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Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development.

Dotto MC, Petsch KA, Aukerman MJ, Beatty M, Hammell M, Timmermans MC - PLoS Genet. (2014)

Bottom Line: Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model.The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3.Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

ABSTRACT
Maize leafbladeless1 (lbl1) encodes a key component in the trans-acting short-interfering RNA (ta-siRNA) biogenesis pathway. Correlated with a great diversity in ta-siRNAs and the targets they regulate, the phenotypes conditioned by mutants perturbing this small RNA pathway vary extensively across species. Mutations in lbl1 result in severe developmental defects, giving rise to plants with radial, abaxialized leaves. To investigate the basis for this phenotype, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects the accumulation of small RNAs in all major classes, and reveal unexpected crosstalk between ta-siRNA biogenesis and other small RNA pathways regulating transposons. Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model. Our analysis identified nine TAS loci, all belonging to the conserved TAS3 family. Information from RNA deep sequencing and PARE analyses identified the tasiR-ARFs as the major functional ta-siRNAs in the maize vegetative apex where they regulate expression of AUXIN RESPONSE FACTOR3 (ARF3) homologs. Plants expressing a tasiR-ARF insensitive arf3a transgene recapitulate the phenotype of lbl1, providing direct evidence that deregulation of ARF3 transcription factors underlies the developmental defects of maize ta-siRNA biogenesis mutants. The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3. Our data indicate that diversity in TAS pathways and their targets cannot fully account for the phenotypic differences conditioned by ta-siRNA biogenesis mutants across plant species. Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well.

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LBL1 affects the accumulation of 21-, 22-, and 24-nt small RNAs.(A) Annotation of loci that accumulate significantly fewer small RNAs in lbl1 than wild-type. (B) Annotation of loci that accumulate significantly more small RNAs in lbl1 compared to wild-type. Tables list the number of loci in each category and bar graphs show their relative frequencies.
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pgen-1004826-g004: LBL1 affects the accumulation of 21-, 22-, and 24-nt small RNAs.(A) Annotation of loci that accumulate significantly fewer small RNAs in lbl1 than wild-type. (B) Annotation of loci that accumulate significantly more small RNAs in lbl1 compared to wild-type. Tables list the number of loci in each category and bar graphs show their relative frequencies.

Mentions: A requirement for LBL1 in the production of phased siRNAs explains, however, only a subset of the small RNA level changes identified in the vegetative apex of lbl1 mutants. A further 68, 161, and 198 loci generating 21-, 22-, or 24-nt small RNAs, respectively, show a significant change (q-value<0.05) in small RNA accumulation of at least 2-fold between wild-type and lbl1 apices (S1 Dataset, Fig. 4A-B), and these could conceivably contribute to the developmental defects of lbl1 mutants. To assess this possibility and to gain insight into the possible function of these LBL1-dependent siRNAs, we first determined whether genes differentially accumulating small RNAs in lbl1 show a corresponding change in transcript levels. In addition to the ARF3 and TAS3 loci discussed above, 23 protein coding genes within the maize filtered and working gene sets show a significant difference in 21-, 22-, or 24-nt small RNA accumulation between wild-type and lbl1 apices (Fig. 4A-B; S1 Dataset). However, only GRMZM2G093276, which encodes a ZIP zinc/iron transport protein, shows a significant increase in transcript levels in lbl1 that is correlated with a decrease in siRNAs at the locus (S4 Dataset). Plants overexpressing ZIP proteins show a reduction in plant height and axillary bud outgrowth [39], [40], but such plants are otherwise morphologically normal. As such, a contribution of ZIP deregulation to the severe polarity defects of lbl1 mutants seems speculative.


Genome-wide analysis of leafbladeless1-regulated and phased small RNAs underscores the importance of the TAS3 ta-siRNA pathway to maize development.

Dotto MC, Petsch KA, Aukerman MJ, Beatty M, Hammell M, Timmermans MC - PLoS Genet. (2014)

LBL1 affects the accumulation of 21-, 22-, and 24-nt small RNAs.(A) Annotation of loci that accumulate significantly fewer small RNAs in lbl1 than wild-type. (B) Annotation of loci that accumulate significantly more small RNAs in lbl1 compared to wild-type. Tables list the number of loci in each category and bar graphs show their relative frequencies.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263373&req=5

pgen-1004826-g004: LBL1 affects the accumulation of 21-, 22-, and 24-nt small RNAs.(A) Annotation of loci that accumulate significantly fewer small RNAs in lbl1 than wild-type. (B) Annotation of loci that accumulate significantly more small RNAs in lbl1 compared to wild-type. Tables list the number of loci in each category and bar graphs show their relative frequencies.
Mentions: A requirement for LBL1 in the production of phased siRNAs explains, however, only a subset of the small RNA level changes identified in the vegetative apex of lbl1 mutants. A further 68, 161, and 198 loci generating 21-, 22-, or 24-nt small RNAs, respectively, show a significant change (q-value<0.05) in small RNA accumulation of at least 2-fold between wild-type and lbl1 apices (S1 Dataset, Fig. 4A-B), and these could conceivably contribute to the developmental defects of lbl1 mutants. To assess this possibility and to gain insight into the possible function of these LBL1-dependent siRNAs, we first determined whether genes differentially accumulating small RNAs in lbl1 show a corresponding change in transcript levels. In addition to the ARF3 and TAS3 loci discussed above, 23 protein coding genes within the maize filtered and working gene sets show a significant difference in 21-, 22-, or 24-nt small RNA accumulation between wild-type and lbl1 apices (Fig. 4A-B; S1 Dataset). However, only GRMZM2G093276, which encodes a ZIP zinc/iron transport protein, shows a significant increase in transcript levels in lbl1 that is correlated with a decrease in siRNAs at the locus (S4 Dataset). Plants overexpressing ZIP proteins show a reduction in plant height and axillary bud outgrowth [39], [40], but such plants are otherwise morphologically normal. As such, a contribution of ZIP deregulation to the severe polarity defects of lbl1 mutants seems speculative.

Bottom Line: Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model.The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3.Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America.

ABSTRACT
Maize leafbladeless1 (lbl1) encodes a key component in the trans-acting short-interfering RNA (ta-siRNA) biogenesis pathway. Correlated with a great diversity in ta-siRNAs and the targets they regulate, the phenotypes conditioned by mutants perturbing this small RNA pathway vary extensively across species. Mutations in lbl1 result in severe developmental defects, giving rise to plants with radial, abaxialized leaves. To investigate the basis for this phenotype, we compared the small RNA content between wild-type and lbl1 seedling apices. We show that LBL1 affects the accumulation of small RNAs in all major classes, and reveal unexpected crosstalk between ta-siRNA biogenesis and other small RNA pathways regulating transposons. Interestingly, in contrast to data from other plant species, we found no evidence for the existence of phased siRNAs generated via the one-hit model. Our analysis identified nine TAS loci, all belonging to the conserved TAS3 family. Information from RNA deep sequencing and PARE analyses identified the tasiR-ARFs as the major functional ta-siRNAs in the maize vegetative apex where they regulate expression of AUXIN RESPONSE FACTOR3 (ARF3) homologs. Plants expressing a tasiR-ARF insensitive arf3a transgene recapitulate the phenotype of lbl1, providing direct evidence that deregulation of ARF3 transcription factors underlies the developmental defects of maize ta-siRNA biogenesis mutants. The phenotypes of Arabidopsis and Medicago ta-siRNA mutants, while strikingly different, likewise result from misexpression of the tasiR-ARF target ARF3. Our data indicate that diversity in TAS pathways and their targets cannot fully account for the phenotypic differences conditioned by ta-siRNA biogenesis mutants across plant species. Instead, we propose that divergence in the gene networks downstream of the ARF3 transcription factors or the spatiotemporal pattern during leaf development in which these proteins act constitute key factors underlying the distinct contributions of the ta-siRNA pathway to development in maize, Arabidopsis, and possibly other plant species as well.

Show MeSH
Related in: MedlinePlus