Nav: Home

A prickly subject: The sea urchin genome is sequenced

November 09, 2006

BAR HARBOR, MAINE -- Nov. 9, 2006 Who would have guessed that the lowly sea urchin, that brain-less, limb-less porcupine of the sea, would be the star of a multi-million dollar, worldwide effort to map out every letter of its genetic code? Or that the information gathered in that effort may eventually lead to new treatments for cancer, infertility, blindness, and diseases like muscular dystrophy and Huntington's Disease?

James Coffman, Ph.D., of the Mount Desert Island Biological Laboratory in Bar Harbor was one of the scientists who helped decode the 814 million pairs of nucleotide bases in the sea urchin's chromosomes. The Human Genome Sequencing Center at Baylor College of Medicine in Texas led the project and announced the completion of the three-year project today. Having the complete genome, Coffman says, "makes doing research on urchins so much easier."

Why would anyone want to do biomedical research on sea urchins? According to Coffman, sea urchins are remarkably similar to humans in many ways, sharing most of the same gene families, and yet differ in a few critical areas besides the obvious physical ones. For one thing, sea urchins have a "extraordinarily complex innate immune system" which is not based on antibodies, like that of jawed vertebrates, but is effective enough to give sea urchins a surprisingly long life span of up to a hundred years or more.

Innate immunity refers to a set of proteins that are "hard wired" to detect unique aspects of bacteria and signal to an organism's cells that there is an intruder. The rich repertoire of such proteins in sea urchins could end up providing new tools for use against infectious diseases.

Sea urchins are also extremely good at dealing with potential chemical threats in their environment through a "defensome" - a group of genes which can sense and then transform and eliminate threats from potentially toxic chemicals. Without this sophisticated response, these chemicals, including heavy metals, can lead to aging, illness and death, so it would be valuable to learn how sea urchins defend themselves against them.

In terms of evolution, sea urchins are in an interesting position between vertebrates and invertebrates. "The sea urchin fills a large evolutionary gap in sequenced genomes," said George Weinstock, Ph.D., co-director of the sea urchin sequencing project. Being more closely related to humans than other invertebrates such as flies and worms, "it allows us to see what went on in evolution after the split between the ancestors that gave rise to humans and insects. The sea urchin genome provided plenty of unexpected rewards and was a great choice for sequencing."

In the 1990s, sea urchins became a valuable fishery in Maine, but their stocks were quickly depleted. Linda Mercer, Director of the Bureau of Resource Management at Maine's Department of Marine Research, welcomed the news of the project's completion: "We are certainly interested in reestablishing the sea urchin population along the Maine coast, and any research that can continue to improve our understanding of sea urchin biology would be helpful."

The DNA that was sequenced came from a male California purple sea urchin, not one of the green sea urchins that live in Maine waters. Purple urchins are found along the west coast from Baja to Alaska, whereas the green ones, close relatives of the purple, are found in cold Northern waters on both the east and west coasts.

All sea urchins, however, have round shells covered with spines. Like the other members of the phylum Echinodermata, which includes starfish and sea cucumbers, they have fivefold symmetry and move by means of hundreds of tiny, adhesive "tube feet." They eat algae with a mouth surrounded by five teeth on the bottom of their shell and excrete through a hole at the top.

The sea urchin has long had a strong fan base among scientists. One reason it was chosen for the genome-sequencing project is the size of the sea urchin research community. Over 140 laboratories are using sea urchins as a primary research organism. Annotation of the sequenced genome was conducted by 240 scientists in 11 countries.

In fact, it was research conducted on sea urchins over a hundred years ago that led to one of the breakthroughs of modern biology, when Theodor Boveri discovered in 1902 that normal development requires that every cell in an embryo have a full set of chromosomes carrying the genetic or inherited material for an organism.

One reason sea urchins have been so popular with scientists is that they are easy to work with. They can live in a laboratory comfortably, release their eggs readily, and have transparent embryos. That makes it easy to observe their fertilization and development, which is surprisingly similar to human embryonic development in some ways. As Dr. Coffman says, "Studying gene function and regulation in early sea urchin embryos is relatively easy compared with other model organisms such as mice, and much faster."

Sea urchins are also incredibly fecund. A single female discharges millions of eggs. In fact, most of an urchin's body mass consists of its reproductive organs, and that's what people are consuming when they eat the "roe" from a sea urchin.

At first glance, sea urchins seem to be inanimate, although people who have been around sea urchins know that the spines will move quickly in reaction to a light touch. The genome project, however, revealed that urchins have genes encoding some of the same sensory proteins involved in vision and hearing in humans. Yet the sea urchin has no eyes and ears, at least as we know them. Some of the visual sensory proteins are localized to an appendage known as the tube foot, and probably function in sensory processes there.

"The sea urchin reminds us of the underlying unity of all life on earth," notes Erica Sodergren, Ph.D., co-leader of the sequencing project. At MDIBL, Dr. Coffman is hoping to exploit that unity to ultimately find new treatments for human diseases and is studying a sea urchin member of one of those shared families of genes known as the "Runx" genes. In vertebrates this family of genes is known to be important for developmental processes such as bone and blood formation, and its mutations are associated with bone disorders and a common form of childhood leukemia.

Now that the sea urchin's genome has been sequenced, Dr. Coffman's work should progress more quickly. "It's incredible," he says. "It's hard for me to imagine not having a genome now."
-end-
The Mount Desert Island Biological Laboratory, founded in 1898, is one of the leading marine research institutions in the world. The nonprofit, independent research institution has a three-fold mission: to promote research and education in the biology of marine organisms; to foster understanding and preservation of the environment; and to advance human health.

Mount Desert Island Biological Laboratory

Related Genome Articles:

A close look into the barley genome
An international consortium, with the participation of the Helmholtz Zentrum München, Plant Genome and Systems Biology Department (PGSB), has published methodologically significant data on the barley genome.
Barley genome sequenced
Looking for a better beer or single malt Scotch whiskey?
From Genome Research: Pathogen demonstrates genome flexibility in cystic fibrosis
Chronic lung infections can be devastating for patients with cystic fibrosis (CF), and infection by Burkholderia cenocepacia, one of the most common species found in cystic fibrosis patients, is often antibiotic resistant.
A three-dimensional map of the genome
Cells face a daunting task. They have to neatly pack a several meter-long thread of genetic material into a nucleus that measures only five micrometers across.
Rhino genome results
A study by San Diego Zoo Global reveals that the prospects for recovery of the critically endangered northern white rhinoceros -- of which only three individuals remain -- will reside with the genetic resources that have been banked at San Diego Zoo Global's Frozen Zoo®.
Science and legal experts debate future uses and impact of human genome editing in Gender & the Genome
Precise, economical genome editing tools such as CRISPR have made it possible to make targeted changes in genes, which could be applied to human embryos to correct mutations, prevent disease, or alter traits.
Genome: It's all about architecture
How do pathogens such as bacteria or parasites manage to hide from their host's immune system?
Accelerating genome analysis
An international team of scientists, led by researchers from A*STAR's Genome Institute of Singapore and the Bioinformatics Institute, have developed SIFT 4G (SIFT for Genomes) -- a software that can lead to faster genome analysis.
Packaging and unpacking of the genome
Single-cell techniques have been used to investigate histone replacement and chromatin remodeling in developing oocytes.
The astounding genome of the dinoflagellate
Dinoflagellates live free-floating in the ocean or symbiotically with corals, serving up -- or as -- lunch to a host of mollusks, tiny fish and coral species.

Related Genome Reading:

Genome (The Extinction Files Book 2)
by A.G. Riddle (Author)

The thrilling conclusion to THE EXTINCTION FILES is finally here!

* * *

A code hidden in the human genome...
Will reveal the ultimate secret of human existence.
And could hold humanity's only hope of survival.


* * *


In 2003, the first human genome was sequenced. But the secrets it held were never revealed.

The truth was discovered thirty years ago, almost by accident. Dr. Paul Kraus had spent his entire career searching for what he called humanity's lost tribes--human ancestors who had gone extinct. When... View Details


Genome: The Autobiography of a Species in 23 Chapters
by Matt Ridley (Author)

The genome's been mapped.
But what does it mean?

Arguably the most significant scientific discovery of the new century, the mapping of the twenty-three pairs of chromosomes that make up the human genome raises almost as many questions as it answers. Questions that will profoundly impact the way we think about disease, about longevity, and about free will. Questions that will affect the rest of your life.

Genome offers extraordinary insight into the ramifications of this incredible breakthrough. By picking one newly discovered gene from each pair of chromosomes and... View Details


The Mysterious World of the Human Genome
by Frank Ryan (Author)

The human genome is indeed a mysterious world, but, as this fascinating book shows, its vital secrets are now being uncovered. The latest studies are revealing exciting new discoveries, such as how the DNA and related chemical compounds in our cells work together to direct the processes of life. Scientists are not only unraveling how life evolved in the ancient past, but are also finding the keys to creating a healthier future.  

How does the minuscule chemical cluster in each of our 100 trillion cells accomplish the amazing feat of creating and maintaining our bodies? Frank Ryan, a... View Details


Adam and the Genome: Reading Scripture after Genetic Science
by Scot McKnight (Author), Dennis R. Venema (Author), Daniel Harrell (Afterword), Tremper Longman III (Afterword)

Genomic science indicates that humans descend not from an individual pair but from a large population. What does this mean for the basic claim of many Christians: that humans descend from Adam and Eve?
Leading evangelical geneticist Dennis Venema and popular New Testament scholar Scot McKnight combine their expertise to offer informed guidance and answers to questions pertaining to evolution, genomic science, and the historical Adam. Some of the questions they explore include:

- Is there credible evidence for evolution?
- Do we descend from a population or are we the offspring of... View Details


The Gene: An Intimate History
by Siddhartha Mukherjee (Author)

THE #1 NEW YORK TIMES BESTSELLER
A New York Times Notable Book
A Washington Post and Seattle Times Best Book of the Year


From the Pulitzer Prize-winning author of The Emperor of All Maladies—a fascinating history of the gene and “a magisterial account of how human minds have laboriously, ingeniously picked apart what makes us tick” (Elle).

“Dr. Siddhartha Mukherjee dazzled readers with his Pulitzer Prize-winning The Emperor of All Maladies in 2010. That achievement was evidently just a warm-up for... View Details


Genomes 4
by T. A. Brown (Author)

Genomes 4 has been completely revised and updated. It is a thoroughly modern textbook about genomes and how they are investigated. As with Genomes 3, techniques come first, then genome anatomies, followed by genome function, and finally genome evolution.  The genomes of all types of organism are covered: viruses, bacteria, fungi, plants, and animals including humans and other hominids.

Genome sequencing and assembly methods have been thoroughly revised including a survey of four genome projects: human, Neanderthal, giant panda, and barley. Coverage of... View Details


Genome: The Autobiography of a Species in 23 Chapters (P.S.) 1st (first) edition
by Matt Ridley (Author)

View Details


The Genome: A Novel
by Sergei Lukyanenko (Author)

A science fiction thriller by the author of Night Watch, the hit novel that inspired two major motion pictures

Five months after the horrific accident that left him near death and worried that he’d never fly again, master-pilot Alex Romanov lands a new job: captaining the sleek passenger vessel Mirror. Alex is a spesh—a human who has been genetically modified to perform particular tasks. As a captain and pilot, Alex has a genetic imperative to care for passengers and crew—no matter what the cost.

His first mission aboard Mirror is to... View Details


Neanderthal Man: In Search of Lost Genomes
by Svante Pääbo (Author)

"[T]his book is a vibrant testimonial to what might be the greatest creation of modern humans: the scientific method." --Salon

Neanderthal Man tells the story of geneticist Svante Pääbo's mission to answer this question: what can we learn from the genomes of our closest evolutionary relatives? Beginning with the study of DNA in Egyptian mummies in the early 1980s and culminating in the sequencing of the Neanderthal genome in 2010, Neanderthal Man describes the events, intrigues, failures, and triumphs of these scientifically rich years through the lens of... View Details


The Developing Genome: An Introduction to Behavioral Epigenetics
by David S. Moore (Author)

Why do we grow up to look, act, and feel as we do? Through most of the twentieth century, scientists and laypeople answered this question by referring to two factors alone: our experiences and our genes. But recent discoveries about how genes work have revealed a new way to understand the developmental origins of our characteristics. These discoveries have emerged from the new science of behavioral epigenetics--and just as the whole world has now heard of DNA, "epigenetics" will be a household word in the near future.

Behavioral epigenetics is important because it explains how our... View Details

Best Science Podcasts 2017

We have hand picked the best science podcasts for 2017. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Simple Solutions
Sometimes, the best solutions to complex problems are simple. But simple doesn't always mean easy. This hour, TED speakers describe the innovation and hard work that goes into achieving simplicity. Guests include designer Mileha Soneji, chef Sam Kass, sleep researcher Wendy Troxel, public health advocate Myriam Sidibe, and engineer Amos Winter.
Now Playing: Science for the People

#448 Pavlov (Rebroadcast)
This week, we're learning about the life and work of a groundbreaking physiologist whose work on learning and instinct is familiar worldwide, and almost universally misunderstood. We'll spend the hour with Daniel Todes, Ph.D, Professor of History of Medicine at The Johns Hopkins University, discussing his book "Ivan Pavlov: A Russian Life in Science."