The Impey lab utilizes functional genomic approaches to characterize the transcriptional and epigenetic networks that regulate stem cell self-renewal and neural differentiation. We developed a novel technology, termed Serial Analysis of Chromatin Occupancy (SACO), that enables the identification of transcription factor target sites or epigenetic marks across entire mammalian genomes. We utilize high-throughput sequencing methodologies (ChIP-Seq and RNA-Seq) to profile transcription factor occupancy, epigenetic modifications, and transcription in an unbiased manner in stem cells and developing neuronal cells. The lab also develops bioinformatics tools to extract and visualize novel biology from functional genomic and transcriptome screens.
Embryonic stem cells (ESCs) derived from the inner cell mass (ICM) of pre-implantation embryos can differentiate into all somatic lineages and have an unlimited capacity for self-renewal. ESCs serve as a model for the study of development specification and as an important resource for cell replacement therapy. The homeodomain transcription factors, Oct3/4 and Nanog, play critical roles in sustaining ES cell pluripotency and self-renewal. ESC pluripotency is also believed to depend on an epigenetic state that facilitates self-renewal and prevents developmental gene silencing. Several lines of evidence suggest that Nanog plays a key role in the establishment of a pluripotency-associated epigenetic state. During reprogramming of somatic cells, extensive epigenetic remodeling occurs, including loss of repressive methylation at pluripotency-associated genes and re-establishment of bivalent histone modifications. Interestingly, forced expression of Nanog not only promotes transfer of pluripotency but markedly facilitates reprogramming of histone and DNA methylation. Nevertheless, the downstream mechanisms by which Nanog regulates the initiation and maintenance of pluripotency remain obscure. The Impey lab has utilized bioinformatic analyses of proprietary ChIP-Seq and RNA-Seq data to identify thousands of Nanog- and Oct3/4 regulated genes in mouse and human embryonic stem cells. Functional screens have identified several novel Nanog targets that directly regulate epigenetic pathways and ESC self-renewal. In particular, we have characterized a histone demthylase that phenocopies the effects of Nanog, complements for Nanog, and is essential for ESC self-renewal. Preliminary data also suggests that Nanog-regulated chromatin modifying enzymes also facilitate reprogramming of somatic cells into induced-pluripotent stem cells. NIH-supported research
Our initial SACO screen profiled targets of the transcription factor CREB, an important regulator of neurogenesis, neuronal maturation, and synaptic plasticity. Additional ChIP-Seq screens revealed a network of ~3-6,000 high-confidence CREB binding sites in neuronal progenitors and mature hippocampal neurons. We recently used ChIP-Seq and RNA-Seq data to identify hundreds of novel CREB target genes. Remarkably, a significant fraction of inducible CREB-dependent genes are not predicted to code for proteins. A major focus of the lab is the characterization of novel non-coding genes and microRNAs in the context of neuronal differentiation. NIH-supported research
- Impey S*., McCorckle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss JM, McWeeney S, Dunn JJ, Mandel G, Goodman RH (2004) Defining the CREB Regulon: A Genome-Wide Analysis of Transcription Factor Regulatory Regions. Cell. 119, 1041-1054. Highlighted on cover
- Vo, N., Klein, M. E., Varlamova, O., Keller, D. M., Yamamoto, T., Goodman, R. H., and Impey, S. (2005). A cAMP-response element binding protein-induced microRNA regulates neuronal morphogenesis. Proc. Natl .Acad Sci U S A 102, 16426-1643. Featured as one of Sciences Signaling Breakthroughs of the Year
- Wayman, G.A., Impey, S., Marks, D., Saneyoshi, T., Grant, W.F., Derkach, V.F., and Soderling T.R. (2006) Activity-dependent Dendritic Arborization Mediated by CaM-kinase I Activation and Enhanced CREB-dependent Transcription of Wnt. Neuron 50, 897-909.
- Cheng HY, Papp JW, Varlamova O, Dziema H, Russell B, Curfman JP, Nakazawa T, Shimizu K, Okamura H, Impey S, Obrietan K. (2007) microRNA modulation of circadian-clock period and entrainment. Neuron 54, 813-29.
- Wayman GA, Davare M, Ando H, Fortin D, Varlamova O, Cheng HY, Marks D, Obrietan K, Soderling TR, Goodman RH, Impey S. (2008) An activity-regulated microRNA controls dendritic plasticity by down-regulating p250GAP. Proc Natl Acad Sci U S A. 105, 9093-8.
- Impey, S*., Davare, M., Lasiek, A., Fortin, D., Ando, H., Varlamova, O., Obrietan, K., Soderling, T.R., Goodman, R.H., and Wayman, G.A. (2009). An activity-induced microRNA controls dendritic spine formation by regulating Rac1-PAK signaling. Mol Cell Neurosci.