Abstract
BackgroundLong non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown.ResultsBy exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic marks. Intriguingly, the inheritance of lncRNA expression patterns in 105 recombinant inbred lines reveals apparent transgressive segregation, and maize lncRNAs are less affected by cis- than by trans-genetic factors.ConclusionsWe integrate all available transcriptomic datasets to identify a comprehensive set of maize lncRNAs, provide a unique annotation resource of the maize genome and a genome-wide characterization of maize lncRNAs, and explore the genetic control of their expression using expression quantitative trait locus mapping.
Highlights
Long non-coding RNAs are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation
While shoot apical meristem (SAM) initiation and development is characterized by distinct transcriptional variation [57], we identified a subset of putative long noncoding RNA (lncRNA) exhibiting distinct expression variation during different stages of SAM ontogeny (Additional file 9)
As previous studies have suggested [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28], a substantial number of lncRNAs exist in mammals and plants, and play important functional roles in human disease, plant development, and other biological processes
Summary
Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. While the central dogma defines the primary role for RNA as a messenger molecule in the process of gene expression, there is ample evidence for additional functions of RNA molecules. These RNA molecules include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs; mainly tRNAs and rRNAs), signal recognition particle (7SL/SRP) RNAs, microRNAs (miRNAs), small interfering RNAs (siRNAs), piwi RNAs (piRNAs) and trans-acting siRNAs (ta-siRNAs), natural cis-acting siRNAs and long noncoding RNAs (lncRNAs). Some lncRNAs have been shown to influence human disease, plant development, and other biological processes [10,11,12,13,14]
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