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05.09.18 MaTaDa method reveals cell-type-specific transcription factor binding in small numbers of mammalian cells

last modified Sep 10, 2018 12:30 PM
The Brand and Surani labs combine expertise to apply the Targeted DamID approach to studying binding of mammalian pluripotency factors
05.09.18 MaTaDa method reveals cell-type-specific transcription factor binding in small numbers of mammalian cells

Fig 5e (extract): Genes differentially expressed in ESCs vs. genes bound by PRDM14 in PGCLCs.

Targeted DamID reveals differential binding of mammalian pluripotency factors

Cheetham SW et al. (2018) Development  Sep 5. pii: dev.170209. DOI: 10.1242/dev.170209. [Epub ahead of print]

 

Abstract from the paper

The precise control of gene expression by transcription factor networks is critical 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 protein/DNA interactions in 100 to 1000 times fewer cells than ChIP.

We mapped the binding sites of 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 to elucidate 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 critical role in PGCLC development.

We show that MaTaDa is a sensitive and accurate method to assess cell type specific transcription factor binding in limited numbers of cells.

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Read more about research in the Brand and Surani labs.

Watch Andrea Brand describe her research in this short video.

Studying development to understand disease

The Gurdon Institute is funded by Wellcome and Cancer Research UK to study the biology of development, and how normal growth and maintenance go wrong in cancer and other diseases.

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