Abstract
Elucidation of the epigenetic basis for cell-type specific gene regulation is key to gaining a full understanding of how the distinct phenotypes of differentiated cells are achieved and maintained. Here we examined how epigenetic changes are integrated with transcriptional activation to determine cell phenotype during differentiation. We performed epigenomic profiling in conjunction with transcriptomic profiling using in vitro differentiation of human primary alveolar epithelial cells (AEC). This model recapitulates an in vivo process in which AEC transition from one differentiated cell type to another during regeneration following lung injury. Interrogation of histone marks over time revealed enrichment of specific transcription factor binding motifs within regions of changing chromatin structure. Cross-referencing of these motifs with pathways showing transcriptional changes revealed known regulatory pathways of distal alveolar differentiation, such as the WNT and transforming growth factor beta (TGFB) pathways, and putative novel regulators of adult AEC differentiation including hepatocyte nuclear factor 4 alpha (HNF4A), and the retinoid X receptor (RXR) signaling pathways. Inhibition of the RXR pathway confirmed its functional relevance for alveolar differentiation. Our incorporation of epigenetic data allowed specific identification of transcription factors that are potential direct upstream regulators of the differentiation process, demonstrating the power of this approach. Integration of epigenomic data with transcriptomic profiling has broad application for the identification of regulatory pathways in other models of differentiation.
Highlights
Over the past two decades the relationship between gene expression and chromatin structure has been increasingly recognized [1,2,3,4]
We found that by integrating epigenetic profiling with whole genome transcriptomic data we were able to determine which molecular signaling events were activated and repressed during adult alveolar epithelial cell differentiation, and we identified epigenetic changes that contributed to these changes
Isolated distal lung epithelial cells offer a compelling model system; primary human alveolar epithelial type 2 (AT2) cells can be purified in large numbers from remnant transplant lung, and can be differentiated in vitro in a manner closely mimicking both normal maintenance and regeneration following lung injury [15,16]
Summary
Over the past two decades the relationship between gene expression and chromatin structure has been increasingly recognized [1,2,3,4]. Elucidation of the histone code and subsequent insights into the functional implications of post-translational modifications of histone tails have begun to provide a mechanistic understanding of the role that chromatin context plays in gene expression. One of the most widely studied histone marks of active gene transcription is acetylation of lysine residues in the Nterminal tail of histone H3. Acetylation of Lysines 9 and 14 (H3K9/14Ac), found at promoters and enhancers of actively transcribed genes [5,6,7], serves as a docking point for chromatin remodeling complexes that open chromatin, facilitating transcriptional activation [8,9,10]. Trimethylation of lysine 27 of histone H3 (H3K27me3) confers repression through binding of the polycomb repressive complex (PRC1/2) and chromatin compaction [11,12,13]. The H3K9/14Ac and H3K27me marks usually occur in distinct cell-type specific genomic regions. Using stem cells to dissect the mechanism(s) by which the differentiated epigenotype is reached may be challenging due to the distant
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
