Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA173230 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:shRNA knockdown of the transcription factor NFYA in H322 and HCT116
| PRJNA288982 | ENA
Project description:Cell type-specific master transcription factors (MTFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that all three subunits of the ubiquitous heterotrimeric CCAAT-binding NF-Y complex are required for the maintenance of embryonic stem cell (ESC) identity, and establish NF-Y as a novel component of the core pluripotency network. Genome-wide occupancy and transcriptomic analyses in ESCs and neurons reveal that not only does NF-Y regulate genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with MTFs. Mechanistically, NF-Y's distinctive DNA-binding mode promotes MTF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a novel function for NF-Y in promoting chromatin accessibility, and suggest that other proteins with analogous structural and DNA-binding properties may function in similar ways. Genome-wide mapping of NF-YA, NF-YB, and NF-YC subunits of the NF-Y complex in mouse ESCs, and microarray gene expression profiling of control knockdown (KD), NF-YA KD, NF-YB KD, NF-YC KD, and NF-YA/NF-YB/NF-YC triple KD ESCs.
2014-08-14 | E-GEOD-56839 | biostudies-arrayexpress
Project description:In contrast to stage-specific transcription factors, the role of ubiquitous transcription factors in neuronal development remains a matter of scrutiny. Here, we demonstrated that a ubiquitous factor NF-Y is essential for neural progenitor maintenance during brain morphogenesis. Deletion of the NF-YA subunit in neural progenitors by using nestin-cre transgene in mice resulted in significant abnormalities in brain morphology, including a thinner cerebral cortex and loss of striatum during embryogenesis. Detailed analyses revealed a progressive decline in multiple neural progenitors in the cerebral cortex and ganglionic eminences, accompanied by induced apoptotic cell death and reduced cell proliferation. In neural progenitors, the NF-YA short isoform lacking exon 3 is dominant and co-expressed with cell cycle genes. ChIP-seq analysis from the cortex during early corticogenesis revealed preferential binding of NF-Y to the cell cycle genes, some of which were confirmed to be downregulated following NF-YA deletion. Notably, the NF-YA short isoform disappears and is replaced by its long isoform during neuronal differentiation. Forced expression of the NF-YA long isoform in neural progenitors resulted in a significant decline in neuronal count, possibly due to the suppression of cell proliferation. Collectively, we elucidated a critical role of the NF-YA short isoform in maintaining neural progenitors, possibly by regulating cell proliferation and apoptosis. Moreover, we identified an isoform switch in NF-YA within the neuronal lineage in vivo, which may explain the stage-specific role of NF-Y during neuronal development.
2024-01-11 | GSE244758 | GEO
Project description:Nuclear Factor Y (NF-Y) is a heterotrimeric transcription factor that binds CCAAT elements. The NF-Y trimer is composed of a Histone Fold Domain (HFD) dimer (NF-YB/NF-YC) and NF-YA, which confers DNA sequence specificity. NF-YA shares a conserved domain with the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) proteins. We show that CONSTANS (CO/B-BOX PROTEIN1 BBX1), a master flowering regulator, forms a trimer with Arabidopsis thaliana NF-YB2/NF-YC3 to efficiently bind the CORE element of the FLOWERING LOCUS T promoter. Using saturation mutagenesis, electrophoretic mobility shift assays, and RNA-sequencing profiling of co, nf-yb, and nf-yc mutants, we identify CCACA elements as the core NF-CO binding site. CO physically interacts with the same HFD surface required for NF-YA association, as determined by mutations in NF-YB2 and NF-YC9, and tested in vitro and in vivo. The co-7 mutation in the CCT domain, corresponding to an NF-YA arginine directly involved in CCAAT recognition, abolishes NF-CO binding to DNA
2022-06-09 | GSE205675 | GEO
Project description:The transcription factor NF-Y promotes cell proliferation and often loses its activity during differentiation through the regulation of NF-YA, the DNA binding subunit of the complex. In stem cell compartments, the shorter NF-YA splice variant (NF-YAs) is abundantly expressed and sustains their expansion. Here, we report that satellite cells, the stem cell population of adult skeletal muscle necessary for its growth and regeneration, express uniquely the longer NF-YA isoform (NF-YAl), majorly associated with cell differentiation. Through the generation of a conditional knock out mouse model that selectively ablates NF-YA in satellite cells, we demonstrate that NF-YA expression, and hence NF-Y activity, is fundamental to preserve the pool of muscle stem cells. Moreover, NF-Y supports their commitment to differentiation and ensures robust regenerative response to muscle injury. Gene expression profiling highlights an unexpected role for NF-Y in stem cell biology and opens a new scenario for NF-Y activity that is dispensable for muscle stem cell proliferation but required for efficient myogenic differentiation.
2021-08-30 | GSE154017 | GEO
Project description:Cell type-specific master transcription factors (MTFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that all three subunits of the ubiquitous heterotrimeric CCAAT-binding NF-Y complex are required for the maintenance of embryonic stem cell (ESC) identity, and establish NF-Y as a novel component of the core pluripotency network. Genome-wide occupancy and transcriptomic analyses in ESCs and neurons reveal that not only does NF-Y regulate genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with MTFs. Mechanistically, NF-Y's distinctive DNA-binding mode promotes MTF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a novel function for NF-Y in promoting chromatin accessibility, and suggest that other proteins with analogous structural and DNA-binding properties may function in similar ways. Genome-wide mapping of NF-YA, NF-YB, and NF-YC subunits of the NF-Y complex in mouse ESCs, and microarray gene expression profiling of control knockdown (KD), NF-YA KD, NF-YB KD, NF-YC KD, and NF-YA/NF-YB/NF-YC triple KD ESCs.
2014-08-14 | E-GEOD-56838 | biostudies-arrayexpress
Project description:In this RNA-seq experiment we identified genes differentially expressed in 12 hpf zebrafish embryos following disruption with dominant negative TALE (PBCAB) or NF-Y (NF-YA DN). We normalized each dominant negative condition to GFP. For PBCAB, we find 646 downregulated and 854 upregulated genes. For NF-YA DN, we find 325 downregulated and 577 upregulated genes. Genes downregulated by PBCAB are enriched for transcription, development, and homeodomain ontologies, while genes downregulated by NF-YA DN are enriched for transcription and cilia ontologies. 74 genes are downregulated by both PBCAB and NF-YA DN; these genes are enriched for transcription, development, and homeodomain ontologies.
2019-12-31 | GSE133459 | GEO
Project description:Investigation of the binding behaviour of Sp1, Sp2, Sp3 and NF-ya, NF-yb and NF-yc in mouse embryonic fibroblasts and of Sp1, Sp2 and Sp3 in HEK-293 cells reveals distinct binding of the seemingly similar transcription factors Sp1/3 and Sp2.
2015-01-30 | E-MTAB-2970 | biostudies-arrayexpress
Project description:Bifunctional Activity of members of the Arabidopsis NF-YA Transcription Factor Family
| PRJNA151793 | ENA
Project description:modENCODE_submission_4811 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); Developmental Stage: Young adult; Genotype: unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Young adult; Target gene nfya-1; Strain OP404(official name : OP404 genotype : unc-119(ed3) III; wgIs404(nfya-1::TY1-GFP-3xFLA; unc-119(+)) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology and Genetics in Dresden description : using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The NFYA-1::EGFP fusion protein is expressed in the correct nfya-1 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the NFYA-1 transcription factor. made_by : Unknown ); temp (temperature) 20 degree celsius
2013-07-11 | E-GEOD-48756 | biostudies-arrayexpress