Category Archives: Genome

Quinoa is harvested in the highlands in Puno region, south-eastern Peru. The crop could help improve global food security. Photograph: ICT/Tomas Munita

The near-complete genome of quinoa was unveiled on Wednesday by scientists who say the grain cultivated centuries ago by Incas in the Andes could help feed a hungry world.

Quinoa is incredibly resilient, and can grow in poor or salty soils, said Mark Tester, a professor at King Abdullah University of Science and Technology in Saudi Arabia and leader of the consortium of scholars that decoded the plants genome.

It could provide a healthy, nutritious food source for the world using land and water that currently cannot be used.

Other major crop plants have been bred for centuries or, more recently, genetically modified to combine optimal traits to boost yield and bolster resistance to pests and climate change. Now, scientists can delve into the quinoa genome as well.

Quinoa has great potential to enhance global food security, Tester said.

The grain thrives at any altitude up to 4,000 metres (13,000 feet) above sea level, in conditions that would leave most food plants struggling. Some strains grow well at temperatures up to 38 degrees.

Best known outside its native region as a health food, quinoa is gluten-free and contains essential amino acids, fibre, vitamins and minerals.

It also scores lower than other crops on the glycaemic index, a measure of how quickly foods raise blood sugar levels a major concern for those with diabetes.

Yet global consumption remains incidental compared with wheat, rice, barley or corn less than 100,000 tonnes a year compared with hundreds of millions of tonnes for each of the other major grains and cereals.

One problem with quinoa is that the plant naturally produces bitter-tasting seeds, Tester explained. The bitterness a natural defence against birds and other pests comes from chemical compounds called saponins. The process for removing these chemicals is labour-intensive and costly, and requires ample use of water.

Another constraint is that quinoa plants tends to have small seed heads and long stalks that can collapse in strong wind or heavy rain.

Despite its agronomic potential, quinoa is still an underutilised crop, with relatively few active breeding programmes, Tester and three dozen colleagues wrote in the journal Nature.

First grown by humans thousands of years ago in the high plateau around Lake Titicaca in the Andes, quinoa is still barely domesticated, the researchers said.

Testers team has already pinpointed genes, including one that controls the production of saponins, that could be altered through breeding or gene editing to enhance quality and yields.

With this new knowledge of quinoa DNA, we can quickly and easily select plants that do not produce bitter substances in the breeding process, said co-author Robert van Loo, a scientist at Wageningen University and Research Centre in the Netherlands. South American varieties could probably be made sweeter with a single gene change, he added.

Most quinoa is grown in three Andean countries: Peru, Ecuador and Bolivia.

The United States and Canada account for nearly 70% of exports, followed by France, the Netherlands and Germany. The price of quinoa has nearly tripled in recent years due to increased demand.

If printed, the sequence of letters corresponding to the quinoa genome comprised of 1.3bn molecular building blocks would take up 500,000 pages.

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Quinoa genome unveiled in search for hardy crop to feed world ... - The Guardian

February 8, 2017 The sequencing of the first high-quality quinoa genome by a KAUST-led research team could one day help transform our ability to feed the world's growing population. Credit: 2017 KAUST Linda Polik

An international team of scientists, including quinoa breeding experts from Wageningen University & Research, published the complete DNA sequence of quinoa the food crop that is conquering the world from South America in Nature magazine on 8 February 2017. Quinoa is rich in essential amino acids and nutritional fibres and does not contain gluten. The crop is important to farmers as it provides a reasonable yield even on poor soils. The new knowledge about quinoa DNA is already being used by breeders who are developing quinoa varieties which grow well in saline soil and still meet the taste requirements of consumers.

The scientists determined the sequence of the DNA-building blocks of the entire quinoa genome. The total length of the DNA, the 'genome', consists over a little over 1.3 billion DNA building blocks (the nucleotides A, C, G or T), divided over 18 chromosomes. Printed on paper this would add up to over 500,000 pages of text.

To map the DNA building blocks, the scientists used a smart combination of various DNA sequencing techniques. While this enabled them to put together ever-larger DNA segments in the computer from the huge amount of DNA information available, it did not lead to the 18 segments which represent the 18 chromosomes. The scientists therefore applied genetic maps that were made by crossbreeding plants to determine how molecular markers were inherited by the offspring. This allowed them to place most of the DNA on 18 large DNA-strains, representing the quinoa chromosomes.

According to Robert van Loo, expert in quinoa breeding at Wageningen University & Research, it was this combination that allowed the scientists to clearly map the DNA. "We were able to determine the location on the chromosome of no less than 85% of the DNA-sequence. This is a major benefit for plant breeders."

Van Loo and his colleagues will be using the new knowledge in various ways, including the development of quinoa varieties which meet the demands of both consumers and farmers. Van Loo: "For example, we discovered mutations which ensure that certain quinoa varieties cannot produce bitter tasting saponins. These 'sweet' varieties do not need to be polished to remove the bitter substances, saving some 15 to 20 per cent. With the new knowledge of quinoa DNA, we can quickly and easily select plants that do not produce bitter substances in the breeding process."

In the future, scientists can probably ensure that specific varieties such as those that are well adapted to the cultivation conditions in a specific region do not produce bitter substances.

"Gene directed mutation breeding could be a good approach in this regard, with varieties that have already proven their value regionally being the starting point," says Van Loo. "The varieties which are currently being grown in South America can probably be made sweet with one specific mutation."

The research was led by the King Abdullah University of Science and Technology in Saudi Arabia, a region with difficult growth conditions for plants and with many poor or even saline soils. Wageningen University & Research provided DNA sequencing experts and breeding scientists to contribute to the research. It was this Wageningen team that made the genetic maps on which the gene which regulates the production of saponin (bitter substance) was found.

Ancient civilisations in the Andes already used quinoa as an important food crop. It faded into the background with the arrival of the Spanish, however, which is why quinoa was never truly 'domesticated' despite being such a good and healthy food crop.

One of the properties that makes quinoa less attractive is the presence of bitter substances on the outside of the seeds. Known as saponins, these substances can be removed from the seeds although the process costs time, money and water. Wageningen University & Research has already developed four varieties without bitter substances since the 1990s.

Quinoa is part of a plant family known for its growing power in extreme conditions, such as in poor soils, at high altitudes and even in saline soils. There are already various quinoa varieties which produce food in places where other food crops, such as wheat and rice, have very poor yields. As a result, quinoa is seen as a crop that can help produce extra food with fewer inputs of water and fertiliser. The new knowledge of the DNA will accelerate the development of extra sustainable quinoa varieties which also meet other demands from farmers and consumers alike.

Explore further: Bitter chemical coating leads to quinoa success

More information: The genome of Chenopodium quinoa, Nature, nature.com/articles/doi:10.1038/nature21370

Journal reference: Nature

Provided by: Wageningen University

The challenge posed by removing a chemical compound from their 'superfood' crop to create a market for WA quinoa led three innovative farmers to build Australia's largest quinoa processing plant in the state's south-west.

To the south of Nash Huber's farm fields are the Olympic Mountains, peaking at nearly 8,000 feet. Due north is the end of a channel of Pacific Ocean waters that separate the United States from Canada.

(HealthDay)The grain quinoa seems safe for people with celiac disease, a new British study suggests.

Consumers can't get enough of the superfood quinoa, healthy grains which originate from and thrive in South America. Wageningen UR has developed three varieties that also do well elsewhere in the world.

Algae is evolving as the next new alternative protein source consumers are anxious to bite into as an ingredient in crackers, snack bars, cereals and breads, according to a July 12th presentation at IFT15: Where Science Feeds ...

The capacity to feed the world's growing population will be greatly improved by developing crops able to tolerate higher soil salinity and salt water irrigation. Researchers at King Abdullah University of Science and Technology ...

An international team of scientists, including quinoa breeding experts from Wageningen University & Research, published the complete DNA sequence of quinoa the food crop that is conquering the world from South America ...

Scientists studying oysters along the Atlantic Coast have discovered a critical clue to understanding why more seafood lovers are getting sick from eating shellfish.

The flashlight fish uses bioluminescent light to detect and feed on its planktonic prey, according to a study published February 8, 2017 in the open-access journal PLOS ONE by Jens Hellinger from Ruhr-University, Bochum, ...

An investigation into the evolution of human walking by looking at how chimpanzees walk on two legs is the subject of a new research paper published in the March 2017 issue of Journal of Human Evolution.

A compound extracted from a deep-water marine sponge collected near the Bahamas is showing potent antibacterial activity against the drug resistant bacteria methicillin-resistant Staphylococcus aureus (MRSA). Also called ...

A group of insects that mimic each other in an effective golden sheen to fight predators has been discovered as the largest in Australia, a collaboration between Masaryk University and Macquarie University researchers has ...

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When Chimeras of Animals can be made, why not mix it up with various food crops?

GM plants owned by big corp is the furthest thing from food security.

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Quinoa genome accelerates solutions for food security (Update) - Phys.Org

The mysterious majority as much as 98 percent of our DNA do not code for proteins. Much of this dark matter genome is thought to be nonfunctional evolutionary leftoversHowever, hidden among this noncoding DNA are many crucial regulatory elements that control the activity of thousands of genes.

[In an] effort to fully map and annotatethe human genome, including this silent majority, the National Institutes of Health (NIH)announced new grant funding for a nationwide project to set up five characterization centersto study how these regulatory elements influence gene expression andcell behavior.

By cataloging the functions of thousands of regulatory sequences, [researchers] hope to develop rules about how to predict and interpret other sequences functions. This would not only help illuminate the rest of the dark matter genome, it could also reveal new treatment targets for complex genetic diseases.

A lot of human diseases have been found to be associated with regulatory sequences, said [Nadav Ahituv, a professor of bioengineering at UC San Francisco]. For example, in genome-wide association studies for common diseases, such as diabetes, cancer and autism, 90 percent of the disease-associated DNA variants are in the noncoding DNA. So its not a gene thats changed, but what regulates it.

The GLP aggregated and excerpted this blog/article to reflect the diversity of news, opinion, and analysis. Read full, original post:The mysterious 98%: Scientists look to shine light on the dark genome

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'Dark genome' could yield answers to complex genetic diseases - Genetic Literacy Project

Genomes in flux: New study reveals hidden dynamics of bird and mammal DNA evolution Science Daily But in some instance it might be more appropriate to call it an overhaul. Over the past 100 million years, the human lineage has lost one-fifth of its DNA, while an even greater amount was added, report scientists. Until now, the extent to which our ...

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Genomes in flux: New study reveals hidden dynamics of bird and mammal DNA evolution - Science Daily

February 6, 2017 Credit: NIH

Evolution is often thought of as a gradual remodeling of the genome, the genetic blueprints for building an organism. But in some instance it might be more appropriate to call it an overhaul. Over the past 100 million years, the human lineage has lost one-fifth of its DNA, while an even greater amount was added, report scientists at the University of Utah School of Medicine. Until now, the extent to which our genome has expanded and contracted had been underappreciated, masked by its relatively constant size over evolutionary time.

Humans aren't the only ones with elastic genomes. A new look at a virtual zoo-full of animals, from hummingbirds to bats to elephants, suggests that most vertebrate genomes have the same accordion-like properties.

"I didn't expect this at all," says the study's senior author Cdric Feschotte, Ph.D., professor of human genetics. "The dynamic nature of these genomes had remained hidden because of the remarkable balance between gain and loss."

Previous research had shown that genome sizes vary widely across different species of insects or plants, a telltale sign of fluctuation. This survey is the first to compare a diverse array of warm-blooded vertebrates, 10 mammals and 24 birds altogether. The study appears online in Proceedings of the National Academies of Sciences (PNAS) during the week of Feb. 6.

Trimming for Takeoff

When evolution repeats itself, there's usually a good reason. For most vertebrates it's not immediately apparent why genome deletions and add-ons typically go hand-in-hand. For flying animals, however, there could be a clue.

Feschotte's foray into the field began five years ago after his research had turned up a paradox. His group and others had found that the genomes of bats were littered with small pieces of DNA, called transposons, that had invaded and copied themselves throughout the flying mammals' genetic material. In particular, this massive transposon amplification had expanded the genome of a species called the microbat by 460 megabases, more genetic material than there is in a pufferfish. Yet the overall size of the bat's genome had remained relatively small in comparison to other mammals, suggesting that while transposons added new DNA, old DNA must have been removed somehow.

"These data begged the question: where did the old DNA go?" says Feschotte. In order to keep their genomes trim, he reasoned, these animals must have been good at jettisoning DNA.

In order to test the hypothesis, his team needed to quantify something that wasn't there, the amount of DNA lost over many millenia. Feschotte and the study's lead author Aurlie Kapusta, Ph.D., a research associate in human genetics, developed methods to extrapolate the amount of DNA that vanished by comparing genome sizes from present day animals to that of their common ancestors.

As they suspected, the microbat lost more DNA over time - three times as much - than it had gained since its divergence from a mammalian ancestor. This bat's cousin, the megabat, slimmed down its genome even more, losing eight times more than had been added.

The findings were a first clue that mammalian genomes were more dynamic than previously thought. But more than that, the data fit in nicely with an idea that scientists had been bantering around for a while. Animals that fly have smaller genomes. One reason could be that the metabolic cost of powered flight imposes a constraint on genome size.

Indeed, expanding the survey to include the bats' compatriots of the skies: woodpeckers, egrets, hummingbirds, and other birds, showed that the genome dynamcis of the two flying mammal species was more like that of the birds than the land-bound mammals. While most mammals trended toward an equilibrium between the amounts of DNA gained and lost over deep evolutionary time, the bats skewed toward shedding DNA over the same time frame.

The biological factors underlying the differences in genome dynamics observed across species are likely to be complex and remains to be explored. But whether streamlining genome content may have allowed flying animals to get off the ground is an intriguing proposal worth investigating, says Feschotte.

"If you look at small parts of the genome, or only one time point, you don't see how the whole genome landscape has changed over time," says Kapusta. 'You can see so much more when you step back and look at the fuller picture."

The work was supported by the National Institutes of Health, and will publish as "Dynamics of genome size evolution in birds and mammals" in PNAS on Feb. 6, 2017.

Explore further: First genome sequence of Amur leopard highlights the drawback of a meat only diet

More information: Dynamics of genome size evolution in birds and mammals, PNAS, http://www.pnas.org/cgi/doi/10.1073/pnas.1616702114

The first whole genome sequence of the Far Eastern Amur leopard is published in the open access journal Genome Biology, providing new insight into carnivory and how it impacts on genetic diversity and population size.

In rare instances, DNA is known to have jumped from one species to another. If a parasite's DNA jumps to its host's genome, it could leave evidence of that parasitic interaction that could be found millions of years latera ...

(PhysOrg.com) -- Researchers at The University of Texas at Arlington have found the first solid evidence of horizontal DNA transfer, the movement of genetic material among non-mating species, between parasitic invertebrates ...

Researchers from the University of Bristol have uncovered one of the reasons for the evolutionary success of flowering plants.

(Phys.org) It has long been known that birds and bats have small genomes, but the cause was uncertain. Now researchers at the University of New Mexico have shown that the genome shrinks over evolutionary time in species ...

In a contribution to an extraordinary international scientific collaboration the University of Sydney found that genomic 'fossils' of past viral infections are up to thirteen times less common in birds than mammals.

Researchers at the Hebrew University of Jerusalem have discovered a survival strategy that harmful bacteria can use to outsmart the human immune response, resulting in more severe and persistent infections and more effective ...

Researchers at the University of Southampton have developed a new 3D system to study human infection in the laboratory.

To the average plant-eating human, the thought of a plant turning the tables to feast on an animal might seem like a lurid novelty.

Evolution is often thought of as a gradual remodeling of the genome, the genetic blueprints for building an organism. But in some instance it might be more appropriate to call it an overhaul. Over the past 100 million years, ...

Conventional wisdom holds that sharks can't be harvested in a sustainable manner because they are long-lived animals. It takes time for them to reproduce and grow in numbers. But, researchers reporting in Current Biology ...

A grisly method by which bacteria dispatch their distant relatives also creates conditions in which the attackers can thrive, research has found.

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Genomes in flux: New study reveals hidden dynamics of bird and ... - Phys.Org

Forbes

'Adam And The Genome' Offers A New Approach To Counter Creationism Forbes Now, they've teamed up to write Adam and the Genome, published by Brazos Press. In eight chapters, they lay out the case for accepting the genomic evidence that the human race is descended from a population of humans that left Africa roughly 50,000 ...

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'Adam And The Genome' Offers A New Approach To Counter Creationism - Forbes

Vertigo3d/iStock

Targeted, genetic modification in humans is no longer in the realm of science fiction. Both the UK and US governments have approved the use of a cheap and accurate DNA-editing technique called CRISPR-Cas9 in human embryos and adults. The technique allows scientists to edit genes with unprecedented precision, efficiency, and flexibility but how does it work and why is it so controversial?

CRISPR, pronounced 'crisper', stands for Clustered Regularly Interspaced Short Palindromic Repeat. The name refers to the way short, repeated DNA sequences in the genomes of bacteria and other microorganisms are organised.

CRISPR was inspired by these organisms defence mechanisms. Bacteria defend themselves from viral attacks by stealing strips of the invading virus DNA, which they splice in their own using an enzyme called Cas. These newly-formed sequences are known as CRISPR. The bacteria make RNA copies of these sequences, which help recognise virus DNA and prevent future invasions.

In 2012, scientists turned CRISPR from a bacterial shield into a gene-editing tool.

They replaced the bacterial CRISPR RNA system with a modified guide RNA. This RNA acts as a kind of wanted poster - it tells a bounty hunter enzyme called CAS9 where to look. The enzyme scans the cell's genome to find a DNA match then slices for the DNA in the cells enzymes. To repair damage at that point, scientists can change or add DNA within the cell.

By feeding CAS9 the right sequence or guide RNA, scientists can cut and paste parts of the DNA sequence, up to 20 bases long, into the genome at any point.

The technique is significant because it gives genetic biologists a powerful tool for gene editing. More importantly, it's cheap. The major impact of CRISPR has been in developing new model systems, cells and animals, that are more rapid to develop and much more accurate than previous genetic models, Dr Ed Wild, from UCL Institute of Neurology, told WIRED.

It gives rise to a huge range of opportunities. Plans are underway to edit allergens in peanuts, create mushrooms that don't brown and breed genetically-engineered mosquitoes that cannot transmit malaria. There is even a project to bring back the woolly mammoth from extinction.

But it doesn't stop there. CRISPR is already being used to edit pig DNA so their organs can be transplanted into humans; China is using CRISPR-edited cells in living humans, to inject cancer-fighting white blood cells into a patient. The technique could also be used to target illnesses such as system fibrosis, sickle-cell anaemia and Huntington's disease.

However, there is a long road ahead. Editing the genomes of embryos is much easier in principle, but many genetic conditions dont require it because a proportion of embryos are naturally free from the mutation already, Dr Wild added.

For example, 50 per cent of embryos from a parent with Huntingtons disease, and 25 per cent of embryos from a couple carrying the mutation that causes cystic fibrosis, would be free from harmful mutations without any need for genome editing.

There are many challenges with viral delivery and concerns about side-effects from turning cells into CRISPR factories, too. The proteins being introduced came from bacteria, so they could trigger the immune system. There are also concerns about the fact it may be impossible to turn them off.

These seem like solvable problems but we know that it will take many years to solve them, Dr Wild told WIRED. In the short term CRISPR will be used to study disease in much more efficient and targeted ways, for example by developing new model systems or by simulating the effect of treatments using genetic editing, Dr Wild says.

In the medium term, it may be used to produce cleaner versions of existing therapeutics, like therapeutic stem cells edited to be closer to the tissue type they are trying to replace.

Want to know more? Come to this year's WIRED Health conference on March 9 at 30 Euston Square. Buy tickets and discover the speakers here.

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CRISPR Cas9 genome editing explained | WIRED UK - Wired.co.uk

February 3, 2017 by Dana Smith Credit: David Senior

After the 2003 completion of the Human Genome Project which sequenced all 3 billion "letters," or base pairs, in the human genome many thought that our DNA would become an open book. But a perplexing problem quickly emerged: although scientists could transcribe the book, they could only interpret a small percentage of it.

The mysterious majority as much as 98 percent of our DNA do not code for proteins. Much of this "dark matter genome" is thought to be nonfunctional evolutionary leftovers that are just along for the ride. However, hidden among this noncoding DNA are many crucial regulatory elements that control the activity of thousands of genes. What is more, these elements play a major role in diseases such as cancer, heart disease, and autism, and they could hold the key to possible cures.

As part of a major ongoing effort to fully map and annotate the functional sequences of the human genome, including this silent majority, the National Institutes of Health (NIH) on Feb. 2, 2017, announced new grant funding for a nationwide project to set up five "characterization centers," including two at UC San Francisco, to study how these regulatory elements influence gene expression and, consequently, cell behavior.

The project's aim is for scientists to use the latest technology, such as genome editing, to gain insights into human biology that could one day lead to treatments for complex genetic diseases.

Importance of Genomic Grammar

After the shortfalls of the Human Genome Project became clear, the Encyclopedia of DNA Elements (ENCODE) Project was launched in September 2003 by the National Human Genome Research Institute (NHGRI). The goal of ENCODE is to find all the functional regions of the human genome, whether they form genes or not.

"The Human Genome Project mapped the letters of the human genome, but it didn't tell us anything about the grammar: where the punctuation is, where the starts and ends are," said NIH Program Director Elise Feingold, PhD. "That's what ENCODE is trying to do."

The initiative revealed that millions of these noncoding letter sequences perform essential regulatory actions, like turning genes on or off in different types of cells. However, while scientists have established that these regulatory sequences have important functions, they do not know what function each sequence performs, nor do they know which gene each one affects. That is because the sequences are often located far from their target genes in some cases millions of letters away. What's more, many of the sequences have different effects in different types of cells.

The new grants from NHGRI will allow the five new centers to work to define the functions and gene targets of these regulatory sequences. At UCSF, two of the centers will be based in the labs of Nadav Ahituv, PhD, and Yin Shen, PhD. The other three characterization centers will be housed at Stanford University, Cornell University, and the Lawrence Berkeley National Laboratory. Additional centers will continue to focus on mapping, computational analysis, data analysis and data coordination.

Cellular Barcodes Reveal Regulatory Function

New technology has made identifying the function and targets of regulatory sequences much easier. Scientists can now manipulate cells to obtain more information about their DNA, and, thanks to high-throughput screening, they can do so in large batches, testing thousands of sequences in one experiment instead of one by one.

"It used to be extremely difficult to test for function in the noncoding part of the genome," said Ahituv, a professor in the Department of Bioengineering and Therapeutic Sciences. "With a gene, it's easier to assess the effect because there is a change in the corresponding protein. But with regulatory sequences, you don't know what a change in DNA can lead to, so it's hard to predict the functional output."

Ahituv and Shen are both using innovative techniques to study enhancers, which play a fundamental role in gene expression. Every cell in the human body contains the same DNA. What determines whether a cell is a skin cell or a brain cell or a heart cell is which genes are turned on and off. Enhancers are the secret switches that turn on cell-type specific genes.

During a previous phase of ENCODE, Ahituv and collaborator Jay Shendure, PhD, at the University of Washington, developed a technique called lentivirus-based massive parallel reporter assay to identify enhancers. With the new grant, they will use this technology to test for enhancers among 100,000 regulatory sequences previously identified by ENCODE.

Their approach pairs each regulatory sequence with a unique DNA barcode of 15 randomly generated letters. A reporter gene is stuck in between the sequence and the barcode, and the whole package is inserted into a cell. If the regulatory sequence is an enhancer, the reporter gene will turn on and activate the barcode. The DNA barcode will then code for RNA in the cell.

Once the researchers see that the reporter gene is turned on, they can easily sequence the RNA in the cell to see which barcode is activated. They then match the barcode back to its corresponding regulatory sequence, which the scientists now know is an enhancer.

"With previous enhancer assays, you had to test each sequence one by one," Ahituv explained. "With our approach, we can clone thousands of sequences along with thousands of barcodes and test them all at once."

Deleting Sequences to Understand Their Role

Shen, an assistant professor in the Department of Neurology and the Institute for Human Genetics, is taking a different approach to characterize the function of regulatory sequences. In collaboration with her former mentor at the Ludwig Institute for Cancer Research and UC San Diego, Bing Ren, PhD, she developed a high-throughput CRISPR-Cas9 screening method to test the function of noncoding sequences. Now, Shen and Ren are using this approach to identify not only which sequences have regulatory functions, but also which genes they affect.

Shen will use CRISPR to edit tens of thousands of regulatory sequences in a large pool of cells and track the effects of the edits on a set of 60 pairs of genes that commonly co-express.

For this work, each cell will be programmed to reflect two fluorescent colors one for each gene when a pair of genes is turned on. If the light in a cell goes out, the scientists will know that its target gene has been affected by one of the CRISPR-based sequence edits. The final step is to sequence each cell's DNA to determine which regulatory sequence edit caused the change in gene expression.

By monitoring the colors of co-expressed genes, Shen will reveal the complex relationship between numerous functional sequences and multiple genes, which was beyond the scope of traditional sequencing techniques.

"Until the recent development of CRISPR, it was not possible to genetically manipulate non-coding sequences in a large scale," said Shen. "Now, CRISPR can be scaled up so that we can screen thousands of regulatory sequences in one experiment. This approach will tell us not only which sequences are functional in a cell, but also which gene they regulate."

Can Dark Matter DNA Treat Disease?

By cataloging the functions of thousands of regulatory sequences, Shen and Ahituv hope to develop rules about how to predict and interpret other sequences' functions. This would not only help illuminate the rest of the dark matter genome, it could also reveal new treatment targets for complex genetic diseases.

"A lot of human diseases have been found to be associated with regulatory sequences," Ahituv said. "For example, in genome-wide association studies for common diseases, such as diabetes, cancer and autism, 90 percent of the disease-associated DNA variants are in the noncoding DNA. So it's not a gene that's changed, but what regulates it."

As the price for sequencing a person's genome has dropped significantly, there is talk about using precision medicine to cure many serious diseases. However, the hurdle of how to interpret mutations in noncoding DNA remains.

"If we can characterize the function and identify the gene targets of these regulatory sequences, we can start to reveal how their mutations contribute to diseases," Shen said. "Eventually, we may even be able to treat complex diseases by correcting regulatory mutations."

Explore further: Biologists unlock code regulating most human genes

Molecular biologists at UC San Diego have unlocked the code that initiates transcription and regulates the activity of more than half of all human genes, an achievement that should provide scientists with a better understanding ...

We have barely begun to crack open the rulebook for the vast noncoding regions of the genome. Two new methods, building on CRISPR advances, may help reveal some of the pages.

Researchers have shown that when parts of a genome known as enhancers are missing, the heart works abnormally, a finding that bolsters the importance of DNA segments once considered "junk" because they do not code for specific ...

Scientists have devised a powerful new tool for understanding how DNA controls gene activity in cells. The tool allows researchers to map at high resolution, across large swaths of a cell's genome, which DNA nucleotides work ...

A team of researchers from the Perelman School of Medicine at the University of Pennsylvania have shed new light on how the structure of regulatory sequences in DNA is packaged in a cell. "This work has implications for better ...

Scientists are using machine learning to identify important sequences of DNA within the mosquito genome that regulate how the insect's cells develop and behave.

To the average plant-eating human, the thought of a plant turning the tables to feast on an animal might seem like a lurid novelty.

Conventional wisdom holds that sharks can't be harvested in a sustainable manner because they are long-lived animals. It takes time for them to reproduce and grow in numbers. But, researchers reporting in Current Biology ...

The ability of malaria parasites to persist in the body for years is linked to the expression of a set of genes from the pir gene family, scientists from the Francis Crick Institute and the Wellcome Trust Sanger Institute ...

A grisly method by which bacteria dispatch their distant relatives also creates conditions in which the attackers can thrive, research has found.

The enemies were thrown together, so the killing began. Brandishing harpoon-like appendages covered in poison, two armies of cholera bacteria stabbed each other, rupturing victims like water balloons. Scientists at the Georgia ...

A new model exploring how evolutionary dynamics work in natural selection has found that phenotypic diversity, or an organism's observable traits, co-evolves with contingent cooperation when organisms with like traits work ...

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The mysterious 98%: Scientists look to shine light on the 'dark genome' - Phys.Org

The American College of Medical Genetics and Genomics (ACMG) has published a statementrecommending caution over the clinicalapplication of genome editing.

The college's 'points to consider'highlighttechnological and ethical concerns that it believes should be addressed before genome-editing technology can be used to treat genetic diseases in humans.

'Our goal in this statement is to draw attention to the opportunities for the treatment of genetic conditions, some of the challenges that are being actively addressed, and the ongoing concern about even greater challenges associated with germline, as opposed to somatic, genome editing,' said ACMG President Gerald Feldman.

While developments in genome editing are occurring rapidly, the technology is not perfect, and the ACMG recommends rigorous medical review of the clinical applications. For treating somaticcells in patients, this involves ensuring that the disease-causing variant is corrected to a form that ends the disease, that no other variants are created, and that cells do not pick up epigenetic changes that could create abnormal function when transplanted back into the individual.

For altering the genome of human embryos, this involves preventing off-target effects, ensuring that editing a disease-causing variant has no harmful epigenetic effects, and considering the potential genetic impact on future generations.

The ACMG also addresses ethical concerns about the effect on society of clinical genome editing. It will need to be decided which variants highly impactful disease-causing variants, minimally impactful disease-causing variants, or non-disease variants should or should not be subject to genome editing.

The statement concludes: 'In light of these potentially serious and far-reaching concerns, the ACMG Board of Directors believes that genome editing in the human embryo is premature and should be subject to vigorous ethical debate and further refinement of technological issues.

'The ACMG will appoint an ad hoc committee to recommend specific areas where it can contribute to this debate.'

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ACMG recommends caution on genome editing - BioNews

The National Institutes of Health today announced eight mapping centers that will help lead the next four-year phase of its Encyclopedia of DNA Elements (ENCODE) Project, whose purpose is to identify all of the functional elements contained in the human genome. These eight laboratories include the Center for Genome Architecture (TC4GA) at Baylor College of Medicine, which will be responsible for mapping how the genome folds inside the nucleus of roughly 100 different types of cells. Led by Dr. Erez Lieberman Aiden, McNair Scholar and assistant professor of genetics at Baylor and Rice University, TC4GA has received $3.3 million to fund its role in the mapping effort.

The ENCODE Project was launched by the NIHs National Human Genome Research Institute (NHGRI) in 2003, in the wake of the completion of the first drafts of the human genomes 3 billion letter sequence. ENCODEs goal is to decode that sequence by cataloging all the functional pieces of the human genome and to determine what each one does. These sequences include both genes and regulatory elements the parts of the genome that control when genes turn on and off. ENCODEs mapping centers play a crucial role in this effort. Each center is responsible for mapping one or more types of DNA sequence elements. The overall goal is to create a catalog that can serve as a resource for the entire scientific community.

The basic idea of the ENCODE project is to create extremely detailed maps of different types of features in the genome, Aiden said. Then, when we put all of these maps together, the whole is much more valuable than each of the parts.

The award to TC4GA marks the first time that ENCODE has funded a center dedicated to producing comprehensive maps of genome folding. Aiden explains that, if stretched out from end-to-end, the DNA in each cell of the human body would be over six feet long. But the DNA has to fold up to fit inside the cell's nucleus, which is less than a thousandth of an inch wide.

This fold is not merely a way of packing a long DNA strand into a tiny space. The folding pattern is different for a heart cell that beats, a brain cell that thinks, or an immune cell that fights disease, Aiden said.

The compact folding within the nucleus leads the genome to bend back on itself, so that two pieces that lie far apart along the DNA molecule like a gene and its regulatory element can come close together in the cell nucleus. Having a better understanding of where these loops occur genome-wide also will lead to a better understanding of gene regulation.

There are certain features that the research community feels are important to know about if we want a better understanding of how the genome works, Aiden said. The goal of the mapping centers is to think about these different types of features in the genome and how to detect and record them in some standardized fashion. It has become increasingly clear that genome folding plays an important role in many cellular processes. So our center will be dedicated to characterizing how the genome folds.

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$3.3M effort to map human genome's intricate folding pattern - Baylor College of Medicine News (press release)