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Targeted DamID reveals differential binding of mammalian pluripotency factors.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Gruhn, Wolfram H 
van den Ameele, Jelle  ORCID logo  https://orcid.org/0000-0002-2744-0810
Krautz, Robert 
Southall, Tony D 

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.

Description

Keywords

ChIP-seq, Embryonic stem cells, Oct4, Prdm14, Primordial germ cells, Targeted DamID, Animals, Binding Sites, Chromatin, DNA Methylation, DNA-Binding Proteins, Genome, Germ Cells, Mice, Mouse Embryonic Stem Cells, Pluripotent Stem Cells, Protein Binding, RNA-Binding Proteins, Transcription Factors

Journal Title

Development

Conference Name

Journal ISSN

0950-1991
1477-9129

Volume Title

145

Publisher

The Company of Biologists
Sponsorship
Wellcome Trust (092545/Z/10/Z)
Wellcome Trust (103792/Z/14/Z)
Wellcome Trust (105839/Z/14/Z)
Royal Society (RP150061)
Wellcome Trust (096738/Z/11/Z)
Wellcome Trust (092096/Z/10/Z)
Cancer Research Uk (None)