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Coordination of mA mRNA Methylation and Gene Transcription by ZFP217 Regulates Pluripotency and Reprogramming

http://www.cell.com/cell-stem-cell/abstract/S1934-5909(15)00412-9?rss=yes by

 

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Figure 1

ZFP217 Is Required to Maintain the Pluripotent State of ESCs

(A) qRT-PCR analysis of Zfp217 expression in MEFs, iPSCs, and ESCs. Data are represented as mean ± SD (n = 3). ∗∗∗p < 0.0005, ∗∗p < 0.005 versus MEFs.

(B and C) qRT-PCR analysis of Zfp217, Pou5f1, Sox2, and Zfp617 during RA-induced differentiation (B) and EB formation (C). Data are represented as mean ± SD (n = 3).

(D and E) qRT-PCR analysis of Zfp217 (D) and representative western blot (E) for ZFP217 upon Nanog, Pou5f1, and Sox2 depletion. The expression of the pluripotency factors was determined to monitor knockdown efficiency. Error bars show ± SD (n = 3). ∗∗∗p < 0.0001 versus control shRNA. For the immunoblots, β-ACTIN was used as a loading control. Asterisk in (E), nonspecific; Ctrl, control.

(F) qRT-PCR (top) and western blot analysis (bottom) to monitor Zfp217 knockdown efficiency. Error bars show ± SD (n = 3). ∗∗∗p < 0.0001 versus control shRNA. For the immunoblot, β-ACTIN was used as a loading control.

(G and H) AP staining of control and Zfp217-depleted ESCs (G). Percentages of ESC colonies were counted and are depicted in (H). UD, undifferentiated; PD, partially differentiated; FD, fully differentiated.

(I) Proliferation rate of control and Zfp217-depleted ESCs relative to shRNA control on day 8. Error bars show ± SD (n = 3). p = 0.01 versus control shRNA.

(J) Cell-cycle distribution of control and Zfp217-depleted ESCs examined by DNA content index. Error bars show ± SD (n = 3). Ns, not significant. p < 0.05 versus control.

(K) Percentage of early apoptotic cells in control and Zfp217-depleted ESCs defined as Annexin V-positive and 7-aminoactinomycin D (7AAD)-negative cells. Error bars show ± SD (n = 3). ∗∗p < 0.005, ∗∗∗p < 0.001 versus control shRNA.

Figure 2

ZFP217 Is Required for Somatic Cell Reprogramming

(A) Schematics of iPSC generation. d, day; IF, immunofluorescence.

(B and C) Representative qRT-PCR analysis for Zfp217 (B) and Nanog (C) during MEF reprogramming.

(D and E) AP staining (D) and quantification (E) of control and Zfp217-depleted iPSCs on day 21. Error bars show ± SD (n = 3). ∗∗∗p < 0.0001 versus control shRNA.

(F) Proliferation rate of control and Zfp217-depleted reprogramming MEFs.

(G) AP staining of reprogramming MEFs overexpressing ZFP217_HA or empty vector on day 15 post-transduction.

(H and I) Number of AP+ (H) and GFP+ (I) colonies in ZFP217_HA relative to empty vector. Error bars show ± SD (n = 3). ∗∗p < 0.001 versus empty vector (EV).

(J) Proliferation rate of reprogramming MEFs transduced with ZFP217_HA or empty vector.

(K) E-CADHERIN (CDH1), SSEA1, and NANOG immunostaining on the indicated days of reprogramming with control or Zfp217 shRNA. The bright field is depicted at the right. Scale bars, 100 μm.

(L) Heatmap illustrating the relative expression of pluripotency, epithelial, and mesenchymal genes measured by qRT-PCR in reprogramming MEFs with control or Zfp217 shRNA on the indicated days.

Figure 3

ZFP217 Is Associated with Both Promoters and Enhancers in ESCs

(A) The relative position of the unique closest ZFP217 peaks with respect to the TSS (x axis) and the log2 fold change in gene expression in response to Zfp217 depletion (y axis).

(B) The number of ZFP217-only-bound genes, activated and bound, and repressed and bound in Zfp217-depleted ESCs.

(C and D) Functional categories of genes activated and bound (C) and repressed and bound (D) upon Zfp217 depletion of ESCs showing the p value for the enrichment of biological process GO term.

(E) The distribution of ZFP217-binding peaks relative to the nearest TSS.

(F) The genomic distribution of ZFP217-binding peaks, including promoters (within 5 kb upstream of the TSS), downstream (within 10 kb downstream of the gene), introns, exons, upstream (within 10 kb upstream of the gene), and intergenic regions.

(G) ZFP217 binding sites (black lines) at active (green), bivalent (dark green), and silent (orange) genes (defined in the Supplemental Experimental Procedures ).

(H and I) ZFP217 de novo motif (H) and ZFP217 binding at known binding motifs for STAT3, KLF4, SP1, and POU5F1 (I) with the corresponding p values.

Figure 4

ZFP217 Positively Regulates the ESC Transcriptome

(A) Scatterplot of upregulated and downregulated genes in control compared with Zfp217-depleted ESCs.

(B) qRT-PCR analysis of pluripotency-associated genes in ESCs transduced with Zfp217_1 or Zfp217_2 compared with control shRNA. Error bars show ± SD (n = 3). p < 0.0001 versus control shRNA.

(C) Luciferase assay of the indicated constructs transfected in control or Zfp217-depleted ESCs. Data are normalized to cytomegalovirus (CMV)-Renilla luciferase and represented relative to the minimal Oct4 promoter. Error bars show ± SD (n = 3). ∗∗p < 0.001; p < 0.05; ns = not significant versus control shRNA.

(D) ChIP-qPCR analysis of ZFP217 (top), LSD1 (center), and POU5F1 (bottom) binding at the Pou5f1, Nanog, and Sox2 loci. The positions of the amplified regions are indicated in Figures S3 A–S3C. E1 and E2, enhancer 1 and enhancer 2, respectively. Error bars show ± SD (n = 3). p < 0.0001; ns, not significant versus immunoglobulin G (IgG) control.

(E) Density maps of ZFP217, LSD1, and POU5F1 ChIP-seq datasets at the TSS. The color scale indicates the ChIP-seq signal in reads per million.

(F) GSEA plots of ZFP217, LSD1, and POU5F1-bound genes during RA-induced differentiation and EB formation. Top: high and low expression of genes is represented in red and blue, respectively. Bottom: functional categories of ZFP217, LSD1, and POU5F1-bound genes using genomic regions enrichment of annotations tool (GREAT) software. NES, normalized enrichment score; FDR, false discovery rate

Figure 5

ZFP217 Interacts with METTL3 and Counteracts Its Activity

(A) The network of associated proteins identified through LC-MS/MS of ZFP217. Black and red lines represent published and novel interactions, respectively.

(B) Ingenuity pathway analysis (IPA) of proteins identified with LC-MS/MS. Left: the molecular and cellular functions. Right: function annotations of the RNA post-transcriptional modification category.

(C) Immunoprecipitation of nuclear extracts from ESCs with antibodies against ZFP217 (left) or METTL3 (right), followed by immunoblotting (IB) with ZFP217, METTL3, and METTL14 antibodies. IgG was used as a control.

(D) Immunoprecipitation (IP) of nuclear extracts pretreated with DNase I or RNase A with antibodies against ZFP217, followed by immunoblotting with ZFP217 and METTL3 antibodies. IgG was used as a control.

(E) qRT-PCR analysis of Mettl3 expression in MEFs, iPSCs, and ESCs. Error bars show ± SD (n = 3). ∗∗∗p < 0.0005 versus MEFs.

(F and G) RT-qPCR analysis of Mettl3 during RA-induced differentiation (F) and EB formation (G). Error bars show ± SD (n = 3).

(H) m6A immunostaining of ESCs transduced with control, Zfp217_1, or Mettl3_1 shRNAs. Nuclei were stained with DAPI. Scale bars, 100 μm.

(I) Dot blot analysis of polyadenylated RNA (poly(A)+) isolated from control and Zfp217_1 shRNA ESCs. The indicated amounts were loaded and detected with m6A antibody. Methylene blue staining was used as a loading control.

(J) LC-MS/MS quantification of the m6A/A ratio in polyadenylated RNA isolated from control and Zfp217_1 knockdown ESCs. Error bars show ± SD (n = 2). p < 0.05 versus control shRNA.

Figure 6

Analysis of ZFP217-Dependent m6A Sites

(A) Cumulative distribution function of log2 peak intensity of m6A-modified sites in control and Zfp217-depleted ESCs.

(B) Functional categories of ZFP217-dependent m6A sites. The p value for the enrichment of biological process GO-term is shown.

(C) GSEA plot of ZFP217-dependent m6A sites during RA-induced differentiation (top) and EB formation (bottom). High and low expression of genes is represented in red and blue, respectively.

(D) Heatmap representing log2 fold change of Zfp217 shRNA ESCs compared with control (left) and Mettl3 knockout (KO) ESCs compared with the WT (right). Red and blue indicate an increase and decrease of m6A peak intensity, respectively.

(E) Distributions of distance between the m6A peak and the nearest consensus site of control and Zfp217-depleted ESCs.

(F) Sequence logo representing the consensus motif following clustering of all enriched motifs in ZFP217-dependent peaks.

(G) The overlapping transcripts of ZFP217 and METTL3 RIP-seq samples.

(H) The coverage at the TSS of genes containing ChIP and RIP peaks or ChIP peaks only with ZFP217 antibodies.

(I) Coverage of ZFP217 signal at the TSS of modified and unmodified genes.

Figure 7

ZFP217 Regulates the Epitranscriptome of Key Pluripotency Factors

(A) ZFP217 ChIP-seq target genes, m6A ZFP217-dependent transcripts, and ZFP217 and METTL3 transcriptomes.

(B) qRT-PCR of Nanog, Sox2, Klf4, and c-Myc after PAR-CLIP with ZFP217-specific antibodies. Shown is the fold enrichment relative to the IgG control. Error bars show ± SD (n = 3). ∗∗p < 0.01, ∗∗∗p < 0.001 versus IgG control.

(C) qRT-PCR of m6A modification at key pluripotency RNAs in control and Zfp217 shRNA. The percentage of input is shown. Error bars show ± SD (n = 3). ∗∗∗p < 0.0001; ns, not significant versus control shRNA.

(D–H) qRT-PCR analysis of Nanog (D), Sox2 (E), Klf4 (F), c-Myc (G), and Stat 3 (H) expression after 8 hr of 5-ethynyl uridine (EU) incorporation in control and Zfp217-depleted ESCs. Error bars show ± SD (n = 2). ∗∗∗p < 0.0001; ∗∗p < 0.001; p < 0.01; ns, not significant versus control shRNA at 8 hr.

(I) Quantification of the RNA binding ability of METTL3 in control and Zfp217-depleted ESCs (from Figure S6 E). RNA binding was normalized to the corresponding pull-down proteins. Error bars show ± SD (n = 2). p < 0.005 versus control shRNA.

(J and K) AP staining of reprogramming MEFs transduced with OSKM in the presence of the indicated shRNA constructs on day 15 (J) and number of AP+ colonies relative to control iPSCs (K). Error bars show ± SD (n = 4). ∗∗∗p < 0.0001 versus Zfp217 shRNA.

(L) ZFP217 function in ESC self-renewal and iPSC reprogramming. In our model, ZFP217 directly regulates the transcription of key pluripotency and reprogramming factors, including Nanog, Sox2, Klf4, and c-Myc, and promotes their stabilization by preventing them from METTL3-mediated m6A aberrant methylation.

Highlights

  • ZFP217 regulates the expression of the core stem cell gene network
  • ZFP217 is required for efficient somatic cell reprogramming
  • ZFP217 interacts with METTL3 and restrains m6A RNA modification
  • Low m6A levels in ESC-related transcripts enable pluripotency and reprogramming

Summary

Epigenetic and epitranscriptomic networks have important functions in maintaining the pluripotency of embryonic stem cells (ESCs) and somatic cell reprogramming. However, the mechanisms integrating the actions of these distinct networks are only partially understood. Here we show that the chromatin-associated zinc finger protein 217 (ZFP217) coordinates epigenetic and epitranscriptomic regulation. ZFP217 interacts with several epigenetic regulators, activates the transcription of key pluripotency genes, and modulates N6-methyladenosine (m6A) deposition on their transcripts by sequestering the enzyme m6A methyltransferase-like 3 (METTL3). Consistently, Zfp217 depletion compromises ESC self-renewal and somatic cell reprogramming, globally increases m6A RNA levels, and enhances m6A modification of the Nanog, Sox2, Klf4, and c-Myc mRNAs, promoting their degradation. ZFP217 binds its own target gene mRNAs, which are also METTL3 associated, and is enriched at promoters of m6A-modified transcripts. Collectively, these findings shed light on how a transcription factor can tightly couple gene transcription to m6A RNA modification to ensure ESC identity.

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