@article {47412,
	title = {Epigenomic landscapes of retinal rods and cones.},
	journal = {eLife},
	volume = {5},
	year = {2016},
	month = {2016 Mar 07},
	abstract = {<p>Rod and cone photoreceptors are highly similar in many respects but they have important functional and molecular differences. Here, we investigate genome-wide patterns of DNA methylation and chromatin accessibility in mouse rods and cones and correlate differences in these features with gene expression, histone marks, transcription factor binding, and DNA sequence motifs. Loss of NR2E3 in rods shifts their epigenomes to a more cone-like state. The data further reveal wide differences in DNA methylation between retinal photoreceptors and brain neurons. Surprisingly, we also find a substantial fraction of DNA hypo-methylated regions in adult rods that are not in active chromatin. Many of these regions exhibit hallmarks of regulatory regions that were active earlier in neuronal development, suggesting that these regions could remain undermethylated due to the highly compact chromatin in mature rods. This work defines the epigenomic landscapes of rods and cones, revealing features relevant to photoreceptor development and function.</p>
},
	issn = {2050-084X},
	doi = {10.7554/eLife.11613},
	author = {Mo, Alisa and Luo, Chongyuan and Davis, Fred P and Mukamel, Eran A and Henry, Gilbert L and Nery, Joseph R and Urich, Mark A and Picard, Serge and Lister, Ryan and Eddy, Sean R and Beer, Michael A and Ecker, Joseph R and Nathans, Jeremy}
}
@article {46852,
	title = {Epigenomic signatures of neuronal diversity in the mammalian brain.},
	journal = {Neuron},
	volume = {86},
	year = {2015},
	month = {2015 Jun 17},
	pages = {1369-1384},
	abstract = {<p>Neuronal diversity is essential for mammalian brain function but poses a challenge to molecular profiling. To address the need for tools that facilitate cell-type-specific epigenomic studies, we developed the first\&nbsp;affinity purification approach to isolate nuclei from genetically defined cell types in a mammal. We\&nbsp;combine this technique with next-generation sequencing to show that three subtypes of neocortical neurons have highly distinctive epigenomic landscapes. Over 200,000 regions differ in chromatin accessibility and DNA methylation signatures characteristic of gene regulatory regions. By footprinting and motif analyses, these regions are predicted to bind distinct cohorts of neuron subtype-specific transcription factors. Neuronal epigenomes reflect both past and present gene expression, with DNA hyper-methylation at developmentally critical genes appearing as a novel epigenomic signature in mature neurons. Taken together, our findings link the functional and transcriptional complexity of neurons to their underlying epigenomic diversity.</p>
},
	issn = {1097-4199},
	doi = {10.1016/j.neuron.2015.05.018},
	author = {Mo, Alisa and Mukamel, Eran A and Davis, Fred P and Luo, Chongyuan and Henry, Gilbert L and Picard, Serge and Urich, Mark A and Nery, Joseph R and Sejnowski, Terrence J and Lister, Ryan and Eddy, Sean R and Ecker, Joseph R and Nathans, Jeremy}
}
