Abstract
BackgroundLong non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Recent studies also identified lncRNAs in plant genomes, revealing a new level of transcriptional complexity in plants. Thousands of lncRNAs have been predicted in the Arabidopsis thaliana genome, but only a few have been studied in depth.ResultsHere we report the identification of Arabidopsis lncRNAs that are expressed during the vegetative stage of development in either the shoot apical meristem or in leaves. We found that hundreds of lncRNAs are expressed in these tissues, of which 50 show differential expression upon an increase in ambient temperature. One of these lncRNAs, FLINC, is down-regulated at higher ambient temperature and affects ambient temperature-mediated flowering in Arabidopsis.ConclusionA number of ambient temperature responsive lncRNAs were identified with potential roles in the regulation of temperature-dependent developmental changes, such as the transition from the vegetative to the reproductive (flowering) phase. The challenge for the future is to characterize the biological function and molecular mode of action of the large number of ambient temperature-regulated lncRNAs that have been identified in this study.
Highlights
Long non-coding RNAs have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level
They have been divided in different categories based on their location in the genome relative to protein-coding genes: natural antisense transcripts (NATs) are Long non-coding RNAs (lncRNAs) transcribed on the opposite strand of a protein-coding gene; long intergenic RNAs are transcribed in intergenic regions; intronic lncRNAs are transcribed from an
Strand-specific libraries were generated from shoot apical meristem (SAM)-enriched tissue of 5 weeks-old Arabidopsis Col-0 plants grown in short-day conditions, and still in the vegetative stage
Summary
Long non-coding RNAs (lncRNAs) have emerged as new class of regulatory molecules in animals where they regulate gene expression at transcriptional and post-transcriptional level. Only a small number of lncRNAs has been functionally characterized and the emerging picture shows that lncRNAs have several modes of action, ranging from transcriptional interference to chromatin looping and mRNA splicing [1, 2, 4]. These lncRNAs act in a wide range of biological processes. Some examples include the lincRNA APOLO, which is involved in auxin response [5], ELENA1, which functions in plant immunity [6], Enod, which plays a role in regulation of sucrose utilization in Severing et al BMC Plant Biology (2018) 18:145 nodules [7] and IPS1, which acts as a mimic of a miRNA target in the control of Pi homeostasis [8]
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