scholarly journals Computational Biology of microRNA-Pluripotency Gene Networks in Embryonic Stem Cells

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Heyao Zhang ◽  
Xuepeng Wang ◽  
Jingsheng Li ◽  
Ronghua Shi ◽  
Ying Ye

Embryonic stem cells (ESCs) can self-renew indefinitely and maintain their pluripotency status. The pluripotency gene regulatory network is critical in controlling these properties and particularly chromatin remodeling complexes. In this review, we summarize the research progresses of the functional and mechanistic studies of BAF complex in mouse ESCs and early embryonic development. A discussion of the mechanistic bases underlying the distinct phenotypes upon the deletion of different BAF subunits in ESCs and embryos will be highlighted.


2016 ◽  
Vol 44 (12) ◽  
pp. 5515-5528 ◽  
Author(s):  
Junko Yamane ◽  
Sachiyo Aburatani ◽  
Satoshi Imanishi ◽  
Hiromi Akanuma ◽  
Reiko Nagano ◽  
...  

2020 ◽  
Vol 32 (2) ◽  
pp. 234
Author(s):  
S. Arcuri ◽  
G. Pennarossa ◽  
F. Gandolfi ◽  
T. Brevini

Cell proliferation, apoptosis, and differentiation are essential processes from the early phases of embryogenesis to adult tissue formation and maintenance. These mechanisms also play a key role in embryonic stem cells (ESCs), which are able to proliferate maintaining pluripotency and, at the same time, give rise to all populations belonging to the three germ layers in response to specific stimuli. ESCs are, therefore, considered a well-established invitro model to study the complexity of these processes. We previously generated porcine and human diploid parthenogenetic embryonic stem cells (ParthESC) that showed many features and regulatory pathways common to biparental ESCs. However, we observed that monoparental cells demonstrated a greater ability to form outgrowths and generate stable three-dimensional (3D) spheroid colonies, which are distinctive signs of high plasticity (Brevini et al. 2010 STCR 6; https://doi.org/10.1007/s12015-010-9153-2). In the present study, we compared porcine and human biparental ESCs and ParthESC. Pluripotency gene expression was analysed and ELISA tests for global DNA methylation and total YAP levels were performed. Our results showed that ParthESCs showed significantly higher expression levels of YAP and TAZ than biparental ESCs. In contrast, the analysis of the upstream genes involved in the Hippo signalling pathway revealed no differences. We demonstrated that YAP remains in a dephosphorylated form, encouraging its nuclear compartmentalization and direct interaction with the nuclear transcription factors TEADs and SMADs, that are also upregulated and maintain pluripotency, repressing differentiation processes (Beyer et al. 2013 Cell Rep. 5, 1611-1624; https://doi.org/10.1016/j.celrep.2013.11.021). These complex regulatory interactions accompanied the overexpression of the pluripotency-related genes OCT4, NANOG, REX1, SOX2, UTF1, and TERT. In parallel, we observed a decrease of DNMT3 and DNMT4 activity that resulted in a global DNA hypomethylation and a chromatin high-permissive state. Altogether, our results demonstrate a significant upregulation of YAP/TAZ activity in monoparental cell lines. This may account for their greater ability to form outgrowths and generate 3D spheroid colonies and increased plasticity compared with biparental counterparts. It is interesting to note that YAP mRNA is supplied and expressed by the oocyte and is maternally inherited (Yu et al. 2016 Cell Res. 26, 275-287; https://doi.org/10.1038/cr.2016.20). Although further clarifications are needed, we hypothesise that its higher expression in ParthESC may be related to the strictly maternal origin of these cells. This study was supported by the Carraresi Foundation. Authors are members of the COST Actions CA16119.


2021 ◽  
Vol 7 ◽  
Author(s):  
Dao-Yin Dong ◽  
Pu-Yu Li

SOX2 overlapping transcript (SOX2-OT) is an evolutionarily conserved long non-coding RNA (lncRNA) whose intronic region contains the transcript of pluripotency gene SRY-box transcription factor 2 (SOX2). It has been suggested that SOX2-OT can regulate its overlapping gene, SOX2. Studies demonstrated that elevated SOX2-OT promotes SOX2 expression in cancer cells, whereas levels of SOX2-OT are inversely correlated with levels of SOX2 in embryonic stem cells. It is not clear why there is a tremendous discrepancy in the regulation of SOX2 by SOX2-OT in cancer cells and embryonic stem cells. Due to the diversified transcription of the SOX2-OT gene, we hypothesize that differential expression of transcripts of the SOX2-OT gene in cancer cells and embryonic stem cells may contribute to the divergence in the regulatory relationship of SOX2-OT and SOX2. A CRISPR screening platform can be leveraged to systemic evaluate which transcript of the SOX2-OT gene may be responsible for upregulation or downregulation of SOX2 in cancer cells and embryonic stem cells, respectively.


2018 ◽  
Vol 47 (3) ◽  
pp. 1600-1600
Author(s):  
Junko Yamane ◽  
Sachiyo Aburatani ◽  
Satoshi Imanishi ◽  
Hiromi Akanuma ◽  
Reiko Nagano ◽  
...  

PLoS ONE ◽  
2006 ◽  
Vol 1 (1) ◽  
pp. e26 ◽  
Author(s):  
Ryo Matoba ◽  
Hitoshi Niwa ◽  
Shinji Masui ◽  
Satoshi Ohtsuka ◽  
Mark G. Carter ◽  
...  

2018 ◽  
Vol 120 (3) ◽  
pp. 4071-4080 ◽  
Author(s):  
Vahideh Assadollahi ◽  
Ebrahim Mohammadi ◽  
Fardin Fathi ◽  
Kambiz hassanzadeh ◽  
Mohamad Bager Khadem Erfan ◽  
...  

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