Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme noncoding-sequence conservation has successfully predicted enhancers that are active in many tissues but has failed to identify substantial numbers of heart-specific enhancers. Here, we used ChIP-Seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over 3,000 candidate heart enhancers genome wide. Compared to enhancers active in othertissues we studied at this time point, most candidate heart enhancers were less deeply conserved in vertebrate evolution. Nevertheless, transgenic mouse assays of 130 candidate regions revealed that most function reproducibly as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary conservation of embryonic enhancers can vary depending on tissue type.
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The authors wish to thank R. Hosseini and S. Phouanenavong for technical support. L.A.P. and E.M.R. were supported by grant HL066681, Berkeley Program for Genomic Applications, which is funded by the National Heart, Lung, and Blood Institute. L.A.P. was also supported by grant HG003988, which is funded by the National Human Genome Research Institute. B.L.B was supported by grants HL64658 and HL89707 from the National Heart, Lung, and Blood Institute. B.R. is supported by funding from the National Human Genome Research Institute and the Ludwig Institute for Cancer Research. Research was conducted at the E.O. Lawrence Berkeley National Laboratory and was performed under the Department of Energy Contract DE-AC02-05CH11231, University of California.
The authors declare no competing financial interests.
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