Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1

Abstract

The compaction of nucleosomal structures creates a barrier for DNA-binding transcription factors (TFs) to access their cognate cis-regulatory elements. Pioneer factors (PFs) such as FOXA1 are able to directly access these cis-targets within compact chromatin. However, how these PFs interplay with nucleosomes remains to be elucidated, and is critical for us to understand the underlying mechanism of gene regulation. Here, we have conducted a computational analysis on a strand-specific paired-end ChIP-exo (termed as ChIP-ePENS) data of FOXA1 in LNCaP cells by our novel algorithm ePEST. We find that FOXA1 chromatin binding occurs via four distinct border modes (or footprint boundary patterns), with a preferential footprint boundary patterns relative to FOXA1 motif orientation. In addition, from this analysis three fundamental nucleotide positions (oG, oS and oH) emerged as major determinants for blocking exo-digestion and forming these four distinct border modes. By integrating histone MNase-seq data, we found an astonishingly consistent, ‘well-positioned’ configuration occurs between FOXA1 motifs and dyads of nucleosomes genome-wide. We further performed ChIP-seq of eight chromatin remodelers and found an increased occupancy of these remodelers on FOXA1 motifs for all four border modes (or footprint boundary patterns), indicating the full occupancy of FOXA1 complex on the three blocking sites (oG, oS and oH) likely produces an active regulatory status with well-positioned phasing for protein binding events. Together, our results suggest a positional-nucleosome-oriented accessing model for PFs seeking target motifs, in which FOXA1 can examine each underlying DNA nucleotide and is able to sense all potential motifs regardless of whether they face inward or outward from histone octamers along the DNA helix axis.

RBPJ binds to consensus and methylated cis elements within phased nucleosomes and controls gene expression in human aortic smooth muscle cells in cooperation with SRF

“…When coupled with our observation that RBPJ binding was frequently observed at the edges of transcriptionally active chromatin regions, these findings suggest that RBPJ may have effects on chromatin state and/or be a reader of chromatin structure. Our demonstration that RBPJ binds to phased nucleosomes (See model in Figure 6E ) is similar to observations made for FOXA2 ( 46 , 47 ), GATA3 ( 48 ) and the progesterone receptor ( 49 ). Like these ‘pioneering’ transcription factors, RBPJ may be involved in recruiting positive remodelers to condensed chromatin.…”

Characterizing protein-DNA binding event subtypes in ChIP-exo data

“…ChExMix identifies three main subclasses in FoxA1 ChIP-exo data. The majority (24,749) of binding events are associated with a subtype that contains FoxA1's cognate DNA binding motif and a ChIP-exo tag distribution shape highly similar to that found in previous ChIP-exo analyses of FoxA transcription factors (Iwafuchi-Doi et al, 2016;Ye et al, 2016;Serandour et al, 2013) (Figure 5A, 5B; Figure S10A,B; Table S3). We thus label this the "direct binding" subtype.…”

“…We compared ChExMix performance in predicting human CTCF (Rhee and Pugh, 2011) and mouse FoxA2 (Iwafuchi-Doi et al, 2016) binding event locations to that of nine ChIP-exo analysis methods, including MultiGPS (Mahony et al, 2014), GEM (Guo et al, 2012), MACS2 (Zhang et al, 2008), MACE (Wang et al, 2014), PeakXus (Hartonen et al, 2016), Peakzilla (Bardet et al, 2013), Q-nexus (Hansen et al, 2016), DFilter (Kumar et al, 2013), and CexoR (Madrigal, 2015). We excluded ChIP-ePENS (Ye et al, 2016) from our evaluation because it requires paired-end ChIP-exo data. Both CTCF and FoxA2 ChIPexo datasets consist of single-end sequencing data.…”

The interaction landscape between transcription factors and the nucleosome

“…Third, the entry and exit of nucleosomal DNA are also close to the dyad; together with the dyad DNA, they provide a scaffold for specific configurations of TFs. FoxA has been suggested to make use of this scaffold to achieve highly specific positioning close to the dyad 20,78 ; this binding mode mimics that of the linker histones H1 and H5 79 . However, the dyad positioning of FoxA is not observed in this study using eDBD, potentially because the full length of FoxA is required for its interaction with the nucleosome 21 .…”