Evolutionary conservation of the eumetazoan gene regulatory landscape

Short talk at the XXXVIII meeting of the Portuguese Genetics Society, June 2013

Transcript

1. Evolutionary conservation of the eumetazoan gene regulatory landscape XXXVIII Jornadas Portuguesas de Genética, June 2013 Michaela Schwaiger, Anna Schönauer, André F. Rendeiro, Carina Pribitzer, Alexandra Schauer, Anna Gilles, Johannes Schinko, David Fredman, and Ulrich Technau University of Vienna, Austria
2. Evolution of biological complexity and body plans in metazoans
3. Gregory, T.R. (2005). Animal Genome Size Database Genome size does not correlate with morphological complexity
4. ~15000 André Karwath Gene number does not correlate with morphological complexity ~24000 Chuya Shinzato ~21000 Richard Avedon ~23000 Kirt L. Onthank
5. We want to inspect whether the evolution of morphological complexity is driven largely by major differences in gene regulation.
6. Metazoa Eumetazoa Bilateral symmetry Third germ layer adapted from Ryan et al. Genome Biology, 2006.
7. Lee et al. Developmental Biology, 2007. Nematostella vectensis (Cnidaria, Anthozoa) First cnidarian genome sequenced. Surprising highly conserved gene repertoire and intron structure. Similar complexity of developmental gene families as vertebrates. Many important genes for development of key bilaterian traits.
8. What we did Comparison of the gene regulatory landscape between a cnidarian (Nematostella vectensis) and bilaterians. Highly reproducible ChIP-seq datasets in two developmental stages (gastrula and planula). H3K36me3 First genome-wide prediction of chromatin states and gene regulatory elements in a non-bilaterian animal.
9. Results & Discussion
10. Conserved distribution of histone modifications across eumetazoan genes
11. Conserved distribution of histone modifications across eumetazoan genes H3K4me1 H3K4me2 H3K4me3 H3K36me3 Gene models
12. H3K4me3 and CpG methylation target mutually exclusive regions In vertebrates, DNA methylation at CpG dinucleotides is found throughout large parts of the genome, but excluded from sites of H3K4 trimethylation. Drosophila and C. elegans lack DNA methylation, but many invertebrates, including Nematostella, methylate CpGs. Gene models H3K4me3 CpG methylation
13. Enhancer chromatin modifications at distal p300/CBP peaks are conserved and correlate with expression We found thousands of peaks distal (> 300bp) from the nearest TSS. Chromatin marks correlate with expression of nearest gene. Distal p300 TSS TES As in vertebrates, H3K4me1 marks all enhancers, while active enhancers are distinguished by the presence of H3K27ac.
14. Enhancer chromatin modifications at distal p300/CBP peaks are conserved and correlate with expression We found thousands of peaks distal (> 300bp) from the nearest TSS. Chromatin marks correlate with expression of nearest gene. Distal p300 TSS TES As in vertebrates, H3K4me1 marks all enhancers, while active enhancers are distinguished by the presence of H3K27ac. As in vertebrates, distal p300 peaks might act as TSSs for non-coding RNAs.
15. -2kb 2kb TSS Annotation of chromatin states and prediction of gene regulatory elements Genome segmented into 6 different chromatin states with HMM model Predicted 2558 gastrula and 4732 planula enhancers, 1543 are shared. 2967 genes are potentially regulated by at least one enhancer. Genes containing stage-specific enhancers have higher expression at the same stage.
16. Complex regulation of transcription factors in Nematostella -log 10 (p-value) Transcriptional regulation, signaling, and developmental processes are significantly enriched
17. Complex regulation of transcription factors in Nematostella Transcription factors are significantly more associated with multiple enhancers than housekeeping genes -log 10 (p-value) Transcriptional regulation, signaling, and developmental processes are significantly enriched
18. Genomic landscape of gene regulation Similarity of genomic distribution of enhancers between Nematostella and Drosophila. Enrichment Depletion Nematostella Enhancers Drosophila Enhancers Zebrafish Enhancers 1.5Gb genome 170Mb genome ~300Mb genome Position of enhancers in orthologs is not conserved: 1) do not share any common ancestry 2) have diverged and may be even bound by different transcription factors.
19. In vivo validation of predicted enhancers 12 in 16 of the tested regions drove expression in a tissue specific pattern at least partially reflecting the expression pattern of the neighboring gene mRNA mOrange mRNA mOrange
20. Final Remarks First genome-wide analysis of gene regulation in a non-bilaterian sheds light on the evolution of regulation in animals. The eumetazoan ancestor already possessed very complex regulation. Complexity of bilaterian body plans in general did not arise through novel gene regulatory mechanisms, but possibly through a re-wiring of a few important interactions in gene regulatory networks. It is necessary to obtain a detailed understanding of gene regulatory networks in cnidarians and bilaterians to understand the evolution of morphological complexity.
21. Acknowledgements Technau lab, Vienna specially Michaela Schwaiger Christiane Wirbelauer and Dirk Schübeler (Antibodies, Blots) Rabih Murr and Andreas Sommer (NGS) Anaïs Bardet (Peakzilla software)