Drought is the most important factor that limits rice production in drought-prone environments. Plant microRNAs (miRNAs) are involved in biotic and abiotic stress responses. Common wild rice (Oryza rufipogon Griff.) contains abundant drought-resistant genes, which provide an opportunity to explore these excellent resources as contributors to improve rice resistance, productivity, and quality. In this study, we constructed four small RNA libraries, called CL and CR from PEG6000-free samples and DL and DR from PEG6000-treated samples, where ‘R’ indicates the root tissue and ‘L’ indicates the shoot tissue. A total of 200 miRNAs were identified to be differentially expressed under the drought-treated conditions (16% PEG6000 for 24 h), and the changes in the miRNA expression profile of the shoot were distinct from those of the root. At the miRNA level, 77 known miRNAs, which belong to 23 families, including 40 up-regulated and 37 down-regulated in the shoot, and 85 known miRNAs in 46 families, including 65 up-regulated and 20 down-regulated in the root, were identified as differentially expressed. In addition, we predicted 26 new miRNA candidates from the shoot and 43 from the root that were differentially expressed during the drought stress. The quantitative real-time PCR analysis results were consistent with high-throughput sequencing data. Moreover, 88 miRNAs that were differentially-expressed were predicted to match with 197 targets for drought-stress. Our results suggest that the miRNAs of O. rufipogon are responsive to drought stress. The differentially expressed miRNAs that are tissue-specific under drought conditions could play different roles in the regulation of the auxin pathway, the flowering pathway, the drought pathway, and lateral root formation. Thus, the present study provides an account of tissue-specific miRNAs that are involved in the drought adaption of O. rufipogon.

Promoters play a very important role in the initiation and regulation of gene transcription. Green-tissue promoter is of great significance to the development of genetically modified crops. Based on RNA-seq data and RT-PCR expression analysis, this study screened a gene, OrGSE (GREEN SPECIAL EXPRESS), which is expressed specifically in green tissues. The study also isolated the promoter of the OrGSE gene (OrGSEp), and predicted many cis-acting elements, such as the CAAT-Box and TATA-Box, and light-responding elements, including circadian, G-BOX and GT1 CONSENSUS. Histochemical analysis and quantification of GUS activity in transgenic Arabidopsis thaliana plants expressing GUS under the control of OrGSEp revealed that this promoter is not only green tissue-specific, but also light-inducible. The ability of a series of 5’-deletion fragments of OrGSEp to drive GUS expression in Arabidopsis was also evaluated. We found that the promoter region from −54 to −114 is critical for the promoter function, and the region from −374 to −114 may contain core cis-elements involved in light response. In transgenic rice expressing GUS under the control of OrGSEp, visualization and quantification of GUS activity showed that GUS was preferentially expressed in green tissues and not in endosperm. OrGSEp is a useful regulatory element for breeding pest-resistant crops.

Common wild rice (Oryza rufipogon Griff.) is the most closely related ancestral species to Asian cultivated rice (Oryza sativa L.). It contains various valuable traits with regard to tolerance to cold, drought and salinity, flowering diversity and many quantitative trait loci with agronomic important traits. Flowering is one of the most important agronomic traits. However, flowering-related transcriptome and how to be regulated by miRNAs have not been estimated in O.rufipogon. To identify how the genes and miRNAs regulating flowering in O.rufipogon. Three O.rufipogon RNA libraries, two vegetative stages (CWRT-V1 and CWRT-V2) and one flowering stage (CWRT-F2) were constructed using leaves tissue and sequenced using Illumina deep sequencing. 27,405, 27,333, 28,979 unique genes were obtained after mapping to the reference genome from CWRT-V1, CWRT-V2 and CWRT-F2, respectively. Then differentially expressed genes (DEGs) were screened and got 1419 unique genes are likely to involve in flower development. Detailed information showed that MADS box and floral meristem identity genes, such as MADS 1, MADS14, Hd1 are involved in common wild rice. Then, combined analysis of miRNA and mRNA expression profiles was performed. Twenty three known miRNA-mRNA pairs and five new candidates were presented an anti-correlationship. Interestingly, 12 miRNAs were negatively correlated with 20 mRNAs encoding flowering-related proteins, indicating that miRNAs regulated target genes to promote flowering in CWRT-F2 group. The results provided here genomic resources for flowering related genes and how these flowering genes were regulated by miRNAs in common wild rice.

The repressive histone modification H3K27me3 plays a causal role in determining gene expression patterns.

Retrotransposons (RTEs), which comprise nearly half of the mammalian genome, are silenced in adult somatic tissues but can be reactivated by physiological stimuli and in diseases. Here, we focus on adult regenerative tissues, particularly blood and skin, where RTE regulation requires a delicate balance between maintaining faithful silencing and harnessing physiological RTE activity to support stem cell maturation, stress responses, and interactions with tissue niches, and excessive reactivation can lead to stem cell exhaustion and tissue dysfunction. We summarize studies of RE-derived nucleic acids that, when aberrantly activated, engage innate immune sensors and trigger antiviral responses, linking RTE activity to inflammatory disorders. We further review experimental evidence in cancer, where RTE reactivation creates a battleground between antiviral defense and immune evasion, and emerging evidence suggesting that RTEs may mediate communication between peripheral tissues and the hematopoietic system. Finally, while experimental evidence is promising, clinical studies targeting RTE activity have produced mixed outcomes. We therefore conclude by highlighting the need for deeper mechanistic investigations.