Archive | February 2017

The CRISPR-Cas system: the latest trend in gene modification

Article written by Rosa Martínez Corral.

In less than a decade, the field of genome engineering has been revolutionised by a series of techniques that now allow to accurately, efficiently and economically modify virtually any point in the genome of any organism. It all started in the early 1990s, when a pattern of repetitive sequences was observed in the DNA of certain bacteria. It was subsequently seen that many other types of bacteria also possess these patterns and, after years of research, these random observations have led to a revolution with strong implications both for research and therapy.

These repetitive sequences were part of a bacterial genomic region now known as CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats. They consist of repetitive DNA sequences that flank DNA fragments from past viral infections. Faced with a new infection by the same virus, the viral DNA fragment generates a complementary RNA molecule. This RNA guides its associated Cas proteins towards the viral genome, and these degrade the DNA of the virus. Therefore, this is a bacterial immune system that, like ours, retains a memory of past infections.

Left: The endogenous CRISPR-Cas system of bacteria. The schema shows how a bacterial genome acquires a fragment of viral DNA. Upon reinfection, it can generate a complementary RNA molecule that specifically guides a Cas protein towards the viral DNA, to degrade it and thus eliminate the infection. Right: The CRISPR-Cas system is used in the laboratory to modify specific points in the genome of organisms.

Left: The endogenous CRISPR-Cas system of bacteria. The schema shows how a bacterial genome acquires a fragment of viral DNA. Upon reinfection, it can generate a complementary RNA molecule that specifically guides a Cas protein towards the viral DNA, to degrade it and thus eliminate the infection.
Right: The CRISPR-Cas system is used in the laboratory to modify specific points in the genome of organisms.

 

But not only that, the CRISPR-Cas system has also proved a useful tool in the laboratory, leading to a series of powerful techniques to modify the DNA of organisms.  In the most widely-used version, an RNA molecule complementary to the region of the genome to be modified is designed in such a way that it guides a Cas protein to make a cut in that specific location. The cell then repairs itself, and depending on the aim and thus how the technique is applied, a mutation can either be repaired or introduced. The first is desirable, for instance, in the case where a genetic defect exists. On the other hand, in order to understand what the function of a genomic region is, scientists often make deleterious mutations to inactivate it and see what the consequence is.

The CRISPR-Cas system is, therefore, a simple and easily scalable tool that allows specific changes to be made to multiple parts of the genome, needing little time and few resources, something unprecedented in the field of genome engineering. For example, to inactivate a gene in a model organism, it was often necessary to cause random mutations and then select those of interest, involving a long and costly process. But with the CRISPR-Cas system this is no longer necessary. It has even been used to make genetic modifications in human embryos, opening new doors to the study of human development and the therapy of inherited genetic diseases.

But there are still problems to be solved. The most important of these is the fact that the system is not perfect and it can make cuts in unintended regions of the genome. It is also necessary to improve the methods that allow the Cas protein and RNA guide to be effective only in specific tissues, particularly if it is to be used as a therapeutic tool.

Further information:

Genomics of aging

On December 12th Vadim Gladyshev from the Harvard Medical School, Boston, USA, gave a conference in a packed room at the PRBB invited by Roderic Guigó from the CRG. Gladyshev investigates the molecular basis for natural changes in longevity and the biological mechanisms involved in aging.

The first part of the conference focused on the mechanisms of aging. Gladyshev’s main question was: why and how do things go wrong with age?

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At the beginning he introduced several aging theories that have contributed most significantly to the aging debate in the research community. Some of them were built in the 50s based on 19th century insights, whereas others are very recent. According to him, these theories are very different, each of them touching on a particular aspect of the aging process and, within that context, each has its merit, but all are incomplete.

He continued with his own view about aging. He suggested that imperfectness of biological processes leads to inevitable damage accumulation – called deleteriome – causing aging. His research group is now characterizing properties of cumulative damage and its impact on the aging process. They also study cancer as a disease of aging.

While the mechanisms of aging and the process of lifespan control may seem highly related topics, he riumaintained that they are different areas. To explain the difference, he used a metaphor of a river, where a lifespan would be equivalent to the time needed for the water to flow from the mountain to the ocean. According to him, the route of the river can be changed to make the journey longer, just like lifespan of humans can be extended. However, the fact that the river flows because of gravity can’t be changed, just like we cannot change the fact that the aging process occurs because of imperfectness. So the cause of aging is different from the determinants of longevity.

The second part of the conference was about mechanisms of lifespan control, trying to answer the questions: why do cells and organisms live as long as they do? and how does Nature adjust lifespan?

myotis_brandtiGladyshev’s research team uses multiple approaches to address this question. One methodology involves studying the genes of exceptionally long-lived mammals, such as the naked mole rat, the Brandt’s bat and the bowhead whale. The Brandt’s bat (Myotis brandtii) is found throughout most of Europe and parts of Asia, and it often lives more than 40 years.

22339537119_5640a2de32_bThe naked mole rat (Heterocephalus glaber) is a burrowing animal commonly found in East Africa, well-adapted to their underground existence. They are characterized by small eyes, short and thin legs, hairless body (hence the common name) and wrinkled pink or yellowish skin. Their large front teeth are used to dig. This animal can live up to 31 years, the record for the longest living rodent.

Gladyshev’s group recently sequenced and analyzed the genomes of these animals, and they discovered some of the adaptations that contribute to their long lifespans. They also identified general gene expression and metabolic changes that associate with longer life.

In addition to the evolutionary study of long-lived animals, Gladyshev’s lab focuses  on cell types that have different lifespan and in long-lived mouse models. They also do analysis across species and cell culture-based profiling in order to find unique and common mechanisms of longevity. Longevity signatures (based on gene expression) identify candidate interventions for lifespan extension. Ultimately, the researchers would like to find treatments or some other approaches which would help extend life span and diminish the consequences of age-related diseases.

At the end of the talk the public showed great interest on Gladyshev’s research, posing many questions  about aging in yeast, epigenetic drift in aging and the relation between lifespan and maturity. In a fruitful and interesting conversation, some in the audience also suggested research approaches such as studying aging in single cells or focusing on the physics of aging.  We’ll have to wait for Gladyshev’s next talk to see if some of these suggestions gave their fruits!

 

A report by Mari Carmen Cebrián

New genes and functional innovation in mammals

In her latest post, Mar Albà, head of the Evolutionary genomics lab at the UPF-IMIM, explains her group’s research into new genes and their role in mammalian-specific adaptations. You can read the paper she refers to in bioRxiv, the preprint server for biology!

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“Many human genes have counterparts in distant species such as plants or bacteria. This is because they share a common origin, they were invented a long time ago in a primitive cell. However, there are some genes that do not have counterparts in other species, or only in a few of them. These genes have been born much more recently. Although they may have appeared by accident, some have acquired useful functions and been preserved by natural selection. We have recently compiled thousands of mammalian-specific gene families and asked which functions they perform. We have found an enrichment in proteins from the immune system, milk, skin and the germ cells. The most recent genes, however, are rarely functionally characterized. The results of this work provide new insights into how new genes originate and what they are selected for.

 
Read our paper at bioRxiv and tell us what you think!
mar.alba@upf.edu”

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