PU.1-Directed Gene Networks in Erythroid Cells Figure 7. PU.1 occupies many of the same gene targets in myeloid and erythroid cells, and PU.1-dependent gene regulation is similar in HSC, myeloid, and erythroid cells. (A) qChIP was performed for PU.1 as described in Materials and Methods with chromatin from 32D cells using primers described in Table S2. An HA antibody was used as an isotype control. The same primers were used to show that PU.1 binds close to these genes in MEL cells and ES-EP (Figure S5). The myogenin gene serves as a negative control. Standard deviations were calculated from triplicate PCR reactions. Similar results were obtained with at least two independent chromatin preparations. (B) Expression data from PU.12/2 cells stimulated to differentiate into macrophages by the restoration of PU.1 [49] and HSC from PU.1 knockdown mice [33] were used to compare with PU.1 dependent gene regulation in early erythroid progenitors from PU.1 knockdown mice. Of the PU.1 bound genes in MEL and ES-EP that displayed a $1.5-fold change in expression, 308 were upregulated and 209 were downregulated. 162 and 265 of these PU.1 dependent genes were annotated in the other 2 datasets. Venn diagrams display the comparisons between the three datasets of these upregulated genes (left) and downregulated genes (right). doi:10.1371/journal.pgen.1001392.g007 PLoS Genetics | www.plosgenetics.org 11 June 2011 | Volume 7 | Issue 6 | e1001392