Targeted DamID reveals differential binding of mammalian pluripotency factors.

TitleTargeted DamID reveals differential binding of mammalian pluripotency factors.
Publication TypeJournal Article
Year of Publication2018
AuthorsCheetham, SW, Gruhn, WH, van den Ameele, J, Krautz, R, Southall, TD, Kobayashi, T, M Surani, A, Brand, AH
JournalDevelopment
Volume145
Issue20
Date Published2018 10 17
ISSN1477-9129
KeywordsAnimals, Binding Sites, Chromatin, DNA Methylation, Genome, Germ Cells, Mice, Mouse Embryonic Stem Cells, Pluripotent Stem Cells, Protein Binding, Transcription Factors
Abstract

The precise control of gene expression by transcription factor networks is crucial to organismal development. The predominant approach for mapping transcription factor-chromatin interactions has been chromatin immunoprecipitation (ChIP). However, ChIP requires a large number of homogeneous cells and antisera with high specificity. A second approach, DamID, has the drawback that high levels of Dam methylase are toxic. Here, we modify our targeted DamID approach (TaDa) to enable cell type-specific expression in mammalian systems, generating an inducible system (mammalian TaDa or MaTaDa) to identify genome-wide protein/DNA interactions in 100 to 1000 times fewer cells than ChIP-based approaches. We mapped the binding sites of two key pluripotency factors, OCT4 and PRDM14, in mouse embryonic stem cells, epiblast-like cells and primordial germ cell-like cells (PGCLCs). PGCLCs are an important system for elucidating primordial germ cell development in mice. We monitored PRDM14 binding during the specification of PGCLCs, identifying direct targets of PRDM14 that are key to understanding its crucial role in PGCLC development. We show that MaTaDa is a sensitive and accurate method for assessing cell type-specific transcription factor binding in limited numbers of cells.

DOI10.1242/dev.170209
Alternate JournalDevelopment
Citation Key10.1242/dev.170209
PubMed ID30185410
PubMed Central IDPMC6215400
Grant List / / Wellcome Trust / United Kingdom
103792 / / Wellcome Trust / United Kingdom
105839 / / Wellcome Trust / United Kingdom
092545 / / Wellcome Trust / United Kingdom
096738 / / Wellcome Trust / United Kingdom
092096 / / Wellcome Trust / United Kingdom
C6946/A14492 / / Cancer Research UK / United Kingdom