The constitutive differential transcriptome of a brain circuit for vocal learning

Abstract

BackgroundThe ability to imitate the vocalizations of other organisms, a trait known as vocal learning, is shared by only a few organisms, including humans, where it subserves the acquisition of speech and language, and 3 groups of birds. In songbirds, vocal learning requires the coordinated activity of a set of specialized brain nuclei referred to as the song control system. Recent efforts have revealed some of the genes that are expressed in these vocal nuclei, however a thorough characterization of the transcriptional specializations of this system is still missing. We conducted a rigorous and comprehensive analysis of microarrays, and conducted a separate analysis of 380 genes by in situ hybridizations in order to identify molecular specializations of the major nuclei of the song system of zebra finches (Taeniopygia guttata), a songbird species.ResultsOur efforts identified more than 3300 genes that are differentially regulated in one or more vocal nuclei of adult male birds compared to the adjacent brain regions. Bioinformatics analyses provided insights into the possible involvement of these genes in molecular pathways such as cellular morphogenesis, intrinsic cellular excitability, neurotransmission and neuromodulation, axonal guidance and cela-to-cell interactions, and cell survival, which are known to strongly influence the functional properties of the song system. Moreover, an in-depth analysis of specific gene families with known involvement in regulating the development and physiological properties of neuronal circuits provides further insights into possible modulators of the song system.ConclusionOur study represents one of the most comprehensive molecular characterizations of a brain circuit that evolved to facilitate a learned behavior in a vertebrate. The data provide novel insights into possible molecular determinants of the functional properties of the song control circuitry. It also provides lists of compelling targets for pharmacological and genetic manipulations to elucidate the molecular regulation of song behavior and vocal learning.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4578-0) contains supplementary material, which is available to authorized users.

Molecular architecture of the zebra finch arcopallium

“…Seeking additional support for these findings, we next re‐examined the ZEBrA database and identified another 171 genes that were general markers of the entire arcopallium or differentially expressed in the various arcopallial domains and/or subdomains defined in the present study (Table ; details in TAble S1). A large subset of these genes ( n = 124) represent RA markers, since they derived from microarray screenings for song nuclei markers (Lovell, Clayton, Replogle, & Mello, ; Lovell, Huizinga, Friedrich, Wirthlin, & Mello, ; Pfenning et al, ). Because of differences in cutting angle and/or covered regions in the brains used to generate ZEBrA, the detailed definitions of arcopallial subdomains differs somewhat across genes.…”

“…The large set of RA markers in ZEBrA derives from microarray screenings (Lovell et al, 2008;Pfenning et al, 2014). While recently validated through microarray re-analysis and confirmatory in situs (Lovell et al, 2018), the contrasting microarray sample was ventrolateral to RA ( fig. S17a in Pfenning et al, 2014), likely within AIv (see Figure 16b).…”

Estrogen and sex-dependent loss of the vocal learning system in female zebra finches

“…The above findings revealed that one gene, CADPS2, which is specialized in juvenile male Area X is also impacted by estrogen manipulation in juvenile females. However, many genes in adults have specialized expression in different song nuclei (Lovell et al, 2008;Lovell et al, 2018;Olson et al, 2015;Pfenning et al, 2014). Prior work from our lab has shown that SLIT1, an axon guidance ligand, has specialized down regulation in RA beginning at PHD20-35 in males and females, but its receptor ROBO1 has specialized upregulation in RA around PHD35, followed by down regulation in adulthood in males with no changes in females (Wang et al, 2015).…”

Curation of microarray oligonucleotides and corresponding ESTs/cDNAs used for gene expression analysis in zebra finches

“…Other oligos were derived from cDNA cloning artifacts, or erroneous sequence selection. By removing and correcting these errors, we generated what we consider the most thorough and accurate constitutive transcriptome of the zebra finch song control system [ 27 ]. We describe this curation effort below.…”