Research
Lines of investigation
• Large-scale annotation of sRNA producing loci in fungi and plants.
• Biology-led tool development for sequencing analysis.
• Data-mining of public data resources.
Small RNAs
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 annotate these features at all.
Lots to learn in fungi
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, exploring shared classes with relationships to fungal lifestyle. Fungi are known to use sRNAs in interactions with other organisms, but it is not clear to what degree this is conserved or common among these interactions.
This work recieved funding from the Fondecyt Iniciacion (#11220727) from ANID in Chile (2022-2025).
We are supported by the Millennium Institute for Integrative Biology (iBio) from ANID. (Young Investigator - Nate).
Research links
Github
Tools for internal and external use
Recent Publications
Nate's google scholar profile