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Background   Nr2e1  (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundreds of target genes, and bind more than 300 co-interacting proteins. However, recognition of the critical role of  Nr2e1  in neural stem cells and neocortex development is relatively recent, thus the molecular mechanisms involved for this nuclear receptor are only beginning to be understood. Serial analysis of gene expression (SAGE), has given researchers both qualitative and quantitative information pertaining to biological processes. Thus, in this work, six LongSAGE mouse libraries were generated from laser microdissected tissue samples of dorsal VZ/SVZ (ventricular zone and subventricular zone) from the telencephalon of wild-type (Wt) and  Nr2e1 -null embryos at the critical development ages E13.5, E15.5, and E17.5. We then used a novel approach, implementing multiple computational methods followed by biological validation to further our understanding of  Nr2e1  in neocortex development.    Results  In this work, we have generated a list of 1279 genes that are differentially expressed in response to altered  Nr2e1  expression during  in vivo  neocortex development. We have refined this list to 64 candidate direct-targets of NR2E1. Our data suggested distinct roles for  Nr2e1  during different neocortex developmental stages. Most importantly, our results suggest a possible novel pathway by which  Nr2e1  regulates neurogenesis, which includes  Lhx2  as one of the candidate direct-target genes, and SOX9 as a co-interactor.    Conclusions  In conclusion, we have provided new candidate interacting partners and numerous well-developed testable hypotheses for understanding the pathways by which  Nr2e1  functions to regulate neocortex development.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1770-3) contains supplementary material, which is available to authorized users.

bmc genomics

Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development