Evolutionary Conservation of the Eumetazoan Gene Regulatory Landscape

Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Research Evolutionary conservation of the eumetazoan gene regulatory landscape Michaela Schwaiger,4 Anna Scho¨nauer,1 Andre´ F. Rendeiro,2 Carina Pribitzer, Alexandra Schauer, Anna F. Gilles,3 Johannes B. Schinko,3 Eduard Renfer, David Fredman, and Ulrich Technau4 Department of Molecular Evolution and Development, Center for Organismal Systems Biology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria Despite considerable differences in morphology and complexity of body plans among animals, a great part of the gene set is shared among Bilateria and their basally branching sister group, the Cnidaria. This suggests that the common ancestor of eumetazoans already had a highly complex gene repertoire. At present it is therefore unclear how morphological diversification is encoded in the genome. Here we address the possibility that differences in gene regulation could con- tribute to the large morphological divergence between cnidarians and bilaterians. To this end, we generated the first genome-wide map of gene regulatory elements in a nonbilaterian animal, the sea anemone Nematostella vectensis. Using chromatin immunoprecipitation followed by deep sequencing of five chromatin modifications and a transcriptional cofactor, we identified over 5000 enhancers in the Nematostella genome and could validate 75% of the tested enhancers in vivo. We found that in Nematostella, but not in yeast, enhancers are characterized by the same combination of histone modifications as in bilaterians, and these enhancers preferentially target developmental regulatory genes. Surprisingly, the distribution and abundance of gene regulatory elements relative to these genes are shared between Nematostella and bilaterian model organisms. Our results suggest that complex gene regulation originated at least 600 million yr ago, predating the common ancestor of eumetazoans. [Supplemental material is available for this article.] It is currently not known to what extent the evolution of mor- differences might underlie apparent morphological differences. phological complexity was driven by changes in gene content or Indeed, the evolution of new body plans is often driven by changes differences in gene regulation. The sea anemone Nematostella vec- in the regulation of gene expression (Carroll 2008; Wittkopp and tensis belongs to cnidarians, the sister group to all bilaterians, Kalay 2011) and many differences between closely related species which diverged from bilaterians more than 600 million yr ago. are caused by changes in cis-regulatory elements that regulate the Cnidarians consist of only two germ layers (endoderm and ecto- expression patterns of their target genes in a modular way (Sucena derm) and have roughly 12–20 morphologically distinct somatic et al. 2003; Jeong et al. 2008; Rebeiz et al. 2009; Chan et al. 2010; cell types. Yet, the Nematostella gene repertoire is surprisingly Frankel et al. 2012). similar to that of vertebrates (Putnam et al. 2007). Despite the In bilaterians, genes are regulated not only by proximal pro- simplicity of its morphology and of gene expression patterns moters, but also by a combination of distal cis-regulatory elements. (Steele et al. 2011; Technau and Steele 2011), the complexity of Each gene can have multiple enhancer elements, which are often developmental gene families (e.g., Wnt, homeobox transcription found at large distances from the gene they regulate (Spitz and factors) in Nematostella is similar to that found in vertebrates Furlong 2012; Ya´n˜ez-Cuna et al. 2012). Therefore, an important (Kusserow et al. 2005; Chourrout et al. 2006; Ryan et al. 2007), and initial step in comparing gene regulation between evolutionary its genome harbors many genes important for the development of distant species is to identify enhancer elements throughout their key bilaterian traits such as mesoderm and bilaterality (Finnerty genomes. Despite their importance, enhancers have been very 2004; Fritzenwanker et al. 2004; Martindale et al. 2004; Technau difficult to locate until recently. However, with the advent of et al. 2005; Steele et al. 2011; Technau and Steele 2011). The simple microarray and next-generation sequencing technologies, ge- body plan of an animal with such a complex gene repertoire led to nome-wide maps of enhancer elements have been predicted in the assumption that the complexity of gene regulation may be human cell lines (Heintzman et al. 2007, 2009; The ENCODE different between bilaterians and nonbilaterians and that these Project Consortium 2012) and several major bilaterian model organisms (Visel et al. 2009a; Gerstein et al. 2010; The modENCODE Consortium et al. 2010; May et al. 2011; Ne`gre et al. 2011; Shen Present addresses: 1Department of Biological and Medical Sciences, et al. 2012). This was achieved not only by mapping the binding Oxford Brookes University, Oxford OX3 0BP, UK; 2Department of Bi- sites of a number of tissue-specific transcription factors (Gerstein 3 ology, University of Aveiro, 3810-193 Aveiro, Portugal; Institut de et al. 2010), but also based on characteristic histone modifications Ge´nomique Fonctionnelle de Lyon (IGFL), Ecole Normale Superieure de Lyon, 69364 Lyon, France and the binding of transcriptional cofactors (Visel et al. 2009a; The 4Corresponding authors E-mail [email protected] E-mail [email protected] Article published online before print. Article, supplemental material, and pub- Ó 2014 Schwaiger et al. This article, published in Genome Research, is avail- lication date are at http://www.genome.org/cgi/doi/10.1101/gr.162529.113. able under a Creative Commons License (Attribution-NonCommercial 3.0 Freely available online through the Genome Research Open Access option. Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/. 24:639–650 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/14; www.genome.org Genome Research 639 www.genome.org Downloaded from genome.cshlp.org on September 24, 2021 - Published by Cold Spring Harbor Laboratory Press Schwaiger et al. modENCODE Consortium et al. 2010; May et al. 2011; Ne`gre et al. H3K4me3 and CpG methylation target mutually exclusive 2011; Shen et al. 2012). Initially, it was shown in mammalian cell regions lines that while H3K4me3 levels are higher at promoters, In vertebrates, DNA methylation at CpG dinucleotides is found H3K4me1 is more enriched at enhancer elements (Heintzman throughout large parts of the genome, but is excluded from sites of et al. 2007, 2009; Supplemental Table S1). This observation has H3K4 methylation (Meissner et al. 2008; Suzuki and Bird 2008; recently been extended to Drosophila as well as vertebrate model Jones 2012; Long et al. 2012). While the invertebrate model or- organisms (Ne`gre et al. 2011; Bogdanovic et al. 2012; Bonn et al. ganisms Drosophila melanogaster and Caenorhabditis elegans lack DNA 2012). It has been suggested that inactive enhancers can be dis- methylation, it has recently been shown that other invertebrates, tinguished from active ones due to the fact that active enhancers including Nematostella vectensis, methylate CpGs throughout many are also associated with acetylated histones (Creyghton et al. 2010; active gene bodies (Feng et al. 2010; Zemach et al. 2010). To test Rada-Iglesias et al. 2010). One of the enzymes that catalyzes the whether the mutually exclusive location of H3K4 methylation and acetylation of histones, the transcriptional cofactor EP300 (also DNA methylation is shared between vertebrates and cnidarians, we known as p300), has been shown to bind to enhancers, and has sorted all genes based on their distribution of H3K4me3 around the recently been used in several studies to predict enhancer elements TSS (Fig. 1B). While the distributions of H3K4me3, H3K4me2, and genome wide (Visel et al. 2009b; May et al. 2011; Ne`gre et al. 2011; H3K27ac are very similar (Fig. 1B; Supplemental Fig. S1), H3K36me3 Shen et al. 2012). Thus, while these studies underlined the com- is enriched within gene bodies of the same genes, starting imme- plexity of cis-regulatory landscapes in vertebrates and insects, their diately after the TSS. CpG methylation localizes to gene bodies evolutionary origin remains unclear, as no studies of nonbilaterian (Zemach et al. 2010) and its levels correlate with H3K36me3 (Fig. animals have been performed. 1B; Supplemental Fig. S3) (P < 2.2 3 10À16). In contrast to Here, we profiled five histone modifications (Supplemental H3K36me3, CpG methylation begins only about 1 kb after the TSS, Table S1) and the binding sites of the Nematostella histone acety- a position where H3K4me3 is no longer enriched, thus suggesting lase p300 throughout the Nematostella genome. Our analysis a mutually exclusive location of H3K4me3 and CpG methylation revealed that the distribution of histone modifications across the in Nematostella. Nematostella genome, relative to genes, as well as their colocaliza- tion with DNA methylation (Zemach et al. 2010), were remarkably Enhancer chromatin modifications at promoter-distal p300 similar to what has been shown in bilaterian model organisms. peaks This allowed us to use this data to predict more than 5000 enhancer elements across two developmental stages of Nematostella. The transcriptional cofactor p300 has been shown to be associated A total of 75% of the predicted enhancers tested in vivo drove with enhancer regions in vertebrates (Visel et al.

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