Song exposure regulates known and novel microRNAs in the zebra finch auditory forebrain

Abstract

BackgroundIn an important model for neuroscience, songbirds learn to discriminate songs they hear during tape-recorded playbacks, as demonstrated by song-specific habituation of both behavioral and neurogenomic responses in the auditory forebrain. We hypothesized that microRNAs (miRNAs or miRs) may participate in the changing pattern of gene expression induced by song exposure. To test this, we used massively parallel Illumina sequencing to analyse small RNAs from auditory forebrain of adult zebra finches exposed to tape-recorded birdsong or silence.ResultsIn the auditory forebrain, we identified 121 known miRNAs conserved in other vertebrates. We also identified 34 novel miRNAs that do not align to human or chicken genomes. Five conserved miRNAs showed significant and consistent changes in copy number after song exposure across three biological replications of the song-silence comparison, with two increasing (tgu-miR-25, tgu-miR-192) and three decreasing (tgu-miR-92, tgu-miR-124, tgu-miR-129-5p). We also detected a locus on the Z sex chromosome that produces three different novel miRNAs, with supporting evidence from Northern blot and TaqMan qPCR assays for differential expression in males and females and in response to song playbacks. One of these, tgu-miR-2954-3p, is predicted (by TargetScan) to regulate eight song-responsive mRNAs that all have functions in cellular proliferation and neuronal differentiation.ConclusionsThe experience of hearing another bird singing alters the profile of miRNAs in the auditory forebrain of zebra finches. The response involves both known conserved miRNAs and novel miRNAs described so far only in the zebra finch, including a novel sex-linked, song-responsive miRNA. These results indicate that miRNAs are likely to contribute to the unique behavioural biology of learned song communication in songbirds.

Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation

“…Contrary to mammals, birds do not have global dosage compensation and they therefore display more pervasive transcriptomic differences between the sexes: The bird Z Chromosome is present in two copies in males, whereas females carry one Z and one W Chromosome, and Z-linked protein-coding genes are, on average, expressed at 1.5-fold higher levels in males (Ellegren et al 2007;Itoh et al 2007;Mank and Ellegren 2009;Julien et al 2012). Consistent with incomplete dosage compensation, the Z-linked miRNA miR-2954-3p was found to be male-biased in birds (Zhao et al 2010;Luo et al 2012), and studies in zebra finch suggested a role for the miRNA in sex-specific song response (Gunaratne et al 2011;Lin et al 2014). The role of miR-2954-3p in non-singing species, such as chicken, has not been extensively explored, although its strongly male-biased expression throughout chicken development hints at a contribution of the miRNA toward the establishment of sex identity in individual cells, especially as this feature is not dependent on gonadal hormones in chicken (Zhao et al 2010).…”

The gene vitellogenin affects microRNA regulation in honey bee (Apis mellifera) fat body and brain

“…But the recent emergence of non-coding RNAs highlights the complexity of the gene expression networks that regulate many biological processes (Mattick and Gagen, 2001). Accordingly, a growing body of evidence has linked microRNA expression and behavioral traits (Kadener et al, 2009;Gunaratne et al, 2011;Jin et al, 2011;Zhan et al, 2011). We herein investigated whether microRNAs may work downstream of Vg in order to effect social changes.…”

“…MicroRNAs are able to act in the regulation of gene expression within (Chen et al, 2007) as well as between tissues . In many organisms, they participate in the regulation of complex behavioral phenotypes, such as migratory behavior of butterflies (Zhan et al, 2011), circadian rhythms of flies (Kadener et al, 2009), food-choice in giant pandas (Jin et al, 2011) and song communication in zebra finches (Gunaratne et al, 2011). Moreover, they are linked to oxidative stress (Hulsmans et al, 2011) as well as immunity (Garbuzov and Tatar, 2010;Fullaondo and Lee, 2012) and lifespan in Drosophila melanogaster (Liu et al, 2012b).…”

Avian transcriptomics: opportunities and challenges

“…In birds, upregulation of miRNAs has been observed in chicken and ducks infected with AIV (Li et al 2015;Wang et al 2012), evall et al 2015). Further, the miRNA profile was altered in the auditory forebrain of Zebra Finches when they heard bird song (Gunaratne et al 2011). This shows that miRNAs are involved in various biological functions in birds, ranging from the immune response to song communication, and that they are likely involved in more functions as well, although they have largely been overlooked so far.…”