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

Mammalian genomes are highly complex and can be regulated at multiple levels, often imposed by a class of RNA molecules, long intervening non-coding RNAs (lincRNAs). Their transcripts are more than 200 nucleotides in length, they are capped, polyadenylated and spliced, similar to mRNAs, but less abundant, but with higher tissue specificity. lincRNAs are versatile and can act on numerous levels and have been linked to development, epigenetic processes and disease. We performed a whole-genome identification of lincRNAs using RNA-seq at two developmental stages of the mouse inner ear sensory epithelium of the cochlea and vestibule. We identified 1,921 lncRNA genes, 1369 of which are intergenic. Of these, 403 are novel, as they were not annotated in the latest Ensembl/GENCODE annotation (Ensembl release 84). We then examined specificity by analyzing the developmental profiles at embryonic day 16.5 and at birth. The spatial and temporal patterns were examined for three lincRNAs, which were in close proximity to genes associated with hearing and deafness. Our findings demonstrate that lincRNAs are prevalent in the sensory epithelium of the mouse cochlea and vestibule and are likely to play key roles in the regulation of critical pathways for hearing and balance. RNA-seq of RNA from two tissues at two developmental times, each with three biological replicates Please note that the P0 samples (GSM2560443-48) are re-analyzed sample records of GSM1975057-62 (in GSE76149).