Transcriptomics

Dataset Information

414

Generation and characterization of a tomato DCL3 silencing mutant


ABSTRACT: DICER-like 3 (DCL3) is a major player in heterochromatic 24-nucleotide siRNA and long miRNA biogenesis and mutants have been characterized from Arabidopsis and rice. Here, a tomato DCL3 mutant was generated through the use of trans-activated artificial microRNA and characterized. Global tomato DCL3 (SlDCL3) silencing was induced by crossing the generated responder line (OP:amiRDCL3) with constitutive driver line. Constitutive trans-activation knocked down SlDCL3 levels by ~77%, resulting in dramatically decreased 24-nucleotide small RNA levels, but a significant increase in 21- and 22- nucleotide small RNAs, which was correlated with specific upregulation of SlDCL4 and SlDCL2b. Moreover, in the majority of small RNA-generating loci an almost complete overlap between the control and 35S>>amiRSlDCL3 siRNA signatures, was observed, strongly suggesting that the reduction in 24-nucleotide siRNAs was compensated by increased biogenesis of 21-22 nt siRNAs from the same genomic sequences. Collectively, these results suggest the requirement of SlDCL3 for the biogenesis of 23-24 nt sRNAs and its substitution by SlDCL4 and SlDCL2b, which function in the biogenesis of 21- and 22-nt small RNAs. In addition, differential expression between control and SlDCL3-silenced small RNAs indicated a significant reduction in the abundance of 24-nt putative long miRNAs, which was validated by northern blots, implicating SlDCL3 in their biogenesis. Examination of small RNA populations in control (35S:LhG4) and SlDCL3 silenced seedlings (35S>>amiRSlDCL3) 2 biological replicates each

ORGANISM(S): Solanum lycopersicum  

SUBMITTER: M Kravchik   S Damodharan  T Arazi  Tzahi Arazi 

PROVIDER: E-GEOD-52265 | ArrayExpress | 2014-03-31

SECONDARY ACCESSION(S): GSE52265SRP032929PRJNA227312

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Generation and characterization of a tomato DCL3-silencing mutant.

Kravchik Michael M   Damodharan Subha S   Stav Ran R   Arazi Tzahi T  

Plant science : an international journal of experimental plant biology 20140226


DICER-like 3 (DCL3) is a major player in heterochromatic 24-nucleotide (nt) small RNA (sRNA) and long microRNA (lmiRNA) biogenesis, and higher plant DCL3 mutants have been characterized from Arabidopsis thaliana and rice. Here, a tomato DCL3 (SlDCL3) mutant was generated through the use of trans-activated artificial miRNA and characterized. Constitutive trans-activation knocked down SlDCL3 levels by ∼64%, resulting in dramatically decreased 24-nt sRNA levels and a significant increase in 21- and  ...[more]

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