Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Which came first, the chicken genome or the egg genome?

10.10.2007
Researchers have answered a similarly vexing (and far more relevant) genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates?

The answers, published online by Nature Genetics on October 7, 2007, provide the first evolutionary history of the duplications in the human genome that are partly responsible for both disease and recent genetic innovations. This work marks a significant step toward a better understanding of what genomic changes paved the way for modern humans, when these duplications occurred and what the associated costs are – in terms of susceptibility to disease-causing genetic mutations.

Genomes have a remarkable ability to copy a long stretch of DNA from one chromosome and insert it into another region of the genome. The resulting chunks of repeated DNA – called “segmental duplications” – hold many evolutionary secrets and uncovering them is a difficult biological and computational challenge with implications for both medicine and our understanding of evolution.

The new evolutionary history, published in Nature Genetics, is from an interdisciplinary team led by biologist Evan Eichler from the University of Washington School of Medicine and computer scientists Pavel Pevzner from University of California, San Diego.

In the past, the highly complex patterns of DNA duplication – including duplications within duplications – have prevented the construction of an evolutionary history of these long DNA duplications.

To crack the duplication code and determine which of the DNA segments are originals (ancestral duplications) and which are copies (derivative duplications), the researchers looked to both algorithmic biology and comparative genomics.

“Identifying the original duplications is a prerequisite to understanding what makes the human genome unstable,” said Pavel Pevzner a UCSD computer science professor who modified an algorithmic genome assembly technique in order to deconstruct the mosaics of repeated stretches of DNA and identify the original sequences. “Maybe there is something special about the originals, some clue or insight into what causes this colonization of the human genome,” said Pevzner.

“This is the first time that we have a global view of the evolutionary origin of some of the most complicated regions of the human genome,” said paper author Evan Eichler, a professor from the University of Washington School of Medicine and the Howard Hughes Medical Institute.

The researchers tracked down the ancestral origin of more than two thirds of these long DNA duplications. In the Nature Genetics paper they highlight two big picture findings.

First, the researchers suggest that specific regions of the human genome experienced elevated rates of duplication activity at different times in our recent genomic history. This contrasts with most models of genomic duplication which suggest a continuous model for recent duplications.

Second, the researchers show that a large fraction of the recent duplication architecture centers around a rather small subset of “core duplicons” – short segments of DNA that come together to form segmental duplications. These cores are focal points of human gene/transcript innovations.

“We found that not all of the duplications in the human genome are created equal. Some of them – the core duplicons – appear to be responsible for recent genetic innovations the in human genome,” explained Pevzner, who is the director of the UCSD Center for Algorithmic and Systems Biology, located at the UCSD division of Calit2.

The authors uncovered 14 such core duplicons.
“We note that in 4 of the 14 cases, there is compelling evidence that genes embedded within the cores are associated with novel human gene innovations. In two cases the core duplicon has been part of novel fusion genes whose functions appear to be radically different from their antecedents,” the authors write in their Nature Genetics paper.

“The results suggest that the high rate of disease caused by these duplications in the normal population – estimated at 1/500 and 1/1000 events per birth – may be offset by the emergence of newly minted human/great-ape specific genes embedded within the duplications. The next challenge will be determining the function of these novel genes," said Eichler.

To reach these insights, the researchers worked to systematically pinpoint the ancestral origin of each human segmental duplication and organized duplication blocks based on their shared evolutionary history.

Pevzner and his associate Haixu Tang (now professor at University of Indiana) applied their expertise in assembling genomes from millions of small fragments – a problem that is not unlike the “mosaic decomposition” problem in analyzing duplications that the team faced.

Over the years, Pevzner has applied the 250-year old algorithmic idea first proposed by 18th century mathematician Leonhard Euler (of the fame of pi) to a variety of problems and demonstrated that it works equally well for a set of seemingly unrelated biological problems including DNA fragment assembly, reconstructing snake venoms, and now dissecting the mosaic structure of segmental duplications.

In the future, the researchers plan to continue their exploration of evolution.

“We want to figure out how the human genome evolved. In the future, we will combine what we know about the evolution within genomes with comparative genomics in order to extend our view of evolution,” said Pevzner.

Daniel Kane | EurekAlert!
Further information:
http://www.ucsd.edu
http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng.2007.9.html

Further reports about: DNA Evolution Genetics Nature Original Pevzner duplicon genomic human genome innovations

More articles from Life Sciences:

nachricht Unique genome architectures after fertilisation in single-cell embryos
30.03.2017 | IMBA - Institut für Molekulare Biotechnologie der Österreichischen Akademie der Wissenschaften GmbH

nachricht Transport of molecular motors into cilia
28.03.2017 | Aarhus University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: A Challenging European Research Project to Develop New Tiny Microscopes

The Institute of Semiconductor Technology and the Institute of Physical and Theoretical Chemistry, both members of the Laboratory for Emerging Nanometrology (LENA), at Technische Universität Braunschweig are partners in a new European research project entitled ChipScope, which aims to develop a completely new and extremely small optical microscope capable of observing the interior of living cells in real time. A consortium of 7 partners from 5 countries will tackle this issue with very ambitious objectives during a four-year research program.

To demonstrate the usefulness of this new scientific tool, at the end of the project the developed chip-sized microscope will be used to observe in real-time...

Im Focus: Giant Magnetic Fields in the Universe

Astronomers from Bonn and Tautenburg in Thuringia (Germany) used the 100-m radio telescope at Effelsberg to observe several galaxy clusters. At the edges of these large accumulations of dark matter, stellar systems (galaxies), hot gas, and charged particles, they found magnetic fields that are exceptionally ordered over distances of many million light years. This makes them the most extended magnetic fields in the universe known so far.

The results will be published on March 22 in the journal „Astronomy & Astrophysics“.

Galaxy clusters are the largest gravitationally bound structures in the universe. With a typical extent of about 10 million light years, i.e. 100 times the...

Im Focus: Tracing down linear ubiquitination

Researchers at the Goethe University Frankfurt, together with partners from the University of Tübingen in Germany and Queen Mary University as well as Francis Crick Institute from London (UK) have developed a novel technology to decipher the secret ubiquitin code.

Ubiquitin is a small protein that can be linked to other cellular proteins, thereby controlling and modulating their functions. The attachment occurs in many...

Im Focus: Perovskite edges can be tuned for optoelectronic performance

Layered 2D material improves efficiency for solar cells and LEDs

In the eternal search for next generation high-efficiency solar cells and LEDs, scientists at Los Alamos National Laboratory and their partners are creating...

Im Focus: Polymer-coated silicon nanosheets as alternative to graphene: A perfect team for nanoelectronics

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are less stable. Now researchers at the Technical University of Munich (TUM) have, for the first time ever, produced a composite material combining silicon nanosheets and a polymer that is both UV-resistant and easy to process. This brings the scientists a significant step closer to industrial applications like flexible displays and photosensors.

Silicon nanosheets are thin, two-dimensional layers with exceptional optoelectronic properties very similar to those of graphene. Albeit, the nanosheets are...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

International Land Use Symposium ILUS 2017: Call for Abstracts and Registration open

20.03.2017 | Event News

CONNECT 2017: International congress on connective tissue

14.03.2017 | Event News

ICTM Conference: Turbine Construction between Big Data and Additive Manufacturing

07.03.2017 | Event News

 
Latest News

'On-off switch' brings researchers a step closer to potential HIV vaccine

30.03.2017 | Health and Medicine

Penn studies find promise for innovations in liquid biopsies

30.03.2017 | Health and Medicine

An LED-based device for imaging radiation induced skin damage

30.03.2017 | Medical Engineering

VideoLinks
B2B-VideoLinks
More VideoLinks >>>