@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} }
 @article{furgurson_loschin_butoto_abugu_gillespie_brown_ferraro_speicher_stokes_budnick_et al._2023, title={Seizing the policy moment in crop biotech regulation: an interdisciplinary response to the Executive Order on biotechnology}, volume={11}, ISSN={["2296-4185"]}, DOI={10.3389/fbioe.2023.1241537}, abstractNote={North Carolina State University Forestry and Environmental Resources, Raleigh, NC, United States, North Carolina State University Genetic Engineering and Society Center, Raleigh, NC, United States, North Carolina State University Applied Ecology, Raleigh, NC, United States, North Carolina State University Crop and Soil Sciences, Raleigh, NC, United States, North Carolina State University Horticultural Science, Raleigh, NC, United States, North Carolina State University Entomology and Plant Pathology, Raleigh, NC, United States, North Carolina State University Food, Bioprocessing and Nutrition Sciences, Raleigh, NC, United States, North Carolina State University Agricultural and Resource Economics, Raleigh, NC, United States, North Carolina State University Communication, Rhetoric, and Digital Media, Raleigh, NC, United States, North Carolina State University Biochemistry, Raleigh, NC, United States, North Carolina State University Plant Biology, Raleigh, NC, United States, North Carolina State University Anthropology, Raleigh, NC, United States}, journal={FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY}, author={Furgurson, Jill and Loschin, Nick and Butoto, Eric and Abugu, Modesta and Gillespie, Christopher J. and Brown, Rebekah and Ferraro, Greg and Speicher, Nolan and Stokes, Ruthie and Budnick, Asa and et al.}, year={2023}, month={Aug} }