@article{utley_edwards_budnick_grotewold_sederoff_2024, title={Camelina circRNA landscape: Implications for gene regulation and fatty acid metabolism}, volume={12}, ISSN={["1940-3372"]}, url={https://doi.org/10.1002/tpg2.20537}, DOI={10.1002/tpg2.20537}, abstractNote={Circular RNAs (circRNAs) are closed-loop RNAs forming a covalent bond between their 3' and 5' ends, the back splice junction (BSJ), rendering them resistant to exonucleases and thus more stable compared to linear RNAs. Identification of circRNAs and distinction from their cognate linear RNA is only possible by sequencing the BSJ that is unique to the circRNA. CircRNAs are involved in the regulation of their cognate RNAs by increasing transcription rates, RNA stability, and alternative splicing. We have identified circRNAs from C. 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 3447 circRNAs from 2763 genes. Most circRNAs originate from a single homeolog of the three subgenomes from allohexaploid camelina and correlate 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.}, journal={PLANT GENOME}, author={Utley, Delecia and Edwards, Brianne and Budnick, Asa and Grotewold, Erich and Sederoff, Heike}, year={2024}, month={Dec} }
 @article{budnick_franklin_utley_edwards_charles_hornstein_sederoff_2024, title={Long- and short-read sequencing methods discover distinct circular RNA pools in <i>Lotus japonicus</i>}, volume={1}, ISSN={["1940-3372"]}, url={https://doi.org/10.1002/tpg2.20429}, DOI={10.1002/tpg2.20429}, abstractNote={AbstractCircular RNAs (circRNAs) are covalently closed single‐stranded RNAs, generated through a back‐splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high‐confidence circRNA‐expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.}, journal={PLANT GENOME}, author={Budnick, Asa and Franklin, Megan J. and Utley, Delecia and Edwards, Brianne and Charles, Melodi and Hornstein, Eli D. and Sederoff, Heike}, year={2024}, month={Jan} }
 @misc{gakpo_hardwick_ahmad_choi_matus_mugisa_ethridge_utley_zarate_2024, title={The need for communication between researchers and policymakers for the deployment of bioengineered carbon capture and sequestration crops}, volume={8}, ISSN={["2571-581X"]}, DOI={10.3389/fsufs.2024.1329123}, abstractNote={Bioengineered/genome-edited carbon capture and sequestration (BE/GEd-CCS) crops are being developed to mitigate climate change. This paper explores how technology, regulation, funding, and social implications, could shape the development and deployment of these crops. We conclude that some of the technological efforts to create BE/GEd-CCS crops may work. Still, stakeholders must agree on generally accepted methods of measuring how much carbon is captured in the soil and its value. The regulatory space for BE/GEd-CCS crops remains fluid until the first crops are reviewed. BE/GEd-CCS crops have received considerable initial funding and may benefit financially more from other federal programs and voluntary carbon markets. BE/GEd-CCS crops may continue perpetuating social equity concerns about agricultural biotechnology due to a lack of oversight. We argue that stakeholders need to pursue a multidisciplinary view of BE/GEd-CCS crops that draw in varying perspectives for effective development and deployment. Communication is needed between researchers and policymakers involved in either developing BE/GEd-CCS crops or developing voluntary carbon markets. We argue for the start of a conversation both across disciplines and between researchers and policymakers about the development and deployment of BE/GEd-CCS crops.}, journal={FRONTIERS IN SUSTAINABLE FOOD SYSTEMS}, author={Gakpo, Joseph Opoku and Hardwick, Andrew and Ahmad, Jabeen and Choi, Jaimie and Matus, Salvador Cruz and Mugisa, Jill Dana and Ethridge, Sandra and Utley, Delecia and Zarate, Sebastian}, year={2024}, month={Jan} }