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A "General" Transcription Factor Regulates Human Mesendodermal Differentiation from hESCs by Shifting Protein-DNA Binding Pattern


During the gastrulation of vertebrate embryos, the epiblast cells differentiate to form three embryo layers: ectoderm, mesoderm and endoderm. The mesendoderm (ME) is considered as the intermediate from the epiblast to the mesoderm and endoderm, and emerges at the very beginning of gastrulation.  

Numerous regulating factors, including signaling pathways, epigenetic modifications, specific transcriptional factors, and cell metabolism, are involved in the modulation of ME formation. These factors are precisely regulated to ensure the proper ME forming. However, there are still many mysteries underlying this process. In addition, most of our knowledge about the ME formation are achieved from animal models, but it remains an open question whether they are the same in human development.  

Recently, Dr. YANG Huang-Tian's group, at Shanghai Institute of Nutrition and Health (SINH), of the Chinese Academy of Sciences (CAS), identified the new function and mechanism of a transcription factor for the specific regulation of ME formation from human embryonic stem cells (hESCs).  

By using the in vitro ME differentiation model, a general transcription factor (GTF), TATA box-binding protein-related factor 3 (TRF3), was found to be significantly up-regulated, accompanying with the transcription initiation of ME genes. However, the expression of TBP and TBPL1, the other two genes coding members of the TATA box-binding protein family, was unchanged. In TRF3 deficient hESCs generated by CRISPR/Cas9, the ME differentiation progress was severely crippled. Interestingly, TRF3 deficiency did not affect the self-renewal and neuroectodermal differentiation of hESCs. Therefore, TRF3 is a critical factor for the human ME specification. Mechanistically, the TRF3 binding profile was significantly shifted to the mesendodermal specification during mesendodermal differentiation of hESCs based on the ChIP-seq analysis. Moreover, ChIP and ChIP-qPCR analysis showed that TRF3 was enriched at core promoter regions of mesendodermal developmental genes, EOMESODERMIN, BRACHYURY, mix paired-like homeobox, and GOOSECOID homeobox, during the mesendodermal differentiation of hESCs. The binding of TRF3 on the promoter of ME genes initiates the expression of these genes and promotes the formation of ME from hESCs.  

These findings reveal that the TBP family member TRF3 is dispensable in the undifferentiated hESCs and the early neuroectodermal differentiation. However, it directs mesendodermal lineage commitment of hESCs via specifically promoting the transcription of key mesendodermal transcription factors. The findings provide new insights into the specific role of the TBP family member during the hESC early lineage commitment and uncover the novel mechanism that “GTF” can switch the hESC state to the early specific lineage by shifting its binding profile.   

The study entitled “TATA box-binding protein-related factor 3 drives the mesendoderm specification of human embryonic stem cells by globally interacting with the TATA box of key mesendodermal genes” was published online in Stem Cell Research & Therapy on 24 May, 2020. This work was completed by a research team led by Dr. YANG Huang-Tian, at the CAS Key Laboratory of Tissue Microenvironment and Tumor of SINH. Dr. LIANG He, Dr. ZHANG Peng and Dr. BAI Huajun are the co-first authors. The study was funded by the grants from the National Natural Science Foundation of China, the National Key R&D Program of China, and the Strategic Priority Research Program of the CAS. 

Schematic representation of TRF3 regulating the ME formation from hESCs. ME, mesendoderm. (Image by Dr. YANG Huang-Tian's group) 

Media Contact:
WANG Jin (Ms.)
Shanghai Institute of Nutrition and Health,
Chinese Academy of Sciences
Email: sibssc@sibs.ac.cn