Similar Datasets
Project description:Pioneer transcription factors such as OCT4 can target silent genes embedded in nucleosome-dense regions. How nucleosome interaction enables transcription factors to target chromatin and determine cell identity remains elusive. Here, we systematically dissect OCT4 to show that nucleosome binding is encoded within the DNA-binding domain and yet can be uncoupled from free-DNA binding. Furthermore, accelerating the binding kinetics of OCT4 to DNA enhances nucleosome binding. In cells, uncoupling nucleosome binding diminishes the ability of OCT4 to individually access closed chromatin, while more dynamic nucleosome binding results in expansive genome scanning within closed chromatin. However, both uncoupling and enhancing nucleosome binding are detrimental to inducing pluripotency from differentiated cells. Remarkably, stable interactions between OCT4 and nucleosomes are continuously required for maintaining the accessibility of pluripotency enhancers in stem cells. Our findings reveal how the affinity and residence time of OCT4-nucleosome complexes modulate chromatin accessibility during cell fate changes and maintenance.
| S-EPMC7611526 | biostudies-literature
Project description:The aim of this study is to dissect the transcription factor OCT4 and reveal which parts of the protein are essential for interaction with nucleosomes and access to closed chromatin. We revealed that the DNA-binding domain mediates the interaction of OCT4 with nucleosomes. Remarkably, nucleosome-binding can be uncoupled from DNA-binding, diminishing the ability of OCT4 to access to closed chromatin, thus losing the pioneer function. We show that the pioneer function of OCT4 is not only essential during reprogramming differentiated cells to pluripotency but also during pluripotency maintenance of embryonic stem cells. Overall, this study shows how pioneer transcription factors interact with nucleosomes to engage the genome and control cellular identity, highlighting that nucleosomes are not always barriers to genome accessibility.
2021-06-24 | GSE168141 | GEO
Project description:Dissecting OCT4 defines the role of nucleosome binding in pluripotency
| PRJNA706206 | ENA
Project description:The aim of this study is to dissect the transcription factor OCT4 and reveal which parts of the protein are essential for interaction with nucleosomes and access to closed chromatin. We revealed that the DNA-binding domain mediates the interaction of OCT4 with nucleosomes. Remarkably, nucleosome-binding can be uncoupled from DNA-binding, diminishing the ability of OCT4 to access to closed chromatin, thus losing the pioneer function. We show that the pioneer function of OCT4 is not only essential during reprogramming differentiated cells to pluripotency but also during pluripotency maintenance of embryonic stem cells. Overall, this study shows how pioneer transcription factors interact with nucleosomes to engage the genome and control cellular identity, highlighting that nucleosomes are not always barriers to genome accessibility .
2021-06-24 | GSE167632 | GEO
Project description:Dissecting OCT4 defines the role of nucleosome binding in pluripotency maintenance
| PRJNA706212 | ENA
Project description:The transcription factors OCT4 and SOX2 are required for generating induced pluripotent stem cells (iPSCs) and for maintaining embryonic stem cells (ESCs). OCT4 and SOX2 associate and bind to DNA in different configurations depending on the arrangement of their individual DNA binding elements. Here we have investigated the role of the different OCT4-SOX2-DNA assemblies in regulating and inducing pluripotency. To this end, we have generated SOX2 mutants that interfere with specific OCT4-SOX2 heterodimer configurations and assessed their ability to generate iPSCs and to rescue ESC self-renewal. Our results demonstrate that the OCT4-SOX2 configuration that dimerizes on a Hoxb1-like composite, a canonical element with juxtaposed individual binding sites, plays a more critical role in the induction and maintenance of pluripotency than any other OCT4-SOX2 configuration. Overall, the results of this study provide new insight into the protein interactions required to establish a de novo pluripotent network and to maintain a true pluripotent cell fate.
| S-EPMC4551974 | biostudies-literature
Project description:The mechanisms whereby the crucial pluripotency transcription factor Oct4 regulates target gene expression are incompletely understood. Using an assay system based on partially differentiated embryonic stem cells, we show that Oct4 opposes the accumulation of local H3K9me2 and subsequent Dnmt3a-mediated DNA methylation. Upon binding DNA, Oct4 recruits the histone lysine demethylase Jmjd1c. Chromatin immunoprecipitation (ChIP) time course experiments identify a stepwise Oct4 mechanism involving Jmjd1c recruitment and H3K9me2 demethylation, transient FACT (facilitates chromatin transactions) complex recruitment, and nucleosome depletion. Genome-wide and targeted ChIP confirms binding of newly synthesized Oct4, together with Jmjd1c and FACT, to the Pou5f1 enhancer and a small number of other Oct4 targets, including the Nanog promoter. Histone demethylation is required for both FACT recruitment and H3 depletion. Jmjd1c is required to induce endogenous Oct4 expression and fully reprogram fibroblasts to pluripotency, indicating that the assay system identifies functional Oct4 cofactors. These findings indicate that Oct4 sequentially recruits activities that catalyze histone demethylation and depletion.
| S-EPMC4333097 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2012-12-01 | E-GEOD-41617 | biostudies-arrayexpress
Project description:Transcription factor binding to genomic DNA is generally prevented by nucleosome formation, in which the DNA is tightly wrapped around the histone octamer. In contrast, pioneer transcription factors efficiently bind their target DNA sequences within the nucleosome. OCT4 has been identified as a pioneer transcription factor required for stem cell pluripotency. To study the nucleosome binding by OCT4, we prepared human OCT4 as a recombinant protein, and biochemically analyzed its interactions with the nucleosome containing a natural OCT4 target, the LIN28B distal enhancer DNA sequence, which contains three potential OCT4 target sequences. By a combination of chemical mapping and cryo-electron microscopy single-particle analysis, we mapped the positions of the three target sequences within the nucleosome. A mutational analysis revealed that OCT4 preferentially binds its target DNA sequence located near the entry/exit site of the nucleosome. Crosslinking mass spectrometry consistently showed that OCT4 binds the nucleosome in the proximity of the histone H3 N-terminal region, which is close to the entry/exit site of the nucleosome. We also found that the linker histone H1 competes with OCT4 for the nucleosome binding. These findings provide important information for understanding the molecular mechanism by which OCT4 binds its target DNA in chromatin.
| S-EPMC7367260 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-08-04 | E-GEOD-56569 | biostudies-arrayexpress