丹羽先生の書いた総説が2018年の”Development” にあります。フリー論文なので、興味ある方はアクセスしてください。 REVIEW The principles that govern transcription factor network functions in stem cells Development 2018 145: dev157420 doi: 10.1242/dev.157420 Published 14 March 2018
Box 1. Glossary 2i culture. This feeder- and serum-free culture condition consists of N2B27 basal medium, MEK inhibitor and GSK3 inhibitor. Inhibition of GSK3 mimics activation of the Wnt signal.
Definitive endoderm. A cell lineage of the post-implantation embryo after gastrulation. Definitive endoderm gives rise to embryonic endoderm cell types.
Embryonic stem cells (ESCs). Pluripotent stem cells (PSCs) derived from blastocyst stage embryos. Mouse ESCs retain the character of PSCs in the epiblast at late blastocyst stage, and continue to self-renew in conventional serum-containing culture with LIF or serum-free 2i culture.
Epiblast stem cells (EpiSCs). PSCs derived from post-implantation embryos. Mouse EpiSCs retain the character of PSCs in epiblast at late egg cylinder stage, and self-renewal in the presence of activin A and Fgf2.
Gene regulatory network. The system controlling the transcriptional activities of all genes in the genome. It consists of multiple layers of molecular mechanisms of genetic and epigenetic regulation.
Jak-Stat3 pathway. Jak is a tyrosine kinase associated with the cytoplasmic domain of the LIF receptor. Jak phosphorylates Stat3, and the phosphorylated form of Stat3 translocates into the nucleus where it acts as a transcription factor.
LIF (leukemia inhibitory factor). LIF is an IL6 family cytokine. The LIF signal is received into the cytoplasm via the transmembrane LIF receptor, which consists of Il6st and Lifr, and is transduced by the Jak-Stat3, PI3K-Akt and Erk-MAPK pathways.
Mediator complex. A complex of 26 subunits that functions as transcriptional co-activator. It interacts with tissue-specific TFs on enhancers and general TFs and RNA polymerase II on promoter regions. These interactions mediate transcriptional activation by TFs.
Mek-Erk pathway. Mek (Erk kinase) and Erk compose the canonical MAPK pathway. LIF signal activates the Mek-Erk pathway via LIF receptor-Grb2-Sos-Ras. The Fgf signal also activates the Mek-Erk pathway via Fgf receptor.
Mesoendoderm. A cell lineage of the post-implantation embryo after gastrulation. Mesoendoderm gives rise to both mesoderm and definitive endoderm.
Neuroectoderm. A cell lineage of the post-implantation embryo after gastrulation. Neuroectoderm gives rise to neuronal cell types.
PI3K-Akt pathway. PI3K is coupled with the cytoplasmic domain of various receptors and produces phosphatidylinositol (3,4,5)-trisphosphate upon stimulation. These lipids then recruit PDK1 and Akt, resulting in activation of the kinase activity of Akt.
Primitive endoderm. The cell lineage located at the surface of the inner cell mass of a late blastocyst stage embryo. Primitive endoderm participates in the formation of yolk sac in post-implantation development. Primitive endoderm is also known as extra-embryonic endoderm.
Super-enhancer. An enhancer is defined as a DNA element that regulates transcription in cis within a certain distance from the promoter element. A super-enhancer is defined as a cluster of enhancers within a certain range of genomic DNA that allows the recruitment of the Mediator complex with higher affinity than a conventional enhancer that lacks such clustering. （スーパーエンハンサーは、従来のエンハンサーよりも高い親和性で転写因子複合体形成したもの。）
Transcriptional bursting. Discontinuous events of transcription. Gene expression occurs as a sum of episodic transcription, and the frequency of transcriptional bursting determines the expression level. The frequency of bursting is regulated by the dynamic recruitment of transcription factors at enhancers.
Trophectoderm. The cell lineage located at the outer layer of a blastocyst stage embryo. Trophectoderm gives rise to a large part of the placenta in post-implantation development.
Trophoblast stem cells (TSCs). The stem cell line derived from trophoblasts. Trophoblasts are a proliferative population of trophectoderm and retain the ability to differentiate into multiple cell types of the placental lineage. TSCs retain the characteristics of trophoblasts in vitro in the presence of Fgf4.
以下がイントロダクション部分です。紫字 In the developmental context, the late stage epiblast of blastocyst stage embryos gives rise to the late post-implantation stage epiblast, suggesting that the primed pluripotent state could represent a direct transition from mESCs. Indeed, culturing mESCs in the culture conditions for EpiSCs (i.e. containing activin A and Fgf2) allows their gradual transition over several passages (Guo et al., 2009). However, to date, there is no way to direct a homogeneous transition of mESCs to the primed state within a few days in culture, as is observed in the developmental context. This suggests that the transition from the naïve to the primed state might not be a direct process. Recently, an intermediate state between naïve and primed was proposed. This state, designated formative pluripotency, is defined by the downregulation of the naïve-specific TFs without the activation of the lineage-primed TFs that are activated in the primed state (Smith, 2017). Although PSCs in the formative state have not been captured stably, epiblast-like cells obtained transiently by the culture of mESCs could be close to it (Hayashi et al., 2011). The dynamic changes in TF binding between mESCs and EpiSCs may support the existence of such an intermediate state as defined by a stable TF network (see figure; dashed lines indicate events that can be induced under artificial conditions) (Matsuda et al., 2017). The transition to the embryonic cell lineages – definitive endoderm, ectoderm and mesoderm – could occur directly from the primed state TF network, but never from the naïve state TF network
Nichols and Smith, 2009らにより、多能性細胞には、ナイーブ型と、プライミング型の二つの異なる状態があることが示されました。 分割卵の着床後、胎内ではスムーズにおきてくる細胞分化ですが、人工的条件 (i.e. containing activin A and Fgf2) で起こさせると、EpiSCsは世代を経て移行していきます。胎内とは異なる経緯をとります。
there is no way to direct a homogeneous transition of mESCs to the primed state within a few days in culture, as is observed in the developmental context. と書かれています。
以下の丹羽先生総説の図をコピーします。 破線は、人工条件下で誘動される可能性のあるイベントを示します）（Matsuda et al。、2017） 。
TFには、General TFsと、Tissue-specific TFs の種類があります。 General TFs は、promoter element に結合して、RNA polymerase II を呼び込み転写を開始し、一方、Tissue-specific TFs はpromoter element 付近のみでなく、離れた部位のenhancerなる部位にも結合できる結果、promoter element がTFs を呼び込み易くなり、TFs リクルートを増強させます。 そして複数のＴＦｓ同士が結合しあって、より強固な構造体となります。 2番目の図を参考にしてください。
以下が、人工的細胞を調べた結果、導かれた細胞発生の仕組みです。丹羽先生は、TFsが細胞の命運を決めている様相を紹介してますが、人工的細胞TS、ES、EpiS を軸に説明してます。 ＞The dynamic changes in TF binding between mESCs and EpiSCs may support the existence of such an intermediate state as defined by a stable TF network