Structural characterization of DNA binding and autoinhibition by the Ets1 transcription factor
Bibliographic record
Abstract
Ets1 belongs to the ETS transcription factor family and plays key roles in regulating eukaryotic gene expression. The affinity of the Ets1 for its cognate DNA sites is autoinhibited by an intrinsically disordered serine-rich region (SRR) and an appended helical inhibitory module (IM). Through transient interactions, the SRR both sterically blocks the ETS domain and allosterically stabilizes the IM to modulate DNA-binding affinity. Calmodulin-dependent kinase II phosphorylation of five serines within the SRR progressively reinforces autoinhibition in response to calcium signaling. Using mutagenesis and quantitative DNA-binding measurements, we demonstrate that phosphorylation-enhanced autoinhibition requires the presence of phenylalanine/tyrosine (ϕ) residues adjacent to the SRR phosphoacceptor serines. The introduction of additional phosphorylated Ser-ϕ-Asp, but not Ser-Ala-Asp, repeats within the SRR dramatically reinforces autoinhibition. NMR spectroscopic studies of phosphorylated and mutated SRR variants, both within their native context and as separate trans-acting peptides, confirmed that the aromatic residues and phosphoserines contribute to the formation of a dynamic complex with the ETS domain. Complementary NMR studies also identified the SRR-interacting surface of the ETS domain, which encompasses its positively-charged DNA recognition interface and an adjacent region of neutral polar and nonpolar residues. Collectively, these studies highlight the role of aromatic residues and their synergy with phosphoserines in an intrinsically disordered regulatory sequence that integrates cellular signaling and gene expression. We also investigated by NMR spectroscopy the interaction of Ets1 with specific and nonspecific oligonucleotides. Upon binding DNA, helices HI-1 and HI-2 of the IM unfold. Thus, autoinibition does not impart DNA-binding specificity. Using amide chemical shift perturbation mapping, we also show that Ets1 binds both specific and non-specific oligonucleotides through its canonical ETS domain interface. However, the non-specific complex is formed by weak and dynamic electrostatic interactions, whereas the specific complex involves well-ordered hydrogen bonds and salt bridges. In support of this conclusion, five lysine sidechains are protected from rapid hydrogen exchange upon binding of specific DNA, whereas only one is stabilized in the non-specific complex. Overall, these data are consistent with Ets1 rapidly finding specific DNA sites within the genome via facilitated diffusion (sliding and hopping) within a vast background of non-specific sequences.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".