Genome-Wide Mapping of Bivalent Histone Modifications in Hepatic Stem/Progenitor Cells
Genome-Wide Mapping of Bivalent Histone Modifications in Hepatic Stem/Progenitor Cells
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DOI：
10.1155/2019/9789240
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发表时间：
2019-01-01
影响因子：
4.3
通讯作者：
Kato, Naoya
中科院分区：
文献类型：
--
作者：
Kanayama, Kengo;Chiba, Tetsuhiro;Kato, Naoya
二价结构域是一种独特的组蛋白修饰标记，其特征在于组蛋白H3在赖氨酸27处的抑制性三甲基化（H3 K27 me 3）和组蛋白H3在赖氨酸4处的活性三甲基化（H3 K4 me 3）标记。这些组蛋白标记的维持和动态解析在调节各种干细胞系统的分化过程中起重要作用。然而，关于它们在肝干/祖细胞中的作用知之甚少。在本研究中，我们进行了染色质免疫沉淀（ChIP）试验，然后高通量DNA测序（ChIP-seq）分析在纯化的delta-like 1蛋白（Dlk（+））肝干/祖细胞，并成功地确定了562个基因的转录起始位点的2kb内显示二价结构域。基因本体分析表明，这些基因在发育功能和分化过程中富集。微阵列分析表明，许多这些基因表现出对肝细胞和胆管细胞谱系分化后的去阻遏。其中，72个基因，包括Cdkn 2a和Sox 4，在向肝细胞或胆管细胞谱系分化后显著上调。在Dlk（+）细胞中敲低Sox 4抑制集落增殖，并导致集落中白蛋白（+）/细胞角蛋白7（+）祖细胞数量增加。这些发现暗示Sox 4表达的去抑制是诱导正常分化过程所必需的。总之，结合ChIP-seq和微阵列分析成功地鉴定了二价基因。这些基因的功能分析将有助于阐明肝干/祖细胞终末分化的表观遗传机制。
The bivalent domain, a distinctive histone modification signature, is characterized by repressive trimethylation of histone H3 at lysine 27 (H3K27me3) and active trimethylation of histone H3 at lysine 4 (H3K4me3) marks. Maintenance and dynamic resolution of these histone marks play important roles in regulating differentiation processes in various stem cell systems. However, little is known regarding their roles in hepatic stem/progenitor cells. In the present study, we conducted the chromatin immunoprecipitation (ChIP) assay followed by high-throughput DNA sequencing (ChIP-seq) analyses in purified delta-like 1 protein (Dlk(+)) hepatic stem/progenitor cells and successfully identified 562 genes exhibiting bivalent domains within 2kb of the transcription start site. Gene ontology analysis revealed that these genes were enriched in developmental functions and differentiation processes. Microarray analyses indicated that many of these genes exhibited derepression after differentiation toward hepatocyte and cholangiocyte lineages. Among these, 72 genes, including Cdkn2a and Sox4, were significantly upregulated after differentiation toward hepatocyte or cholangiocyte lineages. Knockdown of Sox4 in Dlk(+) cells suppressed colony propagation and resulted in increased numbers of albumin(+)/cytokeratin 7(+) progenitor cells in colonies. These findings implicate that derepression of Sox4 expression is required to induce normal differentiation processes. In conclusion, combined ChIP-seq and microarray analyses successfully identified bivalent genes. Functional analyses of these genes will help elucidate the epigenetic machinery underlying the terminal differentiation of hepatic stem/progenitor cells.