Analysis of Neil DNA glycosylases during early Xenopus development
Bibliographic record
Abstract
DNA demethylation plays an important role in development and vertebrate physiology. In active DNA demethylation, 5-methylcytosine (5mC) is iteratively oxidized into 5-hydroxylmethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-caboxylcytosine (5caC) by Ten-eleven-translocation (TET) enzymes. Subsequently, 5fC and 5caC are removed by Thymine DNA glycosylase (TDG) and base excision repair (BER) proteins. In vitro data indicate that Nei-like (NEIL) glycosylases play a crucial role in this context by increasing the enzymatic turnover of TDG in BER. In the first part of my thesis, I analyzed the role of Tet3, Tdg, and especially Neil proteins in active DNA demethylation in Xenopus laevis embryos. Expression analysis showed that tet3, tdg, neil1 and neil3 are expressed during the embryonic development of the central nervous system. Neil2 mRNA is maternally supplied, and its expression level is decreased drastically upon zygotic genome activation (ZGA). Analysis of 5mC and its oxidative derivatives by mass spectrometry supports the cooperation of Tet3, Tdg, and Neil2 in active DNA demethylation in vivo. Antisense Morpholino (MO) knockdown of Tet3, Tdg, Neil2 and Neil3 induces neural crest defects and microcephaly. In the second part of my thesis, I examined the mechanisms leading to the neural crest cell (NCC) defects and microcephaly phenotypes of neil2 MO injected embryos (Neil2 morphants). Whole transcriptome analysis and qPCR expression analysis show that the Tp53 DNA damage pathway is activated in Neil2 morphants. In Neil2 morphant neural plates, pS345 Chk1, Tp53, and active caspase-3 accumulate during NCC differentiation. Knockdown of Tp53 reduces apoptotic cell death and rescues microcephaly in Neil2 morphants. Neural crest defects and microcephaly are recapitulated by treating embryos with the reactive oxygen species (ROS) inducer pyocyanin. This treatment upregulates protein levels of pS345 Chk1, Tp53, and active caspase-3, and activates expression of Tp53 target genes. Pyocyanin and neil2 MO injection show synergistic effects in inducing microcephaly. Furthermore, Neil2 morphants display craniofacial abnormalities, mimicking Treacher-Collins-Syndrome. In summary, my study demonstrates a novel role of Neil2 in cooperation with Tet3 and Tdg in active DNA demethylation during Xenopus embryogenesis. In addition, Neil2 deficiency elicits an oxidative stress-induced, Tp53-dependent DNA damage response, which impairs NCC differentiation. My work emphasizes how defects in BER can lead to a selective lineage defect during embryogenesis.
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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".