Abstract
ABSTRACTThe interaction of proteins and RNA with chromatin underlies the regulation of gene expression. The ability to profile easily these interactions is fundamental for understanding chromatin biology in vivo. DNA adenine methyltransferase identification (DamID) profiles genome-wide protein-DNA interactions without antibodies, fixation or protein pull-downs. Recently, DamID has been adapted for applications beyond simple assaying of protein-DNA interactions, such as for studying RNA-chromatin interactions, chromatin accessibility and long-range chromosome interactions. Here, we provide an overview of DamID and introduce improvements to the technology, discuss their applications and compare alternative methodologies.
Highlights
Techniques that identify the binding of regulatory factors to chromatin are essential for uncovering the mechanisms that maintain and control gene expression
In 2000, Bas van Steensel and Steven Henikoff pioneered the use of DNA adenine methylase identification (DamID) as an alternative to Chromatin immunoprecipitation (ChIP)
chromatin accessibility TaDa (CATaDa) profiling of progenitor and differentiated cell types in the developing Drosophila CNS has identified enriched motifs that correspond to neural transcription factor-binding sites, and cell-type-specific enhancers (Aughey et al, 2018)
Summary
Techniques that identify the binding of regulatory factors to chromatin are essential for uncovering the mechanisms that maintain and control gene expression. Tissue dissociation protocols can result in gene expression artefacts (van den Brink et al, 2017) To address these problems, two DamID methods that allow cell-specific profiling of DNA binding without cell isolation have been developed. If precise temporal control is desired in Gal4-driven experiments, Gal may need to be present to repress Gal activity Another consideration is that the FLP-inducible technique causes an irreversible genetic change, ensuring that all progeny cells in a lineage will express the functioning Dam-fusion. This approach is not suitable to determine the binding sites of proteins in precursor cell types during development.
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