Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation

Proceedings of the National Academy of Sciences of the United States of America
Jérémie BazinJulia Bailey-Serres

Abstract

Eukaryotic transcriptomes contain a major non-protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous (Pi) nutrition. Homodirectional changes in steady-state mRNA abundance and translation were observed for all but 265 annotated protein-coding genes. Of the translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on the principal protein-coding region. Nearly one-half of the 2,382 lncRNAs detected had ribosome footprints, including 56 with significantly altered translation under Pi-limited nutrition. The prediction of translated small ORFs (sORFs) by quantitation of translation termination and peptidic analysis identified lncRNAs that produce peptides, including several deeply evolutionarily conserved and significantly Pi-regulated lncRNAs. Furthermore, we discovered that natural antisense transcripts (NATs) frequently have actively translated sORFs, including five with low-Pi up-regulation that correlated with enhanced tra...Continue Reading

References

Apr 27, 2005·Cell·Edwards AllenJames C Carrington
Jun 16, 2005·Plant Physiology·María Eugenia ZanettiJulia Bailey-Serres
Aug 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Julie MissonMarie-Christine Thibaud
Nov 24, 2005·Current Biology : CB·Hiroaki FujiiJian-Kang Zhu
Mar 1, 2006·BMC Bioinformatics·Joshua S YuanC Neal Stewart
Nov 8, 2006·Plant, Cell & Environment·Matthieu ReymondThierry Desnos
Jul 24, 2007·Nature Genetics·José Manuel Franco-ZorrillaJavier Paz-Ares
Dec 7, 2007·Plant Physiology·Mansour KarimiPierre Hilson
May 20, 2008·Developmental Cell·Brian D GregoryJoseph R Ecker
Jan 31, 2009·EMBO Reports·Felipe F Felippes, Detlef Weigel
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jul 10, 2009·Methods in Molecular Biology·Angelika MustrophJulia Bailey-Serres
Jul 30, 2009·Nature Reviews. Molecular Cell Biology·Mohammad Ali Faghihi, Claes Wahlestedt
Oct 22, 2009·Proceedings of the National Academy of Sciences of the United States of America·Angelika MustrophJulia Bailey-Serres
Jan 26, 2011·Integrative Biology : Quantitative Biosciences From Nano to Macro·Katja BaerenfallerSacha Baginsky
May 3, 2011·Methods in Molecular Biology·Erika Varkonyi-Gasic, Roger P Hellens
Jun 21, 2011·Trends in Plant Science·Benjamin PéretThierry Desnos
Jul 20, 2011·Proceedings of the National Academy of Sciences of the United States of America·Sonja ReilandSacha Baginsky
Jan 19, 2012·PLoS Genetics·Angela BruexJohn Schiefelbein
May 29, 2012·The Plant Cell·Tzu-Yin LiuTzyy-Jen Chiou
Jun 16, 2012·Frontiers in Plant Science·Matthias Hirsch-HoffmannKatja Baerenfaller
Jul 31, 2012·Molecular Cell·Je-Hyun YoonMyriam Gorospe
Sep 1, 2012·Frontiers in Plant Science·Richard A Jorgensen, Ana E Dorantes-Acosta
Sep 8, 2012·Nature·Sarah DjebaliThomas R Gingeras
Mar 26, 2013·The EMBO Journal·Mikhail SchepetilnikovLyubov A Ryabova
May 4, 2013·Molecular Biology and Evolution·Daniel Hupalo, Andrew D Kern
Jul 6, 2013·Cell·Igor Ulitsky, David P Bartel
Jul 25, 2013·The Plant Cell·Kestrel Rogers, Xuemei Chen
Aug 3, 2013·The Arabidopsis Book·Bijoyita Roy, Albrecht G von Arnim

❮ Previous
Next ❯

Citations

Apr 27, 2018·Journal of Experimental Botany·Waleed S AlbihlalPhilip M Mullineaux
Oct 20, 2018·Molecular Omics·Indrek Koppel, Mike Fainzilber
Sep 2, 2018·Journal of Integrative Plant Biology·Zhaoliang ZhangWilliam J Lucas
Apr 21, 2019·Plant & Cell Physiology·Tomoya FujitaShintaro Iwasaki
Dec 5, 2019·The Plant Journal : for Cell and Molecular Biology·Sharon B GraySiobhan M Brady
Jun 28, 2020·Digestive Diseases and Sciences·Zhi-Feng Jiang, Lin Zhang
Jun 20, 2018·Proceedings of the National Academy of Sciences of the United States of America·Yukio KuriharaMinami Matsui
Oct 12, 2019·Science·Mauricio A ReynosoJulia Bailey-Serres
Mar 30, 2020·The Journal of Infectious Diseases·Antón Vila-SanjurjoMariana Leguia
Jan 2, 2019·BMC Genomics·Chao Zeng, Michiaki Hamada
Apr 27, 2019·Frontiers in Genetics·Qi YanXuezhu Feng
May 6, 2020·Wiley Interdisciplinary Reviews. RNA·Ricardo A Urquidi CamachoAlbrecht G von Arnim
Jul 18, 2018·Frontiers in Plant Science·Serina M Mazzoni-Putman, Anna N Stepanova
Jan 13, 2019·Nature Communications·Caihuan TianYuling Jiao
Oct 6, 2020·Frontiers in Plant Science·Xiaoyu YangLin Liu
Jun 14, 2018·Frontiers in Plant Science·Ying-Ping GaiXian-Ling Ji
Jan 29, 2021·Cellular and Molecular Life Sciences : CMLS·Rui VitorinoNobuyoshi Akimitsu
Jan 30, 2021·Neural Regeneration Research·Viviana Nociti, Massimo Santoro
Feb 19, 2021·Nature Communications·Hong ZhangJian Lu
Apr 16, 2020·Trends in Genetics : TIG·Youqiong YeLeng Han
Feb 18, 2021·ELife·Luca MinatiMassimiliano Clamer
Mar 7, 2021·Non-coding RNA·Camille Fonouni-FardeMartin Crespi
May 1, 2021·International Journal of Molecular Sciences·Taeyoung UmSoo Chul Park
May 13, 2019·Molecular Immunology·Swati DahariyaRavi Kumar Gutti
May 17, 2021·BMC Molecular and Cell Biology·Simone G MoroM Mar Albà
Jul 6, 2021·Frontiers in Plant Science·Yan LiangLin Li

❮ Previous
Next ❯

Methods Mentioned

BETA
ribo-seq
affinity purification
RNA-seq
sRNA-seq
acetylation
dsRNA-seq
targeted mutations
transfection
Small
RNA Sequencing

Software Mentioned

Unix
RRS
Bioconductor
R
Cufflinks
Classification SuperViewer
HTSFilter
systemPipeR
RiboTaper

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Proceedings of the National Academy of Sciences of the United States of America
Piyada JuntawongJulia Bailey-Serres
Proceedings of the National Academy of Sciences of the United States of America
Polly Yingshan HsuPhilip N Benfey
DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes
Hongmei LiZhifeng Shao
© 2022 Meta ULC. All rights reserved