PMID:23169531

Citation	Hutchins, AP, Choo, SH, Mistri, TK, Rahmani, M, Woon, CT, Ng, CK, Jauch, R and Robson, P (2013) Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells. Stem Cells 31:269-81
Abstract	Transcription factors (TF) often bind in heterodimeric complexes with each TF recognizing a specific neighboring cis element in the regulatory region of the genome. Comprehension of this DNA motif grammar is opaque, yet recent developments have allowed the interrogation of genome-wide TF binding sites. We reasoned that within this data novel motif grammars could be identified that controlled distinct biological programs. For this purpose, we developed a novel motif-discovery tool termed fexcom that systematically interrogates ChIP-seq data to discover spatially constrained TF-TF composite motifs occurring over short DNA distances. We applied this to the extensive ChIP-seq data available from mouse embryonic stem cells (ESCs). In addition to the well-known and most prevalent sox-oct motif, we also discovered a novel constrained spacer motif for Esrrb and Sox2 with a gap of between 2 and 8 bps that Essrb and Sox2 cobind in a selective fashion. Through the use of knockdown experiments, we argue that the Esrrb-Sox2 complex is an arbiter of gene expression differences between ESCs and epiblast stem cells (EpiSC). A number of genes downregulated upon dual Esrrb/Sox2 knockdown (e.g., Klf4, Klf5, Jam2, Pecam1) are similarly downregulated in the ESC to EpiSC transition and contain the esrrb-sox motif. The prototypical Esrrb-Sox2 target gene, containing an esrrb-sox element conserved throughout eutherian and metatherian mammals, is Nr0b1. Through positive regulation of this transcriptional repressor, we argue the Esrrb-Sox2 complex promotes the ESC state through inhibition of the EpiSC transcriptional program and the same trio may also function to maintain trophoblast stem cells.
Links	PubMed Online version:10.1002/stem.1279
Keywords	Algorithms; Animals; Base Sequence; Chromatin Immunoprecipitation; DAX-1 Orphan Nuclear Receptor/genetics; DAX-1 Orphan Nuclear Receptor/metabolism; DNA/genetics; DNA/metabolism; Embryonic Stem Cells/cytology; Embryonic Stem Cells/metabolism; Gene Expression Regulation, Developmental; Germ Layers/cytology; Germ Layers/growth & development; Germ Layers/metabolism; Mice; Molecular Sequence Data; Protein Binding; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Receptors, Estrogen/genetics; Receptors, Estrogen/metabolism; SOXB1 Transcription Factors/genetics; SOXB1 Transcription Factors/metabolism; Transcription, Genetic
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
MOUSE:ERR2	enables	GO:0003700: DNA-binding transcription factor activity	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
MOUSE:ERR2	enables	GO:0043565: sequence-specific DNA binding	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
MOUSE:ERR2	involved_in	GO:0019827: stem cell population maintenance	ECO:0000315: mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
MOUSE:SMAD1	enables	GO:0043565: sequence-specific DNA binding	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
MOUSE:SOX2	enables	GO:0003700: DNA-binding transcription factor activity	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete
MOUSE:SOX2	involved_in	GO:0019827: stem cell population maintenance	ECO:0000315: mutant phenotype evidence used in manual assertion		P		Seeded From UniProt	complete
MOUSE:SOX2	enables	GO:0043565: sequence-specific DNA binding	ECO:0000314: direct assay evidence used in manual assertion		F		Seeded From UniProt	complete

References

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