Nuclear exclusion of AID limits off target activity by enforcing productive targeting
Bibliographic record
Abstract
Activation induced deaminase (AID) is an enzyme that deaminates deoxycitidine to deoxyuridine on single stranded DNA.AID expression is mostly restricted to antigen activated B-lymphocytes, wherein its activity is critical for both somatic hypermutation (SHM) and class-switch recombination (CSR), which underpin secondary antibody diversification.This is due to the targeted activity of AID at the immunoglobulin (Ig) genes, which encode for the antibody genes.DNA deamination catalyzed by AID initiates the generation of single point mutations for SHM, and double stranded breaks for CSR, both potentially harmful lesions.Importantly, multiple mechanisms regulate AID in order to limit its off-target activity, outside the Ig loci, which has been found to be potentially oncogenic and cytotoxic.For my thesis, I used structure-function studies of AID in order to better understand post-translational regulation of its activity.In a first chapter, evolutionary comparison and structure-function analyses revealed that a structural conformation of a C-terminal domain of AID was required for its association to eEF1A1, which mediated the retention of AID in the cytoplasm.Mutations that disrupted AID cytoplasmic retention, or pharmacological inhibition of eEF1A1, caused AID to accumulate in the nucleus and to generate more mutations on-and off-target.This demonstrated that eEF1A1-dependent retention of AID in the cytoplasm was necessary to restrict its activity.In a second chapter, a structure-function study of AID identified a domain dispensable for its catalytic activity, but critical for SHM and CSR activity in B cells.iii Mutants of this domain were able to functionally distinguish the recruitment of AID to the chromatin from its mutagenic activity in B cells.This revealed that at the chromatin AID requires a licensing step in order to associate with the elongating transcription machinery, and become mutagenic.Interestingly, this licensing is bypassed when AID is forced to accumulate in the nucleus.In a third chapter, studies of the C-terminal region of AID further clarified its role during CSR.This study identified a structural requirement of the C-terminus during CSR, downstream from DNA deamination.This study supports a role for AID, via the Cterminus, to recruit other factors during CSR, likely to mediate proper DNA repair.All together, these studies highlight the intricate regulation of AID activity in B cells.They also suggest that preventing accumulation of AID in the nucleus limits offtarget activity by enforcing a regulatory licensing step at the chromatin.
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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 | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".