ArticleNucleic acids research2016
A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Alternative Splicing of the NF-Y Subunit, NF-YA, in Neuroblastoma Phenotype Heterogeneity.Cancers · 2026Review
- Altered chromatin accessibility and nucleosome positioning landscape upon HDAC and LSD1 inhibition in cancer cell.bioRxiv : the preprint server for biology · 2026Article
- Development and Evaluation of Compact Semi-Synthetic Promoters for Enhanced Antigen Expression in Adenoviral-Vectored Vaccines.Vaccines · 2026Article
- DNA breathing and shape encode distinct mechanisms of transcription factor binding.Bioinformatics advances · 2026Article
- Binding of NF-Y to transposable elements in mouse and human cells.Mobile DNA · 2025Article
- The role(s) of NF-Y in development and differentiation.Cell death and differentiation · 2025Review
- Novel Core Gene Signature Associated with Inflammation-to-Metaplasia Transition in Influenza A Virus-Infected Lungs.International journal of molecular sciences · 2024Article
- The pancancer overexpressed NFYC Antisense 1 controls cell cycle mitotic progression through in cis and in trans modes of action.Cell death & disease · 2024Article
- Natural medicinal compounds target signal transduction pathways to overcome ABC drug efflux transporter-mediated multidrug resistance in cancer.Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy · 2023Review
- Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Characterization of genes associated with TGA7 during the floral transition.BMC plant biology · 2021Article
- NF-Y Subunits Overexpression in HNSCC.Cancers · 2021Article
- Live cell dynamics of the NF-Y transcription factor.Scientific reports · 2021Article
- Transcription factor competition at the γ-globin promoters controls hemoglobin switching.Nature genetics · 2021Article
- Deep neural networks identify sequence context features predictive of transcription factor binding.Nature machine intelligence · 2021Article
- Synergism of Proneurogenic miRNAs Provides a More Effective Strategy to Target Glioma Stem Cells.Cancers · 2021Article
- Structural Variations of the 3D Genome Architecture in Cervical Cancer Development.Frontiers in cell and developmental biology · 2021Article
- On the NF-Y regulome as in ENCODE (2019).PLoS computational biology · 2020Article
- NF-Y Overexpression in Liver Hepatocellular Carcinoma (HCC).International journal of molecular sciences · 2020Article
- Influenza A virus directly modulates mouse eosinophil responses.Journal of leukocyte biology · 2020Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
NF-Y is a trimeric transcription factor (TF), binding the CCAAT box element, for which several results suggest a pioneering role in activation of transcription. In this work, we integrated 380 ENCODE ChIP-Seq experiments for 154 TFs and cofactors with sequence analysis, protein-protein interactions and RNA profiling data, in order to identify genome-wide regulatory modules resulting from the co-association of NF-Y with other TFs. We identified three main degrees of co-association with NF-Y for sequence-specific TFs. In the most relevant one, we found TFs having a significant overlap with NF-Y in their DNA binding loci, some with a precise spacing of binding sites with respect to the CCAAT box, others (FOS, Sp1/2, RFX5, IRF3, PBX3) mostly lacking their canonical binding site and bound to arrays of well spaced CCAAT boxes. As expected, NF-Y binding also correlates with RNA Pol II General TFs and with subunits of complexes involved in the control of H3K4 methylations. Co-association patterns are confirmed by protein-protein interactions, and correspond to specific functional categorizations and expression level changes of target genes following NF-Y inactivation. These data define genome-wide rules for the organization of NF-Y-centered regulatory modules, supporting a model of distinct categorization and synergy with well defined sets of TFs.
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