Why is a Dolphin Not a Cat?

How repurposing non-coding elements in the genome gave rise to the great 'mammalian radiation'

Friday, 30 January 2015

Exploring gene regulation in 20 mammals

provides insights into the mammalian radiation

that occurred over 100 million years ago. Credit:

Spencer Phillips, EMBL-EBI.

New research shows how evolution has given rise to a rich diversity of species by repurposing functional elements shared by all mammals. Published in Cell by scientists at the European Bioinformatics Institute (EMBL-EBI) and the University of Cambridge Cancer Research UK-Cambridge Institute (CRUK CI), the study demonstrates how methods for understanding human biology can be used to understand a broad range of species.

Mammals all share a common ancestor, and they share a lot of the same genes. So what exactly makes a dolphin not a cat, and how did we all start to diverge from one another millions of years ago? Part of the answer lies in how - and when - genes are regulated. This latest research explores the evolution of gene regulation in 20 mammalian species, and provides deep insights into the 'mammalian radiation', a time of rapid morphological evolution that occurred shortly after the asteroid impact that caused the extinction of the dinosaurs.

Leveraging findings from a study comparing the genome sequences of 29 mammals, and with the help of conservation organisations such as the UK Cetacean Strandings Investigation Programme and the Copenhagen Zoo, the team were able to study and compare gene regulation in liver cells from 20 key species including the naked mole rat, human, Tasmanian devil, dolphin and Sei whale.

"What we've shown is that evolution repurposes things that exist in all species, to make each species unique," explains Paul Flicek, head of Vertebrate Genomics at EMBL-EBI.

"By looking at gene promoters and enhancers in many different mammals, we demonstrated that species-specific enhancers come from ancient DNA - that evolution captures DNA that's been around for a long time, and uses it for gene regulation in specific tissues."

Evolution has two ways to turn changes in the genome into differences between species: it can change a protein sequence, or it can change the way promoters or enhancers control that protein's expression. Today's study also shows that in some cases evolution uses both strategies at once. When amino acid sequences evolve very quickly, important regulation changes occur at the same time: the protein-coding sequence and the corresponding regulatory sequence change synergistically.

Gathering the samples - the experimental efforts were led by Diego Villar of CRUK CI - took well over two years, and the experiments themselves produced a staggering volume of data. Analysing the results brought the team to a new frontier in bioinformatics.

"People spend a lot of time and money trying to understand human biology, so most of the tools we have are designed to study human genomes," explains Camille Berthelot of EMBL-EBI, who led the computational work.

"The reference data we have for the less studied species, like the Sei whale or Tasmanian devil, are nothing like the pored-over datasets we have for the human genome. A lot of what we did involved benchmarking, and making sure the methods and algorithms were fit for this kind of comparison."

"What inspired this work was a desire to get on top of the mountain, look out and see what is going on in the landscape of molecular evolution across the breadth of mammalian space," says Duncan Odom of CRUK CI and Wellcome Trust Sanger Institute.

"What's exciting about this study is that we now know we can start to answer questions about the functional genetics of many under-explored species - questions we usually can ask only of humans and mice. We can use tools developed to study humans to understand the biology of all kinds of animals, whether they're blackbirds or elephants, and explore their relationship with one another. This research has given us new insights into mammalian evolution, and proven how powerful these methods can be."

Source: EMBL

Contact: Mary Todd Bergman

Reference:

Enhancer Evolution across 20 Mammalian Species

Diego Villar, Camille Berthelot, Sarah Aldridge, Tim F. Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan T. Erichsen, Anna J. Jasinska, James M.A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom

Cell, Volume 160, Issue 3, p554–566, 29 January 2015, DOI: http://dx.doi.org/10.1016/j.cell.2015.01.006

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Mitochondrial Donation: How Many Women Could Benefit?

Two and a Half Thousand Women Could Benefit from Mitochondrial Donation in the UK

Thursday, 29 January 2015

Almost 2,500 women of child-bearing age in the UK are at risk of transmitting mitochondrial disease to their children, according to the most recent estimates published today in the New England Journal of Medicine.

The research offers the most recent evidence yet of how many families could potentially be helped by new IVF techniques to prevent mitochondrial disease, which would be permitted by new regulations on which a vote in parliament is imminent.

Mitochondrial diseases are caused by inherited mutations in the DNA contained in mitochondria - tiny structures present in every cell that generate energy. Mitochondrial diseases can be devastating and particularly affect tissues that have high energy demands - brain, muscle (including heart), liver and kidney.

New IVF-based techniques have been developed which have the potential to prevent the transmission of serious mitochondrial disease. Known as 'mitochondrial donation' the techniques involve removing faulty mitochondria inherited from the mother and replacing them with the healthy mitochondria of another woman. The nuclear DNA, containing 99.9% of genetic material from the mother and father, remains unchanged.

Researchers at the Wellcome Trust Centre for Mitochondrial Research at Newcastle University, which will be the first to offer mitochondrial donation if parliament agrees to new regulations of the Human Fertilisation and Embryology Act (1990), have now calculated how many women have disease-causing mutations in their mitochondrial DNA in order to estimate how many could potentially benefit. The new regulations only allow for mitochondrial donation to prevent mitochondrial disease and set no precedent for genetic manipulation of nuclear DNA.

They calculate that 2,473 women in the UK, and 12,423 women in the US, aged between 15 and 44 years, are at risk of passing on potentially lethal mitochondrial DNA disease to their children. This equates to an average of 152 births per year in the UK, and 778 births per year in the US.

The estimates were made by identifying the number of women in North East England who are at risk of passing on mitochondrial disease to their children and extrapolating the figure to the rest of the UK, based on the relative number of women of child-bearing age in the North East compared to the UK as a whole. A similar method was used for the US figures. The study did not account for variance due to ethnicity or potentially different fertility rates in different parts of the UK.

Researchers also assessed the fertility of women with mitochondrial DNA mutations. To do this they compared fertility data from their patients' to data about the general population, obtained from the UK Office for National Statistics. They found that mitochondrial mutation has no statistically significant effect on fertility rate.

Dr Gráinne Gorman from the Wellcome Trust Centre for Mitochondrial Research at Newcastle University, and joint first author of the paper, said:

"Our estimate of how many women could benefit from mitochondrial donation is based on our data from North East England, where we have very detailed insight into how many women are affected. We are confident that there are a similar number of women across the UK at risk of passing on mitochondrial disease to their children."

Professor Doug Turnbull, Director of the Wellcome Trust Centre for Mitochondrial Research at Newcastle University, and an author of the paper, said:

"Our findings have considerable implications for all countries that are considering allowing mitochondrial donation techniques. In the UK we are waiting for parliament to decide whether to support these regulations. This would allow women who carry these mutations greater reproductive choice. "

Source: Wellcome Trust 

Contact: Clare Ryan 

Reference:

Mitochondrial Donation: How many women could benefit? 

Gráinne S. Gorman, John P. Grady, Yi Ng, Andrew M. Schaefer, Richard J. McNally, Patrick F. Chinnery, Patrick Yu Wai Man, Mary Herbert, Robert W. Taylor, Robert McFarland, and Doug M. Turnbull

New England Journal of Medicine, January 28, 2015 DOI: 10.1056/NEJMc1500960

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Researchers Reconstruct Early Stages of Embryo Development

Researchers Reconstruct Early Stages of Embryo Development

Tuesday, 04 November 2014

Researchers at the University of Cambridge have managed to reconstruct the early stage of mammalian development using embryonic stem cells, showing that a critical mass of cells – not too few, but not too many – is needed for the cells to being self-organising into the correct structure for an embryo to form.

All organisms develop from embryos: a cell divides generating many cells. In the early stages of this process, all cells look alike and tend to aggregate into a featureless structure, more often than not a ball. Then, the cells begin to 'specialise' into different types of cell and space out asymmetrically, forming an axis which begins to provide a structure for the embryo to develop along.

In animal embryos this stage is followed by a process known as gastrulation: a choreographed movement of the cells that, using the initial axis as a reference, positions the head and the tail, the front and the back. During the process, the cells begin to form three distinct layers: the endoderm, mesoderm and ectoderm, determining which tissues or organs the cells will then develop into.

Professor Alfonso Martinez-Arias from the Department of Genetics at the University of Cambridge, who led the research, says:

"Gastrulation was described by biologist Professor Lewis Wolpert as being 'truly the most important event in your life' because it creates the blueprint of an organism. Axis formation and gastrulation are the two central processes that initiate the development of an organism and are inextricably associated with the embryo. We have managed to recreate this for the first time in the lab."

Professor Martinez-Arias and colleagues, supported by the European Research Council and the Wellcome Trust, have reconstructed these early stages of development using mouse embryonic stem cells. Embryonic stem cells, discovered in the Department of Genetics in the 1980s (for which Sir Martin Evans was awarded the Nobel Prize in Physiology or Medicine 2007), have become an important tool for developmental biology, understanding disease, and in regenerative medicine due to the ability to give rise to all cell types in culture. Over the last few years, they have been used to 'grow' organs including the eye and the cerebral cortex; surprisingly, these structures develop without an axis.

In research published today in the journal Development, the researchers report a way to coax cells to reorganize in the manner that they do in an embryo, creating an axis and undergoing movements and organisations that mimic the process of gastrulation. Over the years researchers have been making aggregates of embryonic stem cells to obtain certain cell types, for example red blood cells. However, these aggregates lack structure and the different cell types emerge in a disorganised fashion. This is the first time that researchers have been able to elicit axis formation, spatial organisation and gastrulation-like movements from aggregates of embryonic stem cells.

The researchers show that if the number of cells aggregated initially is similar to that of a mouse embryo, the cells generate a single axis and this serves as a template for a sequence of events that mimics those of the early embryo. By manipulating the signals that the cells see at a particular time, the researchers were able to influence what type of cell they become and how they are organised. In one of the experiments, for example, activation of a particular signal at the correct time elicits the appearance of the mesoderm, endoderm and ectoderm – the precursors of all cell types – with a spatial organization similar to that of an embryo.

Using this experimental system, the researchers were able to generate the early stages of a spinal cord, which they showed forms as part of the process of gastrulation. This finding complements previous research from the University of Edinburgh and the National Institute for Medical Research which showed that embryonic stem cells can be coaxed into this spinal cord cells; however, the Cambridge researchers showed that in the embryo-like aggregates, the structural organization is more robust and allows for the polarised growth of the tissue.

Professor Martinez-Arias adds:

"It is early days but this system promises insights into the early stages of development and what determines the specification of the different cell types. This will allow more robust protocols for differentiation with cues that mimic those that the cells are subject to in embryos.”

"Most significantly, the system will provide a means to test, experimentally, how a homogeneous group of cells organizes itself in space, a central process in the development of any organism, and the ability to recreate in culture the niches that adult stem cells create during embryogenesis and which have remained elusive experimentally."

Source: University of Cambridge

Contact: Craig Brierley

References:

Symmetry breaking, germ layer specification and axial organisation in aggregates of mouse ES cells

Susanne C. van den Brink, Peter Baillie-Johnson, Tina Balayo, Anna-Katerina Hadjantonakis, Sonja Nowotschin, David A. Turner, and Alfonso Martinez Arias

Development 2014 141:4231-4242; doi:10.1242/dev.113001

Wnt/β-catenin and FGF signalling direct the specification and maintenance of a neuromesodermal axial progenitor in ensembles of mouse ES cells

David A. Turner, Penelope C. Hayward, Peter Baillie-Johnson, Pau Rué, Rebecca Broome, Fernando Faunes, and Alfonso Martinez Arias

Development; 2014 141:4243-4253; doi:10.1242/dev.112979

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Rewiring Stem Cells

Rewiring Stem Cells

Friday, 10 January 2014

This is a set of chromosomes in haploid mouse 
embryonic stem cells. Credit: Martin Leeb. 

A fast and comprehensive method for determining the function of genes could greatly improve our understanding of a wide range of diseases and conditions, such as heart disease, liver disease and cancer.

The method uses stem cells with a single set of chromosomes, instead of the two sets found in most cells, to reveal what causes the "circuitry" of stem cells to be rewired as they begin the process of conversion into other cell types. The same method could also be used to understand a range of biological processes.

Embryonic stem cells rely on a particular gene circuitry to retain their original, undifferentiated state, making them self-renewing. The dismantling of this circuitry is what allows stem cells to start converting into other types of cells - a process known as cell differentiation - but how this happens is poorly understood.

Researchers from the University of Cambridge Wellcome Trust-MRC Stem Cell Institute have developed a technique which can pinpoint the factors which drive cell differentiation, including many that were previously unidentified. The method, outlined in the Thursday (9 January) edition of the journal Cell Stem Cell, uses stem cells with a single set of chromosomes to uncover how cell differentiation works.

Cells in mammals contain two sets of chromosomes – one set inherited from the mother and one from the father. This can present a challenge when studying the function of genes, however: as each cell contains two copies of each gene, determining the link between a genetic change and its physical effect, or phenotype, is immensely complex.

"The conventional approach is to work gene by gene, and in the past people would have spent most of their careers looking at one mutation or one gene," said Dr Martin Leeb, who led the research, in collaboration with Professor Austin Smith.

"Today, the process is a bit faster, but it's still a methodical gene by gene approach because when you have an organism with two sets of chromosomes that's really the only way you can go."

Dr Leeb used unfertilised mouse eggs to generate embryonic stem cells with a single set of chromosomes, known as haploid stem cells. These haploid cells show all of the same characteristics as stem cells with two sets of chromosomes, and retain the same full developmental potential, making them a powerful tool for determining how the genetic circuitry of mammalian development functions.

The researchers used transposons – "jumping genes" – to make mutations in nearly all genes. The effect of a mutation can be seen immediately in haploid cells because there is no second gene copy. Additionally, since embryonic stem cells can convert into almost any cell type, the haploid stem cells can be used to investigate any number of conditions in any number of cell types. Mutations with important biological effects can then rapidly be traced to individual genes by next generation DNA sequencing.

"This is a powerful and revolutionary new tool for discovering how gene circuits operate," said Dr Leeb.

"The cells and the methodology we've developed could be applied to a huge range of biological questions."

Source: University of Cambridge 

Contact: Sarah Collins

Reference:

Genetic Exploration of the Exit from Self-Renewal Using Haploid Embryonic Stem Cells

Martin Leeb, Sabine Dietmann, Maike Paramor, Hitoshi Niwa, Austin Smith

Cell Stem Cell, 09 January 2014, 10.1016/j.stem.2013.12.008

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First 3D Pictures of Chromosome Structure Revealed

'X-shape' not true picture of chromosome structure, new imaging technique reveals

Sunday, 29 September 2013

This is the chromosome structure from single-cell

Hi-C. Credit: Dr. Peter Fraser. Babraham Institute. 

A new method for visualising chromosomes is painting a truer picture of their shape, which is rarely like the X-shaped blob of DNA most of us are familiar with.

Scientists at the BBSRC-funded Babraham Institute, working with the University of Cambridge and the Weizmann Institute, have produced beautiful 3D models that more accurately show their complex shape and the way DNA within them folds up.

The X-shape, often used to describe chromosomes, is only a snapshot of their complexity.

Dr Peter Fraser of the Babraham Institute explains:

"The image of a chromosome, an X-shaped blob of DNA, is familiar to many but this microscopic portrait of a chromosome actually shows a structure that occurs only transiently in cells – at a point when they are just about to divide."

"The vast majority of cells in an organism have finished dividing and their chromosomes don't look anything like the X-shape. Chromosomes in these cells exist in a very different form and so far it has been impossible to create accurate pictures of their structure."

Peter's team has developed a new method to visualise their shape. It involves creating thousands of molecular measurements of chromosomes in single cells, using the latest DNA sequencing technology. By combining these tiny measurements, using powerful computers, they have created a three-dimensional portrait of chromosomes for the first time. This new technology has been made possible thanks to funding from the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC) and the Wellcome Trust.

Dr Fraser added:

"These unique images not only show us the structure of the chromosome, but also the path of the DNA in it, allowing us to map specific genes and other important features. Using these 3D models, we have begun to unravel the basic principles of chromosome structure and its role in how our genome functions."

This latest research, published in Nature, puts DNA into its proper context in a cell, conveying the beauty and complexity of the mammalian genome in a far more effective way than volumes of text previously have. In doing so it shows that the structure of these chromosomes, and the way the DNA within them folds up, are intimately linked to when and how much genes are expressed, which has direct consequences for health, ageing and disease.

Douglas Kell, BBSRC Chief Executive, said:

"Until now, our understanding of chromosome structure has been limited to rather fuzzy pictures, alongside diagrams of the all too familiar X-shape seen before cell division. These truer pictures help us to understand more about what chromosomes look like in the majority of cells in our bodies. The intricate folds help to unravel how chromosomes interact and how genome functions are controlled."

Source: Biotechnology and Biological Sciences Research Council 

Contact: Rob Dawson

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First Child Born Following New Genome Embryo Screening

Validation studies underline accuracy of 'next generation sequencing' for embryo selection in IVF

Tuesday, 09 July 2013

The first birth has been achieved following the analysis of embryos using a new genome sequencing technique which promises to revolutionise embryo selection for IVF. The technique, which has never before been applied in the screening of embryos, is reported today at the annual meeting of ESHRE by Dr Dagan Wells of the NIHR Biomedical Research Centre at the University of Oxford, UK.

The analysis technique is known as "next generation sequencing", a powerful method capable of decoding entire genomes. Vast quantities of DNA data are produced from each sample tested, simultaneously revealing information on the inheritance of genetic disorders, chromosome abnormalities and mitochondrial mutations. Next generation sequencing (NGS) is already revolutionising many areas of genetic research and diagnostics, said Dr Wells, and, when applied to the assessment of embryos, will allow the concurrent analysis of serious inherited disorders and lethal chromosome abnormalities.

"Next generation sequencing provides an unprecedented insight into the biology of embryos," said Dr Wells.

The identification of an embryo destined to implant in the uterus and form a pregnancy remains the holy grail of IVF. On average, only around 30% of embryos currently selected for transfer actually implant. The reason for this high failure rate is unknown, but the prime suspects are unidentified genetic or chromosomal defects. Several genetic screening methods have been introduced over the past decade, but all have been shown to have drawbacks (and have not realised their potential) when tested in randomised clinical trials. This new NGS technique developed by Dr Wells and colleagues, however, seems to overcome the major drawbacks of current methods: 

• Complete chromosome information can be produced revealing abnormalities often responsible for miscarriage;
• Serious gene defects can be identified at the same time;
• The analysis can be completed rapidly (around 16 hours), thus avoiding the need for embryo freezing while awaiting results;
• The test could greatly reduce the costs of embryo screening, which is currently an expensive add-on to IVF.

The study described today was designed to test the accuracy and predictability of NGS in embryo selection. The validation was performed on multiple cells from cell-lines with known chromosome abnormalities, gene defects (cystic fibrosis) or mitochondrial DNA mutations.

Additionally, cells from 45 embryos, previously shown to be abnormal with another testing technique, were reanalysed by NGS in a blinded fashion. After high accuracy had been demonstrated, the method was applied clinically, with cells sampled from seven five-day-old embryos (blastocysts) produced by two couples undergoing IVF. The mothers were 35 and 39 years of age and one couple had a history of miscarriage.

NGS analysis in these two IVF patients identified three chromosomally healthy blastocysts in the first and two in the second; single embryo transfers based upon these results led to healthy pregnancies in both cases. The first pregnancy ended with the delivery of a healthy boy in June.

Dr Wells, who led the international research team behind the study, said:

"Many of the embryos produced during infertility treatments have no chance of becoming a baby because they carry lethal genetic abnormalities. Next generation sequencing improves our ability to detect these abnormalities and helps us identify the embryos with the best chances of producing a viable pregnancy. Potentially, this should lead to improved IVF success rates and a lower risk of miscarriage.”

"In the past few years, results from randomised clinical trials have suggested that most IVF patients would benefit from embryo chromosome screening, with some studies reporting a 50% boost in pregnancy rates. However, the costs of these genetic tests are relatively high, putting them beyond the reach of many patients. Next generation sequencing is a way which could make chromosome testing more widely available to a greater number of patients, improving access by cutting the costs. Our next step is a randomised clinical trial to reveal the true efficacy of this approach - and this will begin later this year."

Source: European Society of Human Reproduction and Embryology 

Contact: Christine Bauquis

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3D Printing Breakthrough with Human Embryonic Stem Cells

3D Printing Breakthrough with Human Embryonic Stem Cells

Tuesday, 05 February 2013

A team of researchers from Scotland has used a novel 3D printing technique to arrange human embryonic stem cells (hESCs) for the very first time.

Printed human organs for testing and 

transplantation. Credit: Heriot-Watt 

University Edinburgh. 

It is hoped that this breakthrough, which has been published today, 5 February, in the journal Biofabrication, will allow three-dimensional tissues and structures to be created using hESCs, which could, amongst other things, speed up and improve the process of drug testing.

In the field of biofabrication, great advances have been made in recent years towards fabricating three-dimensional tissues and organs by combining artificial solid structures and cells; however, in the majority of these studies, animal cells have been used to test the different printing methods which are used to produce the structures.

Co-author of the study, Dr Will Wenmiao Shu, from Heriot-Watt University, said:

"To the best of our knowledge, this is the first time that hESCs have been printed. The generation of 3D structures from hESCs will allow us to create more accurate human tissue models which are essential for in vitro drug development and toxicity-testing. Since the majority of drug discovery is targeting human disease, it makes sense to use human tissues."

In the longer term, this new method of printing may also pave the way for incorporating hESCs into artificially created organs and tissues ready for transplantation into patients suffering from a variety of diseases.

In the study, the researchers, from Heriot-Watt University in collaboration with Roslin Cellab, a stem cell technology company, used a valve-based printing technique, which was tailored to account for the sensitive and delicate properties of hESCs.

The hESCs were loaded into two separate reservoirs in the printer and were then deposited onto a plate in a pre-programmed, uniformed pattern.

Once the hESCs were printed, a number of tests were performed to discern how effective the method was. For example, the researchers tested to see if the hESCs remained alive after printing and whether they maintained their ability to differentiate into different types of cells. They also examined the concentration, characterisation and distribution of the printed hESCs to assess the accuracy of the valve-based method.

"Using this valve-based method, the printed cells are driven by pneumatic pressure and controlled by the opening and closing of a microvalve. The amount of cells dispensed can be precisely controlled by changing the nozzle diameter, the inlet air pressure or the opening time of the valve”, Dr Shu said.

"We found that the valve-based printing is gentle enough to maintain high stem cell viability, accurate enough to produce spheroids of uniform size, and, most importantly, the printed hESCs maintained their pluripotency – the ability to be differentiated into any other cell type."

Roslin Cellab has a track record of applying new technologies to human stem cell systems and will take the lead in developing 3D stem cell printing for commercial uses.

"This world-first printing of human embryonic stem cell cultures is a continuation of our productive partnership with Heriot-Watt. Normally laboratory grown cells grow in 2D but some cell types have been printed in 3D. However, up to now, human stem cell cultures have been too sensitive to manipulate in this way,” Jason King, business development manager of Roslin Cellab, said.

"This is a scientific development which we hope and believe will have immensely valuable long-term implications for reliable, animal-free drug-testing and, in the longer term, to provide organs for transplant on demand, without the need for donation and without the problems of immune suppression and potential organ rejection."

hESCs have received much attention in the field of regenerative medicine. They are originally derived from an early stage embryo to create "stem cell lines" which can be grown indefinitely and differentiate into any cell type in the human body.

"In the longer term, we envisage the technology being further developed to create viable 3D organs for medical implantation from a patient's own cells, eliminating the need for organ donation, immune suppression and the problem of transplant rejection," continued Dr Shu.

Source: Institute of Physics 

Contact: Michael Bishop

Reference:

Development of a valve-based cell printer for the formation of human embryonic stem cell spheroid aggregates

Alan Faulkner-Jones, Sebastian Greenhough, Jason A King, John Gardner, Aidan Courtney and Wenmiao Shu

Biofabrication 2013, 5 015013 doi:10.1088/1758-5082/5/1/015013

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How to Make Stem Cells

Nuclear reprogramming moves a step forward

Monday, 29 October 2012

The idea of taking a mature cell and removing its identity (nuclear reprogramming) so that it can then become any kind of cell, holds great promise for repairing damaged tissue or replacing bone marrow after chemotherapy. Hot on the heels of his recent Nobel prize Dr John B. Gurdon has published today in BioMed Central's open access journal Epigenetics & Chromatin research showing that histone H3.3 deposited by the histone-interacting protein HIRA is a key step in reverting nuclei to a pluripotent type, capable of being any one of many cell types.

All of an individual's cells have the same DNA, yet these cells become programmed, as the organism matures, into different types such as heart, or lung or brain. To achieve this different genes are more or less permanently switched off in each cell lineage. As an embryo grows, after a certain number of divisions, it is no longer possible for cells which have gone down the pathway to become something else. For example heart cells cannot be converted into lung tissue, and muscle cells cannot form bone.

One way to reprogram DNA is to transfer the nucleus of a mature cell into an unfertilized egg. Proteins and other factors inside the egg alter the DNA switching some genes on and other off until it resembles the DNA of a pluripotent cell. However there seem to be some difficulties with this method in completely wiping the cell's 'memory'.

One of the mechanisms regulating the activation of genes is chromatin and in particular histones. DNA is wrapped around histones and alteration in how the DNA is wound changes which genes are available to the cell. In order to understand how nuclear reprogramming works Dr Gurdon's team transplanted a mouse nucleus into a frog oocyte (Xenopus laevis). They added fluorescently tagged histones by microinjection, so that they could see where in the cell and nucleus these histones collected.

Prof Gurdon explained:

"Using real-time microscopy it became apparent that from 10 hours onwards H3.3 (the histone involved with active genes) expressed in the oocyte became incorporated into the transplanted nucleus. When we looked in detail at the gene Oct4, which is known to be involved in making cells pluripotent, we found that H3.3 was incorporated into Oct4, and that this coincided with the onset of transcription from the gene."

Prof Gurdon's team also found that HIRA, a protein required to incorporate H3.3 into chromatin, was also required for nuclear reprogramming.

Dr Steven Henikoff, from the Fred Hutchinson Cancer Research Center, commented:

"Manipulating the H3.3 pathway may provide a way to completely wipe a cell's 'memory' and produce a truly pluripotent cell. Half a century after showing that cells can be reprogrammed this research provides a link to the work of Shinya Yamanaka (who shared the prize), and suggests that chromatin is a sticking point preventing artificially induced reprogramming being used routinely in the clinic."

Source: BioMed Central 

Contact: Hilary Glover

Reference:

HIRA dependent H3.3 deposition is required for transcriptional reprogramming following nuclear transfer to Xenopus oocytes

Jerome Jullien, Carolina Astrand, Emmanuelle Szenker, Nigel Garrett, Genevieve Almouzni and John Gurdon 

Epigenetics & Chromatin (in press)

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How Many Genes in the Human Genome? Human Genome Far More Active than Thought

GENCODE Consortium discovers far more genes than previously thought

Friday, 07 September 2012

The GENCODE Consortium expects the human genome has twice as many genes than previously thought, many of which might have a role in cellular control and could be important in human disease. This remarkable discovery comes from the GENCODE Consortium, which has done a painstaking and skilled review of available data on gene activity.

Among their discoveries, the team describes more than 10,000 novel genes; identify genes that have 'died' and others that are being resurrected. The GENCODE Consortium reference gene catalogue has been one of the underpinnings of the larger ENCODE Project and will be essential for the full understanding of the role of our genes in disease.

The GENCODE Consortium is part of the ENCODE Project that, today, publishes 30 research papers describing findings from their nearly decade-long effort to describe comprehensively all the active regions of our human genome. ENCODE was launched in 2003 after the completion of the Human Genome Project, and brought together an international group of scientists tasked with identifying and describing all functional regions of the human genome sequence.

"We have uncovered a staggering array of genes in our genome, simply because we can examine many genomes in a detail that was not possible a decade ago," says Dr. Jennifer Harrow, GENCODE principle investigator from the Wellcome Sanger Institute. 

"As sequencing technology improves, so we have much more data to explore.

"But our work remains a skilled effort to annotate correctly our human genome - or, more precisely, our human genomes, for each of us differ. These vast texts of genetic information will not give up their secrets easily. GENCODE has made amazing strides to enable immediate access of its reference gene set by other researchers."

The team more accurately described the genes that contain the genetic code to make proteins: they found 20,687 such protein-coding genes, a value that has not changed greatly from previous work. The new set captures far more of the alternative forms of these genes found in different cell types.

More significant are their findings on genes that do not contain genetic code to make proteins - non-coding genes - and the graveyard of supposedly 'dead' genes from which some are emerging, resurrected from the catalogue of pseudogenes.

They mapped and described 9,277 long non-coding genes, a relatively new type that acts, not through producing a protein, but directly through its RNA messenger. Long non-coding RNAs derived from these genes can play a significant part in human biology and disease, but they remain only poorly understood.

"If the Human Genome Project was the baseline for genetics, ENCODE is the baseline for biology, and GENCODE are the parts that make the human biological machine work. Our list is essential to all those who would fix the human machine," said Dr. Tim Hubbard.

The new map of such genetic components gives researchers more avenues to explore in their quest to understand human biology and human disease. Remarkably, the team thinks their job is not complete and believes that there may be another 10,000 of these genes yet to be uncovered.

"Our initial work from the Human Genome Project suggested there were around 20,000 protein-coding genes and that value has not changed greatly," says Professor Roderic Guigo, GENCODE principle investigator from Centre for Genomic Regulation, Barcelona.

"However GENCODE has shown that long non-coding RNAs are far more numerous and important than previously thought"

"The limited knowledge we have of the class of long non-coding RNAs suggests they might play a major role in regulating the activity of other genes. If this is generally true of this group, we have much more to explore than we imagined."

As dramatic, GENCODE has catalogued for the first time a set of more than 11,000 pseudogenes by examining the entire human genome. There is some emerging evidence that many of these genes, too, might have some biological activity.

The GENCODE team predicts that at least 9% of pseudogenes may be active with some controlling the activity of other genes. Pseudogenes have been implicated in many biological activities, such as the prevention of certain elements known to be involved in the development of cancer.

"At the announcement of the Human Genome Project draft sequence, we emphasized this was the end of the beginning, that 'at present most genes - probably tens of thousands - remain a mystery'", says Dr. Tim Hubbard, lead principle investigator of GENCODE from the Wellcome Trust Sanger Institute. 

"Today, we describe many thousands of genes for the first time."

"If the Human Genome Project was the baseline for genetics, ENCODE is the baseline for biology, and GENCODE are the parts that make the human biological machine work. Our list is essential to all those who would fix the human machine."

The GENCODE human reference set will be updated every three months to ensure that models are continually refined and assessed based on new experimental data deposited in the public databases.

Source: Wellcome Trust Sanger Institute 

Contact: Don Powell

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ZenMaster

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For more on stem cells and cloning, go to CellNEWS at

http://cellnews-blog.blogspot.com/

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Gorilla Genome Sheds New Light on Human Evolution

What have we got in common with a gorilla? An insight into human evolution from the gorilla genome sequence 
Wednesday, 07 March 2012

Kamilah from San Diego Zoo.

Researchers announce today that they have completed the genome sequence for the gorilla – the last genus of the living great apes to have its genome decoded. While confirming that our closest relative is the chimpanzee, the team shows that much of the human genome more closely resembles the gorilla than it does the chimpanzee genome.

This is the first time scientists have been able to compare the genomes of all four living great apes: humans, chimpanzees, gorillas and orang-utans. This study provides a unique perspective on our own origins and is an important resource for research into human evolution and biology, as well as for gorilla biology and conservation.

"The gorilla genome is important because it sheds light on the time when our ancestors diverged from our closest evolutionary cousins. It also lets us explore the similarities and differences between our genes and those of gorilla, the largest living primate," says Aylwyn Scally, first author from the Wellcome Trust Sanger Institute.

"Using DNA from Kamilah, a female western lowland gorilla, we assembled a gorilla genome sequence and compared it with the genomes of the other great apes. We also sampled DNA sequences from other gorillas in order to explore genetic differences between gorilla species."

The team searched more than 11,000 genes in human, chimpanzee and gorilla for genetic changes important in evolution. Humans and chimpanzees are genetically closest to each other over most of the genome, but the team found many places where this is not the case. 15% of the human genome is closer to the gorilla genome than it is to chimpanzee, and 15% of the chimpanzee genome is closer to the gorilla than human.

In all three species, genes relating to sensory perception, hearing and brain development showed accelerated evolution – and particularly so in humans and gorillas.

"Our most significant findings reveal not only differences between the species reflecting millions of years of evolutionary divergence, but also similarities in parallel changes over time since their common ancestor," says Dr Chris Tyler-Smith, senior author from the Wellcome Trust Sanger Institute.

"We found that gorillas share many parallel genetic changes with humans including the evolution of our hearing. Scientists had suggested that the rapid evolution of human hearing genes was linked to the evolution of language. Our results cast doubt on this, as hearing genes have evolved in gorillas at a similar rate to those in humans."

This research also illuminates the timing of splits between species. Although we commonly think of species diverging at a single point in time, this does not always reflect reality: species can separate over an extended period of time.

The team found that divergence of gorillas from humans and chimpanzees occurred around ten million years ago. The split between eastern and western gorillas was much more recent, in the last million years or so, and was gradual, although they are now genetically distinct. This split is comparable in some ways to the split between chimpanzees and bonobos, or modern humans and Neanderthals.

"Our research completes the genetic picture for overall comparisons of the great apes," says Dr Richard Durbin, senior author from the Wellcome Trust Sanger Institute,

"After decades of debate, our genetic interpretations are now consistent with the fossil record and provide a way for palaeontologists and geneticists to work within the same framework.”

"Our data are the last genetic piece we can gather for this puzzle: there are no other living great ape genera to study."

Gorillas survive today in just a few isolated and endangered populations in the equatorial forests of central Africa. They are severely threatened and their numbers are diminishing. This research not only informs us about human evolution, but highlights the importance of protecting and conserving the full diversity of these remarkable species.

Source: Wellcome Trust Sanger Institute

Contact: Aileen Sheehy

Reference:

Insights into hominid evolution from the gorilla genome sequence
Aylwyn Scally, Julien Y. Dutheil, LaDeana W. Hillier, Gregory E. Jordan, Ian Goodhead, Javier Herrero, Asger Hobolth, Tuuli Lappalainen, Thomas Mailund, Tomas Marques-Bonet, Shane McCarthy, Stephen H. Montgomery, Petra C. Schwalie, Y. Amy Tang, Michelle C. Ward, Yali Xue, Bryndis Yngvadottir, Can Alkan, Lars N. Andersen, Qasim Ayub, Edward V. Ball, Kathryn Beal, Brenda J. Bradley, Yuan Chen, Chris M. Clee, Stephen Fitzgerald, Tina A. Graves, Yong Gu, Paul Heath, Andreas Heger, Emre Karakoc, Anja Kolb-Kokocinski, Gavin K. Laird, Gerton Lunter, Stephen Meader, Matthew Mort, James C. Mullikin, Kasper Munch, Timothy D. O’Connor, Andrew D. Phillips, Javier Prado-Martinez, Anthony S. Rogers, Saba Sajjadian, Dominic Schmidt, Katy Shaw, Jared T. Simpson, Peter D. Stenson, Daniel J. Turner, Linda Vigilant, Albert J. Vilella, Weldon Whitener, Baoli Zhu, David N. Cooper, Pieter de Jong, Emmanouil T. Dermitzakis, Evan E. Eichler, Paul Flicek, Nick Goldman, Nicholas I. Mundy, Zemin Ning, Duncan T. Odom, Chris P. Ponting, Michael A. Quail, Oliver A. Ryder, Stephen M. Searle, Wesley C. Warren, Richard K. Wilson, Mikkel H. Schierup, Jane Rogers, Chris Tyler-Smith & Richard Durbin
Nature 483, 169–175, 08 March 2012, doi:10.1038/nature10842
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ZenMaster

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For more on stem cells and cloning, go to CellNEWS at
http://cellnews-blog.blogspot.com/

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