Small RNAs (sRNAs) are a widespread and ancient form of gene and genome regulation. They are found in all eukaryotes (except those who have lost them…) and frequently play essential roles in transcriptional regulation, genomic integrity, and interactions between organisms.

MicroRNAs (miRNAs) are perhaps the best-studied (and best-understood) class of sRNAs and are also broadly found in eukaryotes. A large part of why we understand miRNAs so well is because of their relative simplicity to study. However, most organisms produce numerous other types of sRNAs which have received relatively little attention. In fact, most annotation software does not an-notate these features at all.

In fungi, this gap is more pronounced. Sequencing efforts have often only scraped the surface of the breadth of loci that are found in this kingdom. The wide phylogenetic diversity in fungi makes this even more challenging. The main aim of our laboratory is to utilize the wealth of publicly-available small-RNA-sequencing data (from over 60 species) to start to annotate the many types of small RNAs that these organisms produce. This includes exploring the definitions of known classes like miRNAs in fungi.

To do this, we are using available tools as well as developing our own to address challenges specific to fungi. We are interested in using these data tell how sRNAs evolve and function in fungi, explor-ing shared classes with relationships to fungal lifestyle. Fungi are known to use sRNAs in interac-tions with other organisms, but it is not clear to what degree this is conserved or common among these interactions.

Biography

Nathan is a Plant Biologist by training, with a background in computational biology. He received his B.S. from Michigan State University (Plant Biology, 2011) and a Ph.D. from Penn State University (Plant Biology, 2019) within the Huck Institutes for Life Sciences. There, he worked with Professor Mike Axtell, studying trans-species sRNAs in parasitic plants. In 2020, Nathan joined the Millennium Institute for Integrative Biology (iBio) in Chile as a Post-Doc, working with Professors Elena Vidal and Jose Alvarez, researching topics related to gene-regulatory-networks in plants and sRNAs in Fungi. In 2022, Nathan received a Fondecyt Iniciacion award (#11220727), focused on the topics of the sRNA genomics lab. Recently in 2022, he joined the CGB as a Professor Instructor and becoming an Assistant Professor in 2023.

Selected works

From this lab:

Melet, L., Canan, J., Villalobos, P., Vidal-Veuthey, B., González-Toro, F., Orellana, I., Rivas-Pardo, J.A., Cárdenas, J.P., Moraga, C., Castro-Fernandez, V., Johnson, N.R., Vidal, E.A. (2025). Clade-wide proteome analysis shows widespread non-canonical Dcr proteins in fungi. bioRxiv, 2025.04.28.651110.

Johnson, N.R., Gonzalez-Toro, F., and Gomez, B.B. (2025). Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms. Comput. Struct. Biotechnol. J.

Johnson, N.R., Larrondo, L.F., Álvarez, J.M., and Vidal, E.A. (2022). Comprehensive re-analysis of hairpin small RNAs in fungi reveals loci with conserved links. Elife 11.

Prior related works:

Lunardon, A., Johnson, N.R., Hagerott, E., Phifer, T., Polydore, S., Coruh, C., and Axtell, M.J. (2020). Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Genome Res. 30: 497–513.

Johnson, N.R., dePamphilis, C.W., and Axtell, M.J. (2019). Compensatory sequence variation be-tween trans-species small RNAs and their target sites. Elife 8.

Shahid, S., Kim, G., Johnson, N.R., Wafula, E., Wang, F., Coruh, C., Bernal-Galeano, V., Phifer, T., dePamphilis, C.W., Westwood, J.H., and Axtell, M.J. (2018). MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature 553: 82.

Johnson, N.R., Yeoh, J.M., Coruh, C., and Axtell, M.J. (2016). Improved Placement of Multi-Map-ping Small RNAs. G3: g3.116.030452.

Full list of publications

Link to google scholar