title: Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells.
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.
authors.affiliation: Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore. ahutchins@ifrec.osaka-u.ac.jp
authors.forename: Andrew Paul
authors.initials: AP
authors.lastname: Hutchins
authors.forename: Siew Hua
authors.initials: SH
authors.lastname: Choo
authors.forename: Tapan Kumar
authors.initials: TK
authors.lastname: Mistri
authors.forename: Mehran
authors.initials: M
authors.lastname: Rahmani
authors.forename: Chow Thai
authors.initials: CT
authors.lastname: Woon
authors.forename: Calista Keow Leng
authors.initials: CK
authors.lastname: Ng
authors.forename: Ralf
authors.initials: R
authors.lastname: Jauch
authors.forename: Paul
authors.initials: P
authors.lastname: Robson
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D047369:Chromatin Immunoprecipitation; D057137:DAX-1 Orphan Nuclear Receptor / Q000235:genetics / Q000378:metabolism; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D005855:Germ Layers / Q000166:cytology / Q000254:growth & development / Q000378:metabolism*; D000090062:Kruppel-Like Factor 4; D051379:Mice; D008969:Molecular Sequence Data; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D025941:Protein Interaction Mapping; D011960:Receptors, Estrogen / Q000235:genetics / Q000378:metabolism*; D055748:SOXB1 Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D057137:DAX-1 Orphan Nuclear Receptor; C098925:Esrrb protein, mouse; C000715468:Klf4 protein, mouse; D000090062:Kruppel-Like Factor 4; C539966:Nr0b1 protein, mouse; D011960:Receptors, Estrogen; D055748:SOXB1 Transcription Factors; C527783:Sox2 protein, mouse; D004247:DNA