Substantial expression of novel small open reading frames in<i>Oryza sativa</i>

Okamoto, Masanori; Higuchi-Takeuchi, Mieko; Shimizu, Minami; Shinozaki, Kazuo; Hanada, Kousuke

doi:10.4161/psb.27848

Cited by 9 publications

(8 citation statements)

References 26 publications

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“…They then systematically overexpressed 473 sORFs in Arabidopsis and found that 49 of them produced visible phenotypes . Searching for homologs of these 49 sORFs led to the identification of 35 rice sORFs, two‐thirds of which are located within intergenic regions . Therefore, it is likely that many more functional sORFs are still awaiting to be discovered in plant genomes.…”

Section: Functions Of Translated Sorfsmentioning

confidence: 99%

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

Hsu

Benfey

2017

Proteomics

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Peptides encoded by small open reading frames (sORFs, usually <100 codons) play critical regulatory roles in plant development and environmental responses. Despite their importance, only a small number of these peptides have been identified and characterized. Genomic studies have revealed that many plant genomes contain thousands of possible sORFs, which could potentially encode small peptides. The challenge is to distinguish translated sORFs from nontranslated ones. Here, we highlight advances in methodologies for identifying these hidden sORFs in plant genomes, including ribosome profiling and proteomics. We also examine the evidence for new peptides arising from sORFs and discuss their functions in plant development, environmental responses, and translational control.

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Section: Functions Of Translated Sorfsmentioning

confidence: 99%

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

Hsu

Benfey

2017

Proteomics

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“…Previous studies suggest that plant genomes contain more SSP genes than those that have been identified until now and whose function remains to be established ( Hanada et al , 2013 ; Lease and Walker, 2006 , 2010 ; Okamoto et al , 2014 ; Silverstein et al , 2007 ). Indeed, the annotation of genes coding for SSPs is problematic because they harbour fewer characteristics of protein-coding sequences than larger genes and homology search linking sequence and function is restricted to domains coding for just a few amino acid residues conserved across SSP families.…”

Section: Introductionmentioning

confidence: 99%

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

Ghorbani

Lin

Parizot

et al. 2015

EXBOTJ

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“…These diverse functions substantiate the bi-functional nature of ENOD40 . Recent studies in Arabidopsis and rice have identified a number of RNAs similar to ENOD40 that can code for short ORFs [53] , [54] . It is conceivable that these are also potential cncRNAs.…”

Section: Bi-functional Rnas In Plantsmentioning

confidence: 99%

cncRNAs: Bi-functional RNAs with protein coding and non-coding functions

Kumari

Sampath

2015

Seminars in Cell & Developmental Biology

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For many decades, the major function of mRNA was thought to be to provide protein-coding information embedded in the genome. The advent of high-throughput sequencing has led to the discovery of pervasive transcription of eukaryotic genomes and opened the world of RNA-mediated gene regulation. Many regulatory RNAs have been found to be incapable of protein coding and are hence termed as non-coding RNAs (ncRNAs). However, studies in recent years have shown that several previously annotated non-coding RNAs have the potential to encode proteins, and conversely, some coding RNAs have regulatory functions independent of the protein they encode. Such bi-functional RNAs, with both protein coding and non-coding functions, which we term as ‘cncRNAs’, have emerged as new players in cellular systems. Here, we describe the functions of some cncRNAs identified from bacteria to humans. Because the functions of many RNAs across genomes remains unclear, we propose that RNAs be classified as coding, non-coding or both only after careful analysis of their functions.

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Substantial expression of novel small open reading frames inOryza sativa

Cited by 9 publications

References 26 publications

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

Small but Mighty: Functional Peptides Encoded by Small ORFs in Plants

Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays

cncRNAs: Bi-functional RNAs with protein coding and non-coding functions

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