title: Genome wide features, distribution and correlations of NF-Y binding sites.
abstract: NF-Y is a trimeric transcription factor that binds on DNA the CCAAT-box motif. In this article we reviewed and complemented with additional bioinformatic analysis existing data on genome-wide NF-Y binding characterization in human, reaching the following main conclusions: (1) about half of NF-Y binding sites are located at promoters, about 60-80 base pairs from transcription start sites; NF-Y binding to distal genomic regions takes place at inactive chromatin loci and/or DNA repetitive elements more often than active enhancers; (2) on almost half of its binding sites, regardless of their genomic localization (promoters or distal regions), NF-Y finds on DNA more than one CCAAT-box, and most of those multiple CCAAT binding loci present precise spacing and organization of the elements composing them; (3) there exists a well defined class of transcription factors that show genome-wide co-localization with NF-Y. Some of them lack their canonical binding site in binding regions overlapping with NF-Y, hence hinting at NF-Y mediated recruitment, while others show a precise positioning on DNA of their binding sites with respect to the CCAAT box bound by NF-Y. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
authors: Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy; Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Via Amendola 165/A, 70126, Italy.
authors: Federico
authors: F
authors: Zambelli
authors: Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Via Celoria 26, 20133, Italy. Electronic address: giulio.pavesi@unimi.it.
authors: Giulio
authors: G
authors: Pavesi
mesh_terms: D023081:CCAAT-Binding Factor / Q000235:genetics / Q000378:metabolism*; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D055106:Genome-Wide Association Study; D006367:HeLa Cells; D006801:Humans; D020014:K562 Cells; D020218:Response Elements / Q000502:physiology*
chemical_list: D023081:CCAAT-Binding Factor; D002843:Chromatin
keywords: CCAAT box; ChIP-Seq; NF-Y; Transcription regulation