Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Small RNAs in the Physcomitrella dcl4 mutant

ABSTRACT: To study the function of Physcomitrella DCL4, a knockout plant line was created. Small RNAs from ~10-day old protonemata were obtained and sequenced using a SOLiD 2 instrument. A single library each was made from dcl4 mutant protonemata and wild-type protonemata. The dcl4 library was sequenced in four separate technical replicates. The wild-type sample was subject to a single sequencing run.

ORGANISM(S): Physcomitrella patens

SUBMITTER: Michael Axtell

PROVIDER: E-GEOD-18466 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility.

Arif M Asif MA Fattash Isam I Ma Zhaorong Z Cho Sung Hyun SH Beike Anna K AK Reski Ralf R Axtell Michael J MJ Frank Wolfgang W

Molecular plant 20120417 6

Trans-acting small interfering RNAs (ta-siRNAs) are plant-specific siRNAs released from TAS precursor transcripts after microRNA-dependent cleavage, conversion into double-stranded RNA, and Dicer-dependent phased processing. Like microRNAs (miRNAs), ta-siRNAs direct site-specific cleavage of target RNAs at sites of extensive complementarity. Here, we show that the DICER-LIKE 4 protein of Physcomitrella patens (PpDCL4) is essential for the biogenesis of 21 nucleotide (nt) ta-siRNAs. In ΔPpDCL4 mu ...[more]

PMID: 22511605

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Project description:In response to infection, viral genomes are processed by Dicer-like (DCL) ribonuclease proteins into viral small RNAs (vsRNAs) of discrete sizes. vsRNAs are then used as guides for silencing the viral genome. The profile of vsRNAs produced during the infection process has been extensively studied for some group of viruses. However, nothing is known for members of the economically important family Luteoviridae, a group of phloem-restricted viruses. Here, the population of vsRNAs from cotton plants infected with Cotton leafroll dwarf virus (CLRDV), a member of the genus Polerovirus, family Luteoviridae, is characterized.Deep sequencing of small RNAs (sRNAs) from CLRDV-infected cotton leaves was performed. Results showed 21-nt to 24-nt long vsRNAs matching all the viral genome, with a higher frequency of matches in the 3M-CM-"M-BM-^@M-BM-^Y region. Equivalent amounts of sense and antisense vsRNAs were found, and the 22-nt long small RNA class was the most prominent one. Looking for cotton Dcl transcripts levels during infection, we could observe that Dcl4 seems to be up-regulated, while Dcl2 seems to be down-regulated.This is the first report on the profile of sRNAs coming from a plant infected with a member of the family Luteoviridae. Our sequence data strongly suggest that virus-derived double-stranded RNA functions as one of the main precursors of vsRNAsOur results indicate that secondary structures of the viral RNAs are not the main source of the viRNAs observed, as suggested for other viruses. Judging by the profiled size classes, all cotton DCLs might be working to silence the virus. The possible causes for the unexpected high accumulation of 22-nt viRNAvsRNAs are discussed. CLRDV is the causal agent of worldwide cotton pathology named Cotton blue disease. Our results are an important contribution for understanding the molecular mechanisms involved in this and related diseases. Total RNA obtained from leaves of the cotton plant 5 days post-infection with Cotton leafrol dawrf virus (CLRDV) compared to not-infected control.

Dataset Information

Small RNAs in the Physcomitrella dcl4 mutant

Publications

DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility.

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