An Oct4-centered protein interaction network in embryonic stem cells

Abstract

Transcription factors, such as Oct4, are critical for establishing and maintaining pluripotent cell identity. Whereas the genomic locations of several pluripotency transcription factors have been reported, the spectrum of their interaction partners is underexplored. Here, we use an improved affinity protocol to purify Oct4-interacting proteins from mouse embryonic stem cells (ESCs). Subsequent purification of Oct4 partners Sall4, Tcfcp2l1, Dax1, and Esrrb resulted in an Oct4 interactome of 166 proteins, including transcription factors and chromatin-modifying complexes with documented roles in self-renewal, but also many factors not previously associated with the ESC network. We find that Esrrb associated with the basal transcription machinery and also detect interactions between transcription factors and components of the TGF-beta, Notch, and Wnt signaling pathways. Acute depletion of Oct4 reduced binding of Tcfcp2l1, Dax1, and Esrrb to several target genes. In conclusion, our purification protocol allowed us to bring greater definition to the circuitry controlling pluripotent cell identity.

Figure 1

Purification of Oct4 and Its Interacting Proteins (A) Colloidal Coomassie-stained SDS-polyacrylamide gel of a FLAG-Oct4 (F-Oct4) and control purification. Asterisk indicates contaminating band. The F-Oct4 band is indicated. (B) Colloidal Coomassie-stained SDS-polyacrylamide gel of immunoprecipitated endogenous Oct4 and a control immunoprecipitation via IgG. The Oct4 band is indicated. (C and D) Oct4 immunoprecipitates analyzed by western blots with the indicated antibodies. Benzonase (Benzo) was added where indicated. (E) MTA2 immunoprecipitates analyzed by western blots with the indicated antibodies. (F) Subunit stoichiometry of F-Oct4-bound NuRD complex (F-Oct4) compared to anti-Mta2 coimmunoprecipitated NuRD complex (anti-Mta2) by western blot against the indicated NuRD subunits. Asterisk indicates a lighter exposure of the same experiment. See also Figure S1.

Figure 2

Purification of F-Sall4, F-Dax1, F-Tcfcp2l1, F-Esrrb, and Their Interacting Proteins (A) Colloidal Coomassie-stained SDS-polyacrylamide gels of representative purifications of the FLAG-tagged transcription factors and control purifications from the parental ESC line. Arrows indicate the respective FLAG-tagged proteins. (B–E) Summaries of the identified interacting proteins. The average Mascot score and number of identified unique peptides of two purifications without doxycycline addition are indicated for individual proteins or complexes. The number of identified subunits of a complex is between brackets. (F) F-Esrrb or control purifications analyzed by western blots with the indicated antibodies. Benzonase was added where indicated. (G) GST-Esrrb pull-downs analyzed by western blots with the indicated antibodies. Figure S3H (right) shows the purified GST proteins on a Coomassie-stained polyacrylamide gel. See also Figure S2 and Tables S2–S9.

Figure 3

Protein Interaction Network of Oct4 and Its Associated Proteins Sall4, Dax1, Tcfcp2l1, and Esrrb The network represents the proteins present in both purifications (−Dox) of F-Sall4, F-Dax1, F-Tcfcp2l1, or F-Esrrb and/or present in F-Oct4 purifications as in Table 1 (complete lists of identifications and information on Mascot scores, number of identified unique peptides, and emPAI scores are shown in Table 1 and Tables S2–S9). Complexes are shown as larger circles. Yellow coloring indicates importance for ESC self-renewal capacity (see Table 2). See also Figure S3.

Figure 4

Oct4-Dependent Genome Targeting by Dax1, Tcfcp2l1, and Esrrb Left panels indicate genome binding by F-Tcfcp2l1 (A), F-Esrrb (B), and V5-Dax1 (C) at the indicated genomic regions in the absence (−Dox) or presence (+Dox) of doxycycline, as assessed by ChIP against FLAG (F-Tcfcp2l1 and F-Esrrb) or V5 (V5-Dax1) in ZHBTc4 ESCs stably expressing these tagged proteins. The ZHBTc4 parental cell line functions as a specificity control (ZHBTc4). Right panels indicate Oct4 genome binding, as assessed by Oct4 antibody ChIP, on the same regions and in the same ESCs as the corresponding left panels. Note that the addition of doxycycline diminishes expression and thereby genome binding by Oct4. Graphs show the enrichment over a control region (Amylase). SEM is indicated by error bars.