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. 2012 Feb 25;40(4):1438–1445. doi: 10.1093/nar/gkr1010

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© The Author(s) 2012. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Delineation and analysis of cis-NAT promoters. Cis-NATs are initiated from protein-coding gene loci and transcribed in the opposite (antisense) direction. (a) Example of a protein-coding gene locus with a genic promoter that drives transcription in the 5′-to-3′ direction along with a cis-NAT promoter that initiates 3′-to-5′ transcription within the locus. (b) cis-NAT TSSs were defined using clusters of overlapping antisense CAGE tags. Specific cis-NAT TSS locations were taken as the base with the highest density of mapped CAGE tags within the cluster. (c) cis-NAT promoter sequences were taken as genomic regions immediately flanking cis-NAT TSS, and the chromatin environment of cis-NAT promoters was analyzed using ChIP-seq data for histone modification and RNA Pol II binding.