Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants

RNA Biology
Yijun MengMing Chen

Abstract

In this survey, we did a large-scale re-examination of the currently registered plant microRNAs (miRNAs) in miRBase (release 17), which were annotated based on the already established criteria. Huge public small RNA (sRNA) high-throughput sequencing (HTS) data sets were employed to interrogate the accuracy of the miRBase registries based on the secondary structures of the miRNA precursors and the expression levels of the miRNAs and the miRNA*s. Our results raised the caveat that the current miRNA lists in miRBase should be carefully refined, and more strict criteria should be implemented for new miRNA registration. Through this work, we proposed a structure- and expression-based strategy to validate a set of defined miRNA genes, or even to annotate novel ones based on currently available sRNA HTS data sets. We also hope to inspire further research efforts on the manual refinement of the current miRNA gene lists.

References

Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Feb 20, 2003·RNA·Victor AmbrosThomas Tuschl
Dec 19, 2003·Nucleic Acids Research·Sam Griffiths-Jones
Dec 17, 2005·Bioinformatics·Peter SteffenRobert Giegerich
May 4, 2006·Annual Review of Plant Biology·Matthew W Jones-RhoadesBonnie Bartel
Nov 10, 2007·Nucleic Acids Research·Sam Griffiths-JonesAnton J Enright
Jul 18, 2008·Proceedings of the National Academy of Sciences of the United States of America·Zhicheng DongNina Fedoroff
Dec 17, 2008·The Plant Cell·Blake C MeyersJian-Kang Zhu
May 12, 2011·RNA Biology·Thomas B HansenJesper B Bramsen

❮ Previous
Next ❯

Citations

Jan 11, 2014·Trends in Plant Science·Richard S TaylorPhilip C J Donoghue
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Dec 3, 2015·Biochemical Pharmacology·Bisrat T Woldemichael, Isabelle M Mansuy
Jul 8, 2015·Briefings in Functional Genomics·Hikmet BudakBurcu Alptekin
Nov 8, 2014·Nucleic Acids Research·Nathan Wong, Xiaowei Wang
Jan 6, 2017·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Richard S TaylorPhilip C J Donoghue
Oct 27, 2017·Nucleic Acids Research·Xiaogang WuKai Wang
Mar 6, 2018·BMC Genomics·Igor I Titov, Pavel S Vorozheykin
Oct 11, 2019·Nucleic Acids Research·Bastian FrommKevin J Peterson
May 23, 2018·Genome Biology and Evolution·James E TarverPhilip C J Donoghue
Apr 12, 2013·Biology of Reproduction·Dong-bao Chen, Wen Wang
Jun 24, 2017·Journal of Integrative Bioinformatics·Ali M YazbeckJana Hertel
Feb 9, 2017·Frontiers in Plant Science·Burcu AlptekinHikmet Budak
Sep 16, 2017·Nucleic Acids Research·Tobias FehlmannAndreas Keller
Aug 30, 2018·BMC Bioinformatics·Yin LuMarc K Halushka
Mar 2, 2019·Nucleic Acids Research·Julia AllesEckart Meese
Jul 14, 2017·Scientific Reports·Nicole LudwigEckart Meese
Dec 5, 2020·Pharmaceuticals·Orazio Fortunato, Marilena V Iorio
Oct 16, 2020·Journal of the National Cancer Institute·Xinyi LiuXiaowei Wang

❮ Previous
Next ❯

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.