Genomics

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Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts


ABSTRACT: Evolutionary alterations to cis-regulatory sequences are likely to cause adaptive phenotypic complexity, through orchestrating changes in cellular proliferation, identity and communication. For non-model 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 only been 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 genome-wide 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. examination of H3K4me3 in adult fin tissue of the Nile tilapia (Oreochromis niloticus)

ORGANISM(S): Oreochromis niloticus  

SUBMITTER: Axel Meyer  Claudius F Kratochwil    

PROVIDER: E-GEOD-62791 | ArrayExpress| 2015-08-19

SECONDARY ACCESSION(S): SRP049359GSE62791PRJNA265129

REPOSITORIES: GEO, ArrayExpress, ENA

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Mapping active promoters by ChIP-seq profiling of H3K4me3 in cichlid fish - a first step to uncover cis-regulatory elements in ecological model teleosts.

Kratochwil Claudius F CF   Meyer Axel A  

Molecular ecology resources 20141206 4


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 po  ...[more]

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