Genome-wide Analysis of Simultaneous GATA1/2, RUNX1, FLI1, and SCL Binding in Megakaryocytes Identifies Hematopoietic Regulators

Marloes R. Tijssen,Willem H. Ouwehand,Berthold Göttgens,S. Helen Oram,Katrin Ottersbach,Dana C. Bellissimo,Nicola K. Wilson,Anthony R. Green,Anagha Joshi,Ana Cvejic,Rita Ferreira,Rebecca L. Hannah,Xiaonan Wang,Ariel Forrai,Derek L. Stemple,Peter A. Smethurst

doi:10.1016/j.devcel.2011.04.008

Marloes R. Tijssen, Willem H. Ouwehand + Show 14 more

Open Access

https://doi.org/10.1016/j.devcel.2011.04.008

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Abstract

SummaryHematopoietic differentiation critically depends on combinations of transcriptional regulators controlling the development of individual lineages. Here, we report the genome-wide binding sites for the five key hematopoietic transcription factors—GATA1, GATA2, RUNX1, FLI1, and TAL1/SCL—in primary human megakaryocytes. Statistical analysis of the 17,263 regions bound by at least one factor demonstrated that simultaneous binding by all five factors was the most enriched pattern and often occurred near known hematopoietic regulators. Eight genes not previously appreciated to function in hematopoiesis that were bound by all five factors were shown to be essential for thrombocyte and/or erythroid development in zebrafish. Moreover, one of these genes encoding the PDZK1IP1 protein shared transcriptional enhancer elements with the blood stem cell regulator TAL1/SCL. Multifactor ChIP-Seq analysis in primary human cells coupled with a high-throughput in vivo perturbation screen therefore offers a powerful strategy to identify essential regulators of complex mammalian differentiation processes.

Highlights

Complex gene-regulatory networks control all metazoan development (Davidson, 2001)
We have recently reported genome-wide combinatorial interactions for ten key regulators of hematopoietic stem/progenitor cells in the multipotent mouse hematopoietic progenitor cell line 7 (HPC-7) (Wilson et al, 2010a), which revealed combinatorial interactions between a heptad of Transcription factors (TFs) (Scl, Lyl1, Lmo2, Gata2, Runx1, Erg, Fli1)
We have previously shown that the RUNX1 +23 enhancer is bound by GATA2, RUNX1, FLI1, and SCL in mouse progenitor cells (Wilson et al, 2010a), and the SCL +40 enhancer by GATA1 in erythroid cells (Ogilvy et al, 2007)

Summary

SUMMARY

Hematopoietic differentiation critically depends on combinations of transcriptional regulators controlling the development of individual lineages. We report the genome-wide binding sites for the five key hematopoietic transcription factors—GATA1, GATA2, RUNX1, FLI1, and TAL1/SCL—in primary human megakaryocytes. Eight genes not previously appreciated to function in hematopoiesis that were bound by all five factors were shown to be essential for thrombocyte and/or erythroid development in zebrafish. One of these genes encoding the PDZK1IP1 protein shared transcriptional enhancer elements with the blood stem cell regulator TAL1/SCL. Multifactor ChIP-Seq analysis in primary human cells coupled with a high-throughput in vivo perturbation screen offers a powerful strategy to identify essential regulators of complex mammalian differentiation processes

INTRODUCTION

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EXPERIMENTAL PROCEDURES