TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation
Bibliographic record
Abstract
Abstract Cis -regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce Transposase-Accessible Chromosome Conformation Capture (TAC-C), a method integrating ATAC-seq and Hi-C to capture fine-scale chromatin interactions in four major crops: rice, sorghum, maize, and wheat. TAC-C reveals that chromatin interaction frequency aligns with genome size and gene expression, exhibiting distinct loop structures between C3 and C4 plants, particularly in C4-specific enzymes coding genes. Integrating chromatin structure with population genetics data highlights that chromatin loops connect distal regulatory elements to phenotypic variation. Asymmetrical open chromatin interactions among subgenomes, driven by transposon insertions and sequence variations, contribute to biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through chromatin interactions, with enhanced photosynthetic efficiency and starch content in Taspl7&15 mutant. TAC-C provides new insights into the spatial organization of regulatory elements in crops, especially for SPL-mediated photosynthesis regulation in wheat. Teaser TAC-C Reveals Chromatin Interactions and SPL-Mediated Photosynthesis Regulation in Crops.
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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) | 0.002 | 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".