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Targeted DamID reveals differential binding of mammalian pluripotency factors

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Title: Targeted DamID reveals differential binding of mammalian pluripotency factors
Authors: Cheetham, SW
Gruhn, WH
Van den Ameele, J
Krautz, R
Southall, TD
Kobayashi, T
Surani, MA
Brand, AH
Item Type: Journal Article
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.
Issue Date: 15-Oct-2018
Date of Acceptance: 23-Aug-2018
URI: http://hdl.handle.net/10044/1/67190
DOI: https://dx.doi.org/10.1242/dev.170209
ISSN: 0950-1991
Publisher: Company of Biologists Ltd
Journal / Book Title: Development
Volume: 145
Issue: 20
Copyright Statement: © 2018 The Author(s). Published by The Company of Biologists Ltd. http://www.biologists.com/user-licence-1-1/
Keywords: Science & Technology
Life Sciences & Biomedicine
Developmental Biology
ChIP-seq
Embryonic stem cells
Oct4
Prdm14
Primordial germ cells
Targeted DamID
PROTEIN-DNA INTERACTIONS
GERM-CELL SPECIFICATION
EMBRYONIC STEM-CELLS
NAIVE PLURIPOTENCY
GENE-EXPRESSION
READ ALIGNMENT
IN-VITRO
MOUSE
PRDM14
INDUCTION
Animals
Binding Sites
Chromatin
DNA Methylation
Genome
Germ Cells
Mice
Mouse Embryonic Stem Cells
Pluripotent Stem Cells
Protein Binding
Transcription Factors
06 Biological Sciences
11 Medical And Health Sciences
Publication Status: Published
Article Number: dev170209
Online Publication Date: 2018-10-17
Appears in Collections:Faculty of Natural Sciences



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