Genome-wide discovery and characterization of maize long non-coding RNAs

Lin Li, Steven R. Eichten, Rena Shimizu, Katherine Petsch, Cheng Ting Yeh, Wei Wu, Antony M. Chettoor, Scott A. Givan, Rex A. Cole, John E. Fowler, Matthew M.S. Evans, Michael J. Scanlon, Jianming Yu, Patrick S. Schnable, Marja C.P. Timmermans, Nathan M. Springer, Gary J. Muehlbauer

Research output: Contribution to journalArticlepeer-review

374 Scopus citations


Background: 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. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown.Results: By 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.Conclusions: We 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.

Original languageEnglish (US)
Article numberR40
JournalGenome biology
Issue number2
StatePublished - Feb 27 2014

Bibliographical note

Funding Information:
We acknowledge the support of the Minnesota Supercomputing Institute. We thank Dr Ying Zhang from Minnesota Supercomputing Institute for the set-up of the computation environment. We are grateful to the editor and the anonymous reviewers for their helpful comments and suggestions. This work was supported by the National Science Foundation (Genomic Analyses of shoot meristem function in maize-NSF #0820610; Functional Structural Diversity among Maize Haplotypes-NSF #1027527; and Functional Genomics of Maize Gametophytes NSF #0701731). Funding for open access charge: National Science Foundation.


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