Alternative SET/TAFI Promoters Regulate Embryonic Stem Cell Differentiation

Abstract

Embryonic stem cells (ESCs) are regulated by pluripotency-related transcription factors in concert with chromatin regulators. To identify additional stem cell regulators, we screened a library of endogenously labeled fluorescent fusion proteins in mouse ESCs for fluorescence loss during differentiation. We identified SET, which displayed a rapid isoform shift during early differentiation from the predominant isoform in ESCs, SETα, to the primary isoform in differentiated cells, SETβ, through alternative promoters. SETα is selectively bound and regulated by pluripotency factors. SET depletion causes proliferation slowdown and perturbed neuronal differentiation in vitro and developmental arrest in vivo, and photobleaching methods demonstrate SET's role in maintaining a dynamic chromatin state in ESCs. This work identifies an important regulator of pluripotency and early differentiation, which is controlled by alternative promoter usage.

Keywords: SET; TAF-I; TAFI; chromatin; differentiation; embryonic stem cells; epigenetics; histone chaperone; histone dynamics; pluripotency.

Graphical abstract

Figure 1

A SET Isoform Switch during Early ESC Differentiation (A) Time-lapse images of SETα-YFP cells during the first 50 hr of RA-induced ESC differentiation. Scale bar, 50 μm. (B) Schematic showing the gene structure of the two SET isoforms and YFP-SETα. (C) Anti-GFP western blots of SET-YFP during ESC differentiation. GAPDH was used as control. (D) Protein domain model depicting the SETα and SETβ isoforms. Shown are SETα-specific region (blue), SETβ-specific region (violet), dimerization domain (orange), and acidic domain (red). (E and F) qRT-PCR analysis of SETα (E) (^∗p < 0.001, ^∗∗p ≤ 1.6 × 10⁻⁵, 2-tailed Student's t test) and SETβ (F) mRNA level during ESC differentiation (Data are shown as mean ± SD; n = 3 independent experiments). (G) Anti-SET western blots showing SETα and SETβ isoforms during ESC differentiation. GAPDH was used as loading control. Differentiation was carried out in ESC medium with RA (1 μM) and without LIF on gelatin-coated plates. (H) RNA-seq tracks showing evidence for SETα and SETβ expression in ESCs and MEFs.

Figure 2

SETα Expression Is Regulated by Pluripotency Factors in ESCs (A) In silico reverse-ChIP analysis for SET. For every query, our BindDB webtool and pipeline returns the TFs and chromatin modifications that are enriched at the promoter region (proximal or distal). Dark green, binding; light green, no binding. Green, blue, and red boxes depict TFs or histone marks associated with active chromatin, pluripotency, or poised chromatin, respectively. (B) ChIP analysis of pluripotency factors at the SETα promoter (left). SETα gene body corresponding to a region in intron 7 was used as a negative control (right) (data are shown as mean ± SD; n = 3 independent experiments). (C) qRT-PCR analysis of Oct4 and Nanog mRNA levels in Zhbtc4 cells before and after Dox treatment. Expression levels were normalized to GAPDH (data are shown as mean ± SD; n = 3 independent experiments). (D and E) qRT-PCR analysis of SETα (D) and SETβ (E) mRNA levels in Zhbtc4 cells before and after Dox treatment. Expression levels were normalized to GAPDH expression (data are shown as mean ± SD; n = 3 independent experiments). (F) Western blots of SETα, SETβ, and OCT4 in Zhbtc4 cells before and after Dox treatment. GAPDH was used as a loading control. (G) Binding profiles of RNAPII at SETα and SETβ promoters before (0 hr) and after (24 hr) Dox addition. Data are from Rahl et al. (2010).

Figure 3

SET Regulates ESC Proliferation (A) qRT-PCR analysis of SET knockdown efficiency (n = 3 independent biological experiments; ^∗p < 0.005, 2-tailed t test). Expression levels were normalized to GAPDH. Error bars represent ±SD. (B) Western blots of SET in control (Scr-ctrl) and SET-KD cells. GAPDH was used as control. (C) Western blots of pluripotency factors in SET-KD clones. GAPDH was used as control. (D) The number of upregulated (blue) and downregulated (red) genes in undifferentiated SET-KD ESCs (left) and in RA-induced SET-KD cells (right). (E) Reduced proliferation in SET-KD ESCs (^∗p < 0.05, 2-tailed t test). Cell number of SET-depleted ESCs was normalized to Scr-ctrl cell number. Error bars represent ±SD (n = 3 independent biological experiments). (F) Cell-cycle analysis of SET-KD cells. Cell number in each phase was normalized to that of Scr-ctrl (n = 3 independent experiments; error bars represent ±SD; ^∗p < 0.05, 2-tailed t test). (G) KH2-ESC proliferation assay following overexpression (OE) of SETα or SETβ (n = 3 independent experiments; error bars represent ±SD). (H) Representative images of clone formation assay of control (top), SETα-OE (bottom left), and SETβ-OE (bottom right) wells. Colonies were detected with AP staining (pink). (I) Quantification of (H) (n = 3 independent experiments; error bars represent ±SD; ^∗p < 0.05, 2-tailed t test).

Figure 4

SET Regulates ESC Neuronal Differentiation (A) Phase contrast images of Scr-ctrl cells (left) and SET-KD cells (right). SET depletion results in circular colonies and aberrant neuronal differentiation (arrows). Scale bars, 200 μm. (B) Immunofluorescence (IF) for NESTIN (red) and RA-differentiated Scr-ctrl (top) and SET-KD cells (bottom). Nuclei were counterstained with DAPI (blue, right). Note the characteristic circular structures in the KD clones. Scale bar, 200 μm. (C) IF for OCT4 (red) in RA-differentiated Scr-ctrl (left) and SET-KD clones (right). Scale bar, 200 μm. (D) IF for GATA4 (red) in RA-differentiated Scr-ctrl (top) and SET-KD ESCs (bottom). Nuclei were counterstained with DAPI (blue, right). Scale bar, 200 μm. (E and F) Time-course qRT-PCR analysis of pluripotency (E) and differentiation (F) factor levels in Scr-Ctrl and KD clones during RA-induced differentiation. Expression levels were normalized to GAPDH (n = 3 independent biological experiments; error bars represent ±SEM). (G) EBs derived from Scr-ctrl cells (left) and SET-KD clones (right). Note formation of cystic EBs in the SET-KD clones. Scale bar, 500 μm. (H) Normal EB formation in SETα- and SETβ-overexpressing clones. Scale bar, 500 μm. (I) IF for NESTIN (red) in NPCs derived from Scr-ctrl (top) and SET-KD clones (bottom) without addback vectors. Phase-contrast images are shown on the left. Scale bar, 200 μm. (J) Quantification of (I) (n = 3 independent experiments; error bars represent ±SD; ^∗p < 0.02, 2-tailed Student's t test). (K) Western blots using anti-HA antibodies showing HA-SETα and HA-SETβ overexpression in addback clones. Arrowheads indicate SET isoform positions. (L) NESTIN immunostaining (red) in NPCs derived from Scr-ctrl cells (Scr-pN1, left), SET-KD cells (second from left), and in SET-KD-addback SETα (second from right) or SETβ (right) clones. Empty vectors (pN1) were used as controls. Nuclei were counterstained with DAPI (blue). Phase contrast is shown at the bottom. Dotted white lines represent the border between EBs and differentiating NPCs. Scale bars, 100 μm. (M) Quantification of the addback experiments (n = 3 independent experiments; error bars represent ±SD; ^∗p < 0.05, 2-tailed t test). (N) The relative abundance (in percentage) of the different cell types observed during NPC differentiation of Scr-ctrl, SET-KD and the various addback clones. (O) IF for TUJ1 (red) in differentiated neurons derived from Scr-ctrl (top) and SET-KD ESCs (middle and bottom). Nuclei were counterstained with DAPI (blue). Scale bar, 100 μm. (P) Quantification of neuronal differentiation capacity in Scr-ctrl and KD clones (n = 3 independent experiments; error bars represent ±SD; ^∗p < 0.05, 2-tailed Student's t test).

Figure 5

SETα Is Essential for Maintaining the ESC State (A) qRT-PCR analysis of the lineage-specific factors Nestin (blue), Brachyury (red), and Gata4 (green) in SET-control, SETα-OE, and SETβ-OE ESCs and in 4-day differentiated EBs (n = 3 independent experiments; error bars represent ±SD; ^∗p < 0.05; 2-tailed t test). Expression levels were normalized to GAPDH. (B) Experimental layout of NPC differentiation from SET-OE ESCs. (C) Phase-contrast images of continued (top) or transient (bottom) SETα expression during NPC differentiation. Scale bar, 200 μm. (D) Immunostaining for NESTIN in NPCs derived from KH2 cells (left), KH2 cells continually expressing SETα (middle), and KH2 cells transiently expressing SETα (right). Nuclei were counterstained with DAPI (blue). Scale bar, 100 μm. (E) Quantification of the transient and continuous addback experiments (n = 3 independent experiments; error bars represent ±SD; ^∗p < 0.05, 2-tailed Student's t test). (F) FRAP curves of histone H1e-Cherry in control (blue) and SET-KD (red, orange) cells (n = 3 independent experiments; ^∗∗∗p < 10⁻⁴; 2-tailed t test). (G) Kinetic parameters of SET-KD FRAP experiments (H) FRAP curves of H1e-Cherry in control (blue), SETα-OE (red), and SETβ-OE (green) cells (n = 3 independent experiments; ^∗∗p < 0.02, 2-tailed Student's t test). (I) Kinetic parameters of SET-OE FRAP experiments.