Compartmentalization of HP1 Proteins in Pluripotency Acquisition and Maintenance

Abstract

The heterochromatin protein 1 (HP1) family is involved in various functions with maintenance of chromatin structure. During murine somatic cell reprogramming, we find that early depletion of HP1γ reduces the generation of induced pluripotent stem cells, while late depletion enhances the process, with a concomitant change from a centromeric to nucleoplasmic localization and elongation-associated histone H3.3 enrichment. Depletion of heterochromatin anchoring protein SENP7 increased reprogramming efficiency to a similar extent as HP1γ, indicating the importance of HP1γ release from chromatin for pluripotency acquisition. HP1γ interacted with OCT4 and DPPA4 in HP1α and HP1β knockouts and in H3K9 methylation depleted H3K9M embryonic stem cell (ESC) lines. HP1α and HP1γ complexes in ESCs differed in association with histones, the histone chaperone CAF1 complex, and specific components of chromatin-modifying complexes such as DPY30, implying distinct functional contributions. Taken together, our results reveal the complex contribution of the HP1 proteins to pluripotency.

Keywords: Dppa4; H3.3; H3K9M; HP1α knockout; HP1β knockout; HP1γ knockout; Senp7; iPSC; pluripotency; reprogramming.

Figure 1

Differential Localization and Function of HP1γ during Reprogramming (A) Immunofluorescence for HP1γ (top panel) and HP1α (bottom panel) in (i) mouse embryonic fibroblasts (MEFs), (ii) at different time points in reprogramming populations, and (iii) embryonic stem cells (ESCs). Scale bar, 10 μm. Inset: zoomed image of a region (white box). Inset scale bar, 10 μm. (B) (i) Cell counts of punctate, non-punctate, and semi-punctate HP1γ localization in reprogramming MEFs, plotted as a fraction of the total cells counted, N. Semi-punctate refers to a generally more nucleoplasmic localization, but still exhibiting <3 punctate spots. (ii) Colony counts of punctate, non-punctate, and mixed HP1γ localization in reprogramming colonies, plotted as a fraction of the total colonies counted, N. (C) (i) Cell counts of punctate, non-punctate, and semi-punctate HP1α localization in reprogramming MEFs plotted as a fraction of the total cells counted, N. Semi-punctate refers to a generally more nucleoplasmic localization, but still exhibiting <3 punctate spots. (ii) Colony counts of punctate, non-punctate, and mixed HP1α localization in reprogramming colonies, plotted as a fraction of the total colonies counted, N. (D) Top: scheme of experiment. Doxycycline (Dox) induction of reprogramming factors on day 0, small interfering RNA (siRNA) transfection on days indicated by arrows. Nanog-positive iPSCs colonies counted on day 10. Bottom: ratio of iPSC colonies formed upon depletion of HP1γ over non-targeting control show differences between each depletion starting point. Error bars represent SDs of three independent reprogramming experiments. ^∗p < 0.05, ^∗∗p < 0.01 assessed by Student's t test. (E) (i) Immunofluorescence of HP1γ in partially reprogrammed iPSCs (pre-iPSCs). Scale bar, 10 μm. (ii) Top: scheme of experiment. Pre-iPSCs treated with AA + 2i: AA, ascorbic acid; 2i, MAPK inhibitor (PD-0325901) + GSK inhibitor (CHIR-99021). Cells were transfected with siRNA on indicated days. Bottom: percentage of Nanog-GFP cells upon depletion of HP1γ or non-targeting control determined by flow cytometry. Error bars represent SDs of two independent wells from the same experiment. Data from three independent conversion experiments are presented. See also Figures S1 and S2, and Movie S1.

Figure 2

Compartmentalization of HP1γ Complexes in ESCs (A) Immunoblot of HP1γ extracted from ESCs with increasing salt concentrations (left), or micrococcal nuclease (MCN)-mediated extraction with increasing salt concentrations (right). S, supernatant; P, pellet; WNE, whole nuclear extract; Cyto, cytoplasmic. Bottom: numbers indicate quantified fraction of HP1γ from S and P with total S + P = 1. (B) HP1γ-interacting proteins enriched in different extraction methods. Volcano plots show proteins enriched in FLAG-HP1γ of ESC (+Dox) extracted with (i) 0.42 M KCl, (ii) MCN with 0.15 M NaCl, or (iii) MCN with 0.3 M NaCl against uninduced samples (-Dox) as control. Significantly enriched proteins, red; bait, blue; significantly enriched proteins that are also expressed >10-fold higher in ESC compared with MEF, bold red. (C) Venn diagram showing overlaps of enriched proteins between the three extraction conditions as in (B). Known interactors of HP1γ, magenta; previously unidentified interactors of HP1γ, black; previously unidentified interactors of HP1γ that are also expressed 10-fold higher in ESC, bold black. (D) Complexes enriched in FLAG-HP1γ IP-MS of MCN with 0.3 M NaCl overlaid on the STRING Network database. See also Figure S2 and Table S1.

Figure 3

Differential Enrichment of HP1γ-Interacting Proteins in Pre-iPSCs Compared with ESCs (A) Venn diagram showing overlaps of enriched HP1γ interactors from individual analyses in ESCs (as in Figure 2B) and pre-iPSC (as in Figure S3B). Known interactors of HP1, magenta; previously unidentified interactors of HP1, black; interactors of HP1 that are also expressed >5-fold higher in ESC compared to pre-iPSC, bold black. (B) Volcano plot showing quantitative comparison of FLAG-HP1γ IP-MS in ESC versus pre-iPSC. Significantly enriched proteins, red; significantly enriched proteins that are also expressed >5-fold higher in ESC compared to pre-iPSC, bold red. (C) Bar graphs show differential enrichment of HP1γ-interacting proteins as part of complexes between ESCs and pre-iPSCs. Data from two or three independent immunoprecipitation experiments for ESC and pre-iPSC, respectively, are presented. ^∗p < 0.05, ^∗∗p < 0.01, ^∗∗∗p < 0.005, ^∗∗∗∗p < 0.001 assessed by Student's t test. (D) (i) Scheme of experiment: ESCs with dox-inducible FLAG-HP1γ or pre-iPSCs with either FLAG-empty or FLAG-HP1γ were transduced with V5-tagged H3.3 lentivirus followed by immunoprecipitation with FLAG antibody (FLAG-IP). (ii) Immunoprecipitation (IP) with FLAG antibody with immunoblot for V5 and HP1γ. Asterisk (^∗) marks immunoglobulin G (IgG) light chain (25 kDa). (iii) Quantitation of percentage enrichment (elute/input) for V5-H3.3 in pre-iPSC and ESC. Error bars represent SDs of two independent immunoprecipitation experiments. See also Figure S3 and Table S1.

Figure 4

Differential Enrichment of SENP7 in Pre-iPSCs Compared with ESCs (A) (i) IP with FLAG antibody in pre-iPSCs and ESCs with immunoblot for SENP7 and HP1γ. (ii) Quantitation of percentage enrichment (elute/input) for SENP7 in pre-iPSCs and ESCs. Error bars represent SDs of two independent immunoprecipitation experiments. (B) Percentage of Nanog-GFP cells in a pre-iPSC conversion experiment upon depletion of Senp7, HP1γ, both Senp7 and HP1γ, or non-targeting control. Error bars represent SDs of two independent conversion experiments. See also Figure S4.

Figure 5

Interaction of HP1γ with OCT4 and DPPA4 Is Independent of the Presence of HP1α or HP1β and H3K9 Methylation (A) Immunoprecipitation (IP) of endogenous HP1γ with immunoblot for OCT4 and DPPA4. Asterisk (^∗) marks IgG heavy chain (∼55 kDa). (B) IP of endogenous DPPA4 with immunoblot for HP1γ. (C) Confocal immunofluorescence image show regions of colocalization of DPPA4 with HP1γ except in mitotically dividing cells. Scale bar, 10 μm; inset scale bar, 5 μm. (D) Immunofluorescence of HP1α and HP1β ESC knockout cell lines. Scale bar, 10 μm. (E) IP of endogenous HP1γ in Crispr wild-type (WT), HP1α KO, and HP1β KO ESC with immunoblot for OCT4 and DPPA4. (F) Western blot of H3K9me2 and H3K9me3 in FLAG-HP1γ ESC line with V5-tagged H3.3 K9M compared with control V5-tagged H3.3 WT. Cells were treated with doxycycline (Dox) to induce expression of FLAG-HP1γ. (G) IP of FLAG-HP1γ in (i) H3.3 WT ESC and (ii) H3.3 K9M ESC, with immunoblot for OCT4 and DPPA4. See also Figure S5.

Figure 6

Differential Protein Enrichment between HP1α, HP1β, and HP1γ (A) Volcano plots showing quantitative comparison of proteins enriched in (i) HP1γ versus HP1α, or (ii) HP1γ versus HP1β in ESC extracted with MCN + 0.3 M NaCl. Significantly enriched proteins, red; bait, blue; significantly enriched proteins that are also expressed >5-fold higher in ESC, bold red. (B) Bar graphs of differential enrichment of proteins between HP1α, HP1β, and HP1γ within known complexes. Data from two independent immunoprecipitation experiments for each group are presented. (C) (i) IP with FLAG antibody in FLAG-HP1α or FLAG-HP1γ ESC with immunoblot for CHAF1B, DPY30, and FLAG. (ii) Quantitation of percentage enrichment (elute/input) for CHAF1B and DPY30 in FLAG-HP1α or FLAG-HP1γ ESC. Error bars represent SDs of two independent immunoprecipitation experiments. (D) Western blot of co-immunoprecipitation of H3K79me2 with FLAG-HP1γ. (E) Post-translational modifications (PTMs) of HP1α, HP1β, and HP1γ found in ESC in red. Previously unidentified PTMs are in red with yellow highlights. Chromodomain, chromoshadow domain, and hinge domain are indicated. See also Figure S6, Table S2, and Table S3.

Figure 7

Proposed Model of HP1γ Interactions In non-pluripotent cells and reprogramming intermediates, HP1γ interacts with SENP7, which anchors HP1γ to H3K9me2/3 histones in the heterochromatin, depicted as red or yellow circles. HP1γ is also more enriched with linker histone H1 in reprogramming intermediates. During reprogramming, the release of HP1γ from being anchored to the heterochromatin is required to attain pluripotency. In pluripotent cells, HP1γ interacts with histone H3.3 and histone elongation mark H3K79me2. Moreover, OCT4 and DPPA4 are among the interactors of HP1γ in pluripotent cells that occur independently of H3K9me3 but may be dependent on other modifications (black circle).