BMP and WNT-Directed Transcription Factors TCF7L2/TCF4 and SMAD1 Bind to Distinct Hematopoietic-Specific Target Genes Depending on Cell Lineage
Authors: Trompouki Eirini , Bowman Teresa V. , Lawton Lee N , Fan Zi Peng , DiBiase Anthony , Cech Jennifer , Sessa Anna , LeBlanc Jocelyn , Li Pulin , Heffner Garrett , Daley George Q. , Young Richard , Zon Leonard I. 
Published: October 2019

Abstract
Abstract 3870
The BMP and WNT signaling pathways are two highly conserved signaling pathways that cooperate in many developmental processes, ultimately through alteration of transcription via SMAD and TCF transcription factors. These pathways elicit pleiotropic outcomes across cell types, yet only a few cell-specific direct target genes are known for the signaling transcription factors that mitigate these effects. We took a genome-wide approach to define the binding sites of BMP and WNT-directed transcription factors in different hematopoietic lineages. Using heat-shock inducible transgenic fish lines that overexpress BMP2 or WNT8, we demonstrated accelerated marrow recovery following irradiation. Irradiation recovery was blunted by heat shock induced overexpression of the respective inhibitors Chordin and DKK1. Similar to the zebrafish regeneration results, competitive transplants with mouse bone marrow treated with the WNT agonist BIO led to enhanced chimerism. Inhibition of BMP diminished peripheral blood contribution even in the presence of WNT stimulation, suggesting a conserved and cell intrinsic interaction for these signaling pathways in adult stress hematopoiesis. To examine potential target genes that could account for the synergy, we performed chromatin immunoprecipitation with WNT- and BMP-activated transcription factors followed by sequencing (ChIP-seq) in K562 cells. ChIP-seq was performed with TCF7L2/TCF4, a mediator of the WNT pathway, and SMAD1, a mediator of the BMP signaling pathway, and >2000 binding sites were identified for each factor. Motif discovery revealed that the DNA sequences bound by TCF7L2 and SMAD1 were not only enriched for TCF and SMAD binding elements, respectively, but were also enriched for a GATA motif. Comparison of the TCF7L2 and SMAD1 bound genes with published ChIP-Seq data for GATA1 and GATA2 in K562 cells revealed that both signaling factors bind more than 40% of GATA1 bound genes and greater than 70% of GATA2 bound genes. Ingenuity and GSEA analysis revealed that genes important for erythropoiesis were among the genes co-bound by these factors. To evaluate the effect of cell lineage on signaling factor binding, ChIP-seq of TCF7L2 and SMAD1 in U937, a monocytic leukemia cell line, was performed. Motif discovery of sequences bound in U937 found enrichment for an ETS motif, which is bound by the key myeloid transcription factor Pu.1. In addition, TCF7L2 and SMAD1 bound genes in U937 overlapped genes bound by C/EBPalpha in U937 by greater than 70%. These genes are implicated in monocytic development. The overlap of binding between TCF7L2 in K562 and U937 was less than 15% and the overlap of SMAD1 binding sites between the cell lines was less than 10%, indicating a substantial influence of cell lineage on transcription factor binding. Confirmation of cell type selective binding of TCF7L2 and SMAD1 in vivo was accomplished by ChIP of the transcription factors in zebrafish nucleated erythrocytes. Binding of TCF7L2 and SMAD1 in these cells showed that these factors co-bind with GATA1 in many genes with established roles in erythropoiesis. Together our data suggest the co-binding of WNT- and BMP-specific transcription factors with master regulators of each hematopoietic cell type results in regulation of distinct blood genes based on lineage.
(First two authors contributed equally to this work)

Disclosures:
Zon: FATE, Inc.: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties; Stemgent: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.