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Final Report Summary - DEVCOM (European Initial Training Network on Developmental and Computational Biology)

Project context
The ability to manipulate cellular pluripotency and differentiation holds the as yet unrealized promise of regenerative medicine to produce replacement cells and tissues. To this end a deep understanding of the regulation of differentiation potential in the context of normal embryonic development is crucial. The recent revolution in sequencing technology has enabled high throughput and genome-wide analysis of cellular behaviour. The challenge with the new opportunities in genome-scale quantitative data gathering is to reach a more fundamental, systems level understanding of complex biological phenomena such as development and differentiation.

Training of early stage and experienced researchers
DevCom network has trained 15 scientists to bridge the gap between developmental and computational biology, preparing them for the emerging field of “New Biology” in which systems-level, quantitative and computational approaches are fully integrated in the analysis of profound scientific problems related to pluripotency and differentiation. The DevCom research plan revolved around early embryonic regulatory networks and disease networks in vertebrate embryos of the Xenopus and zebrafish model systems. The researchers have been exposed to interdisciplinary training in both academic and business settings. The trainees have acquired technical expertise in embryonic anatomy and development, genomic profiling, sequence conservation and evolutionary relationships of regulatory elements, genetic and chemical screens, mass spectrometry, informatics, statistics and computational modelling. Moreover they have been trained in a range of soft and complementary skills, including management, communication, writing, dissemination, intellectual property, and entrepreneurship, thereby improving the career perspectives of participating fellows and preparing them for leading roles in academia and industry. In addition to being useful to the trainees, the effort has been very beneficial for the training capacity and programs of participating institutions, on which it will have a lasting impact.

Work performed and main results achieved
In DevCom, researchers have been trained to conduct research in a mixed computational and developmental biology environment, mainly using Xenopus and zebrafish as embryo model systems, in addition to mammalian cells cultured in vitro. The use of different model systems has enriched DevCom in several ways. It has allowed them to develop a broad view of the utility of vertebrate model systems, while also enabling powerful analyses of conservation. This has been organized in three interrelated sub-programmes (SPs): SP1, Comparative epigenomics of cis-regulatory elements; SP2, Analysis of transcription factor (TF) networks; SP3, Models for human health.

Sub-programme 1 (SP1): Comparative epigenomics of cis-regulatory elements
In SP1 we have used available epigenomic data to identify and compare, at a genome-wide level, all cis-regulatory elements (enhancers and promoters) that operate at different developmental stages in Xenopus and zebrafish. ESR1 has systematically identified a major recruitment mechanism of the Polycomb Repressor Complex2 that is conserved between Xenopus embryos and mouse ES cells. Such a mechanism has been established in Drosophila in the 1990s but has been elusive in vertebrates. ESR2 has established genome-wide profiles of chromatin accessibility during many different stages of Xenopus development, whereas ESR3 has profiled the chromatin-modifying Ep300 protein at high temporal resolution during development. Comparative analyses of regulatory landscapes has also been performed by ESR6 using zebrafish and amphioxus. These projects have identified key epigenetic modifications and chromatin-modifying enzymes involved at the promoters and enhancers of genes with dynamic developmental expression patterns.

Sub-programme 2 (SP2): Analysis of transcription factor (TF) networks
In this sub-programme, we have used functional and computational approaches to build gene regulatory networks operating during early vertebrate embryogenesis. Chromatin accessibility profiles (ATAC-sequencing) have been used to link gene-regulatory sequences with permissive chromatin state (cf.SP1) to transcription factor binding sites in both Xenopus and zebrafish embryos (ESR2, ESR7). We have used computational strategies to infer regulatory networks based on these data; this has led to the identification of transcription factors that play important roles in the specification of specific cell types during gastrulation. We have used single cell RNA-sequencing to identify and characterize these subpopulations of cells. At the same time, we have explored the genome-wide binding profiles of the important mesendoderm master regulator T (Brachyury), using ventralized and dorsalized embryos as a model system (ESR5). The results indicate that tissue-specific binding of the T transcription factor is dependent on its concentration but is also affected by chromatin accessibility. The dynamic binding of transcription factors to DNA has been investigated using a novel approach to measure affinities by quantitative mass spectrometry (ESR12). The structural aspects of components of interaction networks was addressed using structure homology modelling (ER1). A software tool was developed and made available to this end. Integrated analyses of genomic information, pathway data, protein-protein interaction networks, leading to refinement of the developmental gene regulatory networks.

Sub-programme 3 (SP3): Models for human health
We have exploited the results obtained in SP1 and SP2 to perturb developmental networks, some of which are relevant for disease modelling. In particular, we have modelled Allan-Herndon Dudley Syndrome (ADHS), a rare cognitive development disorder characterized by intellectual and movement impairment (ESR8). It is caused by mutations in the thyroid hormone transporter MCT8 that affects neuronal and muscle development. Thyroid signalling is also perturbed by chemicals (xenobiotics), many of which humans are regularly exposed to. A mixture of 15 chemicals found in amniotic fluid was found to perturb thyroid signalling and early brain development.
The second disease model that has been developed concerns heart failure (ESR9). Cardiac insufficiency is a disease with high socio-economic impact as it affects 6.5 million Europeans. ESR9 has established data supporting that the loss of cardiac regeneration capacity is a consequence increased thyroid hormone signalling.
The third model employs aimed to understand cell migration and metastasis in melanoma (ESR10, 11). Dramatic pigment cell migration phenotypes have been identified in a chemical screen by ESR10. These drug-mediated phenotypes identify specific effector molecules that are important for cellular migration during development. The role of the ADAMTS9 methalloproteinase in this process was also studied (ESR11).
The fourth model aimed to understand how environmental stressors affect health (ER2). Such questions require screening methods that are rapid, sensitive, and yet provide physiological, preferably in vivo, information. This can be done by generating transgenic reporters, for example using amphibian embryos transgenic for GFP reporters of the environmental stressors. To identify candidate regulatory elements for such reporters, RNA-seq was used to monitor genes affected by heavy metal exposure in tadpoles of the amphibian Xenopus laevis (ER2, in collaboration with ESR1). Using genome-wide epigenome data, the putative promoters and enhancers of deregulated genes were identified and further studied.

The research of DevCom has resulted in a total of 18 published articles, with 21 more manuscripts in stages of preparation, review, revision or in press. Published results include analyses of epigenetics in development, the effects of xenobiotic amniotic fluid contaminants on brain development and thyroid hormone signalling, the heart tissue response to resection in the Xenopus model system, and the use of cross-linking immunoprecipitation for topological analysis of chromatin complexes.

Meetings, events and outreach
DevCom started September 1, 2013 and came to a formal close on August 31, 2017. Apart from the kick-off meeting, 4 network meetings were organized, one midterm meeting and 12 workshops on experimental biology, computational biology and soft skills. The workshops were open to scientists from outside the DevCom network. In addition, a small symposium with four external invited speakers was organized in Paris in February 2015.
As part of DevCom outreach and integrated with a workshop on communicating to diverse audiences, DevCom fellows contributed to writing, editing and improving Wikipedia pages relevant to the research areas of DevCom.
An absolute highlight of the DevCom project was the final international conference on Gene-regulatory systems in development. This conference was held in Carmona (Spain) in March 2017 and was organized together with ZENCODE ITN. A total of 21 renowned external speakers was invited. All DevCom early stage researchers presented their work, either orally or in a poster session. Participation was open to scientists outside the DevCom network and total attendance was 130 registrations from many different countries in Europe, USA and Asia.

Further information about the DevCom project can be obtained via the website: www.devcom-itn.eu

Reported by

STICHTING KATHOLIEKE UNIVERSITEIT
Netherlands

Subjects

Life Sciences
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