Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers

Reményi, Attila; Lins, Katharina; Nissen, L. Johan; Reinbold, Rolland; Schöler, Hans R.; Wilmanns, Matthias

doi:10.1101/gad.269303

Cited by 349 publications

(413 citation statements)

References 43 publications

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“…We built 1,250 homology models for Oct4 and Oct6 homodimers using MODELLER 9.17 (https://salilab.org/modeller/) and the following templates (referred by PDB ID): (i) 2xsd—crystal structure of Oct6 homodimer bound to MORE 42; (ii) 1e3o—crystal structure of Oct1 homodimer bound to MORE 17; (iii) 3l1p—crystal structure of Oct4 homodimer bound to a palindromic site different than MORE 44; (iv) 1gt0—crystal structure of the Oct1–Sox2–DNA ternary complex 21. We imposed symmetry restraints on Cα, Cβ, and Cγ atoms to enforce a similar structure of the two monomers.…”

Section: Methodsmentioning

confidence: 99%

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

Jerabek

et al. 2016

EMBO Reports

123

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The transcription factor Oct4 is a core component of molecular cocktails inducing pluripotent stem cells (iPSCs), while other members of the POU family cannot replace Oct4 with comparable efficiency. Rather, group III POU factors such as Oct6 induce neural lineages. Here, we sought to identify molecular features determining the differential DNA‐binding and reprogramming activity of Oct4 and Oct6. In enhancers of pluripotency genes, Oct4 cooperates with Sox2 on heterodimeric SoxOct elements. By re‐analyzing ChIP‐Seq data and performing dimerization assays, we found that Oct6 homodimerizes on palindromic OctOct more cooperatively and more stably than Oct4. Using structural and biochemical analyses, we identified a single amino acid directing binding to the respective DNA elements. A change in this amino acid decreases the ability of Oct4 to generate iPSCs, while the reverse mutation in Oct6 does not augment its reprogramming activity. Yet, with two additional amino acid exchanges, Oct6 acquires the ability to generate iPSCs and maintain pluripotency. Together, we demonstrate that cell type‐specific POU factor function is determined by select residues that affect DNA‐dependent dimerization.

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Section: Methodsmentioning

confidence: 99%

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

Jerabek

et al. 2016

EMBO Reports

123

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“…The complexity of an organ development is manifested through spatiotemporal expression of genes involved in development, which is tightly regulated to a large extent by the combination of transcription factors in multi-protein complexes (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13). In these processes, the binding affinity of transcription factors to their genetic elements, which is crucial for transcription activity, is modulated by cooperative binding: low inherent binding affinity of the individual factors is largely enhanced when they present together by their synergistic action.…”

Section: Introductionmentioning

confidence: 99%

“…One example that shows this plasticity and diverse combinatorial transcription activity is Sox2, which activates its downstream transcriptional targets by forming cooperative complex with various factors in each developmental stage. For example, it maintains pluripotency by partnering with various factors like Oct4 and Nanog (5,7,(11)(12), and controls neurogenesis and retinal developmental by forming complexes with Pax6 (7-10), Otx2 (11), Tlx (12) or Brn2 (13). Therefore, it is essential to investigate the dynamics of their cooperativity to understand functional intricacies involved in the process of transcription.…”

Section: Introductionmentioning

confidence: 99%

Examining Cooperative Binding of Sox2 on DC5 Regulatory Element Upon Complex Formation with Pax6 Through Excess Electron Transfer Assay

Saha¹

2018

Molecular Recognition of DNA Double Helix

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Functional cooperativity among transcription factors on regulatory genetic elements is pivotal for milestone decision-making in various cellular processes including mammalian development. However, their molecular interaction during the cooperative binding cannot be precisely understood due to lack of efficient tools for the analyses of protein-DNA interaction in the transcription complex. Here, we demonstrate that photoinduced excess electron transfer assay can be used for analysing cooperativity of proteins in transcription complex using cooperative binding of Pax6 to Sox2 on the regulatory DNA element (DC5 enhancer) as an example. In this assay, Br U-labelled DC5 was introduced for the efficient detection of transferred electrons from Sox2 and Pax6 to the DNA, and guanine base in the complementary strand was replaced with hypoxanthine (I) to block intra-strand electron transfer at the Sox2-binding site. By examining DNA cleavage occurred as a result of the electron transfer process, from tryptophan residues of Sox2 and Pax6 to DNA after irradiation at 280 nm, we not only confirmed their binding to DNA but also observed their increased occupancy on DC5 with respect to that of Sox2 and Pax6 alone as a result of their cooperative interaction.

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“…As these are less likely to occur randomly in genomic sequence, they offer a means by which binding specificity may arise between TFs and regulatory elements. Composite motifs have been discovered for numerous TF complexes, including FOX : ETS [9], SOX : OCT [10,11] and HOX : PBX [12], a classic example of TF cooperativity. The characteristic spacings within these elements reflect the unique structural mechanisms by which each complex cooperatively binds DNA.…”

Section: Introductionmentioning

confidence: 99%

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

Guturu

Doxey

Wenger

et al. 2013

Phil. Trans. R. Soc. B

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Mapping the DNA-binding preferences of transcription factor (TF) complexes is critical for deciphering the functions of cis -regulatory elements. Here, we developed a computational method that compares co-occurring motif spacings in conserved versus unconserved regions of the human genome to detect evolutionarily constrained binding sites of rigid TF complexes. Structural data were used to estimate TF complex physical plausibility, explore overlapping motif arrangements seldom tackled by non-structure-aware methods, and generate and analyse three-dimensional models of the predicted complexes bound to DNA. Using this approach, we predicted 422 physically realistic TF complex motifs at 18% false discovery rate, the majority of which (326, 77%) contain some sequence overlap between binding sites. The set of mostly novel complexes is enriched in known composite motifs, predictive of binding site configurations in TF–TF–DNA crystal structures, and supported by ChIP-seq datasets. Structural modelling revealed three cooperativity mechanisms: direct protein–protein interactions, potentially indirect interactions and ‘through-DNA’ interactions. Indeed, 38% of the predicted complexes were found to contain four or more bases in which TF pairs appear to synergize through overlapping binding to the same DNA base pairs in opposite grooves or strands. Our TF complex and associated binding site predictions are available as a web resource at http://bejerano.stanford.edu/complex .

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Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers

Cited by 349 publications

References 43 publications

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

Examining Cooperative Binding of Sox2 on DC5 Regulatory Element Upon Complex Formation with Pax6 Through Excess Electron Transfer Assay

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements

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