NF-Y Binding Site Architecture Defines a C-Fos Targeted Promoter Class

Abstract

ChIP-seq experiments detect the chromatin occupancy of known transcription factors in a genome-wide fashion. The comparisons of several species-specific ChIP-seq libraries done for different transcription factors have revealed a complex combinatorial and context-specific co-localization behavior for the identified binding regions. In this study we have investigated human derived ChIP-seq data to identify common cis-regulatory principles for the human transcription factor c-Fos. We found that in four different cell lines, c-Fos targeted proximal and distal genomic intervals show prevalences for either AP-1 motifs or CCAAT boxes as known binding motifs for the transcription factor NF-Y, and thereby act in a mutually exclusive manner. For proximal regions of co-localized c-Fos and NF-YB binding, we gathered evidence that a characteristic configuration of repeating CCAAT motifs may be responsible for attracting c-Fos, probably provided by a nearby AP-1 bound enhancer. Our results suggest a novel regulatory function of NF-Y in gene-proximal regions. Specific CCAAT dimer repeats bound by the transcription factor NF-Y define this novel cis-regulatory module. Based on this behavior we propose a new enhancer promoter interaction model based on AP-1 motif defined enhancers which interact with CCAAT-box characterized promoter regions.

Integrating Peak Colocalization and Motif Enrichment Analysis for the Discovery of Genome-Wide Regulatory Modules and Transcription Factor Recruitment Rules

“…Motif centered analysis on the NF-Y/FOS cobinding peaks identified a second binding motif for NF-Y, with the two CCAAT boxes located with precise spacing on DNA, hinting at two NF-Y molecules forming a complex with FOS (Dolfini et al, 2016;Zambelli and Pavesi, 2017). The same conclusion has been confirmed by independent studies, leading to the interesting hypothesis of a single complex connecting enhancers bound by JUN/FOS to a promoter bound by NF-Y (Haubrock et al, 2016).…”

The Plant NF-Y DNA Matrix In Vitro and In Vivo

“…The DNA sequence-specificity of mammalian NF-Y has been precisely assessed in vitro by saturation mutagenesis and SELEX studies (reviewed in Reference [9]), and later confirmed by ChIP-Seq experiments [3,22]. On the other hand, the selectivity of plant trimers has never been tested.…”

“…The binding of mammalian NF-Y to CCAAT was functionally dissected in numerous mutagenesis studies [9]; binding in vivo was assessed in genomic studies, including by the vast collection of transcription factor binding affinity profiles compiled by the ENCODE consortium [3,20,21,22]. It is quite clear that each nucleotide of the CCAAT box is mandatory for the association, but flanking nucleotides are also extremely important: Overall, a matrix of 10 bp, as originally proposed, turned out to be the target of NF-Y in vivo ([9], and all references therein).…”

Disentangling transcription factor binding site complexity

“…The first cluster follows the motif of NF-Y and the second cluster that of AP-1. Both motifs are known to be enriched in c-fos target regions ( 54 ). Such typical intermixtures that resemble the toy example of Figure 2 amount ∼50% of all cases with \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\hat{M}=2$\end{document} .…”