PLX252883

GSE90455: Genetic determinants and epigenetic effects of pioneer factor binding [RNA-seq]

  • Organsim human
  • Type RNASEQ
  • Target gene
  • Project ARCHS4

Transcription factors (TFs) are the core drivers of gene regulatory networks that control developmental transitions and a complete understanding of how they access, alter and maintain specific gene expression patterns remains an important goal. To begin a systematic dissection of the molecular components that either enable or constrain TF activity, we investigated the genomic occupancy of two distinct TFs, the pioneer factor FOXA2 and the pluripotency-associated factor OCT4 (POU5F1), in both endogenous and ectopic settings. We find that, while stable binding of FOXA2 is highly cell type specific and similar to what is observed for most TFs including OCT4, pioneer activity can be distinguished by notable sampling of additional loci that are occupied in alternative lineages. In our ectopic system, FOXA2 binding can be selectively stabilized at previously sampled sites by co-expressing the lineage specific regulator GATA4. Alternatively, we observe minimal influence of chromatin state on discrete, stabilized binding choices for FOXA2 but a strong bias towards open chromatin for ectopic OCT4 targets. Finally, we demonstrate that FOXA2 binding and nucleosome remodeling at silent loci can occur when the cell cycle is halted in G1, but surprisingly subsequent changes in DNA methylation require DNA replication. Taken together, our results provide several new molecular insights that contribute to our basic understanding of gene regulation and pave the way for a more rational use of ectopic TFs for cellular reprogramming. SOURCE: Sudhir Thakurela HSCRB

View on GEOView in Pluto

Key Features

Enhance your research with our curated data sets and powerful platform features. Pluto Bio makes it simple to find and use the data you need.

Learn More

14K+ Published Experiments

Access an extensive range of curated bioinformatics data sets, including genomic, transcriptomic, and proteomic data.

Easy Data Import

Request imports from GEO or TCGA directly within Pluto Bio. Seamlessly integrate external data sets into your workflow.

Advanced Search Capabilities

Utilize powerful search tools to quickly find the data sets relevant to your research. Filter by type, disease, gene, and more.

Analyze and visualize data for this experiment

Use Pluto's intuitive interface to analyze and visualize data for this experiment. Pluto's platform is equipped with an API & SDKs, making it easy to integrate into your internal bioinformatics processes.

Read about post-pipeline analysis

View QC data and experiment metadata

View quality control data and experiment metadata for this experiment.

Request import of other GEO data

Request imports from GEO or TCGA directly within Pluto Bio.

Chat with our Scientific Insights team