| 2010 |
FOXA1 is a key determinant of estrogen receptor (ER) chromatin binding: nearly all ER-chromatin interactions and ER-dependent gene expression changes depend on FOXA1 presence, and FOXA1 influences genome-wide chromatin accessibility. In tamoxifen-resistant cells, ER binding is independent of ligand but still depends on FOXA1. CTCF was identified as an upstream negative regulator of FOXA1-chromatin interactions. |
ChIP-seq, siRNA knockdown of FOXA1, gene expression analysis, chromatin accessibility assays |
Nature genetics |
High |
21151129
|
| 2019 |
FOXA1 class-1 wing-2 domain mutations enhance chromatin mobility and binding frequency, strongly transactivating a luminal androgen-receptor program. Class-2 C-terminal truncation mutations increase DNA affinity for dominant chromatin binding and promote WNT pathway-driven metastasis via TLE3 inactivation. Class-3 genomic rearrangements reposition a conserved regulatory element (FOXMIND) to drive FOXA1 or other oncogene overexpression. |
Aggregate cohort genomic analysis, functional assays in cell lines, live-cell imaging for chromatin mobility, ChIP-seq |
Nature |
High |
31243372
|
| 2019 |
FOXA1 wing-2 domain mutations confer gain of function in pioneer activity, promoting exaggerated pro-luminal differentiation; R219 mutations at the DNA-contact residue block luminal differentiation and activate a neuroendocrine/mesenchymal program by preferentially binding a non-canonical DNA motif (GTAAAG/A instead of canonical GTAAAC/T). All tested mutants showed gain-of-function in prostate organoid proliferation. |
ATAC-seq, mouse prostate organoid proliferation assays, luciferase reporter assays, ChIP-seq, mutagenesis of 14 FOXA1 variants |
Nature |
High |
31243370
|
| 2020 |
LSD1 (KDM1A) associates with FOXA1 and demethylates FOXA1 at lysine-270 (adjacent to wing-2 region of the DNA-binding domain), positively regulating FOXA1 chromatin binding. LSD1 inhibition globally disrupts FOXA1 chromatin binding and consequently androgen receptor binding and transcriptional output. |
Co-IP, in vitro demethylation assay, ChIP-seq, mutagenesis of K270, in vivo xenograft models |
Nature genetics |
High |
32868907
|
| 2021 |
EZH2 methylates FOXA1 at lysine-295; this methylation is recognized by WD40-repeat protein BUB3, which recruits USP7 deubiquitinase to remove ubiquitination and stabilize FOXA1 protein, thereby promoting prostate cancer cell cycle gene regulation and growth. |
Co-IP, in vitro methylation assay, ubiquitination assay, ChIP-seq, cell proliferation assays, mutagenesis |
Science advances |
High |
33827814
|
| 2023 |
SETD7 methylates FOXA1 at lysine-270 (the same site demethylated by LSD1), acting as the primary methyltransferase that disrupts FOXA1-mediated transcription, functioning as a tumor suppressor in castration-resistant prostate cancer. |
In vitro methylation assay, ChIP-seq, gene expression profiling, loss-of-function studies in prostate cancer cells |
Proceedings of the National Academy of Sciences of the United States of America |
High |
37549269
|
| 2014 |
FOXA1 controls AR cistrome by opening chromatin around FKHD sites to recruit AR to low-affinity half-AREs. Too much FOXA1 creates excessive open chromatin that sequesters AR, reducing its availability; FOXA1 downregulation releases AR to permissively bind AREs genome-wide, enabling androgen-independent AR activity. Thus FOXA1 acts both as AR facilitator and inhibitor depending on expression level. |
ChIP-seq, FOXA1 knockdown/overexpression, gene expression analysis, androgen-independent growth assays |
Nature communications |
High |
24875621
|
| 2016 |
FOXA1 associates with DNA repair complexes and is required for genomic targeting of DNA polymerase β (POLB). This FOXA1-DNA repair complex mediates local DNA demethylation at FOXA1-bound regions in a lineage-specific fashion, coupling DNA demethylation to transcriptional pioneering and estrogen receptor genomic targeting. |
Co-IP, ChIP-seq, whole-genome DNA methylome sequencing, FOXA1 overexpression/depletion, POLB ChIP-seq |
Nature genetics |
High |
27500525
|
| 2016 |
FOXA1 induces TET1 expression by direct binding to its cis-regulatory elements, and physically interacts with TET1 protein through its CXXC domain. TET1 co-occupies FOXA1-dependent enhancers to mediate local DNA demethylation and H3K4 methylation in a feed-forward loop that potentiates FOXA1 recruitment. |
ChIP-seq, Co-IP, gene expression analysis, TET1 knockdown, bisulfite sequencing |
Nucleic acids research |
High |
27257062
|
| 2014 |
SUMOylation of FOXA1 at K6, K389, and K267 regulates its nuclear mobility and transcriptional activity with AR. SUMO-2/3 modification occurs on endogenous FOXA1 in prostate cancer cells. FOXA1 slows nuclear mobility of agonist-bound AR; mutation of SUMO sites further retards FOXA1 mobility and enhances chromatin occupancy and AR-regulated PSA locus activity. |
SUMOylation assays in COS-1 cells, FRAP with mCherry-FOXA1 and EGFP-AR in HEK293, ChIP, gene expression in LNCaP cells, site-directed mutagenesis |
Molecular endocrinology |
High |
25127374
|
| 2023 |
FOXA1 forms submicron-sized condensates through its N- and C-terminal intrinsically disordered regions (IDRs). Both IDRs enable FOXA1 to dissolve condensed chromatin. The DNA-binding capacity contributes to both condensate formation and condensed chromatin dissolution. IDRs are required for genome-wide binding and unpacking of condensed chromatin to regulate breast cancer cell proliferation and migration. |
Live-cell imaging, in vitro condensate assays, ATAC-seq, IDR deletion mutagenesis, functional proliferation/migration assays |
Molecular cell |
High |
38101414
|
| 2021 |
FOXA1 is reprogrammed from androgen-receptor (AR) regulatory elements to neuroendocrine (NE)-specific regulatory elements in treatment-emergent neuroendocrine prostate cancer (NEPC). NEPC requires FOXA1 for proliferation and NE lineage gene expression. Ectopic expression of NE lineage TFs ASCL1 and NKX2-1 in prostate adenocarcinoma cells reprograms FOXA1 to NE regulatory elements. |
ChIP-seq (histone modifications), FOXA1 knockdown in NEPC, ectopic TF expression, patient-derived xenograft profiling |
Nature communications |
High |
33785741
|
| 2019 |
FOXA1 overexpression drives genome-wide enhancer reprogramming through superenhancers in endocrine-resistant breast cancer, activating prometastatic transcriptional programs. HIF-2α was identified as the top high-FOXA1-induced superenhancer target mediating prometastatic effects. |
ChIP-seq, H3K27ac profiling, FOXA1 overexpression, gene expression analysis, functional migration/invasion assays, HIF-2α antagonist treatment |
Proceedings of the National Academy of Sciences of the United States of America |
High |
31826955
|
| 2021 |
FOXA1 binds the STAT2 DNA-binding domain and suppresses STAT2 DNA-binding activity and interferon signaling gene expression in prostate and breast cancer cells, independently of FOXA1 transactivation activity and cancer-associated mutations. |
Co-IP, ChIP, gene expression analysis, FOXA1 overexpression/knockdown, IFN signaling reporter assays |
The Journal of clinical investigation |
High |
34101624
|
| 2020 |
JQ1 directly interacts with FOXA1 and inactivates FOXA1 binding to its interacting repressors TLE3, HDAC7, and NFIC in a BET-independent manner, thereby blocking FOXA1-repressive function and activating invasion genes in prostate cancer. |
Co-IP, ChIP-seq, gene expression analysis, invasion assays, direct binding assay |
The Journal of clinical investigation |
High |
31874106
|
| 2023 |
O-GlcNAcylation of FOXA1 at Thr432, Ser441, and Ser443 regulates FOXA1 protein stability and chromatin assembly, and reshapes the FOXA1 interactome by recruiting methyl-CpG binding protein 2 (MeCP2), redirecting FOXA1 chromatin-binding sites to adhesion-related gene loci to promote breast cancer metastasis. |
Mass spectrometry identification of O-GlcNAc sites, site-specific mutagenesis, Co-IP/interactome analysis, ChIP-seq, in vitro and in vivo metastasis assays |
Science advances |
High |
37595040
|
| 2012 |
FoxA1 depletion causes significant redistribution of both androgen receptor (AR) and glucocorticoid receptor (GR) cistromes in prostate cancer cells in a cell-type- and receptor-specific manner. GR regulates many genes considered AR pathway-specific, and ligand-occupied GR attenuates AR-dependent transcription in the presence of androgen. |
ChIP-seq (AR and GR cistromes), FOXA1 knockdown, gene expression analysis |
Cancer research |
High |
23269278
|
| 2009 |
FoxA1 forms a tripartite interaction with ERα and HDAC7 required for estrogen-mediated repression of RPRM (Reprimo). FoxA1 recruits to the RPRM promoter (marked by H3K4me1/me2) and interacts with HDAC7; estrogen treatment causes decreases in H3K4me1/me2 and release of RNA polymerase II from the RPRM promoter. |
Co-IP, ChIP, siRNA knockdown, gene expression analysis |
Molecular and cellular biology |
High |
19917725
|
| 2024 |
NSD2 H3K36 dimethyltransferase is a requisite subunit of the AR/FOXA1 neo-enhanceosome in prostate cancer: tumor-specific AR enhancers bear a chimeric FOXA1:AR half-motif and critically depend on NSD2 activity. NSD2 inactivation disrupts >65% of the AR cistrome. |
ChIP-seq, NSD2 CRISPR/siRNA knockdown, PROTAC degradation, patient specimen enhancer mapping, gene expression analysis |
Nature genetics |
High |
39251788
|
| 2024 |
Covalent small molecules bind FOXA1 at cysteine C258 within the forkhead DNA-binding domain in a DNA-dependent manner, rapidly remodeling FOXA1 pioneer activity by redistributing FOXA1 binding across the genome and changing chromatin accessibility, likely by relaxing canonical DNA-binding preference and strengthening interactions with suboptimal sequences near C258. |
Chemical proteomics, covalent ligand synthesis, ChIP-seq, ATAC-seq, motif analysis, site-directed mutagenesis |
Molecular cell |
High |
39413792
|
| 2010 |
FOXA1 is required for hormone-induced mammary ductal invasion and terminal end bud formation, and is necessary for ERα expression in the mammary gland and breast cancer cell lines. Foxa1 null glands maintain GATA3 expression but lose ERα, demonstrating that FOXA1 regulates ERα expression but not GATA3 in a hierarchical manner. |
Foxa1 conditional knockout mouse model, immunohistochemistry, Western blot, siRNA knockdown in breast cancer cell lines |
Development (Cambridge, England) |
High |
20501593
|
| 2018 |
FOXA1 induces homodimerization upon binding a compact palindromic DNA element (DIV - diverging half-sites) with strongly positive cooperativity; this homodimerization is constrained by precise half-site spacing and is required for full FOXA1-dependent transcriptional activity. FOXA1 DIV sites show increased chromatin accessibility upon PI3K inhibition. |
EMSA, reporter assays, ChIP-seq re-analysis, structural modeling, SNP allelic analysis |
Nucleic acids research |
Medium |
29669022
|
| 2023 |
FOXA1 targets stable, DNase-resistant nucleosomes using lower nucleoplasmic diffusion and longer residence times to scan compact chromatin, distinct from SOX2 (higher diffusion, shorter residence) and HNF4A (which scans compact chromatin inefficiently). Both pioneer factors target stable nucleosomes whereas the non-pioneer HNF4A targets open chromatin. |
Single-molecule tracking (live-cell imaging), DNase-seq, comparison of multiple TFs |
Cell reports |
High |
37405916
|
| 2016 |
FOXA1 and HDAC2 bind the Slug promoter and directly repress its transcription, acting downstream of NOR1. FOXA1 induces E-cadherin expression in mesenchymal breast cancer cells by suppressing Slug expression; FOXA1 knockdown in epithelial cells upregulates Slug and reduces E-cadherin protein. |
ChIP, Co-IP, luciferase reporter assay, siRNA knockdown, Western blot |
Oncotarget |
Medium |
26934447 28867731
|
| 2016 |
FOXA1 acts as a dual-function transcription factor in ER-negative breast cancer: its repressive function on RELB is mediated by recruitment of corepressor TLE3. FOXA1 regulates ErbB2 signaling genes and is itself regulated transcriptionally by ErbB2 signaling components CREB1, c-Fos, and AP2α. |
ChIP, Co-IP, gene expression analysis, siRNA knockdown |
Neoplasia |
Medium |
22577344
|
| 2021 |
NEDD4 E3 ubiquitin ligase physically interacts with FOXA1, triggers FOXA1 ubiquitination and proteasomal degradation, promoting colon cancer progression. |
Co-IP, ubiquitination assay, luciferase reporter, CHX chase for protein stability |
RNA biology |
Medium |
33530829
|
| 2020 |
ZFP91 ubiquitin ligase ubiquitinates and destabilizes FOXA1 protein, promoting cancer cell growth; ZFP91 knockdown reduces FOXA1 polyubiquitination and enhances cellular sensitivity to chemotherapy in gastric cancer. |
Co-IP, ubiquitination assay, protein stability assay, ZFP91 knockdown |
Carcinogenesis |
Medium |
31046116
|
| 2022 |
CREB5 physically interacts with FOXA1, AR, and other co-factors (GRHL2, HOXB13, TBX3, NFIC) at transcription regulatory elements active in metastatic castration-resistant prostate cancer; CREB5 overexpression extensively reprograms nuclear protein-protein interactions in response to enzalutamide and promotes AR-targeted therapy resistance. |
ChIP-seq, rapid immunoprecipitation and mass spectrometry of endogenous proteins (RIME), gene expression analysis |
eLife |
High |
35550030
|
| 2014 |
FOXA1 physically interacts with androgen receptor (AR) in endometrial cancer cells. FOXA1 and AR co-bind the promoter and enhancer regions upstream of MYC. FOXA1 activates downstream AR targets (XBP1, MYC, ZBTB16, UHRF1) and promotes Notch pathway activation (Notch1, Hes1) in an AR-dependent manner to drive cell proliferation. |
Co-immunoprecipitation, ChIP-PCR, siRNA/shRNA knockdown, overexpression, xenograft model |
BMC cancer |
Medium |
24512546
|
| 2022 |
FOXA1 functions as the primary orchestrator of alternative splicing dysregulation in prostate cancer by binding regulatory regions of splicing-related genes including HNRNPK and SRSF1, controlling trans-acting factor expression to calibrate alternative splicing via an exon definition mechanism. |
ChIP-seq, RNA-seq across 500 prostate cancer transcriptomes, functional knockdown, splicing assays |
Cell reports |
High |
36170835
|
| 2020 |
FOXA1 wing-2 mutations in breast cancer display increased chromatin binding at ER loci upon estrogen stimulation and enhanced ER-mediated transcription without changes in chromatin accessibility. The breast cancer-specific SY242CS mutation opens distinct chromatin regions, activates an alternative cistrome and transcriptome, and structurally mediates stable binding to a non-canonical DNA motif. |
ATAC-seq, ChIP-seq, structural modeling, breast cancer patient cohort analysis, functional assays |
Cancer cell |
High |
32888433
|
| 2024 |
FOXA1 mediates repression of NR3C1 (GR gene) expression via the corepressor TLE3. FOXA1 occupancy at pre-accessible chromatin restricts GR chromatin binding in prostate cancer cells; silencing FOXA1 potentiates GR chromatin binding and transcriptional activity counterintuitively to the classical pioneer factor model. |
ChIP-seq, siRNA knockdown of FOXA1, GR ChIP-seq, gene expression analysis |
Nucleic acids research |
High |
38015476
|
| 2015 |
Nuclear receptor SHP inhibits transcriptional activation of BHMT and cystathionine γ-lyase by FOXA1, identified through ChIP showing SHP-FOXA1 interactions at these metabolic gene loci, establishing FOXA1 as a direct transcriptional activator of homocysteine metabolism genes regulated by SHP. |
ChIP, RNA-seq, metabolomics, SHP-null mouse model |
Gastroenterology |
Medium |
25701738
|
| 2019 |
FOXA1 chromatin accessibility is regulated by DNA hypermethylation (silencing FOXA1 in basal bladder cancer) and by allelic loss; conditional inactivation of Foxa1 and PTEN in luminal/intermediate bladder cells in mice drives squamous differentiation and enhanced carcinogen sensitivity, establishing FOXA1 as a maintainer of urothelial identity. |
Conditional mouse knockout, bisulfite methylation analysis, DNMT inhibitor treatment, carcinogen challenge model |
Oncogene |
Medium |
31636388
|
| 2017 |
FOXA1 directly binds the PLOD2 promoter and activates PLOD2 transcription in lung cancer cells, acting downstream of the EGFR-PI3K/AKT signaling axis to promote NSCLC metastasis through collagen reorganization. |
ChIP, luciferase reporter assay, siRNA knockdown, orthotopic metastasis mouse model |
Cell death & disease |
Medium |
29072684
|
| 2019 |
Chromatin structure and nucleosome compaction dramatically influence TDG-mediated removal of 5-formylcytosine (5fC) from DNA. FOXA1 differentially regulates TDG activity on chromatin, providing direct experimental evidence that FOXA1 pioneer factor activity modulates active DNA demethylation through TDG at enhancers. |
In vitro reconstituted nucleosome array assays with chemically defined 5fC, TDG activity assay, FOXA1 addition experiments |
Journal of the American Chemical Society |
High |
31460763
|
| 2017 |
Twist1 binds to the FOXA1 proximal promoter and recruits the NuRD transcriptional repressor complex to de-acetylate H3K9 and repress RNA polymerase II recruitment, thereby silencing FOXA1 expression. Twist1 also inhibits AP-1 recruitment to the FOXA1 promoter. Silencing of FOXA1 by Twist1 is largely responsible for Twist1-induced migration, invasion and metastasis. |
ChIP, Co-IP, luciferase reporter assay, xenograft mouse model, gain/loss-of-function experiments |
Oncogene |
High |
27524420
|
| 2017 |
FOXA1 inhibits PIK3R1 (PI3Kp85) transcription directly, suppressing PI3K/Akt signaling and hepatocellular carcinoma cell viability and motility in male patients. |
ChIP, luciferase reporter, gain/loss-of-function in HCC cell lines, clinical sample analysis |
Journal of experimental & clinical cancer research |
Medium |
29208003
|
| 2005 |
Foxa1 and Foxa2 have compensatory roles in lung morphogenesis; combined deletion inhibits cell proliferation, epithelial differentiation, and branching. Foxa1 and Foxa2 regulate Shh and Shh-dependent genes in respiratory epithelial cells, influencing mesenchymal gene expression required for branching. |
Foxa2 conditional knockout / Foxa1 null double-mutant mouse model, morphological analysis, gene expression |
The Journal of biological chemistry |
High |
15668254
|
| 2014 |
Conditional deletion of both Foxa1 and Foxa2 (but not Foxa2 alone) from adult dopamine neurons causes striatal dopamine depletion, loss of DAT and AADC expression, decline of Aldh1a1, and progressive dopamine neuron loss resembling Parkinson's disease. |
Tamoxifen-inducible tissue-specific CreERT2 knockout (DATCreERT2), immunohistochemistry, dopamine HPLC, behavioral assays |
Frontiers in cellular neuroscience |
Medium |
25249938
|
| 2021 |
Foxa1 and Foxa2 are required to regulate RNA splicing during positive selection of mouse T cells; their deletion reduces CD4SP and CD8SP T cell development. They control expression of splicing factors (Mbnl1, Sf3b1, Hnrnpa1, etc.) and alter >850 differentially used exons. |
Conditional double knockout mouse model, RNA-seq splicing analysis, gene expression |
Development (Cambridge, England) |
Medium |
34323272
|
| 2015 |
FOXA1 depletion abrogates ~41% of the AR-variant (AR-V) transcriptome in CRPC cells and attenuates AR-V chromatin binding at co-regulated genes, demonstrating that AR-Vs depend on FOXA1 as a pioneer factor for sustaining a pro-proliferative gene signature. |
FOXA1 knockdown, RNA-seq/gene expression profiling, ChIP, cell proliferation assays in CWR22Rv1 |
Oncotarget |
Medium |
26336819
|
| 2015 |
EAF2 co-immunoprecipitates with FOXA1 and downregulates FOXA1 protein levels; EAF2 knockdown enhances FOXA1 protein expression and AR target gene expression, cell proliferation, and migration in prostate cancer cells, which is reversed by FOXA1 knockdown. |
Co-IP, protein stability assay, C. elegans RNAi screen, siRNA knockdown, luciferase reporter, BrdU proliferation assay |
The Prostate |
Medium |
25808853
|
| 2014 |
FOXA1 repression in BRCA1-deficient breast cancer is mediated by EZH2-dependent H3K27me3 deposition and DNMT-mediated promoter methylation. BRCA1 binds EZH2 and negatively regulates its methyltransferase activity; BRCA1 loss enables EZH2/DNMT1/3a/3b-mediated epigenetic silencing of FOXA1. |
ChIP, Co-IP, siRNA knockdown of BRCA1 and EZH2, 5-aza-dC treatment, GSK126 (EZH2 inhibitor) treatment, Brca1-deficient mouse mammary epithelial cells |
Oncogene |
High |
25531315
|
| 2017 |
Pioneer factors FOXA1 and FOXA2 are required for initiation of NKX2-1-negative mucinous lung adenocarcinomas and for activation of their gastric differentiation program. Sequential in vivo recombination shows that FoxA1/2 loss in established KRAS-driven neoplasia drives keratinizing squamous cell carcinoma, demonstrating that FOXA1/2 maintain gastric identity and suppress squamous identity downstream of NKX2-1 loss. |
Conditional mouse knockout, sequential in vivo recombination, gene expression, IHC |
eLife |
High |
30475207
|
| 2022 |
FoxA1/2 knockout in NKX2-1-positive KRAS-driven LUAD causes collapse of a dual pulmonary/gastrointestinal identity state by inducing aberrant NKX2-1 genomic relocalization that actively inhibits tumorigenesis and drives alternative non-proliferative identity programs. |
Conditional CRISPR/genetic knockout in GEMMs and human cell lines, ChIP-seq, RNA-seq, ATAC-seq |
Developmental cell |
High |
35835117
|
| 2010 |
Foxa2 directly binds genomic regions of Gli2 and likely regulates Gli2 expression to attenuate Shh signaling in the ventral midbrain. Foxa1 and Foxa2 positively regulate Shh expression and negatively regulate Gli2 expression to specify ventral midbrain progenitor identity. |
ChIP, conditional knockout in mice (Wnt1cre;Foxa2flox/flox), gain- and loss-of-function studies |
Mechanisms of development |
Medium |
21093585
|
| 2017 |
Pioneer factors FOXA1 and FOXA2 assist selective glucocorticoid receptor (GR) signaling by enabling GR recruitment to the LEFTY1 promoter in human endometrial cells; glucocorticoid-mediated GR recruitment to LEFTY1 depends on FOXA1 and FOXA2, and E2 antagonizes this by reducing recruitment of GR, FOXA1, FOXA2, and active polymerase 2. |
ChIP, siRNA knockdown of FOXA1/FOXA2, luciferase reporter, gene expression analysis in primary and immortalized endometrial cells |
Endocrinology |
Medium |
28938408
|
| 2022 |
FOXA1 repression in bladder cancers with squamous differentiation leads to loss of PD-L1 expression and intrinsic immunotherapy resistance; FOXA1 coordinately regulates lineage identity and immune checkpoint expression in urothelial cells. |
Integrated genomic analysis of human bladder cancer specimens, phylogenetic analysis, FOXA1 expression correlation with PD-L1 and immunotherapy response data |
Nature communications |
Medium |
36323682
|
| 2022 |
FOXA1 binds the imprinting control region of IGF2 and interacts with DNMT1, initiating DNMT1-mediated loss of imprinting (LOI) of IGF2 and autocrine IGF2 secretion in lung adenocarcinoma cells; FOXA1 also suppresses GBA1 expression through IGF2-enhanced ubiquitination to inhibit autophagic cell death. |
ChIP, Co-IP, siRNA knockdown, IGF2 neutralization, IGF1R inhibitor treatment, xenograft model |
Cell death & disease |
Medium |
35974000
|