Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts.
Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For nonmodel organisms with adaptive key innovations, patterns of regulatory evolution have been predominantly limited to targeted sequence-based analyses. Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a technology that has been primarily used in genetic model systems and is a powerful experimental tool to screen for active cis-regulatory elements. Here, we show that it can also be used in ecological model systems and permits genomewide functional exploration of cis-regulatory elements. As a proof of concept, we use ChIP-seq technology in adult fin tissue of the cichlid fish Oreochromis niloticus to map active promoter elements, as indicated by occupancy of trimethylated Histone H3 Lysine 4 (H3K4me3). The fact that cichlids are one of the most phenotypically diverse and species-rich families of vertebrates could make them a perfect model system for the further in-depth analysis of the evolution of transcriptional regulation.
Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany.|Zukunftskolleg, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany.
Claudius F
http://orcid.org/0000-0002-5646-3114
CF
Kratochwil
Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Universitaetsstrasse 10, 78457, Konstanz, Germany.
Axel
A
Meyer
D000818:Animals; D047369:Chromatin Immunoprecipitation; D023681:Cichlids / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism*; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D017422:Sequence Analysis, DNA
D006657:Histones
cichlids; cis-regulatory elements; epigenetics; evolutionary genetics; histone modifications; phenotypic variation; tilapia; transcriptional regulation