scholarly journals Foxd3 controls heterochromatin-mediated silencing of repeat elements in mouse embryonic stem cells and represses the 2-cell transcription program

2021 ◽  
Author(s):  
Deepika Puri ◽  
Birgit Koschorz ◽  
Bettina Engist ◽  
Megumi Onishi-Seebacher ◽  
Devon Ryan ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Stem Cell ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Repeat Element ◽  
Negative Regulator ◽  
Major Satellite ◽  
Satellite Repeats

Repeat element transcription plays a vital role in early embryonic development. Expression of repeats such as MERVL characterises mouse embryos at the 2-cell stage, and defines a 2-cell-like cell (2CLC) population in a mouse embryonic stem cell culture. Repeat element sequences contain binding sites for numerous transcription factors. We identify the forkhead domain transcription factor FOXD3 as a regulator of repeat element transcription in mouse embryonic stem cells. FOXD3 binds to and recruits the histone methyltransferase SUV39H1 to MERVL and major satellite repeats, consequentially repressing the transcription of these repeats by the establishment of the H3K9me3 heterochromatin modification. Notably, depletion of FOXD3 leads to the de-repression of MERVL and major satellite repeats as well as a subset of genes expressed in the 2-cell state, shifting the balance between the stem cell and 2 cell-like population in culture. Thus, FOXD3 acts as a negative regulator of repeat transcription, ascribing a novel function to this transcription factor.

scholarly journals Cancer stem cell induction from mouse embryonic stem cells

2019 ◽  
Author(s):  
Akimasa Seno ◽  
Chikae Murakami ◽  
Bishoy El‑Aarag ◽  
Yoshiaki Iwasaki ◽  
Toshiaki Ohara ◽  
...  
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Embryonic Stem Cells ◽  
Cancer Stem Cell ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Cell Induction

scholarly journals Computer and Statistical Analysis of Transcription Factor Binding and Chromatin Modifications by ChIP-seq data in Embryonic Stem Cell

2012 ◽  
Vol 9 (2) ◽  
pp. 88-100 ◽  
Author(s):  
Yuriy Orlov ◽  
Han Xu ◽  
Dmitri Afonnikov ◽  
Bing Lim ◽  
Jian-Chien Heng ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Stem Cell ◽  
Statistical Analysis ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Embryonic Stem ◽  
Published Data ◽  
Binding Studies ◽  
Chip Sequencing

Summary Advances in high throughput sequencing technology have enabled the identification of transcription factor (TF) binding sites in genome scale. TF binding studies are important for medical applications and stem cell research. Somatic cells can be reprogrammed to a pluripotent state by the combined introduction of factors such as Oct4, Sox2, c-Myc, Klf4. These reprogrammed cells share many characteristics with embryonic stem cells (ESCs) and are known as induced pluripotent stem cells (iPSCs). The signaling requirements for maintenance of human and murine embryonic stem cells (ESCs) differ considerably. Genome wide ChIP-seq TF binding maps in mouse stem cells include Oct4, Sox2, Nanog, Tbx3, Smad2 as well as group of other factors. ChIP-seq allows study of new candidate transcription factors for reprogramming. It was shown that Nr5a2 could replace Oct4 for reprogramming. Epigenetic modifications play important role in regulation of gene expression adding additional complexity to transcription network functioning. We have studied associations between different histone modification using published data together with RNA Pol II sites. We found strong associations between activation marks and TF binding sites and present it qualitatively. To meet issues of statistical analysis of genome ChIP-sequencing maps we developed computer program to filter out noise signals and find significant association between binding site affinity and number of sequence reads. The data provide new insights into the function of chromatin organization and regulation in stem cells.

scholarly journals Identification of Novel miRNAs in Mouse Embryonic Stem Cells, Embryonic Fibroblasts, and Reprogrammed Pluripotent Cells

2019 ◽  
Author(s):  
Botao Zhao ◽  
Chunsun Fan
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Embryonic Stem Cells ◽  
De Novo ◽  
Embryonic Stem ◽  
Induced Pluripotent Stem Cell ◽  
Mouse Embryonic Stem Cells ◽  
Pluripotent Cells ◽  
Embryonic Fibroblasts ◽  
Species Specific

AbstractMicroRNAs (miRNAs) are a class of non-coding small RNAs that function in almost every known cellular activity. MiRNAs play an important role in gene regulation that controls embryonic stem cell (ESC) pluripotency and differentiation, as well as induced pluripotent stem cell (iPSC) reprogramming. In this study, we identified nine novel miRNAs by mining the deep sequencing dataset from mouse embryonic stem cells, mouse embryonic fibroblasts (MEF) and three kinds of reprogrammed pluripotent cells. Most of them are non-conserved but species-specific and cell-specific miRNAs. Eight miRNAs are derived from gene introns, including a “mirtron” miRNA, miR-novel-41. We also showed that miR-novel-27 is a mouse-specific miRNA and the 5′ arm of its precursor hairpin, embedding the mature miR-novel-27, uniquely exists in mouse species but not in any other Placentalia animals. Notably, the 5′ arm of the pre-miR-novel-27 hairpin shows nearly perfect palindrome to the 3′ arm suggesting that it was generated by inverted duplication of the 3′ arm. By this mechanism, the pre-miR-novel-27 hairpin was de novo gained in the mouse genome. This is a new type of de novo miRNA emergence mechanism in animals, which we called “inverted local half hairpin duplication” here. In addition, very limited nucleotide mutants accumulated on the newly emerged 5′ arm since its birth suggesting an especially young evolutionary history of the miR-novel-27 gene.

scholarly journals Assessment of Stem Cell Markers During Long-Term Culture of Mouse Embryonic Stem Cells

2004 ◽  
Vol 44 (1/2) ◽  
pp. 77-91 ◽  
Author(s):  
A. Berrill ◽  
H.L. Tan ◽  
S.C. Wuang ◽  
W.J. Fong ◽  
Andre B.H. Choo ◽  
...  
Keyword(s):  
Stem Cells ◽  
Stem Cell ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Stem Cell Markers ◽  
Cell Markers ◽  
Long Term Culture

scholarly journals Nr0b1 is a negative regulator of Zscan4c in mouse embryonic stem cells

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Setsuko Fujii ◽  
Satomi Nishikawa-Torikai ◽  
Yoko Futatsugi ◽  
Yayoi Toyooka ◽  
Mariko Yamane ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Negative Regulator
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