GONUTS has been updated to MW1.31 Most things seem to be working but be sure to report problems.

Have any questions? Please email us at ecoliwiki@gmail.com

PMID:15024409

From GONUTS
Jump to: navigation, search
Citation

Xie, Z, Johansen, LK, Gustafson, AM, Kasschau, KD, Lellis, AD, Zilberman, D, Jacobsen, SE and Carrington, JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2:E104

Abstract

Multicellular eukaryotes produce small RNA molecules (approximately 21-24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging to gene families that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals, plants encode multiple DCL and RDR proteins. Using a series of insertion mutants of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1), endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic marks and increased transcript accumulation at some loci. Defects in siRNA-generation activity in response to turnip crinkle virus in dcl2 mutant plants correlated with increased virus susceptibility. We conclude that proliferation and diversification of DCL and RDR genes during evolution of plants contributed to specialization of small RNA-directed pathways for development, chromatin structure, and defense.

Links

PubMed PMC350667 Online version:10.1371/journal.pbio.0020104

Keywords

Arabidopsis/genetics; Chromatin/chemistry; Cytosine/chemistry; DNA Methylation; Evolution, Molecular; Exons; Genes, Plant; Green Fluorescent Proteins/chemistry; Heterochromatin/chemistry; Histones/chemistry; Immunoblotting; Introns; Methylation; MicroRNAs/chemistry; Models, Genetic; Molecular Sequence Data; Mutation; Plants/virology; RNA/chemistry; RNA Replicase/chemistry; RNA, Small Interfering/chemistry; RNA, Small Interfering/metabolism; RNA, Viral/genetics; Recombinant Fusion Proteins/chemistry; Software

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

ARATH:RDR2

acts_upstream_of_or_within

GO:0030422: production of siRNA involved in RNA interference

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:RDR1

acts_upstream_of_or_within

GO:0009751: response to salicylic acid

ECO:0000270: expression pattern evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:DCL3

located_in

GO:0005634: nucleus

ECO:0000314: direct assay evidence used in manual assertion

C

Seeded From UniProt

complete

ARATH:DCL3

acts_upstream_of_or_within

GO:0030422: production of siRNA involved in RNA interference

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:RDR1

involved_in

GO:0009751: response to salicylic acid

ECO:0000270: expression pattern evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:RDR2

GO:0070919: production of siRNA involved in chromatin silencing by small RNA

ECO:0000315:

P

Notes: Fig. 1.B. shows that rdr2-1 mutants lacking RDR2 do not accumulate any of the endogenous siRNA tested (siRNA02, AtSN1 siRNA, Cluster2 siRNA, or siRNA1003).

complete
CACAO 8266

ARATH:RDR2

NOT|involved_in

GO:0009751: response to salicylic acid

ECO:0000270: expression pattern evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:RDR2

involved_in

GO:0070919: production of siRNA involved in chromatin silencing by small RNA

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:RDR2

involved_in

GO:0030422: production of siRNA involved in RNA interference

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

See also

References

See Help:References for how to manage references in GONUTS.