The Forkhead Transcription Factor FOXM1 Controls Cell Cycle-Dependent Gene Expression through an Atypical Chromatin Binding Mechanism

Abstract

bThere are nearly 50 forkhead (FOX) transcription factors encoded in the human genome and, due to sharing a common DNA binding domain, they are all thought to bind to similar DNA sequences. It is therefore unclear how these transcription factors are targeted to specific chromatin regions to elicit specific biological effects. Here, we used chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate the genome-wide chromatin binding mechanisms used by the forkhead transcription factor FOXM1. In keeping with its previous association with cell cycle control, we demonstrate that FOXM1 binds and regulates a group of genes which are mainly involved in controlling late cell cycle events in the G 2 and M phases. However, rather than being recruited through canonical RYAAAYA forkhead binding motifs, FOXM1 binding is directed via CHR (cell cycle genes homology region) elements. FOXM1 binds these elements through protein-protein interactions with the MMB transcriptional activator complex. Thus, we have uncovered a novel and unexpected mode of chromatin binding of a FOX transcription factor that allows it to specifically control cell cycle-dependent gene expression. There are nearly 50 different forkhead transcription factors encoded in mammalian genomes, and these proteins all contain the conserved forkhead DNA binding domain (reviewed in references 1 and 2). Forkhead transcription factors are involved in controlling a wide range of biological processes and are aberrantly expressed or regulated in disease states, including cancer (reviewed in reference 2). However, due to sharing a common DNA binding domain, forkhead transcription factors are generally believed to bind to variations of the RYAAAYA motif. Hence, it is unclear how individual forkhead proteins are specifically recruited to the regulatory regions of different cohorts of target genes to control defined biological responses. One key process which is controlled by forkhead transcription factors is the cell cycle and, in particular, the G 2 -M transition. The initial links to G 2 -M control were made with the Saccharomyces cerevisiae forkhead protein Fkh2, which controls the temporal expression of a cluster of genes at this phase of the cell cycle (reviewed in reference 3). More recently, members of the FOXO and FOXM classes of forkhead transcription factors have been linked with controlling the same process in mammalian cells (4-6). In both cases, forkhead transcription factors coordinate the integration of signals from the cell cycle regulatory machinery to transcriptional outputs. This is exemplified by the links to the cell cycle regulated Polo-like kinase PLK1, which is recruited to cell cycle-regulated promoters through promoter elements bound by the forkhead transcription factors FOXM1 and Fkh2, albeit indirectly in the case of Fkh2 (7,8).In mammalian cells, the transcriptional control of a cluster of genes at the G 2 -M transition, is coordinated through promoter elements which typically contain CHR (cell cycle genes homology region) and...

Regulatory signatures of liver regeneration distilled by integrative analysis of mRNA, histone methylation, and proteomics

“…8A). It was previously reported that the CHR is bound by a complex of FOXM1, B-MYB, and MuvB (FOXM1-MMB), resulting in the expression of genes important for the progression of the G 2 /M phase of the cell cycle (26). Interestingly, by analyzing the microarray data, we found that Mybl2 (which encodes B-MYB), Lin9 (which is a component of the MuvB complex), and Foxm1 were transcriptionally up-regulated in the regenerating liver (Fig.…”

“…These results suggested the possibility that STAT3 enhanced the expression and activation of FOXM1, which activated the target genes in the regenerating liver by forming the FOXM1-MMB complex. Using the gene lists from the ChIP-seq experiments of LIN9 and B-MYB performed in proliferating HeLa cells (28) and FOXM1 in U2OS cells (26), a gene set enrichment analysis was performed to investigate whether the FOXM1 target genes were activated transcriptionally during the liver regeneration following PVBL. We found that these gene sets were indeed activated in the regenerating liver (Fig.…”

“…F, gene set enrichment analysis to test whether the FOXM1 target genes were randomly distributed or tended to occur toward the extremes of the list of genes that were differentially expressed during liver regeneration. The left panel shows the analysis using all FOXM1 target genes as a gene set; the middle shows the analysis using the genes with ChIP-seq peaks of FOXM1, LIN9, and B-MYB; and the right shows the analysis using the genes with only FOXM1 peaks (26). Enrichment score (ES), normalized enrichment score (NES), nominal p value (p), false discovery rate (q), and familywise error rate (FWER) are indicated.…”

Screen for multi-SUMO–binding proteins reveals a multi-SIM–binding mechanism for recruitment of the transcriptional regulator ZMYM2 to chromatin

“…ChIP-qPCR was performed at least in duplicate, from at least two independent experiments, and analyzed as described previously (20).…”

Fox transcription factors: from development to disease

“…Its forkhead DNA-binding domain (FHD) shares only 18% sequence identity with that of FoxA1, and FoxM1 has lower affinity for the forkhead consensus binding site than other Fox proteins (Littler et al, 2010). Some investigators have shown that, instead of directly interacting with the DNA of its proliferative targets, FoxM1 attaches to proteins in the DREAM complex -a larger conglomeration of proteins that prevents the transcription of proliferative targets in the quiescent state, but promotes expression of the same targets during the cell cycle (Chen et al, 2013). However, other reports have demonstrated direct binding of FoxM1 to its targets (Sanders et al, 2013).…”