Fig. 6: The nuclear CHD6 interactome is highly enriched for PAR-modified and PAR-associated proteins.
For all statistical analysis in this figure, 2-way ANOVAs followed by Tukey post hoc tests were carried out. ns = not significant (p > 0.05), *p < 0.05. ** p < 0.01. ***p < 0.001.****p < 0.0001. Source data are provided as a Source Data file. Panel a Workflow used for identification of interacting partners of CHD6; this figure was created using Biorender (https://BioRender.com/i42e687) and Microsoft PowerPoint. Panel b CHD6HA was transfected into HEK293T, immunoprecipitated from nuclear cells extracts, and immunoblotted for CHD6 to confirm IP efficacy (with KAP-1 used as a loading control); this data is representative of three biological replicates. Panel c SAINT scores of all identified CHD6-interacting proteins and compared to their fold enrichment above IgG controls. Panel d Partial network of proteins identified exclusively in CHD6HA IP or that exhibited a spectral count fold change > 2 compared to IgG controls. Protein hits were filtered for spectral count > 3 across three biological replicates and nuclear localization using the STRING database. Connections between protein hits are based on physical interactions annotated in the STRING database. See Supplemental Information for complete network and all protein names. Panel e. Network of the highest confidence interacting proteins of CHD6 (highlighted by yellow shading in (c). High confidence hits were determined based on a minimum fold change of 2 (dashed line) and SAINT score of 0.5. Annotated interactions from the BioGRID database are also shown. Nodes with yellow borders indicate known targets of PARP1 activity or proteins that interact with PAR-modified substrates. Panel f. Stacked Venn diagrams illustrate the number of proteins identified in the CHD6 nuclear interactome that also were listed as significant in four published screens identifying substrates for PARylation or PAR-interactors.
