Posts Tagged ‘human genome sequencing’

3-D Mapping of the Human Genome

 :: Posted by American Biotechnologist on 01-04-2012

In the beginning, scientists sequenced the human genome. And the human genome was good…but not good enough.

Next came epigenetics. And epigenetics was also good. But not good enough.

And then scientists thought very hard and invented a technology for producing three-dimensional genome structures. And three-dimensional structures was good. Very good.

In a Nature Biotechnology article published December 25th, 2011, a team of scientists from the University of Southern California, described a method for genome-wide mapping of chromatin interactions known as tethered conformation capture (TCC). The method performs ligations on solid substrates rather than in solution, which helps facilitate a detailed analysis of interactions within and between chromosomes. The team then developed a computational method to translate the TCC data into physical chromatin contacts in a population of three-dimensional genome structures.

Understanding the structure of the genome is crucial to understanding its function as a whole, said Lin Chen, professor of molecular biology at the USC Dornsife College of Letters, Arts and Sciences.

“Everything biological works in the three dimensions,” Chen said. “Therefore, to understand it completely, you have to understand it three-dimensionally.”

By analyzing the differences and similarities in genome structure between various cells, scientists are able to discern what basic principles of 3-D organization are. In addition, the structure allows scientists to see where each gene is located relative to any other gene and how this arrangement is important to cellular functions.

Thanks to USC for contributing to this story.

A user’s guide to the encyclopedia of DNA elements

 :: Posted by American Biotechnologist on 04-21-2011

The international team of the ENCODE, or Encyclopedia Of DNA Elements project, has created an overview of its ongoing large-scale efforts to interpret the human genome sequence.

The April 19 publication of “A User’s Guide to the Encyclopedia of DNA Elements (ENCODE)” in the journal PLoS Biology provides a guide for using the vast amounts of high-quality data and resources produced so far by the project. All of the data, tools to study them, and the paper itself are freely available through multiple websites accessible through encodeproject.org.

“This project requires collaboration from multiple people all over the world at the cutting edge of their fields, working in a coordinated manner to figure out the function of our human genome,” said Dr. Richard Myers, president and director of the HudsonAlpha Institute for Biotechnology and one of the 25 principal investigators of the project. “The importance extends beyond basic knowledge of who and what we are as humans and into understanding of human health and disease.”

The publication demonstrates how ENCODE data can be immediately useful in interpreting associations between single nucleotides and disease, using examples such as the c-Myc gene and cancer. Similar studies are now possible for the thousands of variants identified in genome-wide association studies, addressing mechanistic questions of susceptibility to disease.

Dr. Ewan Birney, senior scientist at the European Bioinformatics Institute and another principal investigator, commented “We knew four years ago, from our publication of ENCODE techniques on 1 percent of the genome, that we had an unprecedented view of how biology works on those regions. By extending our work to the entire genome, we see the immediate impact on the interpretation of noncoding variants identified in genome-wide association studies. These studies are disease-driven but have not always yielded clear next steps, and ENCODE data provide those scientists with some new paths to follow.”

Scientists with the ENCODE Project are applying up to 20 different tests in 108 commonly used cell lines to compile these important data. The current paper not only tells how to find the data, but also explains how to apply the data to interpret the human genome.

One can think of determining the human DNA sequence alone as finding a new language, but without a key to interpret the letters within. The ENCODE project adds data such as where RNA is produced from our DNA, where proteins bind to DNA, and where parts of our DNA are augmented by additional chemical markers. These proteins and chemical additions are keys to understanding how different cells within our bodies are interpreting the language of DNA.

Source: HudsonAlpha via EurekAlert

Epigenetics for friends and family

 :: Posted by American Biotechnologist on 02-09-2011

I often find it difficult explaining to friends and family exactly what I do in the lab. In fact, before I started my graduate work, concepts such as DNA, protein, electrophoresis and gene transfer all seemed to esoteric and foreign. That’s why, whenever I come across an article or video that helps clarify our field of work to the layman, I am inclined to share.

In honor of the 10 year anniversary of the sequencing of the human genome, Joe Kloc of Mother Jones has put together a simple yet elegant explanation of epigenetics.

Check it out by clicking on The Illustrated Guide to Epigenetics.