@article {1483610,
	title = {Enhancer transcription identifies -regulatory elements for photoreceptor cell types},
	journal = {Development},
	volume = {147},
	number = {3},
	year = {2020},
	month = {2020 Feb 05},
	abstract = {Identification of cell type-specific regulatory elements (CREs) is crucial for understanding development and disease, although identification of functional regulatory elements remains challenging. We hypothesized that context-specific CREs could be identified by context-specific non-coding RNA (ncRNA) profiling, based on the observation that active CREs produce ncRNAs. We applied ncRNA profiling to identify rod and cone photoreceptor CREs from wild-type and mutant mouse retinas, defined by presence or absence, respectively, of the rod-specific transcription factor (TF) -dependent ncRNA expression strongly correlated with epigenetic profiles of rod and cone photoreceptors, identified thousands of candidate rod- and cone-specific CREs, and identified motifs for rod- and cone-specific TFs. Colocalization of NRL and the retinal TF CRX correlated with rod-specific ncRNA expression, whereas CRX alone favored cone-specific ncRNA expression, providing quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activity. We validated the activity of novel -dependent ncRNA-defined CREs in developing cones. This work supports differential ncRNA profiling as a platform for the identification of cell type-specific CREs and the discovery of molecular mechanisms underlying TF-dependent CRE activity.},
	issn = {1477-9129},
	doi = {10.1242/dev.184432},
	author = {Perez-Cervantes, Carlos and Smith, Linsin A and Nadadur, Rangarajan D and Hughes, Andrew E O and Wang, Sui and Corbo, Joseph C and Cepko, Constance and Lonfat, Nicolas and Moskowitz, Ivan P}
}
