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The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [RNA-Seq]

ABSTRACT: When stem cells activate a member of the SOX family of pioneer factors, they bind their cognate sequences within condensed chromatin, not only evicting the associated nucleosome, but also recruiting H3K4-monomethylases, which modify flanking nucleosomes to open chromatin and activate one lineage program; simultaneously, pioneer factors also silence alternative fates, but in this case act indirectly, through competing for H3K4-monomethylases pre-existing at the original fate genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE208071 | GEO | 2023/05/05

REPOSITORIES: GEO

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The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [CUT&RUN]

Project description:When stem cells activate a member of the SOX family of pioneer factors, they bind their cognate sequences within condensed chromatin, not only evicting the associated nucleosome, but also recruiting H3K4-monomethylases, which modify flanking nucleosomes to open chromatin and activate one lineage program; simultaneously, pioneer factors also silence alternative fates, but in this case act indirectly, through competing for H3K4-monomethylases pre-existing at the original fate genes.

2023-05-05 | GSE208070 | GEO

The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [ATAC-Seq]

2023-05-05 | GSE208066 | GEO

The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [MINT ChIP-Seq]

2023-05-05 | GSE208069 | GEO

The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-05-05 | GSE208072 | GEO

Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor [RNA-seq]

Project description:Eukaryotic DNA is packaged into chromatin in the nucleus, which restricts the binding of transcription factors (TFs) to the target DNA sites. FOXA1 functions as a pioneer TF to bind condensed chromatin and initiates the opening of local chromatin for gene expression. However, the principles of how FOXA1 recruits to and unpacks the condensed chromatin remain elusive. Here, we revealed that FOXA1 intrinsically undergoes phase separation through its N-PrLD and C-IDR regions, identified as phase separation region (PSR). Notably, the phase separation property confers FOXA1 the ability to dissolve the chromatin condensates. In addition, the DNA-binding capacity of FOXA1 contributes to its phase separation property. Further genome-wide investigation showed that FOXA1 is recruited to and unpacks the condensed chromatin by its PSR to regulate the function of breast cancer cells. This work provides a principal example of how pioneer TFs function to initiate competent chromatin states by phase separation.

2023-12-04 | GSE231363 | GEO

Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor [ATAC-seq]

2023-12-04 | GSE231362 | GEO

Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor [ChIP-seq]

2023-12-04 | GSE231361 | GEO

Phase Separation of FOXA1 Unpacks the Condensed Chromatin to Function as a Pioneer Factor (NIH-3T3 cells)

2023-12-03 | GSE242240 | GEO

Effect of NKX2-5 or ETS1 on GATA4 pioneer activity [fibroblast]

Project description:GATA4 is a pioneer transcription factor. The mechanisms by which pioneer factors select and occupy specific loci, open chromatin, and activate enhancers is not well understood. To address the influence of partner, non-pioneer factors on pioneer factor activity, we analyzed the effect of NKX2-5 or ETS1 on GATA4 pioneer activity. NIH3T3 cells were transduced with lentivirus to obtain stable cell lines that express GFP (control), GATA4 (G), NKX2-5 (N), ETS1 (E), GATA4+NKX2-5 (GN), and GATA4+ETS1 (GE). We measured chromatin accessibility using ATAC-seq, and enhancer activation using H3K27ac. From these measurements we determined GATA4, GATA4+ETS, and GATA4+NKX2-5 pioneer binding, pioneer opening, and pioneer enhancer activation. Our results show that ETS1 or NKX2-5 alter GATA4 pioneer binding, opening, and enhancer activation.

2021-07-01 | GSE155652 | GEO

LNCap cell nucleosome footprint elicits novel noncanonical GATA2 pioneer model

Project description:Purpose: The dynamic nucleosome reorganization is the interplay among nucleosome and regulated by pioneer factors, which can access target DNA sequences on nucleosomes.The goals of this study are revealing the dynamic nucleosome footprint and how GATA2 is capable of resetting crowding array to primed, or accessible edge nucleosome states. Methods: LNCaP cells between passage number 30-35 were used for assay. cell nucleus was extracted, digested by MNase to Mono-nucleosome and ChIP/ChIP-exo was performed, the ChIP products were further used to generate library with illumina ChIP-seq kit. Hi-seq 3000 was used for sequencing and the data was analyzed by MACS2 for peaks. Results: GATA2 is associated with condensed nucleosome states and nucleosomes could unwrapped and be more accessible in pioneer factor GATA2 binding sites. Conclusions: Our study represents the first detailed nucleosome footprint of LNCap cells and analysis of the relationship between pioneer factor GATA2 and nucleosome reorganization in whole genomic DNA. These results demonstrated GATA2 play a critical role in an AR-independent manner in prostate cancer.

2021-04-14 | GSE148935 | GEO

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