Featured Research

from universities, journals, and other organizations

Huge human gene study includes Penn State University research

September 5, 2012
Penn State
The first integrated understanding of how the human genome functions will be published this week -- the triumphant result of a collaborative five-year project called ENCODE, involving more than 440 researchers working in 32 labs worldwide. Penn State's contribution involves using the new ENCODE data to help explain how genetic variants that do not affect the structure of encoded proteins could affect a person's susceptibility to disease.

ENCODE is a massive database cataloging many of the functional elements of the entire collection of human genes -- the human genome. The ENCODE data are being made available to the scientific community and to the public as an open resource. This illustration shows a group of proteins bound to the spiraling strands of DNA, which is the genetic material. A chromosome, composed of tightly coiled DNA, is illustrated in the background. The new papers from the ENCODE consortium show that differences in the way certain proteins interact with DNA in each person play a role in their susceptibility to some common diseases.
Credit: National Institutes of Health

The first integrated understanding of how the human genome functions will be published this week -- the triumphant result of a collaborative five-year project involving more than 440 researchers working in 32 labs worldwide. The Encyclopedia of DNA Elements project, known as ENCODE, will publish simultaneously on Sept. 6 a massive number of scientific papers, including one main integrative paper and five others in Nature; 18 in Genome Research; six in Genome Biology; and other affiliated papers in Science, Cell, and other scientific journals.

Related Articles

During the ENCODE study, researchers found that more than 80 percent of the human genome sequence is linked to biological function. They also mapped more than 4 million regulatory regions where proteins interact with the DNA with exquisite specificity. These findings are a significant advance in understanding the precise and complex controls over the expression of genetic information within a cell.

"Penn State's contribution to the ENCODE project involves using the new ENCODE data to help explain how genetic variants that do not affect the structure of encoded proteins could affect a person's susceptibility to disease," said Ross Hardison, the T. Ming Chu Professor of Biochemistry and Molecular Biology at Penn State and a member of the ENCODE research team. The research, led by Hardison, is highlighted in the main integrative ENCODE paper to be published in the journal Nature.

"Genome-wide association studies can map with high resolution the places on our genomes where variation in the DNA sequence among individual persons affects their likelihood of having diabetes, cardiac disease, any of a large number of autoimmune diseases such as Crohn's disease, and other common diseases," Hardison said. Because most of these genetic variations are not in regions of the DNA that contain the codes for producing proteins, scientists suspected that some of these noncoding regions might have an important role in controlling the expression of genes.

Hardison's team at Penn State worked with others in the ENCODE Consortium to show, on a genome-wide scale, that many of the DNA regions that do not hold codes for proteins do, indeed, have an important role in controlling which genes are turned on and which are turned off. "Moreover, our research has made it possible to generate specific molecular hypotheses for how genetic variants in these DNA regions that control gene expression could affect the susceptibility to disease," Hardison said. "We demonstrate this process using, as an example, a locus associated with Crohn's and a few other autoimmune diseases. It is exciting to see our basic research revealing insights that help the progress of medical science, potentially facilitating a more personalized approach to medical practice."

In addition to Hardison, other Penn State scientists whose work on the ENCODE project is featured among the papers to be published on Sept. 6 include Programmer/Analyst Belinda Giardine, postdoctoral scholars Robert S. Harris and Weisheng Wu, and Professor of Biology and of Computer Science and Engineering Webb Miller.

The overall ENCODE findings bring into much sharper focus the continually active genome in which proteins routinely turn genes on and off using sites that are sometimes at great distances from the genes they regulate; where sites on a chromosome interact with each other, also sometimes at great distances; where chemical modifications of DNA influence gene expression; and where various functional forms of RNA, a form of nucleic acid related to DNA, help regulate the whole system. "The ENCODE catalog is like Google Maps for the human genome," said Elise Feingold, a program director at the National Institutes of Health National Human Genome Research Institute (NHGRI), who helped to start the ENCODE Project. "The ENCODE maps allow researchers to inspect the chromosomes, genes, functional elements and individual nucleotides in the human genome in much the same way."

"During the early debates about the Human Genome Project, researchers had calculated that only a few percent of the sequence encoded proteins, the workhorses of the cell," said Eric D. Green, director of NHGRI. "Early on, some scientists even argued that most of the genome was 'junk.' ENCODE now gives us much more appreciation of the complex molecular ballet that converts genetic information into living cells and organisms, and we can now say that there is very little, if any, junk DNA."

Hundreds of researchers in the United States, United Kingdom, Spain, Singapore and Japan performed more than 1,600 sets of experiments on 147 types of tissue with technologies standardized across the consortium. The experiments relied on innovative uses of new next-generation sequencing technologies enabled, in part, by NHGRI's technology initiative for DNA sequencing. In total, ENCODE generated more than 15-trillion bytes of raw data and its analysis consumed the equivalent of more than 300 years of computer time.

The ENCODE project received principal funding from the National Human Genome Research Institute at the National Institutes of Health. Computation was enabled, in part, through the Penn State Cyberstar Computer, funded by the National Science Foundation (grant OCI-0821527).

More information

The ENCODE Consortium placed the resulting data sets as soon as they were verified for accuracy, prior to publication, in several databases that can be freely accessed by anyone on the Internet. These data sets, as well as more information about ENCODE, are available at the ENCODE project portal http://www.encodeproject.org.

"Because the ENCODE project has generated so much data, we, together with the ENCODE Consortium, have introduced a new way to enable researchers to navigate through the data," said Magdalena Skipper, senior editor at Nature, which produced the freely available publishing platform on the Internet. Since the same topics were addressed in different ways in different papers, the new website, http://www.nature.com/encode/, will allow anyone to follow a topic through all of the papers in the ENCODE publication set in which it appears, by clicking on the relevant "thread" at the Nature ENCODE explorer page. ENCODE scientists believe this tool will illuminate many biological themes emerging from the analyses.

Story Source:

The above story is based on materials provided by Penn State. Note: Materials may be edited for content and length.

Cite This Page:

Penn State. "Huge human gene study includes Penn State University research." ScienceDaily. ScienceDaily, 5 September 2012. <www.sciencedaily.com/releases/2012/09/120905135000.htm>.
Penn State. (2012, September 5). Huge human gene study includes Penn State University research. ScienceDaily. Retrieved March 31, 2015 from www.sciencedaily.com/releases/2012/09/120905135000.htm
Penn State. "Huge human gene study includes Penn State University research." ScienceDaily. www.sciencedaily.com/releases/2012/09/120905135000.htm (accessed March 31, 2015).

Share This

More From ScienceDaily

More Health & Medicine News

Tuesday, March 31, 2015

Featured Research

from universities, journals, and other organizations

Featured Videos

from AP, Reuters, AFP, and other news services

Soda, Salt and Sugar: The Next Generation of Taxes

Soda, Salt and Sugar: The Next Generation of Taxes

Washington Post (Mar. 30, 2015) — Denisa Livingston, a health advocate for the Dinι Community Advocacy Alliance, and the Post&apos;s Abby Phillip discuss efforts around the country to make unhealthy food choices hurt your wallet as much as your waistline. Video provided by Washington Post
Powered by NewsLook.com
UnitedHealth Buys Catamaran

UnitedHealth Buys Catamaran

Reuters - Business Video Online (Mar. 30, 2015) — The $12.8 billion merger will combine the U.S.&apos; third and fourth largest pharmacy benefit managers. Analysts say smaller PBMs could also merge. Fred Katayama reports. Video provided by Reuters
Powered by NewsLook.com
S. Leone in New Anti-Ebola Lockdown

S. Leone in New Anti-Ebola Lockdown

AFP (Mar. 28, 2015) — Sierra Leone imposed a three-day nationwide lockdown Friday for the second time in six months in a bid to prevent a resurgence of the deadly Ebola virus. Duration: 01:17 Video provided by AFP
Powered by NewsLook.com
These Popular Antibiotics Can Cause Permanent Nerve Damage

These Popular Antibiotics Can Cause Permanent Nerve Damage

Newsy (Mar. 27, 2015) — A popular class of antibiotic can leave patients in severe pain and even result in permanent nerve damage. 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.


Breaking News:

More Coverage

Human Genome Far More Active Than Thought: GENCODE Consortium Discovers Far More Genes Than Previously Thought

Sep. 5, 2012 — The GENCODE Consortium expects the human genome has twice as many genes than previously thought, many of which might have a role in cellular control and could be important in human disease. This ... read more

Comprehensive Transcriptome Analysis of Human ENCODE Cells

Sep. 5, 2012 — ENCODE, an international research project led by the National Human Genome Research Institute (NHGRI), has produced and analyzed 1649 data sets designed to annotate functional elements of the entire ... read more

Fast Forward for Biomedical Research: Massive DNA Encyclopedia Scraps the Junk

Sep. 5, 2012 — Today, an international team of researchers reveal that much of what has been called 'junk DNA' in the human genome is actually a massive control panel with millions of switches regulating ... read more

UMASS Medical School Faculty Annotate Human Genome for ENCODE Project

Sep. 5, 2012 — The first comprehensive decoding and annotation of the human genome is being published today by the ENCyclopedia Of DNA Elements (ENCODE) project, an international consortium of scientists from 32 ... read more

UC Santa Cruz Provides Access to Encyclopedia of the Human Genome

Sep. 5, 2012 — The ENCODE project has enabled scientists to assign specific functions for 80 percent of the human genome, providing new insights into the mechanisms of gene regulation and giving biomedical ... read more

Yale Team Finds Order Amidst the Chaos Within the Human Genome

Sep. 5, 2012 — The massive Encyclopedia of DNA Elements (ENCODE) unveiled Sept. 5 reveals a human genome vastly more rich and complex than envisioned even a decade ago. In a key supporting paper published in the ... read more

First Holistic View of How Human Genome Actually Works: ENCODE Study Produces Massive Data Set

Sep. 5, 2012 — The Human Genome Project produced an almost complete order of the 3 billion pairs of chemical letters in the DNA that embodies the human genetic code -- but little about the way this blueprint works. ... read more

Biochemical Functions for Most of Human Genome Identified: New Map Finds Genetic Regulatory Elements Account for 80 Percent of Our DNA

Sep. 5, 2012 — Only about 1 percent of the human genome contains gene regions that code for proteins, raising the question of what the rest of the DNA is doing. Scientists have now begun to discover the answer: ... read more

Allegedly Useless Parts of the Human Genome Fulfil Regulatory Tasks

Sep. 7, 2012 — Heidelberg scientists contribute to the encyclopedia of all functional DNA elements in the human ... read more

Strange & Offbeat Stories


Health & Medicine

Mind & Brain

Living & Well

In Other News

... from NewsDaily.com

Science News

Health News

Environment News

Technology News


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