Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors

Abstract

Cell type-specific master transcription factors (TFs) play vital roles in defining cell identity and function. However, the roles ubiquitous factors play in the specification of cell identity remain underappreciated. Here we show that the ubiquitous CCAAT-binding NF-Y complex is required for the maintenance of embryonic stem cell (ESC) identity and is an essential component of the core pluripotency network. Genome-wide studies in ESCs and neurons reveal that NF-Y regulates not only genes with housekeeping functions through cell type-invariant promoter-proximal binding, but also genes required for cell identity by binding to cell type-specific enhancers with master TFs. Mechanistically, NF-Y's distinct DNA-binding mode promotes master/pioneer TF binding at enhancers by facilitating a permissive chromatin conformation. Our studies unearth a conceptually unique function for histone-fold domain (HFD) protein NF-Y in promoting chromatin accessibility and suggest that other HFD proteins with analogous structural and DNA-binding properties may function in similar ways.

Figure 1. Genomic profiling of NF-YA, NF-YB, and NF-YC binding sites in mouse ESCs

(A) ChIP-Seq read density plot showing NF-YA, NF-YB, and NF-YC occupancy near TSSs of all mouse RefSeq genes. (B) Genome browser shots showing NF-YA, NF-YB, and NF-YC occupancy at gene promoters. (C) ChIP-qPCR validation of the NF-Y occupancy at sites highlighted in (B). Error bars represent S.E.M. of three experiments. (D) Consensus sequence motifs enriched within NF-YA, NF-YB, and NF-YC sites using de novo motif analysis. (E) Overlap among NF-YA, NF-YB, and NF-YC sites (peaks). (F) Genome-wide distribution of the NF-Y sites (union of the NF-YA, NF-YB, and NF-YC sites). Promoter, 500 bp upstream of TSS. (G) Correlation between gene expression levels and NF-Y occupancy near TSSs. See also Figure S1.

Figure 2. NF-Y co-occupies enhancers with ESC-specific master TFs

(A) Frequency distribution of NF-Y sites within 1 kb of TSSs. (B) Proximity of NF-Y sites to TSSs. (C) Levels of DNase I hypersensitivity, H3K4me1, H3K27ac, and H3K4me3 near proximal and distal NF-Y sites. (D) Hi-C interaction density near proximal and distal NF-Y sites. (E) TF binding motifs enriched within distal vs proximal NF-Y sites. CTCF is not enriched at either set of NF-Y sites. (F) Co-occupancy between ESC TFs (Chen et al., 2008; Ho et al., 2011; Ma et al., 2011; Marson et al., 2008) and NF-Y at distal and proximal sites. (G) Gene ontology categories enriched among distal and proximal NF-Y target genes.

Figure 3. NF-Y binds to and regulates core ESC self-renewal and pluripotency genes

(A–B) Genome browser shots showing NF-Y co-occupancy with master ESC TFs (Chen et al., 2008; Ma et al., 2011; Marson et al., 2008) at the enhancers of ESC identity genes (A), and at the promoters/enhancers of differentiation/developmental genes (B). (C) Western blot analysis of NF-YA, NF-YB, and NF-YC in NF-YA knockdown (KD), NF-YB KD, NF-YC KD, or NF-Y triple KD (TKD; KD of all three NF-Y subunits) ESCs 96h after siRNA transfection. Ran is used as a loading control. (D) RT-qPCR analysis of relative mRNA levels of ESC identity genes (left), and differentiation markers (right) in NF-YA KD, NF-YB KD, NF-YC KD, and NF-Y TKD ESCs compared to control KD ESCs 96h after siRNA transfection. Data normalized to Actin, HAZ, and TBP. Error bars, SEM. See also Figure S2.

Figure 4. NF-Y is required for ESC self-renewal and is an essential component of the core pluripotency network

(A) Morphology and alkaline phosphatase staining of NF-YA KD, NF-YB KD, NF-YC KD, and NF-Y TKD ESCs 96h after siRNA transfection. (B) Co-immunostaining of NF-YA and Nanog (left)/NF- YC (right) in control and NF-YA KD ESCs 96h after siRNA transfection. Nuclei counterstained by DAPI. (C) RT-qPCR analysis of relative mRNA levels of differentiation markers in NF-YA KD, NF-YB KD, NF-YC KD, and NF-Y TKD ESCs compared to control KD ESCs 96h after siRNA transfection. Data normalized to Actin, HAZ, and TBP. Error bars, SEM. (D) Number of genes up- and down-regulated in NF-Y TKD ESCs 96h after siRNA transfection, and percent of those that are also bound by NF-Y. (E) Gene expression fold changes upon NF-YA KD, NF-YB KD, NF-YC KD, or NF-Y TKD, measured 96h after siRNA transfection. Experiments performed in triplicates. Only genes that were differentially expressed (FDR ≤ 0.05 and fold change ≥ 2) in NF-Y TKD are shown. (F) Relative gene expression changes of NF-Y regulated genes during the normal course of embryoid body formation (day 14) compared to undifferentiated ESCs. NF-Y regulated genes, ordered as in Figure 4E, were grouped into 50 bins. (G) Principal component analysis of gene expression profiles showing NF-YA KD, NF-YB KD, NF-YC KD, and NF-Y TKD ESCs (all in red) alongside differentiation of ESCs into three different lineages (Nishiyama et al., 2009). Z0–Z5, trophoblast lineage (ESCs differentiating into trophoblast cells from day 0 to day 5; purple); N0–N6, neural lineage (ESCs differentiating into neural lineage from day 0 to day 6; orange); F0–F5, primitive endoderm (PE; embryonal carcinoma cells differentiating into PE from day 0 to day 5; green); ESCs, white; Control KD ESCs, black; A, NF-YA KD; B, NF-YB KD; C, NF-YC KD; ABC, NF-Y TKD. (H) Correlation between global gene expression changes upon NF-YA KD, NF-YB KD, NF-YC KD, and NF-Y TKD and those observed after KD or knockout (KO) of other ESC-associated factors, as previously reported. Rows/columns ordered based on unsupervised hierarchical clustering. TKD, Triple KD; WD, Withdrawal. See also Figures S3 and S4.

Figure 5. NF-Y binding at enhancers is cell type-specific, whereas NF-Y binding at promoters is cell type-invariant

(A) Overlap among NF-Y sites in ESCs (red), neural progenitor cells (NPCs; green), and neurons (blue). (B) Panther pathway enrichment analysis of proximal and distal NF-Y target genes in ESCs and neurons. (C) ChIP-qPCR analysis of NF-YA sites in undifferentiated ESCs and differentiating ESCs (induced by retinoic acid, 96h). Error bars, SEM. (D) Sequence motifs, other than that of NF-Y’s, enriched within distal NF-Y sites in ESCs or neurons, identified using de novo motif analysis. (E) Nanog and CTCF (ENCODE, GSE49847) co-occupancy at promoter-proximal and ESC-specific (red) and neuron-specific (purple) distal NF-Y binding sites. (F) TF occupancy (ChIP-Seq read density) near ESC-specific and neuron-specific distal NF-Y sites in ESCs and neurons. (G) Levels of active enhancer marks H3K4me1 and H3K27ac, and repressive mark H3K27me3 near ESC-specific and neuron-specific distal NF-Y binding sites in ESCs (Creyghton et al., 2010; Ho et al., 2011) and neurons (ENCODE, GSE49847). (H) Model for NF-Y mediated transcriptional regulation of housekeeping and cell identity genes. See also Figures S5 and S6.

Figure 6. Oct4/Sox2 binding is dependent on NF-Y

(A) DNase I hypersensitivity, as measured by DNase-Seq (ENCODE, GSE37074), at distal binding sites for various TFs in ESCs. (B) Nucleosome occupancy, as measured by MNase-Seq (Teif et al., 2012), at distal binding sites for various TFs in ESCs. (C) Brg1 occupancy at distal Brg1 sites colocalized with NF-Y (purple), distal Brg1-only sites (orange), distal NF-Y sites colocalized with Brg1 (cyan). (D) Oct4/Sox2/Nanog/Prdm14 (X) occupancy (Ma et al., 2011; Marson et al., 2008) at distal X sites colocalized with NF-Y (purple), distal X-only sites (orange), and distal NF-Y only sites (blue). (E) NF-Y occupancy at distal NF-Y sites colocalized with X (purple), distal NF-Y only sites (blue), and distal X-only sites (orange). (F) Co-immunoprecipitation and western blot analysis showing NF-YC and Oct4 co-immunoprecipitating with Oct4 and NF-YC, respectively. As a positive control, NF-YC and NF-YA, two subunits of NF-Y complex, co-immunoprecipitates with NF-YA and NF-YC, respectively. (G) Western blot analysis of NF-YA, NF-YC, Oct4, and Sox2 in NF-YA KD ESCs 48h after siRNA transfection. Ran used as a loading control. (H) ChIP-qPCR analysis of sites co-bound by Oct4/Sox2 and NF-Y (purple) or bound by Oct4/Sox2 but not NF-Y (orange) in control or NF-YA KD ESCs. Error bars, SEM. See also Figure S7.

Figure 7. NF-Y facilitates Oct4/Sox2 binding by promoting chromatin accessibility

(A) DNase I hypersensitivity (ENCODE, GSE37074) at NF-Y dependent (purple) and independent (orange) Oct4/Sox2/Nanog/Prdm14 sites in ESCs. (B) DNase I and qPCR analysis of NF-Y dependent and NF-Y independent Oct4/Sox2 sites in ESCs. Error bars, SEM. (C) Nucleosome occupancy (Teif et al., 2012) at NF-Y dependent (purple) and independent (orange) Oct4/Sox2/Nanog/Prdm14 sites in ESCs. (D–E) DNase I and qPCR analysis of NF-Y dependent (D) and NF-Y independent (E) Oct4/Sox2 sites (n = 3) in control and NF-YA KD ESCs. Error bars, SEM. (F) ChIP-qPCR analysis of NF-Y dependent (purple) and NF-Y independent (orange) Oct4/Sox2 sites in Control and NF-YA KD ESCs. Error bars, SEM. (G) Proposed model for NF-Y mediated chromatin accessibility. See also Figure S7.