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In vivo enhancer analysis of human conserved non-coding sequences

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Abstract

Identifying the sequences that direct the spatial and temporal expression of genes and defining their function in vivo remains a significant challenge in the annotation of vertebrate genomes. One major obstacle is the lack of experimentally validated training sets. In this study, we made use of extreme evolutionary sequence conservation as a filter to identify putative gene regulatory elements, and characterized the in vivo enhancer activity of a large group of non-coding elements in the human genome that are conserved in human–pufferfish, Takifugu (Fugu) rubripes, or ultraconserved1 in human–mouse–rat. We tested 167 of these extremely conserved sequences in a transgenic mouse enhancer assay. Here we report that 45% of these sequences functioned reproducibly as tissue-specific enhancers of gene expression at embryonic day 11.5. While directing expression in a broad range of anatomical structures in the embryo, the majority of the 75 enhancers directed expression to various regions of the developing nervous system. We identified sequence signatures enriched in a subset of these elements that targeted forebrain expression, and used these features to rank all 3,100 non-coding elements in the human genome that are conserved between human and Fugu. The testing of the top predictions in transgenic mice resulted in a threefold enrichment for sequences with forebrain enhancer activity. These data dramatically expand the catalogue of human gene enhancers that have been characterized in vivo, and illustrate the utility of such training sets for a variety of biological applications, including decoding the regulatory vocabulary of the human genome.

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Acknowledgements

Research was conducted at the E. O. Lawrence Berkeley National Laboratory, under the Programs for Genomic Application, funded by the National Heart, Lung, and Blood Institute, USA as well as the National Human Genome Research Institute, USA, and performed under a Department of Energy Contract with the University of California.

Author information

Competing interests

Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Correspondence to Len A. Pennacchio.

Supplementary information

  1. Supplementary Table 1.

    A summary of all the human conserved noncoding fragments tested for enhancer activity at embryonic day 11.5. Enhancer ID refers to a unique identifier defined at http://enhancer.lbl.gov. (XLS 37 kb)

  2. Supplementary Table 2.

    A compilation of human-fugu conserved noncoding elements in the human genome. (XLS 208 kb)

  3. Supplementary Table 3.

    The top 30 forebrain enhancer predictions in the human genome. The strategy to generate this list can be found in the Supplementary Methods. (XLS 18 kb)

  4. Supplementary Methods.

    An expanded version of the Materials and Methods. (DOC 61 kb)

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Further reading

Figure 1: A summary of all sequences tested for enhancer activity in transgenic mice.
Figure 2: A 3 Mb region of human chromosome 16 enriched for human– Fugu non-coding conservation flanking the SALL1 gene.
Figure 3: Grouping of positive expression patterns captured in the transgenic mouse enhancer assay.
Figure 4: Application of a forebrain enhancer training set to identify forebrain-specific enhancer sequences elsewhere in the human genome.

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