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Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T-cell differentiation.

Li Q, Zou J, Wang M, Ding X, Chepelev I, Zhou X, Zhao W, Wei G, Cui J, Zhao K, Wang HY, Wang RF - Nat Commun (2014)

Bottom Line: The skewing of T-cell differentiation is concomitant with changes in the expression of key transcription factors and cytokines.H3K27me3 and H3K4me3 levels in Jmjd3-deficient cells are correlated with altered gene expression through interactions with specific transcription factors.Our results identify Jmjd3 as an epigenetic factor in T-cell differentiation via changes in histone methylation and target gene expression.

View Article: PubMed Central - PubMed

Affiliation: Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas 77030, USA.

ABSTRACT
Epigenetic factors have been implicated in the regulation of CD4(+) T-cell differentiation. Jmjd3 plays a role in many biological processes, but its in vivo function in T-cell differentiation remains unknown. Here we report that Jmjd3 ablation promotes CD4(+) T-cell differentiation into Th2 and Th17 cells in the small intestine and colon, and inhibits T-cell differentiation into Th1 cells under different cytokine-polarizing conditions and in a Th1-dependent colitis model. Jmjd3 deficiency also restrains the plasticity of the conversion of Th2, Th17 or Treg cells to Th1 cells. The skewing of T-cell differentiation is concomitant with changes in the expression of key transcription factors and cytokines. H3K27me3 and H3K4me3 levels in Jmjd3-deficient cells are correlated with altered gene expression through interactions with specific transcription factors. Our results identify Jmjd3 as an epigenetic factor in T-cell differentiation via changes in histone methylation and target gene expression.

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Jmjd3 regulates target gene expression by altering H3K4me3 and H3K27me3 levels(a) Western blot of global H3K4me1/me2/me3 and H3K27me1/me2/me3 levels in thymic CD4+ SP T cells. (b) H3K4me3 and H3K27me3 in WT and Jmjd3 cKO CD4 SP T cells were analyzed by genome-wide ChIP-Seq. Venn diagram showing the numbers of genes with H3K27me3 and H3K4me3 modifications in Jmjd3 cKO cells compared with WT cells. (c) Average H3K27me3 profiles in WT and cKO samples at differentially methylated genes. TSS, transcription start site; TES, transcription end site. (d) T cell-related genes were classified into three groups based on H3K4me3 and H3K27me3 modifications in WT and Jmjd3 cKO CD4 SP thymocytes: group I, increased H3K27 and decreased H3K4; group II, unchanged H3K27 and decreased H3K4; and group III, unchanged H3K27 and H3K4. Red frames indicate the 2 kb region around the TSS. Scale bars represent 5kb region. (e) Validation of methylation changes in WT and cKO CD4 SP thymocytes by ChIP-qPCR (*p < 0.05 determined by Student's t-test).
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Figure 6: Jmjd3 regulates target gene expression by altering H3K4me3 and H3K27me3 levels(a) Western blot of global H3K4me1/me2/me3 and H3K27me1/me2/me3 levels in thymic CD4+ SP T cells. (b) H3K4me3 and H3K27me3 in WT and Jmjd3 cKO CD4 SP T cells were analyzed by genome-wide ChIP-Seq. Venn diagram showing the numbers of genes with H3K27me3 and H3K4me3 modifications in Jmjd3 cKO cells compared with WT cells. (c) Average H3K27me3 profiles in WT and cKO samples at differentially methylated genes. TSS, transcription start site; TES, transcription end site. (d) T cell-related genes were classified into three groups based on H3K4me3 and H3K27me3 modifications in WT and Jmjd3 cKO CD4 SP thymocytes: group I, increased H3K27 and decreased H3K4; group II, unchanged H3K27 and decreased H3K4; and group III, unchanged H3K27 and H3K4. Red frames indicate the 2 kb region around the TSS. Scale bars represent 5kb region. (e) Validation of methylation changes in WT and cKO CD4 SP thymocytes by ChIP-qPCR (*p < 0.05 determined by Student's t-test).

Mentions: To determine the mechanisms by which Jmjd3 regulates target gene expression, we tested whether Jmjd3 ablation affects global histone methylation in T cells. H3K27me2 and H3K27me3, but not H3K27me1, levels were increased in Jmjd3-deficient thymic CD4+ SP T cells compared with WT, whereas appreciable changes in H3K4 methylation were not observed (Fig. 6a, Supplementary Fig. 3a, and Supplementary Table 1). This suggests that Jmjd3 deletion specifically increases H3K27 dimethylation and trimethylation in CD4+ T cells. ChIP-Seq analysis on WT and Jmjd3-deficient CD4+ T cells revealed that among the 35,000 RefSeq genes, 2754 genes had increased H3K27me3 levels at approximately 2 kilobases around the transcription start site (TSS) in Jmjd3-deficient CD4+ T cells compared with WT controls. H3K27me3 levels were decreased in 811 genes (Fig. 6b and Supplementary Table 1). H3K4me3 levels were increased in 404 genes and decreased in 114 genes in Jmjd3-deficient CD4+ T cells compared with WT (Fig. 6b and Supplementary Table 1). Analysis of average H3K27me3 levels of the differentially methylated genes revealed that total H3K27me3 methylation levels were increased in both promoter regions and gene bodies in Jmjd3-deficient CD4+ T cells compared with WT cells (Fig. 6c). H3K4me3 is generally correlated with active transcription, whereas H3K27me3 is associated with gene repression. Chromatin regions containing high levels of both H3K4me3 and H3K27me3 are known as ‘bivalent domains’, which are silenced and postulated to be ‘poised’ for activation44,45. T cell-related genes were classified into three groups according to H3K27me3 and H3K4me3 status, and significant differences were found between WT and Jmjd3-deficient CD4+ T cells. Group I genes, including Cd44, Ccnd2, Ifng, Irf4, Ccr2, and Fosl2, in Jmjd3-deficient CD4+ T cells, harbored bivalent domains with increased H3K27me3 and decreased H3K4me3 levels (Fig. 6d and Supplementary Fig. 4a), which paralleled decreased gene expression. Group II genes, including Foxp3, Stat3, Tgfß1, Cxcr3, Cxcr6, Ccr8, and Ccr4, had decreased H3K4me3 and unchanged H3K27me3 levels in Jmjd3-deficient CD4+ T cells, which paralleled their decreased gene expression (Fig. 6d and Supplementary Fig. 4b). Conversely, in group III genes, Tbx21, Gata3, Rorc, Smad3, Maf, and several chemokine receptors, both H3K27me3 and H3K4me3 levels were not dramatically changed (Fig. 6d and Supplementary Fig. 4c). These histone methylation changes were further validated using ChIP-qPCR (Fig. 6e). We found only a few genes that had histone methylation changes at distal regions (Supplementary Fig. 5). These results suggest that Jmjd3 regulates target gene expression primarily through alterations in the histone methylation status of H3K27 and/or H3K4 in the promoter and gene body regions.


Critical role of histone demethylase Jmjd3 in the regulation of CD4+ T-cell differentiation.

Li Q, Zou J, Wang M, Ding X, Chepelev I, Zhou X, Zhao W, Wei G, Cui J, Zhao K, Wang HY, Wang RF - Nat Commun (2014)

Jmjd3 regulates target gene expression by altering H3K4me3 and H3K27me3 levels(a) Western blot of global H3K4me1/me2/me3 and H3K27me1/me2/me3 levels in thymic CD4+ SP T cells. (b) H3K4me3 and H3K27me3 in WT and Jmjd3 cKO CD4 SP T cells were analyzed by genome-wide ChIP-Seq. Venn diagram showing the numbers of genes with H3K27me3 and H3K4me3 modifications in Jmjd3 cKO cells compared with WT cells. (c) Average H3K27me3 profiles in WT and cKO samples at differentially methylated genes. TSS, transcription start site; TES, transcription end site. (d) T cell-related genes were classified into three groups based on H3K4me3 and H3K27me3 modifications in WT and Jmjd3 cKO CD4 SP thymocytes: group I, increased H3K27 and decreased H3K4; group II, unchanged H3K27 and decreased H3K4; and group III, unchanged H3K27 and H3K4. Red frames indicate the 2 kb region around the TSS. Scale bars represent 5kb region. (e) Validation of methylation changes in WT and cKO CD4 SP thymocytes by ChIP-qPCR (*p < 0.05 determined by Student's t-test).
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Figure 6: Jmjd3 regulates target gene expression by altering H3K4me3 and H3K27me3 levels(a) Western blot of global H3K4me1/me2/me3 and H3K27me1/me2/me3 levels in thymic CD4+ SP T cells. (b) H3K4me3 and H3K27me3 in WT and Jmjd3 cKO CD4 SP T cells were analyzed by genome-wide ChIP-Seq. Venn diagram showing the numbers of genes with H3K27me3 and H3K4me3 modifications in Jmjd3 cKO cells compared with WT cells. (c) Average H3K27me3 profiles in WT and cKO samples at differentially methylated genes. TSS, transcription start site; TES, transcription end site. (d) T cell-related genes were classified into three groups based on H3K4me3 and H3K27me3 modifications in WT and Jmjd3 cKO CD4 SP thymocytes: group I, increased H3K27 and decreased H3K4; group II, unchanged H3K27 and decreased H3K4; and group III, unchanged H3K27 and H3K4. Red frames indicate the 2 kb region around the TSS. Scale bars represent 5kb region. (e) Validation of methylation changes in WT and cKO CD4 SP thymocytes by ChIP-qPCR (*p < 0.05 determined by Student's t-test).
Mentions: To determine the mechanisms by which Jmjd3 regulates target gene expression, we tested whether Jmjd3 ablation affects global histone methylation in T cells. H3K27me2 and H3K27me3, but not H3K27me1, levels were increased in Jmjd3-deficient thymic CD4+ SP T cells compared with WT, whereas appreciable changes in H3K4 methylation were not observed (Fig. 6a, Supplementary Fig. 3a, and Supplementary Table 1). This suggests that Jmjd3 deletion specifically increases H3K27 dimethylation and trimethylation in CD4+ T cells. ChIP-Seq analysis on WT and Jmjd3-deficient CD4+ T cells revealed that among the 35,000 RefSeq genes, 2754 genes had increased H3K27me3 levels at approximately 2 kilobases around the transcription start site (TSS) in Jmjd3-deficient CD4+ T cells compared with WT controls. H3K27me3 levels were decreased in 811 genes (Fig. 6b and Supplementary Table 1). H3K4me3 levels were increased in 404 genes and decreased in 114 genes in Jmjd3-deficient CD4+ T cells compared with WT (Fig. 6b and Supplementary Table 1). Analysis of average H3K27me3 levels of the differentially methylated genes revealed that total H3K27me3 methylation levels were increased in both promoter regions and gene bodies in Jmjd3-deficient CD4+ T cells compared with WT cells (Fig. 6c). H3K4me3 is generally correlated with active transcription, whereas H3K27me3 is associated with gene repression. Chromatin regions containing high levels of both H3K4me3 and H3K27me3 are known as ‘bivalent domains’, which are silenced and postulated to be ‘poised’ for activation44,45. T cell-related genes were classified into three groups according to H3K27me3 and H3K4me3 status, and significant differences were found between WT and Jmjd3-deficient CD4+ T cells. Group I genes, including Cd44, Ccnd2, Ifng, Irf4, Ccr2, and Fosl2, in Jmjd3-deficient CD4+ T cells, harbored bivalent domains with increased H3K27me3 and decreased H3K4me3 levels (Fig. 6d and Supplementary Fig. 4a), which paralleled decreased gene expression. Group II genes, including Foxp3, Stat3, Tgfß1, Cxcr3, Cxcr6, Ccr8, and Ccr4, had decreased H3K4me3 and unchanged H3K27me3 levels in Jmjd3-deficient CD4+ T cells, which paralleled their decreased gene expression (Fig. 6d and Supplementary Fig. 4b). Conversely, in group III genes, Tbx21, Gata3, Rorc, Smad3, Maf, and several chemokine receptors, both H3K27me3 and H3K4me3 levels were not dramatically changed (Fig. 6d and Supplementary Fig. 4c). These histone methylation changes were further validated using ChIP-qPCR (Fig. 6e). We found only a few genes that had histone methylation changes at distal regions (Supplementary Fig. 5). These results suggest that Jmjd3 regulates target gene expression primarily through alterations in the histone methylation status of H3K27 and/or H3K4 in the promoter and gene body regions.

Bottom Line: The skewing of T-cell differentiation is concomitant with changes in the expression of key transcription factors and cytokines.H3K27me3 and H3K4me3 levels in Jmjd3-deficient cells are correlated with altered gene expression through interactions with specific transcription factors.Our results identify Jmjd3 as an epigenetic factor in T-cell differentiation via changes in histone methylation and target gene expression.

View Article: PubMed Central - PubMed

Affiliation: Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, Texas 77030, USA.

ABSTRACT
Epigenetic factors have been implicated in the regulation of CD4(+) T-cell differentiation. Jmjd3 plays a role in many biological processes, but its in vivo function in T-cell differentiation remains unknown. Here we report that Jmjd3 ablation promotes CD4(+) T-cell differentiation into Th2 and Th17 cells in the small intestine and colon, and inhibits T-cell differentiation into Th1 cells under different cytokine-polarizing conditions and in a Th1-dependent colitis model. Jmjd3 deficiency also restrains the plasticity of the conversion of Th2, Th17 or Treg cells to Th1 cells. The skewing of T-cell differentiation is concomitant with changes in the expression of key transcription factors and cytokines. H3K27me3 and H3K4me3 levels in Jmjd3-deficient cells are correlated with altered gene expression through interactions with specific transcription factors. Our results identify Jmjd3 as an epigenetic factor in T-cell differentiation via changes in histone methylation and target gene expression.

Show MeSH
Related in: MedlinePlus