scholarly journals Integrated omics approach reveals transcription factor binding associated with regulation of ribosome biogenesis genes in adult neural stem cells

2017 ◽  
Vol 145 ◽  
pp. S160
Author(s):  
Shradha Mukherjee ◽  
Jenny Hsieh
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Neural Stem Cells ◽  
Ribosome Biogenesis ◽  
Transcription Factor Binding ◽  
Adult Neural Stem Cells ◽  
Factor Binding ◽  
Integrated Omics

scholarly journals Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

EMBO Reports ◽  
2015 ◽  
Vol 16 (9) ◽  
pp. 1177-1191 ◽  
Author(s):  
Tapan Kumar Mistri ◽  
Arun George Devasia ◽  
Lee Thean Chu ◽  
Wei Ping Ng ◽  
Florian Halbritter ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Neural Stem Cells ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Selective Influence

scholarly journals Demyelination Regulates the Circadian Transcription Factor BMAL1 to Signal Adult Neural Stem Cells to Initiate Oligodendrogenesis

Cell Reports ◽  
2020 ◽  
Vol 33 (7) ◽  
pp. 108394
Author(s):  
Suihong Huang ◽  
Ming Ho Choi ◽  
Hao Huang ◽  
Xin Wang ◽  
Yu Chen Chang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Neural Stem Cells ◽  
Adult Neural Stem Cells ◽  
Circadian Transcription

scholarly journals Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry

2020 ◽  
Vol 118 (8) ◽  
pp. 2015-2026 ◽  
Author(s):  
Matan Goldshtein ◽  
Meir Mellul ◽  
Gai Deutch ◽  
Masahiko Imashimizu ◽  
Koh Takeuchi ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Embryonic Stem Cells ◽  
Dna Sequence ◽  
Embryonic Stem ◽  
Transcription Factor Binding ◽  
Sequence Repeat ◽  
Factor Binding

scholarly journals Widespread conservation of chromatin accessibility patterns and transcription factor binding in human and chimpanzee induced pluripotent stem cells

2018 ◽  
Author(s):  
Irene Gallego Romero ◽  
Shyam Gopalakrishnan ◽  
Yoav Gilad
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Induced Pluripotent Stem Cells ◽  
Pluripotent Stem Cells ◽  
Related Species ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Closely Related Species ◽  
Factor Binding ◽  
Induced Pluripotent

AbstractChanges in gene regulation have been shown to contribute to phenotypic differences between closely related species, most notably in primates. It is likely that a subset of inter-species regulatory differences can be explained by changes in chromatin accessibility and transcription factor binding, yet there is a paucity of comparative data sets with which to investigate this. Using ATAC-seq, we profiled genome-wide chromatin accessibility in a matched set of 6 human and 6 chimpanzee (Pan troglodytes, our closest living relative) induced pluripotent stem cells from which we have previously collected gene expression data. We examined chromatin accessibility patterns near 20,745 orthologous transcriptions start sites and used a footprinting algorithm to predict transcription factor binding activity in each species. We found that the majority of chromatin accessibility patterns and transcription factor activity are conserved between these two closely related species. Interestingly, interspecies divergence in chromatin accessibility and transcription factor binding in pluripotent cells appear to contribute not to differences in the pluripotent state, but to downstream developmental processes. Put together, our findings suggest that the pluripotent state is extremely stable and potentially subject to stronger evolutionary constraint than other somatic tissues.

scholarly journals A flexible repertoire of transcription factor binding sites and diversity threshold determines enhancer activity in embryonic stem cells

2020 ◽  
Author(s):  
Gurdeep Singh ◽  
Shanelle Mullany ◽  
Sakthi D Moorthy ◽  
Richard Zhang ◽  
Tahmid Mehdi ◽  
...  
Keyword(s):  
Stem Cells ◽  
Transcription Factor ◽  
Embryonic Stem Cells ◽  
Binding Sites ◽  
Embryonic Stem ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Enhancer Activity ◽  
Factor Binding ◽  
Master Regulators

ABSTRACTTranscriptional enhancers are critical for development, phenotype evolution and often mutated in disease contexts; however, even in well-studied cell types, the sequence code conferring enhancer activity remains unknown. We found genomic regions with conserved binding of multiple transcription factors in mouse and human embryonic stem cells (ESCs) contain on average 12.6 conserved transcription factor binding sites (TFBS). These TFBS are a diverse repertoire of 70 different sequences representing the binding sites of both known and novel ESC regulators. Remarkably, using a diverse set of TFBS from this repertoire was sufficient to construct short synthetic enhancers with activity comparable to native enhancers. Site directed mutagenesis of conserved TFBS in endogenous enhancers or TFBS deletion from synthetic sequences revealed a requirement for more than ten different TFBS. Furthermore, specific TFBS, including the OCT4:SOX2 co-motif, are dispensable, despite co-binding the OCT4, SOX2 and NANOG master regulators of pluripotency. These findings reveal a TFBS diversity threshold overrides the need for optimized regulatory grammar and individual TFBS that bind specific master regulators.

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