Abstract
Small (s)RNAs play crucial roles in the regulation of gene expression and genome stability across eukaryotes where they direct epigenetic modifications, post-transcriptional gene silencing, and defense against both endogenous and exogenous viruses. It is known that Chlamydomonas reinhardtii, a well-studied unicellular green algae species, possesses sRNA-based mechanisms that are distinct from those of land plants. However, definition of sRNA loci and further systematic classification is not yet available for this or any other algae. Here, using data-driven machine learning approaches including Multiple Correspondence Analysis (MCA) and clustering, we have generated a comprehensively annotated and classified sRNA locus map for C. reinhardtii. This map shows some common characteristics with higher plants and animals, but it also reveals distinct features. These results are consistent with the idea that there was diversification in sRNA mechanisms after the evolutionary divergence of algae from higher plant lineages.
Highlights
Small (s)RNAs in many organisms are involved in regulation of gene expression at the transcriptional and post-transcriptional (RNA degradation/translational repression) levels, as well as in host defenses against viruses [1]
In order to construct a complete locus map we first obtained a comprehensive collection of 145 sRNA libraries encompassing 54 replicate groups (S3 Table)
To obtain a general overview of the sRNA population within our datasets, we first computed the same intrinsic key determinants found to be informative in the sRNA locus classification of Arabidopsis [5]: locus size, 5’ nucleotide, repetitiveness of genomic mapping locations and abundance of individual sRNA species
Summary
Small (s)RNAs in many organisms are involved in regulation of gene expression at the transcriptional (epigenetic marks) and post-transcriptional (RNA degradation/translational repression) levels, as well as in host defenses against viruses [1]. In eukaryotes, their double stranded or highly structured RNA precursors are processed by Dicer-like (DCL) endonucleases into short 20-25nt RNA duplexes that are bound by Argonaute (AGO) proteins. One of the sRNA strands guides an AGO-containing effector complex toward complementary DNA/ RNA to mediate the various mechanisms of RNA silencing [2]. Due to its small genome, vegetative/sexual reproduction, fast growth, motility and capacity to use acetate as carbon source, the photosynthetic green alga Chlamydomonas reinhardtii deposited on Zenodo (https://doi.org/10.5281/ zenodo.3862401)
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