The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in <i>Arabidopsis</i>
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Bibliographic record
Abstract
Abstract In recent years, eukaryotic long non-coding RNAs (lncRNAs) have been identified as important factors involved in a wide variety of biological processes, including histone modification, alternative splicing and transcription enhancement. The expression of lncRNAs is highly tissue-specific and is regulated by environmental stresses. Recently, a large number of plant lncRNAs have been identified, but very few of them have been studied in detail. Furthermore, the mechanism of lncRNA expression regulation remains largely unknown. Arabidopsis HISTONE DEACETYLASE 6 (HDA6) and LSD1-LIKE 1/2 (LDL1/2) can repress gene expression synergistically by regulating H3Ac/H3K4me. In this research, we performed RNA-seq and ChIP-seq analyses to further clarify the function of HDA6-LDL1/2. Our results indicated that the global expression of lncRNAs is increased in hda6/ldl1/2 and that this increased lncRNA expression is particularly associated with H3Ac/H3K4me2 changes. In addition, we found that HDA6-LDL1/2 is important for repressing lncRNAs that are non-expressed or show low-expression, which may be strongly associated with plant development. GO-enrichment analysis also revealed that the neighboring genes of the lncRNAs that are upregulated in hda6/ldl1/2 are associated with various developmental processes. Collectively, our results revealed that the expression of lncRNAs is associated with H3Ac/H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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) | 0.000 | 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 it