ANNOUNCEMENTS
Non-coding RNAs (ncRNAs) have become important controls on how genes are expressed, especially in reaction to stressful situations. A good system to research the functional roles of ncRNAs in stress responses is the model plant A. thaliana. We present a manually curated database titled "Manually Curated Database for Stress-Associated Non-Coding RNAs in Arabidopsis thaliana" to aid in a thorough study in this field. The database contains a large number of long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) that are related to stress. It offers a useful tool for researchers to investigate the various regulatory processes mediated during stress adaptation in A. thaliana by these ncRNAs.
A user-friendly database interface was created along with data preparation, RNA-seq data reanalysis, stress-specificity scores determination, and literature mining as part of the process. Relevant data on stress-related ncRNAs were acquired and reliability and consistency were assured through comprehensive literature investigation and data pre-processing. The study found distinct expression patterns of ncRNAs under various stress situations by re-analyzing existing RNA-seq data and small RNA-seq data, with 953 and 267 samples. 3,482 (27.34%) of the 12,734 lncRNAs that were examined for mapping were successfully mapped. 3,369 of them (96.75%) showed varied expression in response to different stress samples.
The connection of identified ncRNAs with stressful situations was further assessed by the determination of stress-specificity scores. The stress-responsive matrix score (SRMS) of 1,825 lncRNAs surpassed 0.90, indicating that they were responsive to stress. Notably, 18 lncRNAs showed a stress-responsive matrix value of 1, and 691 lncRNAs had scores higher than 0.99. These results highlight the significant stress responsiveness of lncRNAs as a whole and point to potential regulatory activities that could be further investigated in future studies.
