The regions between the genes that make the long RNA Molecules are contained in the genome. The long intergenic non-codingRNAs are thought to have important functions. A lack of well-annotated lincRNA data has made it difficult to understand their roles.
There have been no systematic genome-wide studies that have confirmed or proposed functions for lincRNAs. Direct comparisons of studies are difficult due to the different data reported.
These barriers inspired researchers to take a comprehensive look at the identity, production and function of lincRNAs in four species in the mustard family.
The plant cell published their results on June 6.
The goal was to generate extensive and more actionable data for researchers to understand lincRNA function.
Nelson, who is the corresponding author of the paper, said that the project started small and mushroomed after they realized they couldn't begin to figure out lincRNA function without having annotated genomes. Everything that went into this paper was lead by Kyle.
The team believes that production and function are limited to certain types of cells. The more common data sets don't cover that level of detail so it's easy to miss something. To give the full picture, our comprehensive approach combines a high-throughput, top-level analysis with a deeper dive into their likely functions.
The study used a unified approach to gathering and annotating lincRNA data. As the body of plant lincRNA data continues to grow, this would allow comparisons across different experiments and species.
The team uploaded their results to CyVerse, a free and open-science workspace where they can store, access and analyze data.
Palos said that they made it easy for others to search their results for lincRNAs involved in a plant trait or pathway of interest.
The team's methods could help resolve long-standing questions with genome-wide association studies that identify correlations between plant traits and genes. Is this variant within other genes or a regulatory element?
Nelson said that before you can determine the variant's effect and how to modify it, you need a properly annotated genome.
In the study, the team processed over 20,000 publicly available data sets from the four mustard species to identify thousands of lincRNAs and then annotated them with information.
The functions were assigned based on the expression patterns of the genes. The team deleted a subset of lincRNAs that appeared to play roles in seed growth and development in the plant.
In addition to ongoing studies of the germination-related lincRNAs, the team is applying its methods to lincRNAs in four more important crops.
We're still very much in the dark when it comes to lincRNAs. It could have an impact on human health and crops alike by helping us understand their fundamental properties.
More information: Kyle Palos et al, Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae, The Plant Cell (2022). DOI: 10.1093/plcell/koac166de.cyverse.org/ data/ds/iplant/
Journal information: Plant Cell
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