This work provides a comprehensive resource for basic studies of telencephalon enhancers. Our targeted screen identified the genomic location of thousands of candidate enhancers putatively active in the embryonic forebrain. The mapping and annotation of the activity patterns of nearly 150 human telencephalon enhancers at histological resolution in transgenic mice provides insight into the regulatory architecture of individual genes that are required for forebrain development and will facilitate studies of molecular genetic pathways by identifying the genomic regions to which upstream transcription factors bind.
Our analysis revealed several cases of enhancers that drive similar patterns and are associated with the same gene (e.g. ) in a manner reminiscent of the ‘shadow enhancers’ observed in invertebrate models (Frankel et al., 2010
; Hong et al., 2008
). The data provided through this work will support the identification of minor spatial activity differences between such enhancers, as well as the functional exploration of their apparent redundancies. It is also remarkable that a large proportion of enhancers examined in this study drove patterns that were at least partially different from all other enhancers examined, highlighting the complexity of the developing forebrain, as well as the regulatory sequence code orchestrating its development.
The motif-based classifiers derived from enhancers active in different subregions of the telencephalon demonstrate the value of systematically annotated enhancer activity data sets for computational studies aimed at deciphering the correlation between the transcription factor binding sites present in an enhancer and its precise spatial activity pattern. Beyond such functional genomic studies, the enhancers identified and characterized in this work provide a comprehensive set of molecular reagents that can be used to target gene expression to defined subregions of the developing brain, or to defined cell states when differentiating stem cells in vitro. This will enable tissue-specific homologous recombination and deletion strategies or expression of reporter and selectable genes, as illustrated in .
Finally, results from this study are expected to enable and facilitate the functional genomic exploration of the role of enhancers in human brain disorders. There is accumulating evidence that non-coding sequence variants, as well as copy number variation in coding and non-coding portions of the genome have important impacts on a wide spectrum of disorders including bipolar, schizophrenia, autism, intellectual disability and epilepsy (Cooper et al., 2011
; Durbin et al., 2010
; International Schizophrenia Consortium, 2008
; Malhotra et al., 2011
; Sebat et al., 2007
; Vacic et al., 2011
; Visel et al., 2009b
; Walsh et al., 2008b
). However, the functional interpretation of non-coding sequence or copy number variants remains a major challenge and few potentially causative connections linking neurological traits to molecular variation in enhancers have been identified (e.g., (Poitras et al., 2010
)). Thus, the systematic mapping and high-resolution analysis of telencephalon enhancers through this work is expected to provide functional genomic insights to guide studies that will mechanistically relate individual non-coding sequence and copy number variants to brain disorders.