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News Article | December 15, 2016
Site: www.eurekalert.org

Genomic analysis of the Iberian lynx confirms that it is one of the species with the least genetic diversity among individuals, which means that it has little margin for adaptation Spanish scientists have sequenced the genome of the Iberian lynx (Lynx pardinus), currently one of the world's most endangered felines. They have confirmed the "extreme erosion" suffered by its DNA. The Iberian lynx has one of the least genetically-diverse genomes. It is even less diverse than other endangered mammals, such as the cheetah or Tasmanian devil, or birds, like the crested ibis or osprey. The study, being published today in the scientific journal Genome Biology, has been coordinated by scientists from the Doñana Biological Station (CSIC). The Centre for Genomic Regulation (CRG) contributed to this research project from the very beginning including several groups and facilities. In particular, the laboratories of Roderic Guigó, Cedric Notredame, and Toni Gabaldón at the Bioinformatics and Genomics Programme as well as the CRG Bioinformatics unit. This is the first mammal genome of reference generated entirely in Spain. The project, financed by Banco Santander and managed by the Fundación General CSIC, has integrated the efforts of 50 scientists from research groups of 12 institutions, two of them from outside Spain, that cover a broad range of disciplines, including bioinformatics, genomics, oncology, evolution and conservation. The scientists have managed to read and organize 2.4 billion letters of DNA from Candiles, a male lynx born in the Sierra Morena lynx population, who now forms part of a program for breeding in captivity. To do so, they have used new sequencing techniques and developed innovative procedures to generate a high-quality draft genome on a limited budget. A total of 21,257 genes were identified, a number similar to that of human beings and other mammals, and they have been compared to those of cats, tigers, cheetahs and dogs. Specifically, Toni Gabaldón's group at the Centre for Genomic Regulation in Barcelona has compared the Iberian lynx genome with those of other species, attempting to identify genes that have lost their function because they have remained isolated and the existence of a small population of specimens of this species. Researchers have found evidence of modifications in genes related with the senses of hearing, sight and smell to facilitate the adaptation of the lynx to its environment, which have enabled them to become exceptional hunters specialized in rabbits as prey. History and diversity of the Iberian lynx With the aim of studying the history and genetic diversity of the species, analysis was conducted on the genomes of another ten Iberian lynxes from Doñana and Sierra Morena, the only two surviving populations on the Iberian Peninsula, which have been isolated from each other for decades. Researchers have also completed a comparative analysis with a European lynx, to discover the bonds between the two lynxes that inhabit Eurasia. The Iberian lynx began to diverge from its sister species, the Eurasian lynx (Lynx lynx) some 300,000 years ago, and the two species became completely separated some 2,500 years ago. Throughout that period, they continued to cross-breed and exchange genes, probably in the periods between glaciations, when the climatology allowed the species to spread and encounter each other on the Iberian Peninsula and in southern Europe. The demographic history of the Iberian lynx has been marked by three historic declines, the last of which took place some 300 years ago, decimating its population. In addition to this, there was a drastic drop in the number of specimens in the 20th century due to its persecution, the destruction of its habitat, and two major viral epidemics suffered by the rabbit, its main food source. Scientists have interpreted these demographic drops as the cause of the low levels of diversity observed, and warn that this could impair the lynx's capacity to adapt to changes in its environment (climate, disease, etc.). Furthermore, existence of multiple potentially harmful genetic variants has been confirmed, which could be contributing to the reduced survival and reproduction rates of the species. This genetic deterioration is especially marked in the Doñana population-smaller, and isolated for a longer period-which has half the genetic diversity of the Sierra Morena group. Nevertheless, the study reflects the situation before the exchange between the two relict populations and their inter-breeding in captivity were begun. These measures, taken within the Iberian lynx conservation program, have led to improvement of the species' genetic situation in recent years. The use of new genomic resources, within the framework of the project, will contribute to optimizing management aimed at preserving the greatest genetic diversity, in addition to diminishing these populations' genetic defects as much as possible. In addition to Doñana Biological Station (EBD-CSIC), also taking part in the project were the National Center for Genomic Analysis (CNAG-CRG); the Centre for Genomic Regulation (CRG); the Spanish National Cancer Research Center (CNIO); the Evolutionary Genomics Group of the Hospital del Mar Medical Research Institute (IMIM); the Institute of Evolutionary Biology (IBE, CSIC-UPF); the University Institute of Oncology of Asturias (IUOPA); the Institut de Biotecnologia i de Biomedicina and the Unit of Cell Culture of the Autonomous University of Barcelona (UAB); the Biological Research Center (CIB-CSIC) and the Catalan Institution for Research and Advanced Studies (ICREA). Furthermore, the project has received the cooperation of a team from College of Veterinary Medicine of Texas A&M University and the Bioinformatics Research Center of the University of Aarhus (Denmark).


In contrast to the cells in the rest of the body, sex cells hold half the number of chromosomes (they are haploid) as a result of this special kind of cell division. In meiosis, a precursor cell —primordial germ cell— produces four spermatozoids during spermatogenesis, while only one oocyte is formed during oogenesis (the other three cells die during the process). Mice deficient in RingoA, generated in Nebreda's Signalling and Cell Cycling Laboratory, are apparently healthy but both sexes are completely sterile. After three years of experiments, IRB Barcelona postdoctoral researchers Petra Mikolcevic and Michitaka Isoda describe the molecular imbalances that occur during meiosis as a result of the absence of this protein. This study sheds new light on a key process for all forms of life that engage in sexual reproduction. "We all start life through meiosis so understanding how this process works is intellectually interesting," says Nebreda. Although meiosis was first described in the late 19th century, "many questions remain unanswered," explains this scientist, holder of a European Research Council grant. "There are no good in vitro models available to study meiosis. It is difficult to extract spermatocytes and to perform studies in plates; they have to be studied in the testicles. And oocytes are even worse because ovules are formed in early stages of development and working with embryos is technically complex." The scientists have discovered that RingoA is a key activator of Cdk2, the protein kinase with which it forms a complex required for meiosis. In fact, the genetic mouse model deficient in Cdk2, which was reported 12 years ago by Mariano Barbacid's group at CNIO, is also viable but sterile and shows the exact same alterations in meiosis as those observed by the researchers at IRB Barcelona. "In biology, if two practically indistinguishable phenotypes are obtained, it is an indication that the proteins have the same function and that they may work together." What was not known until now was that RingoA is the key partner for Cdk2 in meiosis, as Cdk2 normally forms complexes with another family of proteins called cyclins. The study demonstrates that RingoA is active at telomeres—structures that protect the ends of chromosomes and where Cdk2 is also found.  During meiosis, telomeres allow chromosomes to attach to the nuclear membrane, thus allowing them to exchange DNA fragments. This recombination of chromosomes is an essential feature of meiosis. Without the RingoA-Cdk2 complex, the telomeres of the chromosomes do not tether to the membrane but rather float in the nucleus, leading to chaotic recombination. The breaks in DNA needed for fragment exchange are not repaired and thus meiosis is not completed. Consequently, sex cells are not formed. "It would not be unreasonable to consider the development of a male contraceptive based on RingoA-Cdk2 inhibitors," proposes Nebreda. In the same way that women produce oocytes during embryo development, men can produce spermatozoids throughout adulthood. "If the pharmaceutical industry wanted to invest in this field, we have the biochemical techniques set up for the identification of inhibitors." Explore further: Researchers identify first sex chromosome gene involved in meiosis and male infertility More information: Essential role of the Cdk2 activator RingoA in meiotic telomere tethering to the nuclear envelope. Nature Comms. (2016, 30 March): DOI: 10.1038/NCOMMS11084


News Article | December 28, 2016
Site: www.eurekalert.org

The study of the evolution of thousands of bacterial proteins allows deciphering many interactions between human proteins. The results will help to clarify the molecular details of thousands of interactions potentially involved in diseases such as cancer. Cells operate like an incredibly well-synchronized orchestra of molecular interactions among proteins. Understanding this molecular network is essential not only to understand how an organism works but also to determine the molecular mechanisms responsible for a multitude of diseases. In fact, it has been observed that protein interacting regions are preferentially mutated in tumours. The investigation of many of these interactions is challenging. However, a study coordinated by Simone Marsili and David Juan, from Alfonso Valencia's team at the CNIO, will advance our knowledge on thousands of them. The work, published in the journal Proceedings of the National Academy of Sciences (PNAS), demonstrates that it is possible to understand a significant number of interactions among human proteins from the evolution of their counterparts in simpler cells, such as bacteria cells. According to Juan Rodríguez, from the Structural Computational Biology Group at the CNIO and first author of the paper, "the complexity of human beings does not only result from the number of proteins that we have, but primarily from how they interact with each other. However, out of 200,000 protein-protein interactions estimated, only a few thousand have been characterised at the molecular level". It is very difficult to study the molecular properties of many important interactions without reliable structural information. It is this "twilight zone" that, for the first time, CNIO researchers have managed to explore. FROM BACTERIA TO HUMANS TO UNDERSTAND DISEASES Although more than 3,000 million years of evolution separate bacteria and humans, the CNIO team has utilized the information accumulated over thousands of bacterial sequences to predict interactions between proteins in humans. "We have used the protein coevolution phenomenon: proteins that interact tend to experience coordinated evolutionary changes that maintain the interaction despite the accumulation of mutations over time," says David Juan. "We have demonstrated that we can use this phenomenon to detect molecular details of interactions in humans that we share with very distant species. What is most interesting is that this allows us to transfer information from bacteria in order to study interactions in humans that we knew almost nothing about," adds Simone Marsili. These new results may lead to important implications for future research. "A deeper understanding of these interactions opens the door to the modeling of three-dimensional structures that may help us to design drugs targeting important interactions in various types of cancer," explains David Juan. "This knowledge can also improve our predictions of the effects of various mutations linked to tumour development," says Rodríguez. The laboratory of Alfonso Valencia, head of the Structural Biology and Biocomputing Programme, has been working in the field of protein coevolution since the 1990s. This field has significantly advanced in recent years. "Thanks to the amount of biological data that is being generated today, we can use new computational methods that take into account a greater number of factors," explains Valencia. According to the researchers, the pace of innovation in massive experimental techniques is providing additional data, making it possible to design more complex statistical models that provide an ever more complete view of the biological systems, "something particularly important in multifactorial diseases, such as cancer." This work was supported by the Spanish Ministry of Economy and Competitiveness and the European Regional Development Fund.


SUMO protein with the areas marked with ubiquitin in green. Credit: CNIO Three years ago, the research team directed by Óscar Fernández-Capetillo, head of the Genomic Instability Group at the Spanish National Cancer Research Centre (CNIO), obtained, for the first time, a panoramic view of the proteins that intervene in one of the most important and delicate cellular processes: the copying of genetic material during cellular division. They observed that the parts of the genome where the DNA was copied were also very rich in the modification by some very particular proteins, SUMOylations, and poor in others, ubiquitinations, but they were unable to understand why. The continuation of the paper, published today in the Nature Structural & Molecular Biology journal, reveals how the balance between these chemical markers in these regions is, in fact, key for the division of genetic material. During this process, the USP7 protein travels with an entourage of molecules that form part of the replisome—a set of proteins involved in copying the DNA—and eliminates the ubiquitination marks of proteins in the complex, thus explaining the low concentration of ubiquitin in these areas. "USP7 acts as an traffic officer that regulates the marks or traffic signs near the replisome. Eliminating ubiquitin prevents the proteins at the replisome from being expelled, thus favouring their concentration and the DNA copying process," explains Fernández-Capetillo. As the team described in the previous paper, replisomes contain up to 50 different proteins that participate in the delicate process of copying genetic material. Some proteins open DNA's double helix, others twist it to favour copying, others stabilise it, etc. They all move together through the genome to ensure a complete copy. In order to understand the role of USP7 and its cutting action on ubiquitin marks during the DNA copying process, the researchers used advanced protein tools. "We knew that replisome proteins could present both modifications simultaneously [ubiquitinations and SUMOylations], but we did not know how they worked," explains Fernández-Capetillo. "We now know that USP7 eliminates the ubiquitin marks on proteins that are also SUMOylated in replication areas, which explains why there is a low concentration of ubiquitin and high levels of SUMO." This balance between SUMO and ubiquitin establishes a code that regulates the concentration of proteins in the replisome. "If a protein is SUMOylated, it becomes enriched in the replisome, but if it is also ubiquitinated, it is expelled. This is a code of signals or flags that regulates the concentration of factors in the DNA replication area," say the researchers. Apart from being of academic interest, these studies are relevant for chemotherapy. USP7 inhibitors are currently being studied as possible anti-cancer agents in pre-clinical tests. "The model that had been proposed is that the compounds increase p53 levels, resulting in the suicide of tumour cells. Our data indicate that USP7 is essential for genome replication in cells with or without p53." With these data, the authors of the paper warn that these molecules may not be specifically anti-tumour agents. "We believe they inhibit the cell division process regardless of whether the cells are cancerous or healthy and, therefore, their use for treating cancer in the future will have to be reconsidered." Explore further: Researchers 'capture' the replication of the human genome for the first time More information: Emilio Lecona et al. USP7 is a SUMO deubiquitinase essential for DNA replication, Nature Structural & Molecular Biology (2016). DOI: 10.1038/nsmb.3185


Millions of human cells are constantly dividing to repair tissue damage and ensure continuity. This is one of the most complex cellular processes, and in order for it to be successful, cells must produce a copy of their genetic material (DNA). Researchers from the Spanish National Cancer Research Centre (CNIO) have discovered the critical role of the POLD3 protein in this DNA replication process; without POLD3, cells do not divide, and even the embryonic development process may be curtailed.


News Article | November 24, 2016
Site: www.eurekalert.org

Damaged cells send signals to neighboring cells that result in the acquisition of embryonic features, and this may contribute to tissue repair; this could have implications for the treatment of degenerative diseases Cell reprogramming does not happen exactly as we thought. In the pages of the journal Science, a team from the Spanish National Cancer Research Centre (CNIO) has shown that tissue damage is a relevant factor for cells to go back to an embryonic state. Cell reprogramming earned its discoverer, Shinya Yamanaka, the Nobel Prize and opened the door to regenerative medicine. This technique, based on introducing a combination of four genes known as OSKM (for the initials of the genes, OCT4, SOX2, KLF4 and MYC), reverts adult cells to an embryonic-like state, and transforms them into pluripotent cells. However, there are several limitations to this process, such as a very low efficiency and the emergence of a particular type of tumour (known as teratoma), which make cell reprogramming incompatible with its potential clinical use. Manuel Serrano and the Tumour Suppression Group at the CNIO have been working in this field for years. Their innovative approach led them to achieve cell reprogramming within a living organism (in this case, a mouse) in 2013, whereas, until then, reprogramming had been only reported using explanted cells out of the organism. The work now published in Science by Serrano and his team analyses what happens in living tissues when reprogramming is induced using OSKM. What they have seen changes the idea that we had to date about this technique. "The Yamanaka genes are inefficient inducing reprogramming or pluripotency in the highly specialised cells that constitute adult tissues," explains Lluc Mosteiro, who has carried out most of the experimental work. Her observations indicate that tissue damage plays a critical role by complementing the activity of the OSKM genes. This relationship between damage and reprogramming is mediated by a proinflammatory molecule, interleukin-6 (IL6). Without its presence, the OSKM genes are far less efficient inducing the reprogramming process. These findings suggest the following sequence of events: the expression of the OSKM genes results in damage to the cells; accordingly, they secrete IL6; the presence of this molecule induces the reprogramming of some neighbouring cells. Having identified the essential role of IL6, Serrano, Mosteiro and the rest of the team are now working on various pharmacological approaches to enhance the reprogramming efficiency, which could help to improve the regeneration of damaged tissue even in the absence of the Yamanaka genes. Improving the repairing capacity of tissues could have obvious implications for regenerative medicine, including the treatment of multiple pathologies and degenerative processes associated with ageing. Cristina Pantoja and Noelia Alcázar, from the Tumour Suppression Group, Maria A. Blasco and Rosa M. Marión, from the Telomeres and Telomerase Group, and several CNIO Units also participated in this study, among others.


News Article | November 28, 2016
Site: www.medicalnewstoday.com

Cell reprogramming does not happen exactly as we thought. In the pages of the journal Science, a team from the Spanish National Cancer Research Centre (CNIO) has shown that tissue damage is a relevant factor for cells to go back to an embryonic state. Cell reprogramming earned its discoverer, Shinya Yamanaka, the Nobel Prize and opened the door to regenerative medicine. This technique, based on introducing a combination of four genes known as OSKM (for the initials of the genes, OCT4, SOX2, KLF4 and MYC), reverts adult cells to an embryonic-like state, and transforms them into pluripotent cells. However, there are several limitations to this process, such as a very low efficiency and the emergence of a particular type of tumour (known as teratoma), which make cell reprogramming incompatible with its potential clinical use. Manuel Serrano and the Tumour Suppression Group at the CNIO have been working in this field for years. Their innovative approach led them to achieve cell reprogramming within a living organism (in this case, a mouse) in 2013, whereas, until then, reprogramming had been only reported using explanted cells out of the organism. The work now published in Science by Serrano and his team analyses what happens in living tissues when reprogramming is induced using OSKM. What they have seen changes the idea that we had to date about this technique. "The Yamanaka genes are inefficient inducing reprogramming or pluripotency in the highly specialised cells that constitute adult tissues," explains Lluc Mosteiro, who has carried out most of the experimental work. Her observations indicate that tissue damage plays a critical role by complementing the activity of the OSKM genes. This relationship between damage and reprogramming is mediated by a proinflammatory molecule, interleukin-6 (IL6). Without its presence, the OSKM genes are far less efficient inducing the reprogramming process. These findings suggest the following sequence of events: the expression of the OSKM genes results in damage to the cells; accordingly, they secrete IL6; the presence of this molecule induces the reprogramming of some neighbouring cells. Having identified the essential role of IL6, Serrano, Mosteiro and the rest of the team are now working on various pharmacological approaches to enhance the reprogramming efficiency, which could help to improve the regeneration of damaged tissue even in the absence of the Yamanaka genes. Improving the repairing capacity of tissues could have obvious implications for regenerative medicine, including the treatment of multiple pathologies and degenerative processes associated with ageing. Article: Tissue damage and senescence provide critical signals for cellular reprogramming in vivo, Lluc Mosteiro, Cristina Pantoja, Noelia Alcazar, Rosa M. Marión, Dafni Chondronasiou, Miguel Rovira, . . . Manuel Serrano1, Science, doi: 10.1126/science.aaf4445, published on 25 November 2016


News Article | August 18, 2016
Site: www.biosciencetechnology.com

Despite their especially compact structure that is difficult to access, telomeres transcribe information like the rest of the DNA. The RNAs resulting from this process are called TERRA and their function is essential in preserving these protective structures. This is the conclusion of a new study by the Telomere and Telomerase Group at the Spanish National Cancer Research Centre (CNIO), which has also located the part of the human genome where these molecules are "manufactured". This finding is consistent with the observations made two years ago by the same group, lead by Maria A. Blasco. On that occasion, they were working on mouse cells and they observed that the TERRA that protect the 20 chromosomes of this mammal originated exclusively in pair 18 and, to a lesser extent, in number 9. In the case of humans, the results now published in Nature Communications indicate that these RNAs are transcribed exclusively at one point. The researchers analysed 18 RNAs previously proposed as possible TERRA but only those arising from the long arm of chromosome 20 (20q) and at the short arm of chromosome X (Xp) showed TERRA features. To demonstrate that the RNAs transcribed at these two points were, indeed, TERRA, the authors genetically removed both loci using the CRISPR-CAS9 technology. They then noted that while the suppression of Xp had no significant consequences, the suppression of 20q had extremely negative effects on telomeres. "Identification of 20q as one of the major locus for human TERRA generation allows us to address the role of TERRA telomere biology," write the authors. After removing it in various cellular lines, they saw that there was a significant increase in DNA and telomere damage, as well as an increase in chromosome instability. This is the first time that the crucial role of TERRA in the preservation of telomeres has been demonstrated in any organism. "These results are striking because they clearly demonstrate that TERRA play an essential role in cell viability as well as in preserving telomeres; they are just as important to the functioning of telomeres as telomerase or shelterins, the proteins that protect the telomeres," explains Blasco. The discovery of the 20q region as the source of TERRA and the confirmation of the key role played by these RNAs in preserving telomeres opens the door to the study of certain syndromes in which alterations in this chromosomal region have been detected. Also, it offers a new path in the study of patients with telomeric disorders in which, however, no alterations in the genes normally involved -telomerase, shelterins- have been found.


News Article | February 6, 2017
Site: www.medicalnewstoday.com

During the 'in vivo' reprogramming process, cellular telomeres are extended due to an increase in endogenous telomerase. This is the main conclusion of a paper published in Stem Cell Reports by a team from the Spanish National Cancer Research Centre (CNIO). Their observations show, for the first time, that the reprogramming of living tissue results in telomerase activation and telomere elongation; thus reversing one of the hallmarks of aging: 'the presence of short telomeres'. "We have found that when you induce cell dedifferentiation in an adult organism, the telomeres become longer, which is consistent with cellular rejuvenation", explains María A. Blasco, head of the CNIO Telomeres and Telomerase Group and leader of this research. This lengthening of the telomeres is an unequivocal sign of cell rejuvenation, which has been quantified for the first time here in a living organism. Blasco and her colleagues have worked with the so-called "reprogrammable mice" - created by Manuel Serrano, also a CNIO researcher, whose group is also involved in this project. Broadly speaking, the cells of these transgenic animals carry the four Yamanaka factors (OSKM) whose expression is turned on when an antibiotic is administered. In doing so, the cells regress to an embryonic-like state, a condition known as known as pluripotency. In light of the importance of telomeres in tissue regeneration, ageing and cancer, the authors decided to analyse the changes that occur in these protective structures of the chromosomes during the 'in vivo' reprogramming process, which leads to dedifferentiation of the tissues. Their observations indicate that this process entails a lengthening of the telomeres, a marker of cellular rejuvenation. This elongation occurs, according to this research, due to the action of telomerase. "What we have seen for the first time is the induction of telomerase 'in vivo'," explained Blasco and Rosa M. Marion, the leading authors of the paper. "To date, we do not know of any study that describes the induction of endogenous telomerase by defined transcription factors in the context of adult tissues," say the authors. The loss of cell differentiation is a phenomenon that takes place in a physiological context. It occurs during tissue regeneration and also in tumourigenesis. In fact, "this is increasingly considered one of the critical initial steps in cancer development," as stated in the paper. Dedifferentiation induced by 'in vivo' reprogramming, as well as the dedifferentiation associated with the initiation of cancer, involve "similar changes in the telomeres", say the authors. In both of these processes, we see the activation of telomerase and the subsequent elongation of the telomeres. A better knowledge of the changes described in the telomeres during 'in vivo' reprogramming and in pathological processes, such as cancer, will improve our understanding about the molecular events associated with cellular differentiation and, most likely, with other processes that involve cell plasticity. This work has been funded funded by the Spanish Ministry of Economy and Competiveness (PLAN RETOS) and by the Fundación Botín. Article: Common Telomere Changes during In Vivo Reprogramming and Early Stages of Tumorigenesis, Rosa M. Marión, Isabel López de Silanes, Lluc Mosteiro, Benjamin Gamache, Maria Abad, Carmen Guerra, Diego Megías, Manuel Serrano and Maria A. Blasco, Stem Cell Reports, doi: 10.1016/j.stemcr.2017.01.001, published online 2 February 2017.


News Article | November 17, 2016
Site: www.eurekalert.org

The Structural Biology and Biocomputing Programme, together with the National Institute Bioinformatics unit at the Spanish National Cancer Research Centre, has participated coordinating the data analysis and making data accessible in the BLUEPRINT project The International Human Epigenome Consortium (IHEC) publishes simultaneously a collection of 41 papers that contain major advances in the study of the Human epigenome - 24 of which appear today in Cell Press magazines. The Structural Biology and Biocomputing Programme together with the National Institute Bioinformatics unit at the National Cancer Research Center (CNIO) participate signing different studies and leading three of them. One of the great mysteries in biology is how the many different cell types that make up our bodies are derived from a single cell and from one DNA sequence, or genome. We have learned a lot from studying the human genome, but have only partially unveiled the processes underlying cell determination. The identity of each cell type is largely defined by an instructive layer of molecular annotations on top of the genome - the epigenome - which acts as a blueprint unique to each cell type and developmental stage. Unlike the genome, the epigenome changes as cells develop and in response to changes in the environment. Defects in the factors that read, write and erase the epigenetic blueprint are involved in many diseases. The comprehensive analysis of the epigenomes of healthy and abnormal cells will facilitate new ways to diagnose and treat various diseases, and ultimately lead to improved health outcomes. A collection of 41 coordinated papers now published by scientists from across the International Human Epigenome Consortium (IHEC) sheds light on these processes, taking global research in the field of epigenomics a major step forward. A set of 24 manuscripts has been released as a package in Cell and Cell Press-associated journals, and an additional 17 papers have been published in other high-impact journals. The Structural Biology and Biocomputing Programme, together with the National Institute Bioinformatics unit at the CNIO, headed by Alfonso Valencia, has participated coordinating the data analysis and making data accessible in the BLUEPRINT project, the major European partner framed in IHEC with 42 partner organisations, representing 33 academic groups and 9 companies (mostly Small and Medium Enterprises (SMEs)) from 12 European countries. "Our work has been making the data accessible to the other research groups," explains Valencia. "The project has generated a large volume of epigenomic data and it was necessary to develop the methods and systems to analyze them." And that is what they have done, with the aim of "facilitating the analysis of biological information". The major contribution has been the BLUEPTRINT Data Analysis Portal an interface that facilitates interactive exploration of genomic regions, genes, and pathways in the context of differentiation of hematopoietic lineages (visit at: http://blueprint-data. ) In addition to this role of data management, Valencia's group has led several works in which they have developed their own systems of analysis. For example, the use of assortativity for the analysis of the 3D configuration of the genome, published in Genome Biology. "It has been a very positive experience because it has provided us with tools that have served to analyze the data of this project and that in the future will serve for the analysis of the data that are generated in epigenomics," says Valencia. "BLUEPRINT has produced more new science and more understanding of blood cell disease than we could have imagined at the outset," "We have made the data of >1000 datasets publicly available" says Henk Stunnenberg from Radboud University, The Netherlands, former Chair of the IHEC International Scientific Steering Committee and coordinator of the EU-funded BLUEPRINT project. "Moreover, we have forged an alliance of researchers and innovative companies from around Europe and, working closely with international partners, we already see results that, in time, will improve the lives of patients." These papers represent the most recent work of IHEC member projects from Canada, the European Union, Germany, Japan, Singapore, and the United States. The collection of publications showcases the achievements and scientific progress made by IHEC in core areas of current epigenetic investigations.

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