“Open” Stem Cell Chromosomes Reveal New Possibilities for Diabetes

Researchers map chromosomal changes that must take place before stem cells can be used to produce pancreatic and liver cells 

Thursday, 02 April 2015

These are pancreatic cells derived from

embryonic stem cells. Credit: UC San Diego

School of Medicine. 

Stem cells hold great promise for treating a number of diseases, in part because they have the unique ability to differentiate, specializing into any one of the hundreds of cell types that comprise the human body. Harnessing this potential, though, is difficult. In some cases, it takes up to seven carefully orchestrated steps of adding certain growth factors at specific times to coax stem cells into the desired cell type. Even then, cells of the intestine, liver and pancreas are notoriously difficult to produce from stem cells. Writing in Cell Stem Cell April 2, researchers at University of California, San Diego School of Medicine have discovered why.

It turns out that the chromosomes in laboratory stem cells open slowly over time, in the same sequence that occurs during embryonic development. It isn’t until certain chromosomal regions have acquired the “open” state that they are able to respond to added growth factors and become liver or pancreatic cells. This new understanding, say researchers, will help spur advancements in stem cell research and the development of new cell therapies for diseases of the liver and pancreas, such as type 1 diabetes.

“Our ability to generate liver and pancreatic cells from stem cells has fallen behind the advances we’ve made for other cell types,” said Maike Sander, MD, professor of paediatrics and cellular and molecular medicine and director of the Pediatric Diabetes Research Center at UC San Diego.

“So we haven’t yet been able to do things like test new drugs on stem cell-derived liver and pancreatic cells. What we have learned is that if we want to make specific cells from stem cells, we need ways to predict how those cells and their chromosomes will respond to the growth factors.”

Sander led the study, together with co-senior author Bing Ren, PhD, professor of cellular and molecular medicine at UC San Diego and Ludwig Cancer Research member.

Chromosomes are the structures formed by tightly wound and packed DNA. Humans have 46 chromosomes – 23 inherited from each parent. Sander, Ren and their teams first made maps of chromosomal modifications over time, as embryonic stem cells differentiated through several different developmental intermediates on their way to becoming pancreatic and liver cells. Then, in analysing these maps, they discovered links between the accessibility (openness) of certain regions of the chromosome and what they call developmental competence – the ability of the cell to respond to triggers like added growth factors.

“We’re also finding that these chromosomal regions that need to open before a stem cell can fully differentiate are linked to regions where there are variations in certain disease states,” Sander says.

In other words, if a person were to inherit a genetic variation in one of these chromosomal regions and his or her chromosome didn’t open up at exactly the right time, he or she could hypothetically be more susceptible to a disease affecting that cell type. Sander’s team is now working to further investigate what role, if any, these chromosomal regions and their variations play in diabetes.

Source: UCSD

Contact: Heather Buschman

Reference:

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

Allen Wang, Feng Yue, Yan Li, Ruiyu Xie, Thomas Harper, Nisha A. Patel, Kayla Muth, Jeffrey Palmer, Yunjiang Qiu, Jinzhao Wang, Dieter K. Lam, Jeffrey C. Raum, Doris A. Stoffers, Bing Ren, Maike Sander

Cell Stem Cell, Volume 16, Issue 4, p386–399, 2 April 2015, DOI: http://dx.doi.org/10.1016/j.stem.2015.02.013

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The ISSCR Issues Statement on Human Germ Line Genome Modification

The International Society for Stem Cell Research has released a statement calling for a moratorium on attempts to apply nuclear genome editing of the human germ line in clinical practice

Sunday, 22 March 2015

In a statement released on Thursday, the International Society for Stem Cell Research called for a moratorium on attempts at clinical application of nuclear genome editing of the human germ line to enable more extensive scientific analysis of the potential risks of genome editing and broader public discussion of the societal and ethical implications.

Technologies used to introduce changes into the DNA sequence of cells have advanced rapidly, making genome editing increasingly simple. Genome editing is feasible, not just in the somatic cells of an adult organism, but also in early embryos, as well as the gametes (sperm and egg) that carry the inheritable, germ line DNA. Research involving germ line nuclear genome editing has been performed to date in many organisms, including mice and monkeys, and applications to human embryos are possible.

The ISSCR statement raises significant ethical, societal and safety considerations related to the application of nuclear genome editing to the human germ line in clinical practice. Current genome editing technologies carry risks of unintended genome damage, in addition to unknown consequences. Moreover, consensus is lacking on what, if any, therapeutic applications of germ line genome modification might be permissible.

The statement calls for a moratorium on attempts to apply nuclear genome editing of the human germ line in clinical practice, as scientists currently lack an adequate understanding of the safety and potential long term risks of germ line genome modification. Moreover, the ISSCR asserts that a deeper and more rigorous deliberation on the ethical, legal and societal implications of any attempts at modifying the human germ line is essential if its clinical practice is ever to be sanctioned.

In calling for the above moratorium, the ISSCR is not taking a position on the clinical testing of mitochondrial replacement therapy, a form of germ line modification that entails replacing the mitochondria (found outside the nucleus) in the eggs of women at risk of transmitting certain devastating diseases to their children.

Source: International Society for Stem Cell Research

Contact: Michelle Quivey

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NIH-Supported Researchers Map Epigenome of More Than 100 Tissue and Cell Types

NIH-Supported Researchers Map Epigenome of More Than 100 Tissue and Cell Types

Thursday, 19 February 2015

Much like mapping the human genome laid the foundations for understanding the genetic basis of human health, new maps of the human epigenome may further unravel the complex links between DNA and disease. The epigenome is part of the machinery that helps direct how genes are turned off and on in different types of cells.

Researchers supported by the National Institutes of Health Common Fund's Roadmap Epigenomics Program have mapped the epigenomes of more than 100 types of cells and tissues, providing new insight into which parts of the genome are used to make a particular type of cell. The data, available to the biomedical research community, can be found at the National Center for Biotechnology Information website.

Reference epigenomes are available for more than 100 cell and tissue types.
Credit: Image courtesy of Nature and Roadmap Epigenomics Consortium. 

"This represents a major advance in the ongoing effort to understand how the 3 billion letters of an individual's DNA instruction book are able to instruct vastly different molecular activities, depending on the cellular context," said NIH Director Francis Collins, M.D., Ph.D.

"This outpouring of data-rich publications, produced by a remarkable team of creative scientists, provides powerful momentum for the rapidly growing field of epigenomics."

Researchers from the NIH Common Fund's Roadmap Epigenomics Program published a description of the epigenome maps in the journal Nature. More than 20 additional papers, published in Nature and Nature-associated journals, show how these maps can be used to study human biology.

"What the Roadmap Epigenomics Program has delivered is a way to look at the human genome in its living, breathing nature from cell type to cell type," said Manolis Kellis, Ph.D., professor of computer science at the Massachusetts Institute of Technology, Cambridge, and senior author of the paper.

Understanding epigenomics

Almost all human cells have identical genomes that contain instructions on how to make the many different cells and tissues in the body. During the development of different types of cells, regulatory proteins turn genes on and off and, in doing so, establish a layer of chemical signatures that make up the epigenome of each cell. In the Roadmap Epigenomics Program, researchers compared these epigenomic signatures and established their differences across a variety of cell types. The resulting information can help us understand how changes to the genome and epigenome can lead to conditions such as Alzheimer's disease, cancer, asthma, and foetal growth abnormalities.

An epigenomic signature can be made on the

genome in two ways, both of which play a role in

turning genes off or on. The first occurs when

chemical tags called methyl groups are attached

to a DNA molecule directly (DNA methylation).

The second occurs when a variety of chemical

tags attach to the tails of histone proteins that

package DNA (histone modifications). Credit:

Image courtesy of John Stamatoyannopoulos

and Rae Senarighi. 

The value of epigenomic data

Researchers can now take data from different cell types and directly compare them.

"Today, sequencing the human genome can be done rapidly and cheaply, but interpreting the genome remains a challenge," said Bing Ren, Ph.D., professor of cellular and molecular medicine at the University of California, San Diego, and co-author of the Nature paper and several of the associated papers.

"These 111 reference epigenome maps are essentially a vocabulary book that helps us decipher each DNA segment in distinct cell and tissue types. These maps are like snapshots of the human genome in action."

"This is the most comprehensive catalogue of epigenomic data from primary human cells and tissues to date," said Lisa Helbling Chadwick, Ph.D., project team leader and a program director at the National Institute of Environmental Health Sciences (NIEHS), part of NIH.

"This coordinated effort, along with uniform data processing, makes it much easier for researchers to make direct comparisons across the entire data set."

"Researchers from the 88 projects supported by the program, including those from this recent series of papers, have propelled the development of new epigenomic technologies," said John Satterlee, Ph.D., co-coordinator of the Roadmap Epigenomics Program, and program director at the National Institute on Drug Abuse (NIDA), part of NIH. Satterlee added that the work of this program has served as a foundation for continued exploration of the human epigenome through the International Human Epigenome Consortium.

"With this increased understanding of the full epigenome, and the datasets available to the entire scientific community, the NIH Common Fund is striving to catalyse future research, to aid the understanding of how epigenomics plays a role in human diseases, with the expectation that further studies will identify early indications of disease and targets for therapeutics," said James Anderson, M.D., Ph.D., director of NIH Division of Program Coordination, Planning, and Strategic Initiatives that oversees the NIH Common Fund.

NIDA, NIEHS, and the National Institute on Deafness and Other Communication Disorders are co-administrators of the NIH Common Fund's Epigenomics Program.

Source: National Institute of Environmental Health Sciences

Contact: Robin Mackar

Reference:

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium

Nature, (2015); doi: 10.1038/nature14248

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A Protein Required for Integrity of Induced Pluripotent Stem Cells

SIRT1 is necessary for telomere elongation and genome integrity during cell reprogramming

Monday, 21 April 2014

This image shows chromosome abnormalities in

reprogrammed cells in which SIRT1 protein has

been removed (in red). Credit: Centro Nacional

de Investigaciones Oncologicas. 

Cell reprogramming converts specialised cells such as nerve cells or skin cells towards an embryonic stem cell state. This reversal in the evolutionary development of cells also requires a reversal in the biology of telomeres, the structures that protect the ends of chromosomes; whilst under normal conditions telomeres shorten over time, during cell reprogramming they follow the opposite strategy and increase in length.

A study published today in the journal Stem Cell Reports, from the Cell Publishing Group, reveals that the SIRT1 protein is needed to lengthen and maintain telomeres during cell reprogramming. SIRT1 also guarantees the integrity of the genome of stem cells that come out of the cell reprogramming process; these cells are known as iPS cells (induced Pluripotent Stem cells).

The study has been carried out by the Spanish National Cancer Research Centre's Telomeres and Telomerase Group, in collaboration with the CNIO's Transgenic Mice Core Unit.

Since the Japanese scientist Shinya Yamanaka first obtained iPS cells from adult tissue in 2006, regenerative medicine has become one of the most exciting and rapidly developing fields in biomedicine. There is a very ambitious aim, given the ability to differentiate iPS cells into any type of cell; this would allow for the regeneration of organs damaged by diseases such as Alzheimer, diabetes or cardiovascular diseases.

The nature of iPS cells however is causing intense debate. The latest research shows that chromosome aberrations and DNA damage can accumulate in these cells.

"The problem is that we don't know if these cells are really safe", says María Luigia De Bonis, a postdoctoral researcher of the Telomeres and Telomerase Group who has done a large part of the work.

In 2009, the same CNIO laboratory discovered that telomeres increase in length during cell reprogramming (Marion et al., Cell Stem Cell, 2009); this increase is important as it allows stem cells to acquire the immortality that characterises them.

One year later, it was demonstrated that the levels of SIRT1 — a protein belonging to the sirtuin family and that is involved in the maintenance of telomeres, genomic stability and DNA damage response — are increased in embryonic stem cells. The question CNIO researchers asked was: is SIRT1 involved in cell reprogramming?

Safer Stem Cells

Employing mouse models and cell cultures as research tools in which SIRT1 had been removed, the team has discovered that this protein is necessary for reprogramming to occur correctly and safely.

"We observed cell reprogramming in the absence of SIRT1, but over time the produced iPS cells lengthen telomeres less efficiently and suffer from chromosome aberrations and DNA damage," says De Bonis.

"SIRT1 helps iPS cells to remain healthy," she concludes.

The authors describe how this protective effect on iPS cells is, in part, mediated by the cMYC regulator. SIRT1 slows the degradation of cMYC, which results in an increase in telomerase (the enzyme that increases telomere length) in cells.

The study sheds light on how cell reprogramming guarantees the healthy functioning of stem cells. This knowledge will help to overcome barriers that come out of the use of iPS cells so they may be used in regenerative medicine.

Source: Centro Nacional de Investigaciones Oncologicas (CNIO) 

Contact: Nuria Noriega

Reference:

SIRT1 Is Necessary for Proficient Telomere Elongation and Genomic Stability of Induced Pluripotent Stem Cells

Maria Luigia De Bonis, Sagrario Ortega, Maria A. Blasco

Stem Cell Reports (2014), http://dx.doi.org/10.1016/j.stemcr.2014.03.002

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Study Dispels Theories of Human Y Chromosome's Demise

Stripped-down chromosome retains key genes for fertility

Friday, 10 January 2014

A comparison of Y chromosomes in eight African and eight European men dispels the common notion that the Y's genes are mostly unimportant and that the chromosome is destined to dwindle and disappear.

"The Y chromosome has lost 90 percent of the genes it once shared with the X chromosome, and some scientists have speculated that the Y chromosome will disappear in less than 5 million years," said evolutionary biologist Melissa A. Wilson Sayres, a Miller Postdoctoral Fellow in the Department of Integrative Biology at the University of California, Berkeley, and lead author of the new analysis.

Some mammals have already lost their Y chromosome, though they still have males and females and reproduce normally. And last month, researchers reported shuffling some genes in mice to create Y-less males that could produce normal offspring, leading some commentators to wonder whether the chromosome is superfluous.

"Our study demonstrates that the genes that have been maintained, and those that migrated from the X to the Y, are important, and the human Y is going to stick around for a long while," she said.

Wilson Sayres and co-author Rasmus Nielsen, UC Berkeley professor of integrative biology, show in a paper published online today (Jan. 9, 2014) in PLOS Genetics that patterns of variation on the Y chromosome among the 16 men are consistent with natural selection acting to maintain the gene content there, much of which has been shown to play a role in male fertility. The Y chromosome's puny size – it contains 27 unique genes versus thousands on the other chromosomes – is a sign it is lean and stripped down to essentials.

"Melissa's results are quite stunning. They show that because there is so much natural selection working on the Y chromosome, there has to be a lot more function on the chromosome than people previously thought," Nielsen said.

Variations in Y chromosomes are used to track how human populations moved around the globe, and according to Nielsen, the new research will help improve estimates of humans' evolutionary history.

"Melissa has shown that this strong negative selection – natural selection to remove deleterious genes – tends to make us think the dates are older than they actually are, which gives quite different estimates of our ancestors' history," Nielsen said.

Y has degraded over past 200 million

Before about 200 million years ago, when mammals were relatively new on Earth, early versions of the sex chromosomes, X and Y, were just like other pairs of chromosomes: with each generation, they swapped a few genes so that offspring were a mix of their parents' genes. Fertilized eggs that got two proto-Xs became females and eggs with a proto-X and proto-Y became males.

But for some reason, Wilson Sayres said, the gene that triggers the cascade of events that result in male features became fixed on the Y chromosome and attracted other male-specific genes, such as those that control development of the testes, sperm and semen. Many of these turned out to be harmful for females, so the X and Y stopped swapping genes and the two chromosomes began to evolve separately.

"Now the X and Y do not swap DNA over most of their lengths, which means that the Y cannot efficiently fix mistakes, so it has degraded over time," she said.

"In XX females, the X still has a partner to swap with and fix mistakes, which is why we think the X hasn't also degraded."

Wilson Sayres was fascinated by the strange history of the sex chromosomes and in particular the lack of genetic variation worldwide on the Y chromosome compared to the variety seen in DNA on the non-sex chromosomes. This variation, though used to chart human history, was poorly characterized across the entire Y chromosome.

"Y chromosomes are more similar to each other than we expect," said Wilson Sayres.

"There has been some debate about whether this is because there are fewer males contributing to the next generation, or whether natural selection is acting to remove variation."

Did fewer males contribute genes to Y chromosome?

The UC Berkeley researchers demonstrated that if fewer males were the only cause of the low variability, it would mean that fewer than 1 in 4 males throughout history had passed on their Y chromosome each generation. Variations in other human chromosomes, including the X chromosome, make this an unlikely scenario. Instead, they showed that the low variation can be explained by intense natural selection, that is, a strong evolutionary pressure to weed out bad mutations that ended up trimming the chromosome down to its essentials.

"We show that a model of purifying selection acting on the Y chromosome to remove harmful mutations, in combination with a moderate reduction in the number of males that are passing on their Y chromosomes, can explain low Y diversity," Wilson Sayres said.

The researchers also found that all 27 genes on the Y chromosome – the 17 that humans retain after 200 million years, and 10 more recently acquired but poorly understood genes – are likely affected by natural selection. Most of the newer genes, called ampliconic genes, are present in multiple copies on the chromosome and loss of one or more copies has been linked to male infertility.

"These ampliconic regions that we haven't really understood until now are evidently very important and probably should be investigated and studied for fertility," she said.

Wilson Sayres was able to precisely measure Y variability because for the first time she compared variation on a person's Y chromosome with variation on that person's other 22 chromosomes (called autosomes), the X chromosome and the mitochondrial DNA. She used whole genome data from 16 men whose DNA had been sequenced by the Mountain View-based company Complete Genomics Inc., which has the most accurate sequences of the Y chromosome. The company was recently acquired by BGI, the Beijing Genome Institute.

Cross-population studies of variation in the Y chromosome are in their infancy, she said, noting that of the more than 36 mammalian genomes sequenced to date, complete Y chromosomes are only available for three. Most of the 1,000+ human genomes already sequenced do not have sufficiently accurate coverage of the Y to make this type of comparison among individuals, but advances in technology to better characterize DNA will facilitate future analyses of the Y chromosome, she said.

Source: University of California - Berkeley 

Contact: Robert Sanders

Reference:

Natural Selection Reduced Diversity on Human Y Chromosomes

Melissa A. Wilson Sayres, Kirk E. Lohmueller and Rasmus Nielsen

PLOS Genetics, January 09, 2014, DOI: 10.1371/journal.pgen.1004064

See also:

Why is Y Disappearing?

Male sex chromosome losing genes by rapid evolution
CellNEWS - Friday, 17 July 2009 

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Study Finds a Patchwork of Genetic Variation in the Brain

Salk scientists find a surprising degree of variation among genomes of individual neurons from the same brain

Saturday, 02 November 2013

It was once thought that each cell in a person's body possesses the same DNA code and that the particular way the genome is read imparts cell function and defines the individual. For many cell types in our bodies, however, that is an oversimplification. Studies of neuronal genomes published in the past decade have turned up extra or missing chromosomes, or pieces of DNA that can copy and paste themselves throughout the genomes.

The only way to know for sure that neurons from the same person harbour unique DNA is by profiling the genomes of single cells instead of bulk cell populations, the latter of which produce an average. Now, using single-cell sequencing, Salk Institute researchers and their collaborators have shown that the genomic structures of individual neurons differ from each other even more than expected. The findings were published November 1 in Science.

This is Salk scientist Fred H. Gage, professor in

the Laboratory of Genetics. Credit: Courtesy

of the Salk Institute for Biological Studies. 

"Contrary to what we once thought, the genetic makeup of neurons in the brain aren't identical, but are made up of a patchwork of DNA," says corresponding author Fred Gage, Salk's Vi and John Adler Chair for Research on Age-Related Neurodegenerative Disease.

In the study, led by Mike McConnell, a former junior fellow in the Crick-Jacobs Center for Theoretical and Computational Biology at the Salk, researchers isolated about 100 neurons from three people posthumously. The scientists took a high-level view of the entire genome – looking for large deletions and duplications of DNA called copy number variations or CNVs – and found that as many as 41 percent of neurons had at least one unique, massive CNV that arose spontaneously, meaning it wasn't passed down from a parent. The CNVs are spread throughout the genome, the team found.

The miniscule amount of DNA in a single cell has to be chemically amplified many times before it can be sequenced. This process is technically challenging, so the team spent a year ruling out potential sources of error in the process.

"A good bit of our study was doing control experiments to show that this is not an artefact," says Gage.

"We had to do that because this was such a surprise – finding out that individual neurons in your brain have different DNA content."

This is research collaborator Michael McConnell

of the University of Virginia. Credit: Courtesy

of the Salk Institute for Biological Studies.

The group found a similar amount of variability in CNVs within individual neurons derived from the skin cells of three healthy people. Scientists routinely use such induced pluripotent stem cells (iPSCs) to study living neurons in a culture dish. Because iPSCs are derived from single skin cells, one might expect their genomes to be the same.

"The surprising thing is that they're not," says Gage.

"There are quite a few unique deletions and amplifications in the genomes of neurons derived from one iPSC line."

Interestingly, the skin cells themselves are genetically different, though not nearly as much as the neurons. This finding, along with the fact that the neurons had unique CNVs, suggests that the genetic changes occur later in development and are not inherited from parents or passed to offspring.

It makes sense that neurons have more diverse genomes than skin cells do, says McConnell, who is now an assistant professor of biochemistry and molecular genetics at the University Of Virginia School Of Medicine in Charlottesville.

"The thing about neurons is that, unlike skin cells, they don't turn over, and they interact with each other," he says.

"They form these big complex circuits, where one cell that has CNVs that make it different can potentially have network-wide influence in a brain."

Spontaneously occurring CNVs have also been linked to risk for brain disorders such as schizophrenia and autism, but those studies usually pool many blood cells. As a result, the CNVs uncovered in those studies affect many if not all cells, which suggests that they arise early in development.

The purpose of CNVs in the healthy brain is still unclear, but researchers have some ideas. The modifications might help people adapt to new surroundings encountered over a lifetime, or they might help us survive a massive viral infection. The scientists are working out ways to alter genomic variability in iPSC-derived neurons and challenge them in specific ways in the culture dish.

This is research collaborator Ira Hall of the

University of Virginia. Credit: Courtesy of the

Salk Institute for Biological Studies. 

Cells with different genomes probably produce unique RNA and then proteins. However, for now, only one sequencing technology can be applied to a single cell.

"If and when more than one method can be applied to a cell, we will be able to see whether cells with different genomes have different transcriptomes (the collection of all the RNA in a cell) in predictable ways," says McConnell.

In addition, it will be necessary to sequence many more cells, and in particular, more cell types, notes corresponding author Ira Hall, an associate professor of biochemistry and molecular genetics at the University of Virginia.

"There's a lot more work to do to really understand to what level we think the things we've found are neuron-specific or associated with different parameters like age or genotype," he says.

Source: Salk Institute 

Contact: Kat Kearney

Reference:

Mosaic Copy Number Variation in Human Neurons

Michael J. McConnell, Michael R. Lindberg, Kristen J. Brennand, Julia C. Piper, Thierry Voet, Chris Cowing-Zitron, Svetlana Shumilina, Roger S. Lasken, Joris R. Vermeesch, Ira M. Hall, Fred H. Gage

Science 1 November 2013:Vol. 342 no. 6158 pp. 632-637, DOI: 10.1126/science.1243472

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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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A New Gene Essential for Nuclear Reprogramming

The article describes the role of TRF1, a protector of telomeres in cell pluripotency

Wednesday, 05 June 2013

Researchers are still fascinated by the idea of the possibility of reprogramming the cells of any tissue, turning them into cells with the capacity to differentiate into cells of a completely different type — pluripotent cells — and they are still striving to understand how it happens.

A group from the Spanish National Cancer Research Centre (CNIO), headed by researcher Ralph P. Schneider, from the Telomeres and Telomerase Group led by María A. Blasco, publishes this week an article in Nature Communications on the discovery of a new gene called TRF1 that is essential for nuclear reprogramming.

It is also known that TRF1 is indispensable for protecting telomeres, the ends of chromosomes. Existing evidence suggests that the length of telomeres and pluripotency — the capacity of a cell to differentiate into multiple cell types — are related. Pluripotent cells, for example, have very long telomeres — a previous finding at CNIO — but until now no protective protein for the telomeres had been found that was essential for pluripotency.

To investigate the connection between telomeres and pluripotency, researchers generated a 'reporter' mouse: they linked together the TRF1 gene and the gene coding for a green fluorescent protein and created a lineage of mice carrying this new genetic baggage. In these animals, the green fluorescent protein acts as a label to show expression of TRF1.

They discovered that TRF1 is an excellent marker for stem cells, both in adult stem cells — those that are found in tissues and the different organs of the body — and embryonic stem cells. It is also the case with 'induced pluripotent' stem cells (iPS cells), which are pluripotent cells that come from artificially reprogrammed specialised cells.

In the case of tissues, the authors write:

"TRF1 distinguishes adult stem cells and is indispensable for their functioning".

The discovery is useful for both identifying and eventually isolating the stem cell population in tissues, something that is important for the development of regenerative medicine. The cells in which TRF1 is expressed are also the most pluripotent.

In iPS cells, the same thing happens. The authors explain that:

"The expression of TRF1 is an indicator of pluripotency. Those iPS cells that express the highest levels of TRF1 are also the most pluripotent. Furthermore, we demonstrate that TRF1 is necessary for the induction and maintenance of pluripotency, inhibiting the triggering of DNA damage responses and apoptosis ('cell suicide')".

Source: Centro Nacional de Investigaciones Oncologicas (CNIO) 

Reference:

TRF1 is a stem cell marker and is essential for the generation of induced pluripotent stem cells

Ralph P. Schneider, Ianire Garrobo, Miguel Foronda, Jose A. Palacios, Rosa M. Marión, Ignacio Flores, Sagrario Ortega, Maria A. Blasco

Nature Communications, doi:10.1038/ncomms2946

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Researchers Chart Epigenomic of Stem Cells that Mimic Early Human Development

Collaborative study will help overcome hurdles to using stem cells to treat diseases and injuries

Thursday, 09 May 2013

Scientists have long known that control mechanisms known collectively as "epigenetics" play a critical role in human development, but they did not know precisely how alterations in this extra layer of biochemical instructions in DNA contribute to development.

Now, in the first comprehensive analysis of epigenetic changes that occur during development, a multi-institutional group of scientists, including several from the Salk Institute for Biological Studies, has discovered how modifications in key epigenetic markers influence human embryonic stem cells as they differentiate into specialized cells in the body. The findings were published May 9 in Cell.

Professor Joseph R. Ecker, Plant Molecular and

Cellular Biology Laboratory, Howard Hughes

Medical Institute and Gordon and Betty Moore

Foundation Investigator, Salk International

Council Chair in Genetics. Credit:  Courtesy of 

the Salk Institute for Biological Studies.

"Our findings help us to understand processes that occur during early human development and the differentiation of a stem cell into specialized cells, which ultimately form tissues in the body," says co-lead author Joseph R. Ecker, a professor and director of Salk's Plant Molecular and Cellular Biology Laboratory and holder of the Salk International Council Chair in Genetics.

Scientists have established that the gene expression program encoded in DNA is carried out by proteins that bind to regulatory genes and modulate gene expression in response to environmental cues. Growing evidence now shows that maintenance of this process depends on epigenetic marks such as DNA methylation and chromatin modifications, biochemical processes that alter gene expression as cells divide and differentiate from embryonic stem cells into specific tissues. Epigenetic modifications - collectively known as the epigenome - control which genes are turned on or off without changing the letters of the DNA alphabet (A-T-C-G), providing cells with an additional tool to fine-tune how genes control the cellular machinery.

In their study, the Salk researchers and their collaborators from several prominent research institutions across the United States examined the beginning state of cells, before and after they developed into specific cell types. Starting with a single cell type-the H1 human embryonic stem cell - the most widely studied stem cell line to date - the team followed the cells' epigenome from development to different cell states, looking at the dynamics in changes to epigenetic marks from one state to another. Were they methylated, an essential process for normal development, or unmethylated?  

What happened to the cells during development? What regulatory processes occurred in the cell lineage?

The scientists found sections of the DNA that activate regulatory genes, which in turn control the activity of other genes, tend to have different amounts of letters of the DNA alphabet, "C" and "G" specifically, depending on when these regulatory genes are turned on during development.  

Additionally, regulatory genes that control early development are often located on stretches of DNA called methylation valleys, or DMVs, that are generally CG rich and devoid of epigenetic chemical modifications known as methylation. Consequently, these genes have to be regulated by another epigenetic mechanism, which the authors found were chemical changes called chromatin modifications. Chromatin is the mass of material-DNA and proteins-in a cell's nucleus that helps to control gene expression.

On the other hand, genes active in more mature cells whose tissue type is already determined tend to be CG poor and regulated by DNA methylation. The results suggest that distinct epigenetic mechanisms regulate early and late states of embryonic stem cell differentiation.

"Epigenomic studies of how stem cells differentiate into distinct cell types are a great way to understand early development of animals," says Ecker, who is also a Howard Hughes Medical Institute and Gordon and Betty Moore Foundation Investigator.

"If we understand how these cells' lineages originate, we can understand if something goes right or wrong during differentiation. It's a very basic study, but there are implications for being able to produce good quality cell types for various therapies."

For example, says Matthew Schultz, a graduate student in Ecker's lab, "understanding how development plays out normally could give us clues about how to reverse the process and turn normal adult cells into stem cells to regenerate tissues."

One area where the findings may help is in the study of tumour development. In normal tissue, DMVs are unmethylated, but in cancer, especially breast, colon and lung cancer, they are hypermethylated, suggesting, says Ecker, that alterations in the DNA methylation machinery might be an important mechanism aiding tumour development. He says further investigation is required to develop a greater understanding of this process.

Source: Salk Institute for Biological Studies

Contact: Andy Hoang

Reference:

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

Wei Xie, Matthew D. Schultz, Ryan Lister, Zhonggang Hou, Nisha Rajagopal, Pradipta Ray, John W. Whitaker, Shulan Tian, R. David Hawkins, Danny Leung, Hongbo Yang, Tao Wang, Ah Young Lee, Scott A. Swanson, Jiuchun Zhang, Yun Zhu, Audrey Kim, Joseph R. Nery, Mark A. Urich, Samantha Kuan, Chia-an Yen, Sarit Klugman, Pengzhi Yu, Kran Suknuntha, Nicholas E. Propson, Huaming Chen, Lee E. Edsall, Ulrich Wagner, Yan Li, Zhen Ye, Ashwinikumar Kulkarni, Zhenyu Xuan, Wen-Yu Chung, Neil C. Chi, Jessica E. Antosiewicz-Bourget, Igor Slukvin, Ron Stewart, Michael Q. Zhang, Wei Wang, James A. Thomson, Joseph R. Ecker, and Bing Ren
Cell, 09 May 2013, 10.1016/j.cell.2013.04.022

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