Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development

Scientific Reports
Danillo PinhalCesar Martins

Abstract

MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage,...Continue Reading

References

Jun 5, 2002·Genome Research·W James KentDavid Haussler
Mar 6, 2003·Genome Research·John S TaylorYves Van de Peer
Sep 26, 2003·Nature·Yoontae LeeV Narry Kim
Oct 22, 2003·Cell·Anastasia KhvorovaSumedha D Jayasena
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 24, 2004·Nature Reviews. Genetics·Lin He, Gregory J Hannon
Nov 3, 2004·Nature Reviews. Genetics·Hiroaki Kitano
May 28, 2005·Science·Erno WienholdsRonald H A Plasterk
Aug 23, 2005·FEBS Letters·Erno Wienholds, Ronald H A Plasterk
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Jan 20, 2006·Nature·Gerhard M SchrattMichael E Greenberg
Feb 18, 2006·Molecular Cell·Christian P PetersenPhillip A Sharp
Mar 15, 2006·Cell·Ronald H A Plasterk
Jun 1, 2006·Nature Genetics·Eugene BerezikovRonald H A Plasterk
Jul 14, 2006·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Lorenzo F SempereKevin J Peterson
Oct 31, 2006·Nature Genetics·Eugene BerezikovRonald H A Plasterk
Mar 9, 2007·Genes & Development·Joel R NeilsonPhillip A Sharp
Sep 21, 2007·Nucleic Acids Research·S Sai Lakshmi, Shipra Agrawal
Jan 17, 2008·Nature Reviews. Genetics·Witold FilipowiczNahum Sonenberg
Feb 22, 2008·Proceedings of the National Academy of Sciences of the United States of America·Alysha M HeimbergKevin J Peterson
Apr 1, 2008·Nature Structural & Molecular Biology·Katsutomo OkamuraEric C Lai
Apr 18, 2008·Sexual Development : Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation·A CnaaniT D Kocher
May 10, 2008·Bioinformatics·Kay PrüferJanet Kelso
May 24, 2008·Molecular Cell·Ulf Andersson ØromAnders H Lund
May 31, 2008·BMC Genomics·Elizabeth J ThatcherJames G Patton
Nov 19, 2008·BMC Bioinformatics·Stephan H BernhartPeter F Stadler
Feb 26, 2009·Cell·Phillip A Sharp
Mar 25, 2009·Bioinformatics·Eric P NawrockiSean R Eddy
Sep 17, 2009·Genome Research·Elzo de WitEugene Berezikov
Feb 2, 2010·Nature·Foteini ChristodoulouDetlev Arendt
Jun 11, 2010·Annual Review of Biochemistry·Marc Robert FabianWitold Filipowicz
Sep 8, 2010·Genome Biology and Evolution·Antonio MarcoSam Griffiths-Jones
Oct 6, 2010·BMC Genomics·Ludwig Christian G HinskeLucila Ohno-Machado
Nov 30, 2010·BMC Bioinformatics·Ari Löytynoja, Nick Goldman
Dec 21, 2010·Genome Biology and Evolution·Yong-Hwee E LohJ Todd Streelman
Feb 1, 2011·Briefings in Bioinformatics·Melissa J HubiszAdam Siepel
Sep 14, 2011·Nucleic Acids Research·Marc R FriedländerNikolaus Rajewsky
Nov 19, 2011·Nature Reviews. Genetics·Eugene Berezikov
Jan 3, 2012·Genome Biology·Nicole CloonanSean M Grimmond
Aug 1, 2012·Sexual Development : Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation·T T BizuayehuI Babiak
Aug 14, 2012·Trends in Genetics : TIG·Corine T NeilsenCameron P Bracken

❮ Previous
Next ❯

Citations

Sep 27, 2019·Scientific Reports·Peiwen XiongPaolo Franchini
May 28, 2019·Epigenetics : Official Journal of the DNA Methylation Society·Tomasz PodgorniakJorge M O Fernandes
Dec 4, 2019·Briefings in Bioinformatics·Fabian KernAndreas Keller
Jul 11, 2021·General and Comparative Endocrinology·Sajid M AlviChun Peng
Sep 22, 2021·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Amanda Oliveira RibeiroDanillo Pinhal

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
Illumina Sequencing
Illumina-sequencing

Software Mentioned

RNAalifold
TreeBest
BLAST
Drosha
UEA small RNA Workbench
phyloP
Python scripts
Galaxy
RealTime Analysis
PHAST package

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.