The double identity of NF-Y: a transcription factor with an histone code

Transcription is governed by DNA-binding proteins that recognize specific sequences in regulatory regions, in the context of chromatin. Histone tails have a plethora of different post-translational modifications which can influence the establishment of other epigenetic marks. Associated with the establishment of active chromatin, H2B K120 mono-ubiquitination is required for H3K4me3 and H3K79me2 methylations. One of the most widespread promoter elements is the CCAAT box, bound by the NF-Y trimer. Two of NF-Y subunits have an H2A-H2B-like structure. By using a NF-Y DNA-binding dominant negative we established the causal relationship between NF-Y binding and positioning of methyl marks: the decrease of NF-Y binding in CCAAT promoters leads to a decrease of H3K4me3, H3K79me2, a removal of components of the H3K4 methylating MLL complex and a transcriptional repression. The H2B-like subunit of NF-Y is mono-ubiquitinated in vivo in Lysine 140 of the histone fold domain, which structurally corresponds to the H2B K120. Micrococcal nuclease Re-ChIP assays allowed the separation of NF-Y-Ub, in promoters, from H2B-Ub in transcribed areas. A NF-YBK140R mutant causes an impaired deposition of H3K4m3 and H3K79m2 in CCAAT box promoters and transcriptional repression of NF-Y targets genes, acting as a dominant negative. We propose a scenario whereby NF-Y is a variant sequence-specific histone a-la-H2B that marks transcription units containing the CCAAT recognition sequence, making chromatin locally accessible to the histone modifying machines that would account for further modifications.