Abstract
During development eukaryotic gene expression is coordinated by dynamic changes in chromatin structure. Measurements of accessible chromatin are used extensively to identify genomic regulatory elements. Whilst chromatin landscapes of pluripotent stem cells are well characterised, chromatin accessibility changes in the development of somatic lineages are not well defined. Here we show that cell-specific chromatin accessibility data can be produced via ectopic expression of E. coli Dam methylase in vivo, without the requirement for cell-sorting (CATaDa). We have profiled chromatin accessibility in individual cell-types of Drosophila neural and midgut lineages. Functional cell-type-specific enhancers were identified, as well as novel motifs enriched at different stages of development. Finally, we show global changes in the accessibility of chromatin between stem-cells and their differentiated progeny. Our results demonstrate the dynamic nature of chromatin accessibility in somatic tissues during stem cell differentiation and provide a novel approach to understanding gene regulatory mechanisms underlying development.
Highlights
During the development of a multicellular organism, gene expression is tightly regulated in response to spatially and temporally restricted signals
We show that Chromatin Accessibility profiling using Targeted DamID (CATaDa) yields comparable results to both FAIRE and ATAC-seq methods, indicating that it is a reliable and reproducible method for investigating chromatin states
To determine if CATaDa produces an accurate reflection of chromatin accessibility, we compared data acquired using this approach with commonly used alternative techniques
Summary
During the development of a multicellular organism, gene expression is tightly regulated in response to spatially and temporally restricted signals. Chromatin states vary widely across developmental stages and cell types. Functional regions of a genome, including promoters and enhancers, can be identified by their relative lack of nucleosomes. These regions of “open chromatin” can be assayed by their accessibility to extrinsic factors. Chromatin is highly accessible in pluripotent cell types such as embryonic stem (ES) cells, but is compacted following differentiation [2]. It has been suggested that this open chromatin represents a permissive state to which multiple programmes of gene regulation may be rapidly applied upon differentiation [3]
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