Genome-wide discovery and characterization of maize long non-coding RNAs
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Li, Lin; Eichten, Steven R; Shimizu, Rena; Petsch, Katherine; Yeh, Cheng-Ting; Wu, Wei; Chettoor, Antony M; Givan, Scott A; Cole, Rex A; Fowler, John E; Evans, Matthew M S; Scanlon, Michael J; Yu, Jianming; Schnable, Patrick S; Timmermans, Marja C P; Springer, Nathan M; Muehlbauer, Gary J
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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,...[Show more]
dc.contributor.author | Li, Lin | |
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dc.contributor.author | Eichten, Steven R | |
dc.contributor.author | Shimizu, Rena | |
dc.contributor.author | Petsch, Katherine | |
dc.contributor.author | Yeh, Cheng-Ting | |
dc.contributor.author | Wu, Wei | |
dc.contributor.author | Chettoor, Antony M | |
dc.contributor.author | Givan, Scott A | |
dc.contributor.author | Cole, Rex A | |
dc.contributor.author | Fowler, John E | |
dc.contributor.author | Evans, Matthew M S | |
dc.contributor.author | Scanlon, Michael J | |
dc.contributor.author | Yu, Jianming | |
dc.contributor.author | Schnable, Patrick S | |
dc.contributor.author | Timmermans, Marja C P | |
dc.contributor.author | Springer, Nathan M | |
dc.contributor.author | Muehlbauer, Gary J | |
dc.date.accessioned | 2015-12-23T23:14:00Z | |
dc.date.available | 2015-12-23T23:14:00Z | |
dc.identifier.issn | 1465-6906 | |
dc.identifier.uri | http://hdl.handle.net/1885/95193 | |
dc.description.abstract | 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. | |
dc.publisher | BioMed Central | |
dc.rights | © 2014 Li et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. | |
dc.source | Genome Biology | |
dc.subject | databases, genetic | |
dc.subject | exons | |
dc.subject | gene expression regulation, plant | |
dc.subject | molecular sequence annotation | |
dc.subject | open reading frames | |
dc.subject | rna, long noncoding | |
dc.subject | zea mays | |
dc.subject | genome, plant | |
dc.subject | transcription, genetic | |
dc.title | Genome-wide discovery and characterization of maize long non-coding RNAs | |
dc.type | Journal article | |
local.description.notes | Imported from ARIES | |
local.identifier.citationvolume | 15 | |
dc.date.issued | 2014-02-27 | |
local.identifier.absfor | 060102 | |
local.identifier.ariespublication | U3488905xPUB1254 | |
local.publisher.url | http://www.biomedcentral.com/ | |
local.type.status | Published Version | |
local.contributor.affiliation | Li, Lin, University of Minnesota, United States of America | |
local.contributor.affiliation | Eichten, Steven, College of Medicine, Biology and Environment, CMBE Research School of Biology, Division of Plant Sciences, The Australian National University | |
local.contributor.affiliation | Shimizu, Rena, Cornell University, United States of America | |
local.contributor.affiliation | Petsch, Katherine , Cold Spring Harbor Laboratory, United States of America | |
local.contributor.affiliation | Yeh, Cheng-Ting, Iowa State University, United States of America | |
local.contributor.affiliation | Wu, Wei, Iowa State University, United States of America | |
local.contributor.affiliation | Chettoor, Antony M, Carnegie Institution for Science, United States of America | |
local.contributor.affiliation | Givan, Scott A , University of Missouri, United States of America | |
local.contributor.affiliation | Cole, Rex A , Oregon State University, United States of America | |
local.contributor.affiliation | Fowler, John E , Oregon State University,, United States of America | |
local.contributor.affiliation | Evans, Matthew M S , Carnegie Institution for Science, United States of America | |
local.contributor.affiliation | Scanlon, Michael J , Cornell University, United States of America | |
local.contributor.affiliation | Yu, Jianming, Iowa State University, United States of America | |
local.identifier.essn | 1474-760X | |
local.bibliographicCitation.issue | 2 | |
local.bibliographicCitation.startpage | R40 | |
local.identifier.doi | 10.1186/gb-2014-15-2-r40 | |
local.identifier.absseo | 820401 | |
dc.date.updated | 2016-02-24T09:58:03Z | |
local.identifier.scopusID | 2-s2.0-84899045771 | |
Collections | ANU Research Publications |
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