 M. ...
Breaking Biology News(10 mins):
(Date:6/27/2016)... ... June 27, 2016 , ... ... innovative medical technologies, services and solutions to the healthcare market. The company's primary ... various distribution, manufacturing, sales and marketing strategies that are necessary to help companies ...
(Date:6/27/2016)... , June 27, 2016  Liquid Biotech ... announced the funding of a Sponsored Research Agreement ... circulating tumor cells (CTCs) from cancer patients.  The ... in CTC levels correlate with clinical outcomes in ... These data will then be employed to support ...
(Date:6/24/2016)... discussions on a range of subjects including policies, debt and ... Poloz. Speaking at a lecture to the Canadian ... to the country,s inflation target, which is set by both ... "In certain areas there needs to be ... why not sit down and address strategy together?" ...
(Date:6/24/2016)... ... 24, 2016 , ... While the majority of commercial spectrophotometers and fluorometers use ... 6000i models are higher end machines that use the more unconventional z-dimension of 20mm. ... from the bottom of the cuvette holder. , FireflySci has developed several Agilent ...
Breaking Biology Technology: