Biology subjects

Utley, D.

Publications and source records attributed to Utley, D..

3 recordsLinked to original sources

bioRxiv2026

Identification of Potential Regulatory Non-Coding RNAs in Lotus Japonicus Symbiosis

O_LISymbiosis between legumes and rhizobia is beneficial on nutrient-poor soils, as it enables the fixation of atmospheric N2. To establish this symbiosis, gene expression in both the host plant and the symbiont has to be regulated. To understand the underlying RNA-mediated regulation of host gene expression, we designed experiments to identify competing endogenous networks involving circular RNA, microRNA, and linear transcripts during symbiosis, using wt and symbiosis-deficient Lotus japonicus mutants with the rhizobium Mesorhizobium loti (M. loti). C_LIO_LICircRNA, miRNA, and linear transcripts were identified from Lotus japonicus wildtype and CCamK mutant (ccamk-13; snf-1) seedlings without inoculation or with M. loti inoculation using deep short-read sequencing with rRNA-depletion and random primers. C_LIO_LIDifferentially expressed miRNAs showed negative correlations to predicted target genes and may regulate symbiotic processes. The symbiosis essential iron-sensor LjnsRING/BRUTUS expresses a circRNA which was upregulated in symbiotic treatments. This circRNA may act as a target mimic and contribute to nodule longevity. CircRNAs are predicted to act predominantly as trans-regulatory molecules with similar frequencies in Arabidopsis thaliania, Oryza sativa, and Lotus japonicus. C_LIO_LIWe identified novel miRNAs, long noncoding RNAs, and circRNAs, and nominated several as potential new regulatory non-coding RNAs that may act as target mimics to stabilize genes and support symbiosis. C_LI SummarySymbiosis between Lotus japonicus and Mesorhizobium loti involves treatment-specific regulation of competing endogenous RNA networks involving circular RNA, miRNA, and linear transcripts.

plant biology↗

bioRxiv2025

Circular RNAs in Lotus japonicus Responses to Nutrient Supply and Symbiotic Interactions

Symbiotic relationships, such as those formed between legumes and rhizobia or arbuscular mycorrhizal (AM) fungi, function by enhancing the nutrient uptake into the plant. The establishment and coordination of the symbiotic interactions requires changes in gene expression in the host and microbe. Circular RNAs (circRNAs) can function through sponging of microRNAs (miRNAs), resulting in changes in transcript abundances. We identified 15,252 unique nuclear circRNAs in Lotus japonicus under different nutrient conditions and symbiotic interactions with rhizobia or AMF. Our results revealed treatment-specific circRNAs and circRNAs originating from key genes in the Common Symbiosis Pathway, suggesting their potential role in the establishment of these symbioses. We validated select circRNAs potentially involved in the regulation of symbiosis and predicted miRNA recognition elements (MREs) that were only created by the backsplice junction of circRNAs. Backsplice-generated MREs represent an additional mechanism through which circRNAs may modulate abundances and translation of mRNAs. Our sequencing approach using random hexamer primers also enabled us to simultaneously characterize the transcriptome of the symbionts and host.

plant biology↗

bioRxiv2024

Camelina CircRNA Landscape: Implications for Gene Regulation and Fatty Acid Metabolism

Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3 and 5 ends, the backsplice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from its cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in regulation of their cognate RNAs by increasing transcription rates, RNA stability and alternative splicing. We have identified circRNAs from Camelina sativa that are associated with the regulation of germination, light response, and lipid metabolism. We sequenced light-grown and etiolated seedlings after 5 or 7 days post-germination and identified a total of 3,447 circRNAs from 2,763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlates with higher ratios of alternative splicing of their cognate genes. A network analysis shows the interactions of select miRNA:circRNA:mRNAs for regulation of transcript stabilities where circRNA can act as a competing endogenous RNA. Several key lipid metabolism genes can generate circRNA and we confirmed the presence of KASII circRNA as a true circRNA. CircRNA in camelina can be a novel target for breeding and engineering efforts. Core ideasO_LIFirst discovery of 3,447 genic and 307 intergenic unique putative circRNAs from Camelina sativa. C_LIO_LIWe identified circRNAs that were regulated in response to seedling de-etiolation. C_LIO_LIMost circRNAs originate from only one homeolog of the three subgenomes in this allohexaploid Camelina. C_LIO_LIAlternative splicing of exon skipping and intron retention positively correlate with circRNA occurrence. C_LIO_LIValidation of KASII circRNAs as an example of lipid metabolism pathways potentially regulated by circRNA. C_LI

plant biology↗