scholarly journals Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Yoko Itahana ◽  
Jinqiu Zhang ◽  
Jonathan Göke ◽  
Leah A. Vardy ◽  
Rachel Han ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Histone Modifications ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
P21 Promoter

Human embryonic stem cells are characterized by distinct patterns of histone modifications in comparison with cells of feeder layer

2008 ◽  
Vol 2008 (Spring) ◽  
Author(s):  
Eva Bartova ◽  
Abdrea Harnicarova ◽  
Jana Krejci ◽  
Gabriela Galiova ◽  
Stanislav Kozubek
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Histone Modifications ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Feeder Layer

scholarly journals Rewiring of transcription factor binding in differentiating human embryonic stem cells is constrained by DNA sequence repeat symmetry

2018 ◽  
Author(s):  
Matan Goldshtein ◽  
David B. Lukatsky
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Embryonic Stem Cells ◽  
Dna Binding ◽  
Dna Sequence ◽  
Histone Modifications ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Sequence Repeat ◽  
Dna Repeat

ABSTRACTWe analyze design principles of transcription factor (TF) recognition by genomic DNA in differentiating human embryonic stem cells for 36 TFs and five histone modifications in four developmental layers, using the data recently measured by Tsankov et al. This analysis reveals that DNA sequence repeat symmetry plays a central role in defining TF-DNA binding preferences across different developmental layers. In particular, we find that different TFs bind similar symmetry patterns within a given developmental layer. While the TF cluster content undergoes modifications upon transitions between different developmental layers, most TFs possess dominant preferences for similar DNA repeat symmetry types. Histone modifications also exhibit strong preferences for similar DNA repeat symmetry patterns, with the symmetry strength differentiating between different histone modifications. Overall, our findings show that despite the enormous sequence complexity of the TF-DNA binding landscape in differentiating human embryonic stem cells, this landscape can be quantitatively characterized in simple terms, using the notion of DNA sequence repeat symmetry.

scholarly journals Functional dissection of the enhancer repertoire in human embryonic stem cells

2017 ◽  
Author(s):  
Tahsin Stefan Barakat ◽  
Florian Halbritter ◽  
Man Zhang ◽  
André F. Rendeiro ◽  
Christoph Bock ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Transposable Elements ◽  
Histone Modifications ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Housekeeping Genes ◽  
List Type ◽  
Enhancer Activity ◽  
Enhancer Function

SummaryEnhancers are genetic elements that regulate spatiotemporal gene expression. Enhancer function requires transcription factor (TF) binding and correlates with histone modifications. However, the extent to which TF binding and histone modifications can functionally define active enhancers remains unclear. Here we combine chromatin immunoprecipitation with a massively parallel reporter assay to identify functional enhancers in human embryonic stem cells (hESCs) genome-wide in a quantitative unbiased manner. While active enhancers associate with TFs, only a minority of regions marked by NANOG, OCT4, H3K27ac and H3K4me1 function as enhancers, with activity changing markedly with culture conditions. Our analysis also reveals a novel enhancer set associated with housekeeping genes. Moreover, while transposable elements associate with putative enhancers only some exhibit activity. Similarly, within super-enhancers, large tracts are non-functional, with activity restricted to small sub-domains. This catalogue of validated enhancers provides a valuable resource for further functional dissection of the regulatory genome.HighlightsA catalog of functional enhancers in hESCs including a novel housekeeping classActive enhancers feature specific transcription factors and transposable elementsMajor shifts in enhancer activity occur during induction of naive pluripotencySuper-enhancers consist of small units with enhancer function

Ethanol alters cell cycle gene expression in human embryonic stem cells

2016 ◽  
Vol 01 (03) ◽  
pp. 201-208 ◽  
Author(s):  
Malini Krishnamoorthy ◽  
Brian Gerwe ◽  
Jamie Heimburg-Molinaro ◽  
Rachel Nash ◽  
Jagan Arumugham ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Human Embryonic Stem Cells ◽  
Embryonic Stem ◽  
Cell Cycle Gene ◽  
Cell Cycle Gene Expression
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