Genome Research, volume 29, issue 9, pages 1464-1477

Distinct types of short open reading frames are translated in plant cells

Fesenko Igor ¹

Kirov Ilya ²

Kniazev Andrey ¹

Khazigaleeva Regina ¹

Lazarev Vassili ^{3, 4}

Kharlampieva Daria ⁵

Grafskaia Ekaterina ^{3, 4}

Zgoda Viktor ⁶

Butenko Ivan ⁵

Arapidi Georgy ^{3, 7}

Mamaeva Anna ¹

Ivanov Vadim ¹

Govorun Vadim M. ⁵

Hide authors affiliations Show authors affiliations: 7 affiliations

Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation. |

Laboratory of marker-assisted and genomic selection of plants, All-Russian Research Institute of Agricultural Biotechnology, 127550 Moscow, Russian Federation. |

3Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russian Federation |

⁴

4Moscow Institute of Physics and Technology (National Research University), 141701 Dolgoprudny, Moscow Region, Russian Federation |

⁵

Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435, Moscow, Russian Federation |

⁶

Laboratory of System Biology, Institute of Biomedical Chemistry, 119121 Moscow, Russian Federation. |

⁷

1Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, Russian Federation |

Publication type: Journal Article

Publication date: 2019-08-06

Cold Spring Harbor Laboratory

Journal: Genome Research

Quartile SCImago

Quartile WOS

Impact factor: 7

ISSN: 10889051, 15495469

DOI: 10.1101/gr.253302.119

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Genetics

Genetics (clinical)

Abstract

Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of 10 plant species examined. Mass spectrometry analysis of proteomic and peptidomic data sets suggested that tens of sORFs located on distinct parts of mRNAs and long noncoding RNAs (lncRNAs) are translated, including conserved sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Functional analysis of four lncRNA-encoded peptides showed that sORFs-encoded peptides are involved in regulation of growth and differentiation in moss. Knocking out lncRNA-encoded peptides resulted in a decrease of moss growth. In contrast, the overexpression of these peptides resulted in a diverse range of phenotypic effects. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.

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Citations by journals

	1 2
Frontiers in Plant Science	Frontiers in Plant Science, 2, 4.55% Frontiers in Plant Science 2 publications, 4.55%
Plants	Plants, 2, 4.55% Plants 2 publications, 4.55%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 2, 4.55% International Journal of Molecular Sciences 2 publications, 4.55%
FEBS Journal	FEBS Journal, 2, 4.55% FEBS Journal 2 publications, 4.55%
Nucleic Acids Research	Nucleic Acids Research, 2, 4.55% Nucleic Acids Research 2 publications, 4.55%
Horticulture Research	Horticulture Research, 2, 4.55% Horticulture Research 2 publications, 4.55%
Nature Communications	Nature Communications, 1, 2.27% Nature Communications 1 publication, 2.27%
Agronomy	Agronomy, 1, 2.27% Agronomy 1 publication, 2.27%
Frontiers in Cellular and Infection Microbiology	Frontiers in Cellular and Infection Microbiology, 1, 2.27% Frontiers in Cellular and Infection Microbiology 1 publication, 2.27%
Plant Molecular Biology	Plant Molecular Biology, 1, 2.27% Plant Molecular Biology 1 publication, 2.27%
Parasitology Research	Parasitology Research, 1, 2.27% Parasitology Research 1 publication, 2.27%
3 Biotech	3 Biotech, 1, 2.27% 3 Biotech 1 publication, 2.27%
Computers in Biology and Medicine	Computers in Biology and Medicine, 1, 2.27% Computers in Biology and Medicine 1 publication, 2.27%
Data in Brief	Data in Brief, 1, 2.27% Data in Brief 1 publication, 2.27%
aBIOTECH	aBIOTECH, 1, 2.27% aBIOTECH 1 publication, 2.27%
Trends in Cell Biology	Trends in Cell Biology, 1, 2.27% Trends in Cell Biology 1 publication, 2.27%
Genomics	Genomics, 1, 2.27% Genomics 1 publication, 2.27%
Methods	Methods, 1, 2.27% Methods 1 publication, 2.27%
Molecular Plant	Molecular Plant, 1, 2.27% Molecular Plant 1 publication, 2.27%
Current Opinion in Chemical Biology	Current Opinion in Chemical Biology, 1, 2.27% Current Opinion in Chemical Biology 1 publication, 2.27%
ChemBioChem	ChemBioChem, 1, 2.27% ChemBioChem 1 publication, 2.27%
IEEE/ACM Transactions on Computational Biology and Bioinformatics	IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, 2.27% IEEE/ACM Transactions on Computational Biology and Bioinformatics 1 publication, 2.27%
DNA Research	DNA Research, 1, 2.27% DNA Research 1 publication, 2.27%
International Journal of Biological Macromolecules	International Journal of Biological Macromolecules, 1, 2.27% International Journal of Biological Macromolecules 1 publication, 2.27%
Bioresource Technology	Bioresource Technology, 1, 2.27% Bioresource Technology 1 publication, 2.27%
Journal of Biomolecular Structure and Dynamics	Journal of Biomolecular Structure and Dynamics, 1, 2.27% Journal of Biomolecular Structure and Dynamics 1 publication, 2.27%
Journal of Chemical Information and Modeling	Journal of Chemical Information and Modeling, 1, 2.27% Journal of Chemical Information and Modeling 1 publication, 2.27%
Methods in Molecular Biology	Methods in Molecular Biology, 1, 2.27% Methods in Molecular Biology 1 publication, 2.27%
Plant Cell	Plant Cell, 1, 2.27% Plant Cell 1 publication, 2.27%

	1 2

Citations by publishers

	1 2 3 4 5 6 7 8 9
Elsevier	Elsevier, 9, 20.45% Elsevier 9 publications, 20.45%
Springer Nature	Springer Nature, 8, 18.18% Springer Nature 8 publications, 18.18%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 5, 11.36% Multidisciplinary Digital Publishing Institute (MDPI) 5 publications, 11.36%
Frontiers Media S.A.	Frontiers Media S.A., 3, 6.82% Frontiers Media S.A. 3 publications, 6.82%
Wiley	Wiley, 3, 6.82% Wiley 3 publications, 6.82%
IEEE	IEEE, 3, 6.82% IEEE 3 publications, 6.82%
Oxford University Press	Oxford University Press, 3, 6.82% Oxford University Press 3 publications, 6.82%
American Chemical Society (ACS)	American Chemical Society (ACS), 2, 4.55% American Chemical Society (ACS) 2 publications, 4.55%
Taylor & Francis	Taylor & Francis, 1, 2.27% Taylor & Francis 1 publication, 2.27%
American Society of Plant Biologists	American Society of Plant Biologists, 1, 2.27% American Society of Plant Biologists 1 publication, 2.27%
	1 2 3 4 5 6 7 8 9

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Fesenko I. et al. Distinct types of short open reading frames are translated in plant cells // Genome Research. 2019. Vol. 29. No. 9. pp. 1464-1477.

GOST all authors (up to 50) Copy

Fesenko I., Kirov I., Kniazev A., Khazigaleeva R., Lazarev V., Kharlampieva D., Grafskaia E., Zgoda V., Butenko I., Arapidi G., Mamaeva A., Ivanov V., Govorun V. M. Distinct types of short open reading frames are translated in plant cells // Genome Research. 2019. Vol. 29. No. 9. pp. 1464-1477.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1101/gr.253302.119

UR - https://doi.org/10.1101%2Fgr.253302.119

TI - Distinct types of short open reading frames are translated in plant cells

T2 - Genome Research

AU - Fesenko, Igor

AU - Kirov, Ilya

AU - Kniazev, Andrey

AU - Khazigaleeva, Regina

AU - Lazarev, Vassili

AU - Kharlampieva, Daria

AU - Grafskaia, Ekaterina

AU - Zgoda, Viktor

AU - Butenko, Ivan

AU - Arapidi, Georgy

AU - Mamaeva, Anna

AU - Ivanov, Vadim

AU - Govorun, Vadim M.

PY - 2019

DA - 2019/08/06 00:00:00

PB - Cold Spring Harbor Laboratory

SP - 1464-1477

IS - 9

VL - 29

SN - 1088-9051

SN - 1549-5469

ER -

BibTex |

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BibTex Copy

@article{2019_Fesenko,

author = {Igor Fesenko and Ilya Kirov and Andrey Kniazev and Regina Khazigaleeva and Vassili Lazarev and Daria Kharlampieva and Ekaterina Grafskaia and Viktor Zgoda and Ivan Butenko and Georgy Arapidi and Anna Mamaeva and Vadim Ivanov and Vadim M. Govorun},

title = {Distinct types of short open reading frames are translated in plant cells},

journal = {Genome Research},

year = {2019},

volume = {29},

publisher = {Cold Spring Harbor Laboratory},

month = {aug},

url = {https://doi.org/10.1101%2Fgr.253302.119},

number = {9},

pages = {1464--1477},

doi = {10.1101/gr.253302.119}

}

MLA

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MLA Copy

Fesenko, Igor, et al. “Distinct types of short open reading frames are translated in plant cells.” Genome Research, vol. 29, no. 9, Aug. 2019, pp. 1464-1477. https://doi.org/10.1101%2Fgr.253302.119.

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Cold Spring Harbor Laboratory

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Genome Research

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Quartile WOS

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10889051 (Print)
15495469 (Electronic)

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