Wednesday, February 18, 2009

ChIP-seq accurately predicts tissue-specific activity of enhancers

by Francisco Barriga
During the last decade, high throughput sequencing has given rise to an astounding amount of information regarding protein coding regions, yet very little is known about distant regulatory sequences, namely enhancers, particularly because they are scattered throughout the vast non-coding portion of the genome. In a recent issue of Nature, Visel and collaborators utilize ChIP-Seq (See [Techniques] Analyzing the genome-wide chromatin landscape: ChIP-Seq) to identify a subset of such distant-acting enhancers across the entire human genome.
[transcription][molecular biology]

They address this question by chromatin immunoprecipitation of the ubiquitously-expressed enhancer-associated protein p300 in different tissues in the mouse embryo followed by high-throughput sequencing. Interestingly the authors find that p300 binds (as a cofactor) to
different enhancer elements in the different tissues analyzed during embryo development, highlighting the importance of distant regulatory elements in appropriate gene expression and how the differential gene expression profiles may be achieved among these tissues.

Besides finding these tissue specific regions, they also validate them as bonna fide enhancers in the tissues that were predicted by p300 binding, through the use of transgenic reporter assays, showing the robustness of their findings.

An interesting fact that arose from the aforementioned studies is that p300 binding sites were generally associated with evolutionarily constrained non-coding sequences in mammalian genomes, underlying their importance in different organisms. Finally, by comparing the genomic distribution of p300 with gene expression data from the studied tissues, the authors show that there is a correlation between p300-enriched regions in embryonic tissues and the transcriptional regulation of neighboring genes, giving further functional support to their discoveries.

In conclusion, high-throughput in vivo mapping of proteins’ binding sites can then be used as an accurate means for identifying functional elements across entire genomes.

The authors conclude:

A generalized picture of the epigenetic marks and proteins associated with different types of functional non-coding elements has started to emerge from genome-wide chromatin studies. We can now begin to use these signatures to unravel gene regulation on a genomic scale in the context of living organisms.

Here's the abstract and reference:

ChIP-seq accurately predicts tissue-specific activity of enhancers.

Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA.

Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.

A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.

Axel Visel, Matthew J. Blow, Zirong Li, Tao Zhang, Jennifer A. Akiyama, Amy Holt, Ingrid Plajzer-Frick, Malak Shoukry, Crystal Wright, Feng Chen, Veena Afzal, Bing Ren, Edward M. Rubin, Len A. Pennacchio (2009). ChIP-seq accurately predicts tissue-specific activity of enhancers Nature, 457 (7231), 854-858 DOI: 10.1038/nature07730