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Prediction and validation of gene regulatory elements active in human development


Embryonic development relies on well-tuned expression of thousands of genes across developing tissues and organs. Gene regulatory regions such as enhancers control these gene expression patterns, and properly functioning regulatory regions are vital for healthy development. To better characterize genes and regulatory regions that are important in embryonic development, we developed a new approach to identify developmental enhancers and a database of genes with known developmental functions, validated our predictions in transgenic mouse and zebrafish enhancer assays, and applied these tools to several interesting questions in embryonic development.

While many large-scale studies have investigated the location and function of enhancers in specific developmental tissues and timepoints, a general predictor of developmental enhancers was lacking. To leverage the massive amount of available data and fill this void, we developed EnhancerFinder, a computational tool that integrates thousands of genetic and epigenetic datasets to predict tissue-specific developmental enhancers. With this tool we predicted over 80,000 developmental enhancers, plus tissue specificity for thousands of these predicted enhancers.

We surveyed the enhancer landscape across the whole genome and found that predicted enhancers tend to cluster around developmental genes and that genes near tissue-specific enhancers are expressed in relevant tissues. We tested 12 developmental enhancers in transgenic mouse and zebrafish enhancer assays and found that 10 candidate enhancers validated with consistent expression patterns in at least one of the animal models. One cluster of these validated enhancers near developmental transcription factor FOXC1 pointed us towards a specific developmental brain structure known to be involved in cerebral malformations. We further investigated these candidate enhancers and developed a model for a possible non-coding genetic cause of the brain development disorder Dandy-Walker malformations.

We developed an improved framework for predicting enhancers, cataloged thousands of genes with developmental functions, predicted tens of thousands of novel developmental enhancers in the human genome that validate well in animal models, and showed applications of these tools in several interesting questions in developmental biology. We hope other researchers will be able to use these tools to further their own investigations in gene regulation during embryonic development.

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