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The Versatile Small RNAs in the Unicellular Microalga Chlamydomonas reinhardtii

Yingshan Li, University of Nebraska - Lincoln


Small RNA-mediated silencing termed RNA interference (RNAi) involves in endogenous gene regulation and genome defense. The microalga Chlamydomonas reinhardtii is a classic model organism in basic biology research. Chlamydomonas has a complete set of key RNAi components, including three Argonautes (AGOs) and three Dicer-like (DCL) proteins, and a variety of endogenous small RNAs (sRNAs). In recent years, research has only focused on the canonical sRNAs, mainly microRNAs (miRNAs), in Chlamydomonas. The bona fide miRNAs are a group of 20-22 nucleotides (nt) sRNAs that depend on DCL3 in their biogenesis and associate with AGO3 to target complementary transcripts for translational repression or degradation. However, the functions and biogenesis of other types of sRNAs are poorly understood. In this dissertation, I present my research, using a combination of in-silico analysis and experiments, on two types of non-canonical sRNAs, namely the long sRNAs and tRNA-derived fragments (tRFs). In the first project, I discovered a type of uncommonly long sRNAs (>26 nt) that associate preferentially with AGO1. Somewhat reminiscent of animal PIWI-interacting RNAs, these long sRNAs are derived from moderately repetitive genomic clusters and their biogenesis appears to be Dicer-independent. The long sRNA encoding sequences have been conserved and duplicated within core Chlamydomonas species. Moreover, the expression of several long sRNAs increases substantially under nutrient deprivation, correlating with the downregulation of putative target transcripts. In the second project, I demonstrate that Chlamydomonas produces abundant tRFs that are accurately derived from tRNAs encoded in both the nuclear and the plastid genomes. The biogenesis of tRFs appears to be Dicer-independent. However, tRFs are loaded into AGO effector complexes and associate preferentially with AGO1. Moreover, reporter assays revealed that cytoplasmic tRFs can repress complementary transcripts in a miRNA-like manner. We also observed a dynamic profile of tRF abundance upon different stresses, suggesting that tRFs may have a role in responses to changing environmental conditions. Together, these data could contribute to a more comprehensive understanding of sRNAs in microalgae.

Subject Area

Biology|Molecular biology

Recommended Citation

Li, Yingshan, "The Versatile Small RNAs in the Unicellular Microalga Chlamydomonas reinhardtii" (2022). ETD collection for University of Nebraska-Lincoln. AAI29999178.