Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation.
Histone modification profiling reveals differential signatures associated with human embryonic stem cell self-renewal and differentiation.
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DOI：
10.1002/pmic.201500231
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发表时间：
2016-02
期刊：
影响因子：
3.4
通讯作者：
Garcia BA
中科院分区：
文献类型：
--
作者：
Bhanu NV;Sidoli S;Garcia BA
在这项研究中，我们使用调节自我更新或分化的药物处理的人胚胎干细胞（hESCs）的表观基因组变化来追踪发育阶段。基于显微镜、qPCR和流式细胞术，我们将处理结果分类为诱导多能性（hESC、氟比洛芬和加替沙星）、中内胚层（青藤碱）、分化（Cyamarin、地高辛、洋地黄毒苷、司来吉林和茶氨酸）和谱系定型（RA）。当我们分析组蛋白PTM印记这些基因和蛋白质的表达，上述分类是重新排列。H3K4、9、14、18、56和122以及H4K5、8、12和16处的超乙酰化作为hESC的多能性特征出现。甲基化，尤其是H3在K9、K20、K27和K36处的甲基化表征了分化起始，如在无药物对照和氟比洛芬中所见。青藤碱处理的细胞聚集在“分化起始物”附近，与流式细胞术一致，其中它诱导中内胚层，沿着cyamarin和可能的selegnine。由RA和茶氨酸诱导的神经外胚层表现出H3上的甲基化转移到H3.3。通过流式细胞术和组蛋白PTM聚类，用加替沙星、氟比洛芬、洋地黄毒苷和地高辛处理的细胞似乎还不是谱系定型或混合细胞类型。总之，我们的中等通量组蛋白PTM分析方法突出了微妙的表观遗传特征，使我们能够预测即使在具有相似表型和基因表达的分化细胞中的分化谱系进展。
In this study, we trace developmental stages using epigenome changes in human embryonic stem cells (hESCs) treated with drugs modulating either self-renewal or differentiation. Based on microscopy, qPCR and flow cytometry, we classified the treatment outcome as inducing pluripotency (hESC, flurbiprofen and gatifloxacin), mesendoderm (sinomenine), differentiation (cyamarin, digoxin, digitoxin, selegeline and theanine) and lineage-commitment (RA). When we analyzed histone PTMs that imprinted these gene and protein expressions, the above classification was reassorted. Hyperacetylation at H3K4, 9, 14, 18, 56 and 122 as well as H4K5, 8, 12 and 16 emerged as the pluripotency signature of hESCs. Methylations especially of H3 at K9, K20, K27 and K36 characterized differentiation initiation as seen in no-drug control and fluribiprofen. Sinomenine-treated cells clustered close to “differentiation initiators”, consistent with flow cytometry where it induced mesendoderm, along with cyamarin and possibly selegnine. Neurectoderm, induced by RA and theanine manifested methylations on H3 shifts to H3.3. By both flow cytometry and histone PTM clustering, it appears that cells treated with gatifloxacin, flurbiprofen, digitoxin and digoxin were not yet lineage-committed or mixed cell types. Taken together, our moderate-throughput histone PTM profiling approach highlighted subtle epigenetic signatures that permitted us to predict divergent lineage progression even in differentiating cells with similar phenotype and gene expression.