Final Report Summary - GREENLINCS (Functional roles of long noncoding RNAs in drought stress responses of Arabidopsis)
The traditional view that protein coding genes are the only regulatory elements in the genome has been challenged by the discovery of miRNA genes and more recently by the discovery of transcription units producing long intergenic non-coding (linc)RNAs. Recent work in yeast and mammals indicate that lincRNAs play important regulatory roles in cell differentiation, organ development and responses to stress. These non-coding units have been suggested to be important orchestrators of gene expression, acting at the transcriptional and/or post-transcriptional levels. Still, very little is known about lincRNAs and in particular, plant lincRNAs.
In this project we have used two photosynthetic model species, the model dicot plant, Arabidopsis thaliana, and the model diatom, Phaeodactylum tricornutum, to investigate these novel molecular actors in the context of abiotic stress in photosynthetic organisms. We have identified several lincRNAs whose expression levels are changed in response to different abiotic stresses, namely drought (in Arabidopsis) and phosphate stress (in Arabidopsis and Phaeodactylum), by Tiling arrays and RNA-Sequencing (http://chualab.rockefeller.edu/cgi-bin/gb2/gbrowse/arabidopsis/(opens in new window)). These lincRNAs in both model systems were further characterized and their expression in response to different stress intensities (drought and/or phosphate stress) was quantified by qPCR. Most of the lincRNAs that were validated had no detectable expression under normal conditions but were significantly up regulated under stress and in specific organs in the case of the model plant (shoot and/or root), further supporting an active role in the stress response.
To study the functional role of these non-coding genes, transgenic plants harboring constructs for knockout/knockdown, inducible and over-expressing the selected lincRNAs genes were made. Several Arabidopsis mutants carrying T-DNA insertions in the lincRNA gene loci from the Salk mutant populations (http://signal.salk.edu(opens in new window)) were also selected. Transgenic plants and mutant homozygous lines have been thoroughly phenotyped, both physiologically and molecularly, under different drought and phosphate stress trials, in parallel to the wild type plants. Manipulation of the expression levels of these candidate lincRNAs has helped to further uncover their putative targets as well as provided insights to the specific lincRNA function(s) under stress. These findings open novel routes to explore the function and regulatory roles of lincRNAs in photosynthetic organisms while addressing the evolutionary significance of the non-protein coding transcriptome. Ultimately, this has the potential to provide new regulatory candidate genes for genetic engineering for stress tolerance in crop plants.
In this project we have used two photosynthetic model species, the model dicot plant, Arabidopsis thaliana, and the model diatom, Phaeodactylum tricornutum, to investigate these novel molecular actors in the context of abiotic stress in photosynthetic organisms. We have identified several lincRNAs whose expression levels are changed in response to different abiotic stresses, namely drought (in Arabidopsis) and phosphate stress (in Arabidopsis and Phaeodactylum), by Tiling arrays and RNA-Sequencing (http://chualab.rockefeller.edu/cgi-bin/gb2/gbrowse/arabidopsis/(opens in new window)). These lincRNAs in both model systems were further characterized and their expression in response to different stress intensities (drought and/or phosphate stress) was quantified by qPCR. Most of the lincRNAs that were validated had no detectable expression under normal conditions but were significantly up regulated under stress and in specific organs in the case of the model plant (shoot and/or root), further supporting an active role in the stress response.
To study the functional role of these non-coding genes, transgenic plants harboring constructs for knockout/knockdown, inducible and over-expressing the selected lincRNAs genes were made. Several Arabidopsis mutants carrying T-DNA insertions in the lincRNA gene loci from the Salk mutant populations (http://signal.salk.edu(opens in new window)) were also selected. Transgenic plants and mutant homozygous lines have been thoroughly phenotyped, both physiologically and molecularly, under different drought and phosphate stress trials, in parallel to the wild type plants. Manipulation of the expression levels of these candidate lincRNAs has helped to further uncover their putative targets as well as provided insights to the specific lincRNA function(s) under stress. These findings open novel routes to explore the function and regulatory roles of lincRNAs in photosynthetic organisms while addressing the evolutionary significance of the non-protein coding transcriptome. Ultimately, this has the potential to provide new regulatory candidate genes for genetic engineering for stress tolerance in crop plants.