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Review
. 2019 Mar 15;146(6):dev173666.
doi: 10.1242/dev.173666.

DamID as a versatile tool for understanding gene regulation

Gabriel N Aughey  1 , Seth W Cheetham  2 , Tony D Southall  3
Affiliations
Review

DamID as a versatile tool for understanding gene regulation

Gabriel N Aughey et al. Development. .

Abstract

The 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.

Keywords: Chromatin; DamID; Gene regulation; Genomics.

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Conflict of interest statement

Competing interestsThe authors declare no competing or financial interests.

Figures

Fig. 1.
Fig. 1.
Methods for cell-specific DamID profiling. (A) TaDa allows cell-specific low-level expression of Dam by attenuating its translation using an upstream ORF. (B) Cell type-specific expression of FLP can remove a stop cassette from in between a minimal promoter and the Dam ORF, allowing low-level expression of Dam in the cells of interest.
Fig. 2.
Fig. 2.
DamID as a versatile tool for studying genome biology. (A) Profiling of transcription factors (TFs) and chromatin-modifying enzymes. (B) Analysis of transcription by profiling Pol II occupancy. (C) Profiling of chromatin accessibility using untethered Dam (CATaDa). (D) Profiling the interaction of non-coding RNAs with DNA using an MCP-Dam fusion (RNA-DamID). (E) Identification of transcription factor co-binding using split DamID. (F) Identification of specific long-range DNA interactions by tethering Dam to a specific locus. (G) Live imaging of DNA that has associated with a specific protein (e.g. lamin).
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