Large-scale identification of mirtrons in Arabidopsis and rice.

PloS One
Yijun Meng, Chaogang Shao

Abstract

A new catalog of microRNA (miRNA) species called mirtrons has been discovered in animals recently, which originate from spliced introns of the gene transcripts. However, only one putative mirtron, osa-MIR1429, has been identified in rice (Oryza sativa). We employed a high-throughput sequencing (HTS) data- and structure-based approach to do a genome-wide search for the mirtron candidate in both Arabidopsis (Arabidopsis thaliana) and rice. Five and eighteen candidates were discovered in the two plants respectively. To investigate their biological roles, the targets of these mirtrons were predicted and validated based on degradome sequencing data. The result indicates that the mirtrons could guide target cleavages to exert their regulatory roles post-transcriptionally, which needs further experimental validation.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Jun 28, 2005·Nucleic Acids Research·Yuanji Zhang
Dec 17, 2005·Bioinformatics·Peter SteffenRobert Giegerich
May 4, 2006·Annual Review of Plant Biology·Matthew W Jones-RhoadesBonnie Bartel
Nov 16, 2006·Bioinformatics·Snorre A HelvikPål Saetrom
Dec 16, 2006·Nucleic Acids Research·Cameron JohnsonVenkatesan Sundaresan
Jun 26, 2007·Nature·J Graham RubyDavid P Bartel
Oct 30, 2007·Molecular Cell·Eugene BerezikovEric C Lai
Nov 10, 2007·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
May 27, 2008·Trends in Plant Science·Michael J Axtell, John L Bowman
Jun 11, 2008·Nature Biotechnology·Marcelo A GermanPamela J Green
Jun 17, 2008·Trends in Plant Science·John W S BrownManuel Echeverria
Aug 9, 2008·Genome Research·Qian-Hao ZhuChris Helliwell
Oct 23, 2008·Nucleic Acids Research·Tanya BarrettRon Edgar
Jan 24, 2009·Nature Reviews. Molecular Cell Biology·V Narry KimMikiko C Siomi
Feb 26, 2009·Cell·Richard W Carthew, Erik J Sontheimer
Feb 26, 2009·Cell·Olivier Voinnet
Jul 7, 2009·Annual Review of Cell and Developmental Biology·Xuemei Chen
Dec 29, 2009·Nature Genetics·Eugene BerezikovEric C Lai
Jul 3, 2010·Molecular Genetics and Genomics : MGG·Keita MiyoshiHaruhiko Siomi
Jan 26, 2011·Briefings in Bioinformatics·Yijun MengMing Chen
May 31, 2011·Nucleic Acids Research·Xinbin Dai, Patrick Xuechun Zhao
Jun 30, 2011·Biochimie·Jakub O Westholm, Eric C Lai

❮ Previous
Next ❯

Citations

Jan 18, 2013·BMC Genomics·Katarzyna KruszkaZofia Szweykowska-Kulinska
Nov 2, 2013·BMC Plant Biology·Aliki KapazoglouAthanasios S Tsaftaris
Nov 14, 2012·Briefings in Functional Genomics·Nicolás G BolognaJavier F Palatnik
Feb 22, 2016·Rice·Patricia Baldrich, Blanca San Segundo
Jun 27, 2012·Wiley Interdisciplinary Reviews. RNA·Helen J CurtisMatthew J A Wood
Jun 27, 2015·Functional & Integrative Genomics·Hikmet Budak, B Ani Akpinar
Jun 4, 2015·Cellular and Molecular Life Sciences : CMLS·Fabian Afonso-Grunz, Sören Müller
Feb 9, 2017·Trends in Genetics : TIG·Iben Daugaard, Thomas Birkballe Hansen
Dec 15, 2017·Briefings in Functional Genomics·Xiaoxia MaYijun Meng
Feb 23, 2019·Journal of Integrative Plant Biology·Yan ZhouXiaocheng Jiang
Aug 14, 2019·Journal of Biomolecular Structure & Dynamics·Sevgi Marakli
Feb 7, 2020·Nucleic Acids Research·Anushree NarjalaPadubidri V Shivaprasad
Jan 6, 2017·Nucleic Acids Research·Florent HubéClaire Francastel
Sep 28, 2018·Plant Methods·Umidjon ShapulatovAlexander R van der Krol
Dec 29, 2012·Journal of Genetics·G D YangC C Zheng
Jun 6, 2018·Frontiers in Genetics·Dongliang YuYijun Meng
May 21, 2021·Functional & Integrative Genomics·Sailaja BhogireddyHimabindu Kudapa
May 19, 2021·Biotechnology and Bioengineering·Hui ZhouBu-Jun Shi
Jun 23, 2021·Wiley Interdisciplinary Reviews. RNA·Uzma SalimPerumal Vivekanandan
Jul 15, 2021·Journal of Experimental Botany·Carlos Hernán Barrera-RojasFabio Tebaldi Silveira Nogueira

❮ Previous
Next ❯

Methods Mentioned

BETA
degradome sequencing

Software Mentioned

RNAshapes
miRU
BLAST

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.