Data and analysis from the project published in Nature Communications
We are pleased to announce that the work of this project has been published in April, 2014 in the journal Nature Communications
. The publication is accessible here
. The analysis of the data was performed collaboratively with a team from Mexico, led by Stefan de Folter, professor at the Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO) in Irapuato. The paper and our collaborative work is described in an article published in the University of Delaware news
Aims of the Project
The goal of this work is to develop extensive sequence resources of plant small RNAs (21 to 24 nucleotides) from representative species across the plant kingdom. These data will enable functional and evolutionary studies of microRNAs (miRNA) and short-interfering RNAs (siRNAs). Small RNAs have a demonstrated and important role in plant development, stress responses, and epigenetic regulation primarily through their role in transcriptional and post-transcriptional silencing of specific target genes and other loci. While most studies have been limited to Arabidopsis, the little that is known about small RNA diversity and evolution suggests that miRNAs are a well-conserved gene regulatory system dating back to lower plants and green algae.
In the current proposal, our hypothesis is that most if not all plants utilize important small RNA signaling networks and different plant families are likely to have both common and lineage-specific miRNAs or other small RNAs with important biological roles that have yet to be characterized even at a superficial level. The data that we propose to generate will allow the experimental characterization of the majority of biologically important small RNAs for a range of plant species, with key focused studies in the Solanaceae and Poaceae families.
This work will result in the identification of numerous small RNAs that likely have important roles in plant biology, and it will develop considerable resources for future genomics studies by many other research groups. This work will provide the foundation for functional analyses of selected small RNAs discovered in this study, and will demonstrate the conservation of miRNAs known to play important biological roles based on ongoing studies in Arabidopsis, rice and other plant species. In addition to providing the foundation and tools for future studies, this project will generate important public resources including an extensive database of classified small RNAs.
Plant miRNAs and Endogenous siRNAs
Two major types of small RNAs (21 to 24 nucleotides in size), known as small interfering RNAs (siRNAs) and microRNAs (miRNAs) are present in a wide variety of eukaryotic organisms. Both types of molecules are processed from double-stranded RNA by RNase III enzymes called DICERs. Though siRNAs and miRNAs are similar in size, their biogenesis and often their functions are substantially different. siRNAs are processed from longer double-stranded RNA molecules and represent both strands of the RNA. In plants, transcriptional silencing can be triggered by either histone modifications or DNA methylation, both of which can result from targeting by endogenous siRNAs. Most of the endogenous siRNAs in plants match to repetitive sequences such as transposons, retrotransposons and centromeric repeats that are often heterochromatic. siRNAs may also be incorporated into a multi-protein complex known as RISC, where they can act as guides to target and degrade complementary mRNA molecules.
January 2010 database update
We are pleased to announce the addition of new sequence tags for the whole Green algae section in this new database release. Older datasets have been completely replaced by higher quality and/or larger sequencing data. Users are welcome to find detailed information for each new library within the downloadable material in the 'Project data 'section. The new data are available for all purposes of analysis in the tool section of the website as well. We must also acknowledge that two small RNA libraries (from avocado fruit and grapevine leaves respectively) were found to have been swapped and mistakenly made available with the wrong description in the preliminary release of Oct 2008. We very much apologize for the inconvenience and welcome you to browse the new corrected data.