Kanayama Kengo, Chiba Tetsuhiro, Oshima Motohiko, Kanzaki Hiroaki, Koide Shuhei, Saraya Atsunori, Miyagi Satoru, Mimura Naoya, Kusakabe Yuko, Saito Tomoko, Ogasawara Sadahisa, Suzuki Eiichiro, Ooka Yoshihiko, Maruyama Hitoshi, Iwama Atsushi, Kato Naoya
Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan.
Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
Stem Cells Int. 2019 Apr 1;2019:9789240. doi: 10.1155/2019/9789240. eCollection 2019.
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 2 kb 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 and , were significantly upregulated after differentiation toward hepatocyte or cholangiocyte lineages. Knockdown of 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 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.
“双价结构域”是一种独特的组蛋白修饰特征，其特点是组蛋白H3赖氨酸27位点的抑制性三甲基化（H3K27me3）和组蛋白H3赖氨酸4位点的活性三甲基化（H3K4me3）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发挥着重要作用。然而，关于它们在肝干细胞/祖细胞中的作用知之甚少。在本研究中，我们对纯化的δ样1蛋白（Dlk）肝干细胞/祖细胞进行了染色质免疫沉淀（ChIP）分析，随后进行高通量DNA测序（ChIP-seq）分析，并成功鉴定出562个在转录起始位点2 kb范围内呈现双价结构域的基因。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，这些基因中的许多在向肝细胞和胆管细胞谱系分化后表现出去抑制。其中，包括[具体基因1]和[具体基因2]在内的72个基因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[具体基因]可抑制集落增殖，并导致集落中白蛋白/细胞角蛋白7祖细胞数量增加。这些发现表明，[具体基因]表达的去抑制是诱导正常分化过程所必需的。总之，ChIP-seq和微阵列分析相结合成功鉴定出双价基因。对这些基因的功能分析将有助于阐明肝干细胞/祖细胞终末分化的表观遗传机制。
