Daily Archives: February 6, 2017

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

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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)