New technologies accelerate the exploration of non-coding RNAs in horticultural plants

Degao Liu; Ritesh Mewalal; Rongbin Hu; Gerald A. Tuskan; Xiaohan Yang

doi:10.1038/hortres.2017.31

New technologies accelerate the exploration of non-coding RNAs in horticultural plants

Degao Liu, Ritesh Mewalal, Rongbin Hu, Gerald A. Tuskan, Xiaohan Yang

Research output: Contribution to journal › Review article › peer-review

57 Scopus citations

Abstract

Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPRassociated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.

Original language	English
Article number	31
Journal	Horticulture Research
Volume	4
DOIs	https://doi.org/10.1038/hortres.2017.31
State	Published - Jul 5 2017

Funding

We thank Dr Zong-Ming Cheng (University of Tennessee) and the reviewers for their critical review and instructive comments on our manuscript. This research is supported by the Department of Energy (DOE), Office of Science, Genomic Science Program under Award Number DE-SC0008834. Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the US DOE under Contract Number DE-AC05- 00OR22725. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).

Funders	Funder number
DOE Public Access Plan
United States Government
U.S. Department of Energy	DE-AC05- 00OR22725
Office of Science	DE-SC0008834
Oak Ridge National Laboratory
University of Tennessee

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10.1038/hortres.2017.31

Cite this

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title = "New technologies accelerate the exploration of non-coding RNAs in horticultural plants",

abstract = "Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPRassociated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.",

author = "Degao Liu and Ritesh Mewalal and Rongbin Hu and Tuskan, {Gerald A.} and Xiaohan Yang",

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AU - Liu, Degao

AU - Mewalal, Ritesh

AU - Hu, Rongbin

AU - Tuskan, Gerald A.

AU - Yang, Xiaohan

PY - 2017/7/5

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N2 - Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPRassociated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.

AB - Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPRassociated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs.

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New technologies accelerate the exploration of non-coding RNAs in horticultural plants

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