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.

DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory organ of Corti

“…Motifs for several known inner ear TFs were found enriched within all LMRs analyzed, such as Atoh1, Stat3, Gata3, Sox10 and Sox2 and were also correlated with available inner ear SE transcriptomes [6,8]. It is clear from the TFBS enrichment heatmap across time points that some motifs are enriched at one time point and not others, likely reflecting a temporal dimension to the relevance of the binding of TF and their asserted regulation.…”

“…We also examined the regions associated with deafness loci with unknown genes described in the Hereditary Hearing Loss Homepage (http://hereditaryhearingloss.org/). Chromosomal regions, derived from microsatellite markers or coordinates of cytogenetic bands, were located in the relevant manuscripts, identified in hg19, and converted to the homologous mouse interval (mm10) [8]. We identified SE LMRs in all of these regions, suggesting they may be associated with deafness in humans.…”

“…We compared available transcriptomic data available for SE [6,8] to the DMR dynamics at genes promoters ( Fig. 5a-b) and genebodies ( Fig.…”

“…In order to relate to the interaction of DNA methylation and the expression level of genes, we focused on genes that exhibit an expected correlation between gene expression in our RNA seq data [8] and the DevTrans DMRs (Fig. 5d); specifically, the negative correlation between DNA methylation of CpG on gene promoter and the gene's differential expression and positive [8] plotted against the gene associated DMR differential methylation score. a DMRs analyzed in the CpG context and residing in gene promoters.…”

“…Transcriptomic approaches have been taken in order to elucidate the genetic determinants that drive each decision during the development and differentiation process of the inner ear sensory organs [4][5][6]. RNA high-throughput sequencing studies of the SE have led to the identification and characterization of non-coding RNAs, including microRNAs and long non-coding (lnc)RNAs [7,8]. RNA transcriptomic analysis at single-cell level has been undertaken in this tissue [9][10][11], setting the stage for understanding the role of the individual cell types encompassing the SE tissue.…”