Dataset Information

Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems.

ABSTRACT: Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction. To help address this need, we performed a whole-genome identification of lncRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 3,239 lncRNA genes, most of which were intergenic (lincRNAs) and 721 are novel. We examined temporal and tissue specificity by analyzing the developmental profiles on embryonic day 16.5 and at birth. The spatial and temporal patterns of three lncRNAs, two of which are in proximity to genes associated with hearing and deafness, were explored further. Our findings indicate that lncRNAs are prevalent in the sensory epithelium of the mouse inner ear and are likely to play key roles in regulating critical pathways for hearing and balance.

SUBMITTER: Ushakov K

PROVIDER: S-EPMC5561060 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems.

Ushakov Kathy K Koffler-Brill Tal T Rom Aviv A Perl Kobi K Ulitsky Igor I Avraham Karen B KB

Scientific reports 20170817 1

Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a r ...[more]

PMID: 28819115

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Project description:BackgroundLong noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an important seed oil crop worldwide and the target of many genetic improvement activities. To understand better the function of lncRNAs in regulating plant metabolic activities, we carried out a genome-wide lncRNA identification of lncRNAs in Brassica napus with a focus on lncRNAs involved in lipid metabolism. Twenty ribosomal RNA depleted strand specific RNA-seq (ssRNA-seq) datasets were generatred using RNAs isolated from B. napus seeds at four developmental stages. For comparison we also included 30 publically available RNA-seq datasets generated from poly(A) enriched mRNAs isolated from from various Brassica napus tissues in our analysis.ResultsA total of 8905 lncRNA loci were identified, including 7100 long intergenic noncoding RNA (lincRNA) loci and 1805 loci generating long noncoding natural antisense transcript (lncNAT). Many lncRNAs were identified only in the ssRNA-seq and poly(A) RNA-seq dataset, suggesting that B. napus has a large lncRNA repertoire and it is necessary to use libraries prepared from different tissues and developmental stages as well as different library preparation approaches to capture the whole spectrum of lncRNAs. Analysis of coexpression networks revealed that among the regulatory modules are networks containing lncRNAs and protein-coding genes related to oil biosynthesis indicating a possible role of lncRNAs in the control of lipid metabolism. One such example is that several lncRNAs are potential regulators of BnaC08g11970D that encodes oleosin1, a protein found in oil bodies and involved in seed lipid accumulation. We also observed that the expression levels of B. napus lncRNAs is positively correlated with their conservation levels.ConclusionsWe demonstrated that the B. napus genome has a large number of lncRNA and that these lncRNAs are expressed broadly across many developmental times and in different tissue types. We also provide evidence indicating that specific lncRNAs appear to be important regulators of lipid biosynthesis forming regulatory networks with transcripts involved in lipid biosynthesis. We also provide evidence that these lncRNAs are conserved in other species of the Brassicaceae family.

Dataset Information

Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems.

Publications

Genome-wide identification and expression profiling of long non-coding RNAs in auditory and vestibular systems.

Similar Datasets

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