Conserved sex-biased DNA methylation patterns target key developmental genes and non-recombining region of the guppy sex chromosome
Bibliographic record
Abstract
ABSTRACT Understanding the regulatory mechanisms that control sexually dimorphic gene expression is a key part of understanding the processes that govern the rate of sex chromosome evolution and phenotypic sex differences. Epigenetic modifications play a major role in tissue-specific gene expression regulation and have been hypothesized to dramatically impact the speed of sex chromosome divergence. The guppy sex chromosomes are an emerging model for studying the initial stages of divergence between the X and Y. In this study, we use comparative epigenomics to identify conserved sex-specific DNA methylation patterns in gonad and muscle tissue between the Trinidadian guppy ( Poecilia reticulata ) and its sister species, Endler’s guppy ( Poecilia wingei ). We find that the oldest part of the guppy sex chromosome shows a conserved pattern of male hypomethylation, consistent with a key role in testis-specific gene expression. This pattern provides a potential mechanism for theoretical predictions that sex chromosome divergence can occur remarkably quickly in evolutionary time, and without widespread degradation of the Y chromosome gene content. Our cross-species comparative epigenomic analysis also provides a robust comparative framework to understand constraints of epigenetic programming. We observe conserved, testis-specific hypomethylated regions near key autosomal developmental genes and a potentially imprinted locus. These observations are consistent with DNA methylation in testis from other vertebrates, and suggest broad conservation of DNA methylation patterns in these regions. Our comparative framework reveals conserved DNA methylation differences between males and females across two related species, providing novel insights into the relationship between epigenetic and evolutionary processes.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 | 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) | 0.002 | 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".