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Mapping active promoters by Ch IP ‐seq profiling of H3K4me3 in cichlid fish – a first step to uncover cis‐regulatory elements in ecological model teleosts
Author(s) -
Kratochwil Claudius F.,
Meyer Axel
Publication year - 2015
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12350
Subject(s) - biology , cichlid , h3k4me3 , profiling (computer programming) , fish <actinopterygii> , promoter , computational biology , evolutionary biology , ecology , gene , fishery , genetics , gene expression , computer science , operating system
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 (Ch IP ‐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 Ch IP ‐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.