Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds

G3 : Genes - Genomes - Genetics
Mohammad Reza Bakhtiarizadeh, Seyed Alireza Salami

Abstract

Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the ...Continue Reading

References

Mar 8, 2000·Mechanisms of Development·X CaubitL Fasano
Oct 20, 2001·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·B XueM B Zemel
Jul 18, 2002·Progress in Lipid Research·John E Cronan, Grover L Waldrop
Nov 2, 2005·International Journal of Obesity : Journal of the International Association for the Study of Obesity·M KaamanI Dahlman
May 10, 2006·PLoS Genetics·Vladimir B BajicYoshihide Hayashizaki
Apr 25, 2007·Biochemical and Biophysical Research Communications·Yasnory T F SasakiTetsuro Hirose
May 9, 2007·Nucleic Acids Research·Andreas UntergasserJack A M Leunissen
Jun 15, 2010·BMC Genomics·Angela CánovasRamona N Pena
Apr 29, 2011·The Journal of Immunology : Official Journal of the American Association of Immunologists·Salima SadallahJürg A Schifferli
Mar 20, 2012·Nature Methods·Tamás NepuszAlberto Paccanaro
Jun 22, 2012·Molecular Biology Reports·Hirokazu MatsumotoHideyuki Mannen
Feb 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Lei SunJohn L Rinn
Mar 16, 2013·Animal Genetics·B MoioliF Napolitano
Mar 26, 2013·Gene·Mohammad Reza BakhtiarizadehEsmaeil Ebrahimie
Jul 6, 2013·Cell·Igor Ulitsky, David P Bartel
Oct 31, 2013·Diabetes·Arianna MarinoMassimo Federici
Jan 28, 2014·Nature·Anamaria NecsuleaHenrik Kaessmann
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Oct 22, 2014·Nucleic Acids Research·Xiu Cheng QuekMarcel E Dinger
Jan 20, 2015·Nature Genetics·Matthew K IyerArul M Chinnaiyan
Feb 19, 2015·Nature Biotechnology·Mihaela PerteaSteven L Salzberg
Mar 10, 2015·Nature Methods·Daehwan KimSteven L Salzberg
Nov 21, 2015·Nucleic Acids Research·Yi ZhaoRunsheng Chen
Nov 26, 2015·Nucleic Acids Research·Zhi-Liang HuJames M Reecy
Dec 17, 2015·Nature Reviews. Genetics·Jeffrey J Quinn, Howard Y Chang
Mar 16, 2016·Molecular Metabolism·Zheng Chen
Mar 24, 2016·Genome Génome / Conseil National De Recherches Canada·Mohammad Reza BakhtiarizadehSeyed Alireza Salami
May 5, 2016·Nucleic Acids Research·Maxim V KuleshovAvi Ma'ayan

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Datasets Mentioned

BETA
PRJNA508203

Methods Mentioned

BETA
RNA-Seq
electrophoresis
cDNA
cDNA library construction
GTPase

Software Mentioned

HMMER
blast search
AnimalQTLdb
ilncRNA
BLASTn
Cytoscape
R
RepeatMasker
Hisat2
cummerbund R package

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