In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has...
BACKGROUND: The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and
biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation,
has been limited in B. distachyon to studies examining a few samples or that rely on computational...
In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora...
In RNA-directed silencing pathways, ternary complexes result from small RNA-guided ARGONAUTE (AGO) associating with target transcripts. Target transcripts are often silenced through direct cleavage (slicing), destabilization through slicer-independent turnover mechanisms, and translational repression. Here, wild-type and active-site defective forms of several Arabidopsis thaliana AGO proteins involved in posttranscriptional silencing were...
Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory RNAs found in fungi, plants, and animals. Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however, the specific roles of most endogenous siRNAs are unclear. The helicase gene eri-6/7 was identified in the...
In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...
Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Background: Short RNAs, and in particular microRNAs, are important regulators of gene
expression both within defined regulatory pathways and at the epigenetic scale. We investigated
the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the
sequenced Populus trichocarpa using a concatenation strategy in combination with...
Endogenous small RNAs (endo-siRNAs) interact with Argonaute (AGO) proteins to mediate
sequence-specific regulation of diverse biological processes. Here, we combine deep-sequencing and
genetic approaches to explore the biogenesis and function of endo-siRNAs in C. elegans. We describe
conditional alleles of the dicer-related helicase, drh-3, that abrogate both RNA interference and...
The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA
populations. However, these methods have been limited by several factors, including representational artifacts and lack of
established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing
and...