Professor Nicholas Hastie CBE FRS, Medical Research Council, UK
Professor Nicholas Hastie CBE FRS, Medical Research Council, UK
The evolution of global enhancers
Professor Denis Duboule, University of Geneva and EPFL Lausanne, Switzerland
Abstract
In this paper, I will discuss potential mechanisms underlying the emergence of regulatory landscapes and their subsequent evolutionary recruitment in various developmental contexts. The long-range control of Hox genes during the development of the limbs and the external genitals will be used as an example, as well as the regulation of these genes during gut development.
The gastrointestinal tract is composed of a series of morphological sub-divisions, specialized in various functions associated with food breakdown and nutrients absorbtion. In mammals, the diet can considerably differ from one species to the other, depending on particular environmental adaptations. To digest the cellulose associated with vegetarian components, mammals belonging to the so-called hindgut fermenters, rely upon the caecum, a specialized gastrointestinal organ branching from the intestinal tract at the transition between the small and the large intestines. The molecular mechanisms underlying both the positioning, the budding and the extension of the caecum, which in some species can be longer than the gut itself, only starts to be understood, and was shown to require the concerted expression of several Hox genes, in particular members of the HoxA and HoxD clusters.
To try and understand how these genes are controlled during the morphogenesis of the caecum, we isolated and characterized the regulatory elements necessary for the transcription of Hoxd genes during the budding of this structure. We observe that an unusual number of enhancer sequences, with related specificities, are located within a gene desert flanking the HoxD cluster on its telomeric side. We also document the presence, within this large DNA interval, of a long non-coding RNA, speficically expressed in the growing caecum, which is involved in cis in the transcriptional regulation of Hoxd genes in this organ. We propose a model for the acquisition of multiple enhancer sequences with comparable activities, based on the existence of a regulatory structure that facilitates successive evolutionary recruitments of such sequences.
Co-authors:
Saskia Delpretti, Thomas Montavon, Nicolas Lonfat, Ecole Polytechnique Fédérale, Switzerland
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Professor Denis Duboule, University of Geneva and EPFL Lausanne, Switzerland
Professor Denis Duboule, University of Geneva and EPFL Lausanne, Switzerland
Denis Duboule earned his PhD in Biology in 1984. He is currently Professor of Developmental genetics and genomics at the Federal Institute of Technology in Lausanne and Chairman of the department of Genetics and Evolution of the University of Geneva, Switzerland. Since 2001, he is also the director of the Swiss national research centre ‘Frontiers in Genetics’. Duboule has a longstanding interest in the function and regulation of Hox genes, a family of genes responsible for the organization and evolution of animal body plans. These genes have been a paradigm to understand embryonic patterning, in developmental, evolutionary and pathological contexts. He is an elected member of several academies and has received many awards, amongst which the Louis-Jeantet Prize for Medicine in 1998. He has four children, bikes a Look KX and plays a Gibson 355 SV stereo.
The pluripotent 3D genome
Professor Wouter de Laat, Hubrecht Institute, The Netherlands
Abstract
Pluripotent stem cells (PSCs), such as embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs), have the unique capacity to differentiate into any somatic cell type. Microscopically, PSCs show minimal clustering of facultative heterochromatic regions such as centromeres and appear to have a more open chromatin structure, which is thought to reflect their ability to activate large portions of the genome upon differentiation. Yet, the three-dimensional organization of the pluripotent genome is not well understood. Here, we applied 4C technology to compare structural features of somatic and pluripotent genomes. In contrast to somatic cells, in PSCs, long-range contacts between inactive chromatin domains are nearly absent, however, active chromatin contacts do occur. Upon differentiation, cells lose the PSC-specific topology and adopt a somatic chromatin architecture. Conversely, the structural specifics of the pluripotent genome are regained during iPSC reprogramming. Finally, we describe a unique contact network of pluripotency genes centered around binding sites of the pluripotency factors Nanog, Oct 4 and Sox2. Collectively, our work reveals a PSC-specific DNA interaction network, which, we speculate, enhances the robustness of pluripotency.
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Professor Wouter de Laat, Hubrecht Institute, The Netherlands
Professor Wouter de Laat, Hubrecht Institute, The Netherlands
Wouter de Laat studied biology at the Utrecht University Utrecht. During his PhD (1998) at the Erasmus University Rotterdam (Prof. Jan Hoeijmakers) he investigated the molecular mechanism of nucleotide excision repair. He identified one of the nucleases and characterized the interplay between repair factors at the site of the lesion. As a postdoc, he joined the group of Prof. Frank Grosveld to work on beta-globin gene activation. In 2000 he received a career grant (Vidi) to work on long-range gene activation. His group used 3C technology, and later developed 4C technology, to demonstrate chromatin loops between genes and enhancers and to uncover long-range DNA contacts within and between chromosomes. In 2008 he received an ERC Young Investigator Grant. In September 2008 de Laat moved his group to the Hubrecht Institute, where he continued his work on genome structure and function. In January 2009 he was appointed professor in Biomedical Genomics at the University Medical Center Utrecht.
Maps of open chromatin from association signals to function
Dr Panos Deloukas, Wellcome Trust Sanger Institute, UK
Abstract
Genome-wide association (GWA) studies have been very successful in identifying genetic loci associated with complex traits, including disease. Many GWA signals map outside protein-coding regions suggesting that the underlying functional variants may influence phenotype through regulation of gene expression.
We used FAIRE (formaldehyde-assisted isolation of regulatory elements) coupled with sequencing to map nucleosome-depleted regions (NDRs), which mark active regulatory elements, in primary human megakaryocytes, erythroblasts and monocytes. Our data suggest that (i) cell type-specific NDRs can guide the identification of regulatory variants and (ii) sequence variants associated with the corresponding platelet and erythrocyte traits are enriched in NDRs in a cell type-dependent manner. As a proof-of-concept, we investigated the molecular mechanism of the 7q22.3 platelet volume locus.
We identified a megakaryocyte-specific NDR harbouring the index SNP which differentially binds the transcription factor EVI1 and affects PIK3CG gene expression in platelets. Gene expression profiling of Pik3cg knockout mice indicated that PIK3CG is associated with gene pathways with an established role in platelet function.
Finally, we applied FAIRE maps in characterizing two low-frequency SNPs at the RBM8A locus, which is involved in thrombocytopenia with absent radii (TAR), a rare congenital malformation syndrome.
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Dr Panos Deloukas, Wellcome Trust Sanger Institute, UK
Dr Panos Deloukas, Wellcome Trust Sanger Institute, UK
Panos Deloukas is Senior Group Leader ‘Genetics of Complex Traits in Humans’, department of Human Genetics, Wellcome Trust Sanger Institute. He is Fellow of the European Society of Cardiology and honorary member of the TwinsUnit at KCL, UK. He obtained his BSc in chemistry from the Aristotelian University of Thessaloniki, Greece (1986), his MSc in microbiology from the University ParisVII, France (1987) and his PhD in molecular biology from the Biozentrum, University of Basel, Switzerland (1992). He worked as post-doctoral fellow at Hoffmann-La Roche in Basel, Switzerland and joined the Sanger Centre in 1994.
He led the sequencing of chromosomes 10 and 20 in the Human Genome Project. He went on to study common sequence variation (HapMap project) and since 2005 is investigating the molecular basis of common disease and variable response to drugs focusing on coronary artery disease. He has been a founder member of the Wellcome Trust Case-Control Consortium and co-Chair of the Immunochip and the CardiogramPlus consortia; is member of several global consortia (GIANT, GLGC, IBPC-GWAS, IWPC). He has authored and co-authored more than 220 papers in peer-reviewed journals.
Deciphering the cis-regulatory code
Dr Eileen Furlong, EMBL, Germany
Abstract
Embryonic development is controlled by precise patterns of temporal and spatial gene expression, which in turn are controlled by the activity of transcription factors converging on cis-regulatory modules (CRMs) or enhancer elements. The location and even combinatorial occupancy of CRMs can be experimentally measured using ChIP-seq at specific stages of development, at high-resolution. A current major challenge however, is to understand their function in terms of spatio-temporal enhancer activity. We have recently developed a new method to obtain cell-type specific signatures of chromatin state or transcription factor occupancy within the context of a developing multicellular embryo (Batch Tissue Specific ChIP: BiTS-ChIP). Using this method, we have measured chromatin modifications and RNA polymerase II occupancy in a specific tissue type at developmental stages before and after cell fate specification. The data revealed heterogeneous combinations of chromatin marks linked to active enhancers. Using a Bayesian network, we show that chromatin state is sufficient to predict, not just the location, but activity state of regulatory elements, accurately distinguishing between enhancers in an active versus inactive state. The model also revealed that Pol II occupancy and H3K79me3, a modification associated with Pol II elongation, are highly predictive for the precise timing of enhancer activity. Pol II occupancy is tightly correlated with both the timing and location of transcription factor occupancy suggesting that it may be recruited there by transcription factors. We are currently investigating how this relates to enhancer activation and three-dimensional looping interactions with promoter elements.
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Dr Eileen Furlong, EMBL, Germany
Dr Eileen Furlong, EMBL, Germany
Eileen Furlong received her PhD at University College Dublin, Ireland and did her post-doctoral research at Stanford University, California. She has been at group leader at the European Molecular Biology Laboratory (EMBL) since Oct 2002. Since January 2009 she is a senior scientist and joint chair of the Genome Biology department at EMBL, Heidelberg.
Her work has been instrumental in developing and applying genomic approaches to multicellular developing embryos. This includes developing an automated transgenic embryo sorter, tiling arrays and protocols for ChIP-chip experiments and a new method to study cell-type specific changes in regulatory state during metazoan development.
Her group’s research interests focus on understanding how transcriptional networks drive developmental progression using Drosophila mesoderm specification as a model system. For this purpose, the group combines genomic, genetic and bioinformatics approaches to uncover basic principles of transcription and to gain predictive insights into cell fate decisions.