Featured Research

from universities, journals, and other organizations

Powerful sequencing technology decodes DNA folding pattern

Date:
April 11, 2012
Source:
Ludwig Institute for Cancer Research
Summary:
Using a powerful DNA sequencing methodology, researchers have now investigated the three-dimensional structure of DNA folds in the nucleus of a chromosome. The findings provide scientists with a greater understanding about the basic principles of DNA folding and its role in gene regulation.

Chromosomes 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 now, 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.


Story Source:

The above story is based on materials provided by Ludwig Institute for Cancer Research. Note: Materials may be edited for content and length.


Journal Reference:

  1. Jesse R. Dixon, Siddarth Selvaraj, Feng Yue, Audrey Kim, Yan Li, Yin Shen, Ming Hu, Jun S. Liu, Bing Ren. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 2012; DOI: 10.1038/nature11082

Cite This Page:

Ludwig Institute for Cancer Research. "Powerful sequencing technology decodes DNA folding pattern." ScienceDaily. ScienceDaily, 11 April 2012. <www.sciencedaily.com/releases/2012/04/120411132208.htm>.
Ludwig Institute for Cancer Research. (2012, April 11). Powerful sequencing technology decodes DNA folding pattern. ScienceDaily. Retrieved October 23, 2014 from www.sciencedaily.com/releases/2012/04/120411132208.htm
Ludwig Institute for Cancer Research. "Powerful sequencing technology decodes DNA folding pattern." ScienceDaily. www.sciencedaily.com/releases/2012/04/120411132208.htm (accessed October 23, 2014).

Share This



More Health & Medicine News

Thursday, October 23, 2014

Featured Research

from universities, journals, and other organizations


Featured Videos

from AP, Reuters, AFP, and other news services

Ebola Fears Keep Guinea Hospitals Empty

Ebola Fears Keep Guinea Hospitals Empty

AP (Oct. 23, 2014) Fears of Ebola are keeping doctors and patients alike away from hospitals in the West African nation of Guinea. (Oct. 23) Video provided by AP
Powered by NewsLook.com
Orthodontist Mom Jennifer Salzer on the Best Time for Braces

Orthodontist Mom Jennifer Salzer on the Best Time for Braces

Working Mother (Oct. 22, 2014) Is your child ready? Video provided by Working Mother
Powered by NewsLook.com
U.S. Issues Ebola Travel Restrictions, Are Visa Bans Next?

U.S. Issues Ebola Travel Restrictions, Are Visa Bans Next?

Newsy (Oct. 22, 2014) Now that the U.S. is restricting travel from West Africa, some are dropping questions about a travel ban and instead asking about visa bans. Video provided by Newsy
Powered by NewsLook.com
More People Diagnosed With TB In 2013, But There's Good News

More People Diagnosed With TB In 2013, But There's Good News

Newsy (Oct. 22, 2014) The World Health Organizations says TB numbers rose in 2013, but it's partly due to better detection and more survivors. Video provided by Newsy
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:

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

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