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:5/3/2016)... , May 3, 2016  Neurotechnology, a provider ... MegaMatcher Automated Biometric Identification System (ABIS) , ... multi-biometric projects. MegaMatcher ABIS can process multiple complex ... any combination of fingerprint, face or iris biometrics. ... SDK and MegaMatcher Accelerator , which ...
(Date:4/28/2016)... SAN FRANCISCO and BANGALORE, India ... part of EdgeVerve Systems, a product subsidiary of Infosys (NYSE: ... service provider, today announced a global partnership that ... convenient way to use mobile banking and payment services. ... Mobility is a key innovation area for financial services, but ...
(Date:4/28/2016)... -- First quarter 2016:   , Revenues ... first quarter of 2015 The gross margin was 49% ... and the operating margin was 40% (-13) Earnings per ... from operations was SEK 249.9 M (21.2) , Outlook ... 7,000-8,500 M. The operating margin for 2016 is estimated ...
Breaking Biology News(10 mins):
(Date:5/6/2016)... May 6, 2016 Recent studies show that ... prescription pain medication when treating certain types of pain. ... therapy, doctors can go right to the source instead ... an educational organization, provides physician training about the benefits ... feature to find physicians across the United ...
(Date:5/6/2016)... (PRWEB) , ... May 06, 2016 , ... ... their most recent release, Clinical Studio Version 4.1, greatly improves performance of the ... oncology, where protocols often generate tremendous volumes of data to be collected on ...
(Date:5/6/2016)... ... May 06, 2016 , ... This June 3-6, SonoDepot ... an exclusive sales and service provider of the ALPINION line, reps will educate attendees ... conference for healthcare technology management. The event draws more than 2,200 biomedical equipment technicians, ...
(Date:5/5/2016)... ... May 05, 2016 , ... ... agreement to acquire Algynomics, a research-stage pain diagnostics company. The Algynomics ... at increased risk for the development of chronic pain, which will allow targeted ...
Breaking Biology Technology: