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Regulation of DNA methylation dictates Cd4 expression during the development of helper and cytotoxic T cell lineages


During development, progenitor cells with binary potential give rise to daughter cells that have distinct functions. Heritable epigenetic mechanisms then lock in gene-expression programs that define lineage identity. Regulation of the gene encoding the T cell–specific coreceptor CD4 in helper and cytotoxic T cells exemplifies this process, with enhancer- and silencer-regulated establishment of epigenetic memory for stable gene expression and repression, respectively. Using a genetic screen, we identified the DNA-methylation machinery as essential for maintaining silencing of Cd4 in the cytotoxic lineage. Furthermore, we found a requirement for the proximal enhancer in mediating the removal of DNA-methylation marks from Cd4, which allowed stable expression of Cd4 in helper T cells. Our findings suggest that stage-specific methylation and demethylation events in Cd4 regulate its heritable expression in response to the distinct signals that dictate lineage 'choice' during T cell development.

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Figure 1: DNA-methylation enzymes are essential for 'silencing' CD4 expression in cytotoxic T cells.
Figure 2: Silencer-dependent DMR in the first intron of Cd4.
Figure 3: Hypermethylation of Cd4 in immature thymocytes.
Figure 4: E4P is required for hypomethylation of the Cd4 locus in the helper T cell lineage.
Figure 5: A decrease in DNMT1 activity 'rescues' CD4 expression in Cd4E4PΔ/E4PΔ helper T cells.
Figure 6: Demethylation of the Cd4 locus occurs late in helper-lineage differentiation and is largely independent of ThPOK.
Figure 7: Hydroxymethylation of Cd4 TSS-proximal sites in MHC class II–selected CD4+CD8lo cells.

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We thank R. Jaenisch (Whitehead Institute for Biomedical Research) for Dnmt1L2 and Dnmt1chip mouse strains; the University of Massachusetts Medical School RNAi Core Facility for shRNAs; A. Cuesta and A. Chen for technical help; and members of the Littman laboratory for discussion. Supported by the US National Institutes of Health (R00DK091508 to J.R.H., 5 T32 CA009161-36 to M.S., and GM033977 to M.R.G.), the Jane Coffin Childs Fund (J.R.H.), the Cancer Research Institute (M.S. and P.D.I.) and the Howard Hughes Medical Institute (M.R.G. and D.R.L.).

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Authors and Affiliations



M.S. performed E4P rescue experiments, proliferation assays in thymus and T4-βGT analysis; J.R.H. did the genetic screen and follow-up analyses; M.S. and K.D. did the analyses of Cd4 locus-wide methylation and nucleosome sequencing, with bioinformatics support from D.A.; P.D.I. performed oxidative bisulfite analysis; M.S. and C.G. performed amplicon bisulfite sequencing; S.G. and M.R.G. provided the mouse shRNA retroviral pools; and M.S., J.R.H. and D.R.L. designed the experiments and wrote the manuscript with input from the other authors.

Corresponding author

Correspondence to Dan R Littman.

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The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 DNA-methylation machinery is essential for silencing of Cd4 in cytotoxic T cells.

(a) Scheme for the retroviral shRNA screen. (b) Histogram showing CD4 expression (MFI) in WT cytotoxic T cells infected with a Dnmt1 shRNA-GFP retrovirus (shaded area) or sham shRNA-GFP retrovirus (open area). Representative of 2 independent experiments. (c) Cytotoxic CD4-8+ cells from Dnmt1Chip/Chip animals were loaded with e670 and cultured in vitro for 4 days after infection with Dnmt1 shRNA retroviruses. Virus-infected cells were selected with puromycin. Gates define non-, low-, medium- and highly-cycled cells (i.e. e670 dilution), and the percentage of cells de-repressing CD4 in each gate is indicated. The red line shows the CD4 staining level used to determine de-repression. Representative of 2 independent experiments.

Supplementary Figure 2 Reproducibility and coverage of locus-wide bisulfite sequencing.

Genomic DNA was prepared from biological replicates of the indicated samples, and then subjected to bisulfite CATCH-seq (Cd4 TSS +/- ~75kb). (a) For each replicate, the fraction methylation at CpG dinucleotides with at least 30x coverage is graphed. Linear regressions were performed (red lines) and R2 calculated. (b) The median CpG sequencing coverage for the indicated samples is graphed. Error bars represent the 5th and 95th percentiles for CpG sequencing coverage.

Supplementary Figure 3 Silencer-dependent DMR in the first intron of Cd4.

Naïve (Thy1.2+CD44loCD62L+CD25-) WT CD4+, WT CD8+ and Cd4S4Δ/S4Δ CD4+8+ cells were isolated from LNs. Their genomic DNA was either isolated immediately or after 5 days of in vitro population expansion, using CFSE-labeling and dilution to identify and sort cells that had completed at least 5 divisions. Genomic DNA was then subjected to CATCH-seq. Percent CpG methylation was graphed on the UCSC genome browser for (a) Chromosome 6, positions 124,746,000-124,909,000 and (b) Chromosome 6, positions124,814,000-124,855,000 (UCSC Mus musculus genome assembly mm9). UCSC genes are indicated below the graphs. The samples correspond to those Fig. 2. Biological replicates were derived from two experiments.

Supplementary Figure 4 Hypermethylation of the Cd4 locus in the cytotoxic lineage and immature T cell progenitors.

To confirm locus-wide bisulfite sequencing, two amplicons were chosen for targeted bisulfite sequencing (a-b, d-h) and four amplicons were chosen for methylation-sensitive restriction enzyme digest analysis (c) (locus (not drawn to scale) and CpG analysis map at top: S4: Silencer; black arrow: TSS; lollipops: CpG dinucleotides; blue bars: bisulfite sequencing amplicons; purple arrows: HpaII sites with positions relative to TSS). (a-b) Naïve WT CD4+ and CD8+ T cells were sorted, genomic DNA was prepared and bisulfite treated, and amplicons were cloned and sequenced. Filled circles indicate methylated CpG dinucleotides and empty circles indicate unmethylated CpG dinucleotides. Colored bars correspond to amplicons in map. The 5’ and 3’ amplicon methylation patterns are shown in (a) and (b), respectively. Data are from 3 mice from two experiments. (c) HpaII digestion of genomic DNA from naïve WT CD4+, WT CD8+ and Cd4S4Δ/S4Δ CD8+ T cells was assessed by qPCR at the indicated CpG dinucleotides. HpaII digests only unmethylated-CCGG motifs; thus, percent-undigested DNA corresponds to percent methylation. All samples were normalized to an HpaII-insensitive loading control amplicon in the Cd4 locus. Graphs represent the average (± s.d.) (n=2 for WT CD4+ and WT CD8+) or amount of undigested DNA (n=1 for Cd4S4Δ/S4Δ) are shown. Data are representative of at least two 2 experiments. Average (± s.d.) of percent methylation from locus-wide bisulfite sequencing of biological replicates is presented in the graphs on the left for each CpG (n=2; samples correspond to those in Fig. 2 ). (d) CFSE-labeled naïve WT CD4+ and CD8+ T cell populations were expanded for 5 d in vitro with anti-CD3, anti-CD28 and IL-2, and cells that had undergone at least 6 divisions were sorted and subjected to bisulfite sequencing of the 3’ amplicon (n = 1, one experiment). (e) CFSE-labeled naïve WT CD4+ and CD8+ T cells were injected into Rag2-/- mice, and 20 days later CFSE-negative cells were sorted (>10 divisions) and subjected to amplicon bisulfite sequencing of the 3’ amplicon (n = 1, one experiment). (f) DN3 and WT DP T cells were sorted and the 5’ amplicon was sequenced as in (a). (g-h) Bisulfite analysis of the 3’ intronic amplicon from WT (g) and Cd4S4Δ/S4Δ (h) DP cells. (f-h) Data are from 1 (DN3), 2 (Cd4S4Δ/S4Δ DP) or 3 (DP) mice from three experiments.

Supplementary Figure 5 Nucleosome positioning correlates with CD4 expression rather than with DNA methylation.

Nuclei from the indicated samples were isolated and treated with micrococcal nuclease, and mono-nucleosome fragments from the Cd4 locus ~ +/-75kb were analyzed by CATCH-seq (without bisulfite treatment). The upper density graphs show nucleosome occupancy (blue = high nucleosome density, white: naked DNA). The lower graphs show coordinate-specific CpG methylation (data from samples in Fig. 2-4; red = hyper-methylation, green = hypo-methylation). Tracks were graphed with the IGV browser platform (Chromosome 6, positions 124,831,500-124,838,486 (UCSC Mus musculus genome assembly mm9)). For clarity, yellow lines separate CD4 high- and low-expressing samples (above and below, respectively). The red arrowhead indicates a region in which nucleosome paucity is highly correlated with CD4 expression. Replicate samples are from two experiments.

Supplementary Figure 6 E4P controls proximal demethylation events early in T cell development.

CATCH-seq was performed on sorted populations of WT DN3 (Thy1.2+Lin-CD25+CD44-), WT and Cd4E4PΔ/E4PΔ DP (TCRβloCD24+CD69-CD4+CD8+), naïve (Thy1.2+CD25-CD44loCD62L+) WT CD4+, WT CD8+, Cd4E4PΔ/E4PΔ CD4+ T, and Cd4S4Δ/S4Δ CD8+ T cells. The heat map depicts percentage CpG methylation from -9270bp to -15869bp relative to the Cd4 TSS (Chromosome 6, positions 124847307-124853906; UCSC Mus musculus genome assembly mm9). The approximate location of the region within the Cd4 locus is indicated above (genes, S4 and E4P are noted), and the lone CpG within the proximal enhancer is indicated below the heat map (green arrow head). Replicates are from 2 independent mice or pools of mice from two independent experiments. 7 CpG dinucleotides in this region experienced complete or partial demethylation at the DN3 to DP transition, and this hypo-methylated state was preserved in mature T cell lineages. E4P is responsible for de-methylation before the DN3 stage (note Cd4E4PΔ/E4PΔ DP hyper-methylation compared to DN3 cells), as well as at the DN3 to DP transition (note that DN3 vs. DP differentially methylated CpG dinucleotides are all highly methylated in Cd4E4PΔ/E4PΔ DP cells).

Supplementary Figure 7 Diminished Dnmt1 activity ‘rescues’ CD4 expression in Cd4E4PΔ/E4PΔ helper T cells.

(a-c) Naïve CD4+ T cells (Thy1.2+CD25-CD8-CD44loCD62L+) from DNMT1-deficient and control mice, both with deletions of E4P, were CFSE labeled and stimulated in vitro with anti-CD3, anti-CD28 and IL-2. Analysis was performed at 96 h and 120 h, to determine (a) the percentage of CD4+ cells, (b) the MFI of the CD4+ cells, and (c) the percentage of CD4+ cells at each cell division as measured by CFSE dilution. Representative of at least 4 independent experiments. (d-e) CFSE stained Cd4E4PΔ/E4PΔ CD4+ T cells were stimulated for 24 h with anti-CD3 and anti-CD28, infected with retroviral vectors expressing Puro, RFP and either Dnmt1 shRNA in a mir30 context (red, shDnmt1) or an empty mir30 (blue, vector). Transduced cells were maintained with puromycin selection and analyzed by gating for RFP+ cells. (a) The percentage of CD4+ cells, as well as the CD4 MFI of CD4+ cells, was measured by flow cytometry at 72 h, 96 h and 120 h. (b) CFSE dilution was used to measure the percentage CD4+ cells in each generation at 72 h, 96 h and 120 h. Representative of at least 4 independent experiments.

Supplementary Figure 8 ThPOK expression and cell division during helper T lineage differentiation.

(a) Helper and cytotoxic T cell differentiation can be traced by CD4, CD8 and GFP (from the Zbtb7bGFP allele) expression (Egawa, T. & Littman, D.R. ThPOK acts late in specification of the helper T cell lineage and suppresses Runx-mediated commitment to the cytotoxic T cell lineage. Nat. Immunol. 9, 1131–1139 10.1038/ni.1652 (2008)). Upon positive selection, DP T cells (A gate) up-regulate CD69 and TCRβ (not shown) and down-regulate CD8 expression, becoming CD4+CD8lo (B gate). MHCI-selected cells then up-regulate CD8 expression (D gate) before finally down-regulating HSA (not shown) and silencing CD4 expression (E gate). MHCII-selected Zbtb7bGFP/+ cells begin to express GFP at the CD4+CD8lo stage (green filled circles, B gate), before fully down regulating CD8 and HSA (C gate and not shown). In Zbtb7bGFP/GFP MHCII-selected cells, GFP expression is still induced at the CD4+CD8lo stage (green filled circles, B gate), but cells then up-regulate CD8 (D gate) before extinguishing CD4 expression to become GFP+ cytotoxic T cells (E gate). (b) To sort CD4+CD8lo cells at different stages of helper cell differentiation, we enriched Zbtb7bGFP/+ and Zbtb7bGFP/GFP thymocytes for TCRβ expression using MACS beads, before sorting HSA+CD69+CD4+CD8lo cells (middle panel) based on Zbtb7b expression: GFP- (MHCI- or early MHCII-selected), GFPmid (MHCII-selected, initiating commitment) and GFP+ (MHCII-selected, late commitment). (c) MHCII-selected CD4SP (Zbtb7bGFP/+) and CD8SP (Zbtb7bGFP/GFP) thymocytes were MACS enriched for TCRβ+ expression, before gating of HSA-TCRβhiCD69-GFP+ cells and sorting of CD4+CD8- and CD4-CD8+ cells, respectively. (b-c) Stainings are representative of at least 3 experiments. (d) Scheme for thymic injection to assess cell division during helper T cell development. (e-f) 106 Tg(TcraTcrb)425Cbn(OT-IItg)+Δ/ΔH2-AbIΔ/Δ CD45.2+ and 107 CD45.2- DP cells (HSA+CD69-CD4+CD8+) were CFSE-labeled and injected intra-thymically into CD45.2- recipients. Tg(TcraTcrb)425Cbn+Δ/ΔH2-AbIΔ/Δ were used to ensure a homogenous population of unselected DP cells that would differentiate into the helper lineage. After four days, mice were sacrificed and thymocytes were analyzed for phenotype and CFSE dilution. (e) Gating of host and donor-derived cells in recipient thymus at day 4 after injection. (f) CFSE levels in cells from gates indicated in (e). Note that injected DP thymocytes do not dilute CFSE following positive selection. Representative of at least 2 experiments.

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Sellars, M., Huh, J., Day, K. et al. Regulation of DNA methylation dictates Cd4 expression during the development of helper and cytotoxic T cell lineages. Nat Immunol 16, 746–754 (2015).

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