A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs

Abstract

Gene regulation involves the orchestrated action of multiple regulators to fine-tune the expression of genes. Hierarchical interactions and co-regulation among regulators are commonly observed in biological systems, leading to complex regulatory networks. Small RNA (sRNAs) have been shown to be important regulators of gene expression due to their involvement in multiple cellular processes. In plants, microRNA (miRNAs) and phased small interfering RNAs (phasiRNAs) correspond to two well-characterized types of sRNAs involved in the regulation of posttranscriptional gene expression, although information about their targets and interactions with other gene expression regulators is limited. We describe an extended sRNA-mediated regulatory network in Arabidopsis thaliana that provides a reference frame to understand sRNA biogenesis and activity at the genomewide level. This regulatory network combines a comprehensive evaluation of phasiRNA production and sRNA targets supported by degradome data. The network includes 17% of genes in the A. thaliana genome, representing~50% annotated gene ontology (GO) functional categories. Approximately 14% of genes with GO annotations corresponding to regulation of gene expression were found to be under sRNA control. The unbiased bioinformatic approach used to produce the network was able to detect 107 PHAS loci (regions of phasiRNA production), 5,047 active phasiRNAs (~70% of which were non-canonical), and reconstruct 17 regulatory modules resulting from complex regulatory interactions between different sRNA-regulatory pathways. Known regulatory modules like miR173-TAS-PPR/TPR and miR390-TAS3-ARF/F-box were faithfully reconstructed and expanded, illustrating the accuracy and sensitivity of the methods and providing confidence for the validity of findings of previously unrecognized modules. The network presented here includes a 2X increase in the number of identified PHAS loci, a large complement (~70%) of non-canonical phasiRNAs, and the most comprehensive

Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology

“…The phasiRNAs accumulation dropped at 21 dpi, suggesting the sRNA-mediated defenses in the recovery phenotype ( Prigigallo et al, 2019 ). Similar examples can also be found in Arabidopsis plants infected with CMV ( Vargas-Asencio and Perry, 2020 ).…”

“…The TAS2-3′D6(-) can target two PPR genes, namely, At1g12770 and Atg63130 ( Allen et al, 2005 ). The cascading effect thus spawns secondary and tertiary phasiRNAs to expand the domain of complex control by a single initiator 22-nt miRNA ( Vargas-Asencio and Perry, 2020 ). TAS2 transcripts harbor several short reading frames of peptides, which are translated and get associated with TAS2 transcripts in the polysome fractions.…”

“…Some miRNAs are overexpressed, resulting in overproduction of PhasiRNAs, whereas in other cases, PhasiRNAs disappear altogether. Such alterations lead to fine-tuning of the host genes related to resistance, susceptibility, or tolerance toward the infecting virus ( Vargas-Asencio and Perry, 2020 ). Zheng et al (2015) examined the PhasiRNA loci in uninfected papaya and papaya ringspot virus (PRSV)-infected papaya.…”

The unique dual targeting of AGO1 by two types of PRMT enzymes promotes phasiRNA loading in Arabidopsis thaliana

“…Among the siRNA down-loaded in AGO1 in atprmt5 , a significant subset coloured in the volcano plots corresponds to phased-type siRNAs (phasiRNAs) which exhibit a 5′U preference in their 5′ terminal position ( Supplementary Figure S11A, B ). We can find tasiRNAs produced from TAS1 and TAS3 non-coding loci coloured in yellow, phasiRNAs produced from loci that have been previously identified in the work of Vargas-Asencio and Perry in 2020 ( 57 ) coloured in pink and siRNA produced from RDR6 dependent targets coloured in green ( 58 ) ( Supplementary Figure S10E ). Supporting the hypothesis of a defect in AGO1 loading for the corresponding siRNAs in atprmt5 mutants, their levels are barely affected in the input fractions (Figures 6B and S10E , right panels).…”

CWLP and PRP940 form plasma-membrane nanodomain complexes with aquaporins, interact with PP2A and contribute to dehydration tolerance

“…CWLP is transcribed bi- directionally, producing a reverse complementary long non-coding RNA ( lncRNA At3g22121 ), which terminates 132 nucleotides downstream of CWLP transcription start site. The double-stranded RNA forming region of 852 nucleotides produces natural antisense small interfering RNAs (NAT-siRNAs) in a phased fashion (91, 92). According to Genevestigator, low levels of lcRNA are present in seeds, xylem, and root pericycle tissues (Fig.…”