title: Characteristics of long non-coding RNAs in the Brown Norway rat and alterations in the Dahl salt-sensitive rat.
abstract: Long non-coding RNAs (lncRNAs) are potentially important mediators of genomic regulation. lncRNAs, however, remain poorly characterized in the rat model organism widely used in biomedical research. Using poly(A)-independent and strand-specific RNA-seq, we identified 1,500 to 1,800 lncRNAs expressed in each of the following tissues of Brown Norway rats: the renal cortex, renal outer medulla, liver, cardiac left ventricle, adrenal gland, and hypothalamus. Expression and the binding of histone H3K4me3 to promoter regions were confirmed for several lncRNAs. Rat lncRNA expression appeared to be more tissue-specific than mRNA. Rat lncRNAs had 4.5 times fewer exons and 29% shorter transcripts than mRNA. The median cumulative abundance of rat lncRNAs was 53% of that of mRNA. Approximately 28% of the lncRNAs identified in the renal outer medulla appeared to lack a poly(A) tail. Differential expression of 74 lncRNAs was detected in the renal outer medulla between Dahl SS rats, a model of salt-sensitive hypertension, and salt-insensitive, congenic SS.13(BN26) rats fed a high-salt diet. Two of the differentially expressed lncRNAs, which were confirmed, were located within the congenic region and contained several sequence variants. The study identified genome-wide characteristics of lncRNAs in the rat model and suggested a role of lncRNAs in hypertension.
authors.affiliation: 1] Department of Nephrology and Rheumatology, Shanghai JiaoTong University Affiliated Sixth People's Hospital, Shanghai, China [2] Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA [3] Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.affiliation: Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310029, China.
authors.forename: Liping
authors.initials: L
authors.lastname: Li
authors.affiliation: Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang 310029, China.
authors.forename: Haiming
authors.initials: H
authors.lastname: Xu
authors.affiliation: 1] Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA [2] Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
authors.forename: Chun
authors.initials: C
authors.lastname: Yang
authors.affiliation: Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA.
authors.forename: Allen W
authors.initials: AW
authors.lastname: Cowley
authors.affiliation: Department of Nephrology and Rheumatology, Shanghai JiaoTong University Affiliated Sixth People's Hospital, Shanghai, China.
authors.forename: Niansong
authors.initials: N
authors.lastname: Wang
authors.affiliation: 1] Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA [2] Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA [3] Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.
authors.forename: Pengyuan
authors.initials: P
authors.lastname: Liu
authors.affiliation: 1] Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA [2] Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, WI, USA.
authors.forename: Mingyu
authors.initials: M
authors.lastname: Liang
mesh_terms: D000818:Animals; D056426:Genetic Loci; D006657:Histones / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000378:metabolism*; D051381:Rats; D011914:Rats, Inbred BN; D020303:Rats, Inbred Dahl; D017423:Sequence Analysis, RNA; D017673:Sodium Chloride, Dietary / Q000378:metabolism; D059467:Transcriptome
chemical_list: D006657:Histones; D062085:RNA, Long Noncoding; D017673:Sodium Chloride, Dietary