Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins

Abstract

Maintenance of pluripotency is regulated by a network of transcription factors coordinated by Oct4, Sox2, and Nanog (OSN), yet a systematic investigation of the composition and dynamics of the OSN protein network specifically on chromatin is still missing. Here we have developed a method combining ChIP with selective isolation of chromatin-associated proteins (SICAP) followed by mass spectrometry to identify chromatin-bound partners of a protein of interest. ChIP-SICAP in mouse embryonic stem cells (ESCs) identified over 400 proteins associating with OSN, including several whose interaction depends on the pluripotent state. Trim24, a previously unrecognized protein in the network, converges with OSN on multiple enhancers and suppresses the expression of developmental genes while activating cell cycle genes. Consistently, Trim24 significantly improved efficiency of cellular reprogramming, demonstrating its direct functionality in establishing pluripotency. Collectively, ChIP-SICAP provides a powerful tool to decode chromatin protein composition, further enhanced by its integrative capacity to perform ChIP-seq.

Keywords: biotinylation; chromatin; embryonic stem cells; pluripotency; protein interactions; proteomics; reprogramming.

Graphical abstract

Figure 1

Principles of ChIP-SICAP Similar to a ChIP experiment, DNA proteins are crosslinked by formaldehyde, and fixed chromatin is sheared to small fragments by sonication (1). Following immunoprecipitation with a suitable antibody (2), DNA is biotinylated by TdT and biotin-ddUTP (3). The antibody is denatured by SDS (4), and chromatin is retrieved along with interacting proteins on streptavidin beads (5). Following extensive washing (6), isolated chromatin fragments are heated to reverse the crosslinks (7). Finally, proteins are digested and identified by mass spectrometry (8).

Figure 2

Comparing Performance of ChIP-SICAP to ChIP-MS and RIME Using Nanog as the Bait (A) Enriched proteins ranked by abundance. (B) Relative abundance of various protein classes. Stacked bars show the abundance of Nanog interactors (light green), other chromatin/DNA binding proteins (dark green), ribosomal proteins (amber), ribonucleoproteins (orange), and other cytoplasmic proteins (burnt orange) relative to the total protein abundance within each method. PTP, potential true positive. PFP, potential false positive. (C) Total MS intensity (top panel) and number of peptides (bottom panel) produced from antibody and protein A contamination. (D) Cumulative distribution of abundance-ranked proteins within the four datasets for various protein classes. Asterisk indicates cytoplasmic proteins that are neither Nanog interactor nor chromatin/DNA binder nor ribosomal nor ribonucleoprotein. See also Figure S2 and Table S1.

Figure 3

Comparative ChIP-SICAP between 2iL and Serum Conditions (A) Scatterplots indicating the distribution and reproducibility of protein ratios in the three ChIP-SICAP experiments using Nanog, Oct4, and Sox2 as bait proteins. Proteins identified by the no-antibody control are not shown. (B) Differential chromatin interaction of proteins involved in stem cell maintenance, nucleosomes, and de novo DNA methylation among the three ChIP-SICAP experiments. (C) Overlap among proteins identified to colocalize with the three pluripotency master regulators. Proteins identified with no antibody control were subtracted. (D) GO annotation of the proteins identified by ChIP-SICAP with Oct4, Sox2, and Nanog. (E) Fold change of proteins and their modifications, comparing ChIP-SICAP data between 2iL and serum growth conditions. See also Figure S3 and Table S2.

Figure 4

Integration of OSN ChIP-SICAP and Association of TRIM24 to the Pluripotency Network (A) Hierarchical clustering of proteins identified by ChIP-SICAP using Oct4, Sox2, Nanog, and Cdh1 as bait proteins. Coloring was done according to ChIP-SICAP 2iL/serum protein ratio (log2). Zoom-in of the top cluster shows the enrichment of known (green) and so-far-unknown OSN-associated proteins (black). (B) Trim24 ChIP-seq signal in 2iL and serum conditions compared to OSN signal in non-superenhancers (nonSE). (C) Same as in (B), but for superenhancers (SE), as defined in (Whyte et al., 2013). (D) Heatmap showing differentially expressed genes after Trim24 knockdown (fold change > 1.5, FDR < 0.01). T KD, Trim24 knockdown; P KD, p53 knock down; T+P KD, double knockdown of Trim24 and p53. See also Figure S4, Table S3, and Table S4.

Figure 5

Mechanism and Function of Trim24 (A) Genetic interaction between Trim24 and p53. The scatterplot shows the genes differentially expressed after Trim24 knockdown. The effect of p53 knockdown on Trim24-target genes (y axis) was calculated by dividing expression change after p53-Trim24 double knockdown by expression change after Trim24 knockdown. Red dots indicate genes with a Trim24-binding site (<10 kb from the gene). Blue dots indicate genes with a p53-binding site (<10 kb from the gene). (B) Trim24 increases the efficiency of reprogramming. (Left) iPS colonies were generated with Oct4, Sox2, Klf4, and c-Myc (OSKM) (bottom) or OSKM plus Trim24 (top) to compare the efficiency of reprogramming based on the number of Oct4-EGFP-positive colonies. (Right) Bar chart indicates the mean of three wells transduced by the vectors separately (error bars indicate SD; p value, Student’s t test). See also Figure S5, Table S4, and Table S5.

Figure 6

Retrieving DNA and Peptides from the Same ChIP-SICAP Assay (A) After tryptic digestion, peptides are cleaned up by SP3 protocol (Hughes et al., 2014) using magnetic beads. DNA remains in solution while peptides are trapped on the beads and can be retrieved separately for sequencing and mass spectrometry. (B) Enrichment of peaks called in a normal Nanog ChIP-seq in comparison to their enrichment after isolation of DNA via ChIP-SICAP. Green dots indicate top 10,000 enriched peaks. Red dots indicate peaks <2-fold enriched by ChIP-SICAP. (C) Aligned ChIP-seq profiles for Nanog near the Nanog locus. Traces indicate profiles after DNA retrieval via classical ChIP-seq (top) and ChIP-SICAP (middle) compared to ChIP-seq data from Whyte et al. (2013) (bottom). See also Figure S6 and Table S7.