Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Powerful sequencing technology decodes DNA folding pattern

12.04.2012
Findings provide tools for better understanding of the human genome

hromosomes are strands of DNA that contain the blueprint of all living organisms. Humans have 23 pairs of chromosomes that instruct how genes are regulated during development of the human body. While scientists have developed an understanding of the one-dimensional structure of DNA, until today, little was known about how different parts of DNA are folded next to each other inside the nucleus.

Using a powerful DNA sequencing methodology, researchers at the Ludwig Institute for Cancer Research have now investigated the three-dimensional structure of DNA folds in the nucleus of a chromosome. The findings published in the April 11 issue of Nature provide scientists with a greater understanding about the basic principles of DNA folding and its role in gene regulation.

"In any biology textbook, when you look at a diagram of how genes are depicted, it is invariably a one-dimensional line. In reality, genes are arranged in such a way that two parts of the gene may be distal to each other linearly, but very close in 3-D," said Dr. Bing Ren, Member of the Ludwig Institute for Cancer Research and Professor of Cellular and Molecular Medicine at the University of California, San Diego. "With the knowledge of how DNA folds inside the nucleus, we now have a more complete picture of the regulatory process of genes. That is the primary reason we sought to tackle this problem." The spatial organization is intimately linked to its role in the body.

Ludwig researchers used a sequencing-based method called Hi-C to examine the 3-D structure of chromosomes. "With this technology, we were able to build a map of pair-wise interactions from each chromosome, and from that, extrapolate the basic folding pattern of the DNA. What we learned is that they fold into many local domains termed topological domains, which are on average one million base pairs in size. By way of comparison, the whole human genome is just over three billion base pairs in size," explained lead researcher, Jesse Dixon, a graduate student in Dr. Ren's lab.

In examining the interaction map, Dr. Ren's team discovered that topological domains are the basic unit of folding. The team confirmed their findings by comparing it among different cell types. In each type, the folding of DNA into topological domains was constant.

A parallel study by researchers at Institut Curie and the University of Massachusetts Medical School support Ludwig researchers' findings. By focusing on the mouse X chromosome segment in embryonic stem cells, as well as neuronal cells and fibroblasts, researchers showed that this segment adhered to similar folding patterns as the ones found by Ren's team. They further showed that this organization could be linked to gene regulation.

"This is just the beginning of a very exciting area of research focused on the understanding of nuclear processes from a three-dimensional point of view. We know that some cancers, including many leukemias, are caused by the translocation of two genes. It's not clear how these translocations are regulated or whether they result from random events. It's possible that the spatial structure of the chromosome can provide clues about how these translocations occur and, more importantly, how we can prevent them or at least mitigate their effect," concluded Dr. Ren.

Co-authors on the paper include Siddarth Selvaraj of the Ludwig Institute for Cancer Research and the University of California, San Diego; Feng Yue, Audrey Kim, Yan Li and Yin Shen of the Ludwig Institute for Cancer Research; and Ming Hu and Jun S. Liu of Harvard University. Development of the new Hi-C technique used in the study was pioneered by a team of researchers including Job Dekker, professor and co-director of the Program in Systems Biology at the University of Massachusetts Medical School.

This work was supported by funding from the Ludwig Institute for Cancer Research, the California Institute for Regenerative Medicine, the National Institutes of Health and the Rett Syndrome Research Foundation.

About The Ludwig Institute for Cancer Research

LICR is an international non-profit organization committed to improving the understanding and control of cancer through integrated laboratory and clinical discovery. Leveraging its worldwide network of investigators and the ability to sponsor and conduct its own clinical trials, the Institute is actively engaged in translating its discoveries into applications for patient benefit. Since its establishment in 1971, the Institute has expended more than $1.5 billion on cancer research.

For further information please contact Rachel Steinhardt, rsteinhardt@licr.org or +1-212-450-1582

Rachel Steinhardt | EurekAlert!
Further information:
http://www.licr.org

More articles from Life Sciences:

nachricht A Map of the Cell’s Power Station
18.08.2017 | Albert-Ludwigs-Universität Freiburg im Breisgau

nachricht On the way to developing a new active ingredient against chronic infections
18.08.2017 | Deutsches Zentrum für Infektionsforschung

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Fizzy soda water could be key to clean manufacture of flat wonder material: Graphene

Whether you call it effervescent, fizzy, or sparkling, carbonated water is making a comeback as a beverage. Aside from quenching thirst, researchers at the University of Illinois at Urbana-Champaign have discovered a new use for these "bubbly" concoctions that will have major impact on the manufacturer of the world's thinnest, flattest, and one most useful materials -- graphene.

As graphene's popularity grows as an advanced "wonder" material, the speed and quality at which it can be manufactured will be paramount. With that in mind,...

Im Focus: Exotic quantum states made from light: Physicists create optical “wells” for a super-photon

Physicists at the University of Bonn have managed to create optical hollows and more complex patterns into which the light of a Bose-Einstein condensate flows. The creation of such highly low-loss structures for light is a prerequisite for complex light circuits, such as for quantum information processing for a new generation of computers. The researchers are now presenting their results in the journal Nature Photonics.

Light particles (photons) occur as tiny, indivisible portions. Many thousands of these light portions can be merged to form a single super-photon if they are...

Im Focus: Circular RNA linked to brain function

For the first time, scientists have shown that circular RNA is linked to brain function. When a RNA molecule called Cdr1as was deleted from the genome of mice, the animals had problems filtering out unnecessary information – like patients suffering from neuropsychiatric disorders.

While hundreds of circular RNAs (circRNAs) are abundant in mammalian brains, one big question has remained unanswered: What are they actually good for? In the...

Im Focus: RAVAN CubeSat measures Earth's outgoing energy

An experimental small satellite has successfully collected and delivered data on a key measurement for predicting changes in Earth's climate.

The Radiometer Assessment using Vertically Aligned Nanotubes (RAVAN) CubeSat was launched into low-Earth orbit on Nov. 11, 2016, in order to test new...

Im Focus: Scientists shine new light on the “other high temperature superconductor”

A study led by scientists of the Max Planck Institute for the Structure and Dynamics of Matter (MPSD) at the Center for Free-Electron Laser Science in Hamburg presents evidence of the coexistence of superconductivity and “charge-density-waves” in compounds of the poorly-studied family of bismuthates. This observation opens up new perspectives for a deeper understanding of the phenomenon of high-temperature superconductivity, a topic which is at the core of condensed matter research since more than 30 years. The paper by Nicoletti et al has been published in the PNAS.

Since the beginning of the 20th century, superconductivity had been observed in some metals at temperatures only a few degrees above the absolute zero (minus...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Call for Papers – ICNFT 2018, 5th International Conference on New Forming Technology

16.08.2017 | Event News

Sustainability is the business model of tomorrow

04.08.2017 | Event News

Clash of Realities 2017: Registration now open. International Conference at TH Köln

26.07.2017 | Event News

 
Latest News

A Map of the Cell’s Power Station

18.08.2017 | Life Sciences

Engineering team images tiny quasicrystals as they form

18.08.2017 | Physics and Astronomy

Researchers printed graphene-like materials with inkjet

18.08.2017 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>