Small RNA pathways in plants Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/w3763880r

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  • miRNA-guided cleavage initiates entry of primary transcripts into the trans-acting siRNA (tasiRNA) biogenesis pathway involving RNA-DEPENDENT RNA POLYMERASE6 (RDR6), DICER-LIKE 4 (DCL4), and SUPPRESSOR OF GENE SILENCING3 (SGS3). Arabidopsis thaliana TAS1 and TAS2 families yield tasiRNA that form through miR173- guided initiation cleavage on the 5’ side of the siRNA-generating regions. The TAS3 family yields tasiRNA that form through miR390-guided initiation cleavage on the 3’ side of the siRNA-generating regions. miR390 also functions in a non-cleavage mode on the 5’ side of the siRNA-generating regions. TAS1 and TAS2 tasiRNA target several transcripts encoding pentatricopeptide repeat (PPR) proteins and proteins of unknown function. TAS3 tasiRNA regulate mRNAs encoding several AUXIN RESPONSE FACTORs. miRNA-guided cleavage initiates entry of primary transcripts into the trans-acting siRNA (tasiRNA) biogenesis pathway involving RNA-DEPENDENT RNA POLYMERASE6 (RDR6), DICER-LIKE 4 (DCL4), and SUPPRESSOR OF GENE SILENCING3 (SGS3). Arabidopsis thaliana TAS1 and TAS2 families yield tasiRNA that form through miR173- guided initiation cleavage on the 5’ side of the siRNA-generating regions. The TAS3 family yields tasiRNA that form through miR390-guided initiation cleavage on the 3’ side of the siRNA-generating regions. miR390 also functions in a non-cleavage mode on the 5’ side of the siRNA-generating regions. TAS1 and TAS2 tasiRNA target several transcripts encoding pentatricopeptide repeat (PPR) proteins and proteins of unknown function. TAS3 tasiRNA regulate mRNAs encoding several AUXIN RESPONSE FACTORs. miRNA-guided cleavage initiates entry of primary transcripts into the trans-acting siRNA (tasiRNA) biogenesis pathway involving RNA-DEPENDENT RNA POLYMERASE6 (RDR6), DICER-LIKE 4 (DCL4), and SUPPRESSOR OF GENE SILENCING3 (SGS3). Arabidopsis thaliana TAS1 and TAS2 families yield tasiRNA that form through miR173- guided initiation cleavage on the 5’ side of the siRNA-generating regions. The TAS3 family yields tasiRNA that form through miR390-guided initiation cleavage on the 3’ side of the siRNA-generating regions. miR390 also functions in a non-cleavage mode on the 5’ side of the siRNA-generating regions. TAS1 and TAS2 tasiRNA target several transcripts encoding pentatricopeptide repeat (PPR) proteins and proteins of unknown function. TAS3 tasiRNA regulate mRNAs encoding several AUXIN RESPONSE FACTORs. The TAS1c and TAS3a loci were modified to produce synthetic (syn) tasiRNA to target an endogenous transcript encoding PHYTOENE DESATURASE (PDS). TAS1c- and TAS3a-based syn-tasiRNA were used to test the unique requirement for miR173 and miR390 in routing TAS1c and TAS3a transcripts, respectively, through the RDR6/SGS3/DCL4-dependent tasiRNA pathway. miR173 was unique in its ability to initiate TAS1c-based syn-tasiRNA formation. Surprisingly, targeting by miR173 was sufficient to route non-TAS transcripts into the tasiRNA pathway as well. AGO1 is shown to associate with miR173, and to be required for TAS1 and TAS2 tasiRNA formation, indicating that the miR173-AGO1 complex functions in a distinct mode from other miRNA-AGO1 complexes. TAS3, but not TAS1 and TAS2, tasiRNA are shown to require ARGONAUTE7 (AGO7) and to regulate the juvenile-to-adult phase transition through suppression of ARF3 mRNA. miR390-AGO7 complexes are shown to function in either cleavage or non-cleavage modes at two target sites in TAS3a transcripts. The AGO7 cleavage, but not the non-cleavage, function could be provided by AGO1, but only when AGO1 was guided to a modified target site through an alternate miRNA. AGO7 was highly selective for interaction with miR390, and miR390 in turn was excluded from association with AGO1 due entirely to an incompatible 5’ adenosine. Analysis of AGO1, AGO2 and AGO7 revealed a potent 5’ nucleotide discrimination function for some, although not all, ARGONAUTEs. miR390 and AGO7, therefore, evolved as a highly specific miRNA guide/effector protein pair to function at two distinct tasiRNA biogenesis steps.
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