Enriched expression and developmental regulation of the middle-weight neurofilament (NF-M) gene in song control nuclei of the zebra finch

Emergence of sex-specific transcriptomes in a sexually dimorphic brain nucleus

We present the transcriptomic changes underlying the development of an extreme neuroanatomical sex difference. The robust nucleus of the arcopallium (RA) is a key component of the songbird vocal motor system. In zebra finch, the RA is initially monomorphic and then atrophies in females but grows up to 7-fold larger in males. Mirroring this divergence, we show here that sex-differential gene expression in the RA expands from hundreds of predominantly sex chromosome Z genes in early development to thousands of predominantly autosomal genes by the time sexual dimorphism asymptotes. Male-specific developmental processes include cell and axonal growth, synapse assembly and activity, and energy metabolism; female-specific processes include cell polarity and differentiation, transcriptional repression, and steroid hormone and immune signaling. Transcription factor binding site analyses support female-biased activation of pro-apoptotic regulatory networks. The extensive and sex-specific transcriptomic reorganization of RA provides insights into potential drivers of sexually dimorphic neurodevelopment.

Friedrich et al. demonstrate extensive transcriptomic sex differences underlying the sexually dimorphic development of vocal nucleus RA in the songbird brain. They find sex-specific gene regulation linked to distinct biological processes, developmental shifts in the relative signal from sex chromosome to autosomal genes, and evidence of female-biased pro-apoptotic regulatory networks.

Intramuscular antagonism of the G-protein coupled estrogen receptor 1 partially affects dimorphic characteristics of the syrinx, but is ineffective within the neural song circuit of zebra finches

Within the zebra finch song system, robust sex differences exist that enable singing behavior in males, but not females. Estradiol is a potent contributor to this process, but how and through which receptor(s) it acts is not clear. Historically, pharmacological manipulations of nuclear estrogen receptors have yielded conflicting results possibly due to method of drug delivery. More recently, the membrane bound G-protein coupled estrogen receptor 1 (GPER1) has also been identified as a potential candidate, but its function has not been fully described. To further investigate the role of GPER1, and the importance of the route of drug administration, a specific antagonist (G-15) was intramuscularly administered to zebra finches for 25 days, starting on the day of hatching. G-15 significantly decreased muscle fiber sizes of ventralis and dorsalis in the syrinx of males only. Dimorphic characteristics of the neural song system were unaffected by this manipulation in either sex. These results contrast with a study in which G-15 was intracranially delivered. In males, select song nuclei were decreased in volume, and in females, syrinx muscle fiber size was increased. Together, these results support the hypothesis that estrogens acting through GPER1 influence dimorphic development of the song system, and that method of drug administration is important in this species.

HDAC3 Inhibitor RGFP966 Modulates Neuronal Memory for Vocal Communication Signals in a Songbird Model

Epigenetic mechanisms that modify chromatin conformation have recently been under investigation for their contributions to learning and the formation of memory. For example, the role of enzymes involved in histone acetylation are studied in the formation of long-lasting memories because memory consolidation requires gene expression events that are facilitated by an open state of chromatin. We recently proposed that epigenetic events may control the entry of specific sensory features into long-term memory by enabling transcription-mediated neuronal plasticity in sensory brain areas. Histone deacetylases, like HDAC3, may thereby regulate the specific sensory information that is captured for entry into long-term memory stores (Phan and Bieszczad, 2016). To test this hypothesis, we used an HDAC3-selective inhibitor (RGFP966) to determine whether its application after an experience with a sound stimulus with unique acoustic features could contribute to the formation of a memory that would assist in mediating its later recognition. We gave adult male zebra finches limited exposure to unique conspecific songs (20 repetitions each, well below the normal threshold to form long-term memory), followed by treatment with RGFP966 or vehicle. In different groups, we either made multi-electrode recordings in the higher auditory area NCM (caudal medial nidopallidum), or determined expression of an immediate early gene, zenk (also identified as zif268, egr-1, ngfi-a and krox24), known to participate in neuronal memory in this system. We found that birds treated with RGFP966 showed neuronal memory after only limited exposure, while birds treated with vehicle did not. Strikingly, evidence of neuronal memory in NCM induced by HDAC3-inhibition was lateralized to the left-hemisphere, consistent with our finding that RGFP966-treatment also elevated zenk expression only in the left hemisphere. The present findings show feasibility for epigenetic mechanisms to control neural plasticity underlying the formation of specific memories for conspecific communication sounds. This is the first evidence in zebra finches that epigenetic mechanisms may contribute to gene expression events for memory of acoustically-rich sensory cues.

Dynamic gene expression in the song system of zebra finches during the song learning period

The brain circuitry that controls song learning and production undergoes marked changes in morphology and connectivity during the song learning period in juvenile zebra finches, in parallel to the acquisition, practice and refinement of song. Yet, the genetic programs and timing of regulatory change that establish the neuronal connectivity and plasticity during this critical learning period remain largely undetermined. To address this question, we used in situ hybridization to compare the expression patterns of a set of 30 known robust molecular markers of HVC and/or area X, major telencephalic song nuclei, between adult and juvenile male zebra finches at different ages during development (20, 35, 50 days post-hatch, dph). We found that several of the genes examined undergo substantial changes in expression within HVC or its surrounds, and/or in other song nuclei. They fit into broad patterns of regulation, including those whose expression within HVC during this period increases (COL12A1, COL 21A1, MPZL1, PVALB, and CXCR7) or decreases (e.g., KCNT2, SAP30L), as well as some that show decreased expression in the surrounding tissue with little change within song nuclei (e.g. SV2B, TAC1). These results reveal a broad range of molecular changes that occur in the song system in concert with the song learning period. Some of the genes and pathways identified are potential modulators of the developmental changes associated with the emergence of the adult properties of the song control system, and/or the acquisition of learned vocalizations in songbirds.

Core and region-enriched networks of behaviorally regulated genes and the singing genome

Songbirds represent an important model organism for elucidating molecular mechanisms that link genes with complex behaviors, in part because they have discrete vocal learning circuits that have parallels with those that mediate human speech. We found that ~10% of the genes in the avian genome were regulated by singing, and we found a striking regional diversity of both basal and singing-induced programs in the four key song nuclei of the zebra finch, a vocal learning songbird. The region-enriched patterns were a result of distinct combinations of region-enriched transcription factors (TFs), their binding motifs, and presinging acetylation of histone 3 at lysine 27 (H3K27ac) enhancer activity in the regulatory regions of the associated genes. RNA interference manipulations validated the role of the calcium-response transcription factor (CaRF) in regulating genes preferentially expressed in specific song nuclei in response to singing. Thus, differential combinatorial binding of a small group of activity-regulated TFs and predefined epigenetic enhancer activity influences the anatomical diversity of behaviorally regulated gene networks.

Amphiphysin I but not dynamin I nor synaptojanin mRNA expression increased after repeated methamphetamine administration in the rat cerebrum and cerebellum

Dopamine increases/decreases synaptic vesicle recycling and in schizophrenia the proteins/mRNA is decreased. We isolated cDNA clone, similar to amphiphysin 1 (vesicle protein) mRNA from the neocortex of rats injected repeatedly with methamphetamine using polymerase chain reaction (PCR) differential display. This clone is highly homologous to the 3' region of the human amphiphysin gene. PCR extension study using a primer specific for the rat amphiphysin 1 gene and a primer located within the clone revealed that it is the 3' UTR region of the rat amphiphysin 1 gene. Furthermore, in situ hybridization revealed that amphiphysin 1 mRNA is expressed in the cerebrum, medial thalamus, hippocampus and cerebellum. In the cerebellum, amphiphysin mRNA expression was confined to upper granule cell layer. Repeated methamphetamine administration increased amphiphysin I mRNA expression in both anterior part of the cerebrum, and the cerebellum. However, the repeated administration did not alter mRNA expression of the other vesicle proteins, synaptotagmin I, synapsin I, synaptojanin and dynamin I, we conclude that the repeated administration selectively increased amphiphysin 1 mRNA expression. Thus, amphiphysin 1 does not work as synaptic recycling, but it is suggested, as a part of pathogenesis of brain tissue injury (under Ca²⁺ and Mg²⁺ devoid environment) in repeated methamphetamine-injected states, the gene regulate actin-asssembly, learning, cell stress signaling and cell polarity.

Organization and development of zebra finch HVC and paraHVC based on expression of zRalDH, an enzyme associated with retinoic acid production

The zRalDH gene encodes an aldehyde dehydrogenase associated with the conversion of retinaldehyde (the main vitamin A metabolite) into retinoic acid and its expression is highly enriched in the song control system of adult zebra finches (Taeniopygia guttata). Within song control nucleus HVC, zRalDH is specifically expressed in the neurons that project to area X of the striatum. It is also expressed in paraHVC, commonly considered a medial extension of HVC that is closely associated with auditory areas in the caudomedial telencephalon. Here we used in situ hybridization to generate a detailed analysis of HVC and paraHVC based on expression of zRalDH for adult zebra finches of both sexes and for males during the song-learning period. We demonstrate that the distribution of zRalDH-positive cells can be used for accurate assessments of HVC and paraHVC in adult and juvenile males. We describe marked developmental changes in the numbers of zRalDH-expressing cells in HVC and paraHVC, reaching a peak at day 50 posthatch, an effect potentially due to dynamic changes in the population of X-projecting cells in HVC. We also show that zRalDH-expressing cells in adult females, although much less numerous than in males, have a surprisingly broad distribution along the medial-to-lateral extent of HVC, but are lacking where paraHVC is found in adult males. Our study thus contributes to our understanding of the nuclear organization of the song system and the dynamics of its developmental changes during the song-learning period.

Uncovering molecular biomarkers that correlate cognitive decline with the changes of hippocampus' gene expression profiles in Alzheimer's disease

BACKGROUND

Alzheimer's disease (AD) is characterized by a neurodegenerative progression that alters cognition. On a phenotypical level, cognition is evaluated by means of the MiniMental State Examination (MMSE) and the post-mortem examination of Neurofibrillary Tangle count (NFT) helps to confirm an AD diagnostic. The MMSE evaluates different aspects of cognition including orientation, short-term memory (retention and recall), attention and language. As there is a normal cognitive decline with aging, and death is the final state on which NFT can be counted, the identification of brain gene expression biomarkers from these phenotypical measures has been elusive.

METHODOLOGY/PRINCIPAL FINDINGS

We have reanalysed a microarray dataset contributed in 2004 by Blalock et al. of 31 samples corresponding to hippocampus gene expression from 22 AD subjects of varying degree of severity and 9 controls. Instead of only relying on correlations of gene expression with the associated MMSE and NFT measures, and by using modern bioinformatics methods based on information theory and combinatorial optimization, we uncovered a 1,372-probe gene expression signature that presents a high-consensus with established markers of progression in AD. The signature reveals alterations in calcium, insulin, phosphatidylinositol and wnt-signalling. Among the most correlated gene probes with AD severity we found those linked to synaptic function, neurofilament bundle assembly and neuronal plasticity.

CONCLUSIONS/SIGNIFICANCE

A transcription factors analysis of 1,372-probe signature reveals significant associations with the EGR/KROX family of proteins, MAZ, and E2F1. The gene homologous of EGR1, zif268, Egr-1 or Zenk, together with other members of the EGR family, are consolidating a key role in the neuronal plasticity in the brain. These results indicate a degree of commonality between putative genes involved in AD and prion-induced neurodegenerative processes that warrants further investigation.

Conservation and expression of IQ-domain-containing calpacitin gene products (neuromodulin/GAP-43, neurogranin/RC3) in the adult and developing oscine song control system

Songbirds are appreciated for the insights they provide into regulated neural plasticity. Here, we describe the comparative analysis and brain expression of two gene sequences encoding probable regulators of synaptic plasticity in songbirds: neuromodulin (GAP-43) and neurogranin (RC3). Both are members of the calpacitin family and share a distinctive conserved core domain that mediates interactions between calcium, calmodulin, and protein kinase C signaling pathways. Comparative sequence analysis is consistent with known phylogenetic relationships, with songbirds most closely related to chicken and progressively more distant from mammals and fish. The C-terminus of neurogranin is different in birds and mammals, and antibodies to the protein reveal high expression in adult zebra finches in cerebellar Purkinje cells, which has not been observed in other species. RNAs for both proteins are generally abundant in the telencephalon yet markedly reduced in certain nuclei of the song control system in adult canaries and zebra finches: neuromodulin RNA is very low in RA and HVC (relative to the surrounding pallial areas), whereas neurogranin RNA is conspicuously low in Area X (relative to surrounding striatum). In both cases, this selective downregulation develops in the zebra finch during the juvenile song learning period, 25-45 days after hatching. These results suggest molecular parallels to the robust stability of the adult avian song control circuit.

Synapsins are late activity-induced genes regulated by birdsong

The consolidation of long-lasting sensory memories requires the activation of gene expression programs in the brain. Despite considerable knowledge about the early components of this response, little is known about late components (i.e., genes regulated 2-6 h after stimulation) and the relationship between early and late genes. Birdsong represents one of the best natural behaviors to study sensory-induced gene expression in awake, freely behaving animals. Here we show that the expression of several isoforms of synapsins, a group of phosphoproteins thought to regulate the dynamics of synaptic vesicle storage and release, is induced by auditory stimulation with birdsong in the caudomedial nidopallium (NCM) of the zebra finch (Taeniopygia guttata) brain. This induction occurs mainly in excitatory (non-GABAergic) neurons and is modulated (suppressed) by early song-inducible proteins. We also show that ZENK, an early song-inducible transcription factor, interacts with the syn3 promoter in vivo, consistent with a direct regulatory effect and an emerging novel view of ZENK action. These results demonstrate that synapsins are a late component of the genomic response to neuronal activation and that their expression depends on a complex set of regulatory interactions between early and late regulated genes.

Dietary retinoic acid affects song maturation and gene expression in the song system of the zebra finch

Vitamin A, an essential nutrient, is required in its acidic form (retinoic acid) for normal embryogenesis and neuronal development, typically within well-defined concentration ranges. In zebra finches, a songbird species, localized retinoic acid synthesis in the brain is important for the development of song, a learned behavior sharing significant commonalities with speech acquisition in humans. We tested how dietary retinoic acid affects the development of song behavior and the brain's system for song control. Supplemental doses of retinoic acid given to juveniles during the critical period for song learning resulted in more variable or plastic-like songs when the birds reached adulthood, compared to the normal songs of vehicle-fed controls. We also observed that several genes (brinp1, nrgn, rxr-alpha, and sdr2/scdr9) had altered levels of expression in specific nuclei of the song system when comparing the experimental and control diet groups. Interestingly, we found significant correlations between gene expression levels in nuclei of the anterior forebrain pathway (lMAN and area X) and the degree of variability in the recorded songs. We observed, however, no major morphological effects such as changes in the volumes of song nuclei. Overall, our results lend further support to a fundamental role of retinoic acid in song maturation and point to possible molecular pathways associated with this action. The data also demonstrate that dietary content of Vitamin A can affect the maturation of a naturally learned complex behavior.

Birdsong "transcriptomics": neurochemical specializations of the oscine song system

Background

Vocal learning is a rare and complex behavioral trait that serves as a basis for the acquisition of human spoken language. In songbirds, vocal learning and production depend on a set of specialized brain nuclei known as the song system.

Methodology/Principal Findings

Using high-throughput functional genomics we have identified ∼200 novel molecular markers of adult zebra finch HVC, a key node of the song system. These markers clearly differentiate HVC from the general pallial region to which HVC belongs, and thus represent molecular specializations of this song nucleus. Bioinformatics analysis reveals that several major neuronal cell functions and specific biochemical pathways are the targets of transcriptional regulation in HVC, including: 1) cell-cell and cell-substrate interactions (e.g., cadherin/catenin-mediated adherens junctions, collagen-mediated focal adhesions, and semaphorin-neuropilin/plexin axon guidance pathways); 2) cell excitability (e.g., potassium channel subfamilies, cholinergic and serotonergic receptors, neuropeptides and neuropeptide receptors); 3) signal transduction (e.g., calcium regulatory proteins, regulators of G-protein-related signaling); 4) cell proliferation/death, migration and differentiation (e.g., TGF-beta/BMP and p53 pathways); and 5) regulation of gene expression (candidate retinoid and steroid targets, modulators of chromatin/nucleolar organization). The overall direction of regulation suggest that processes related to cell stability are enhanced, whereas proliferation, growth and plasticity are largely suppressed in adult HVC, consistent with the observation that song in this songbird species is mostly stable in adulthood.

Conclusions/Significance

Our study represents one of the most comprehensive molecular genetic characterizations of a brain nucleus involved in a complex learned behavior in a vertebrate. The data indicate numerous targets for pharmacological and genetic manipulations of the song system, and provide novel insights into mechanisms that might play a role in the regulation of song behavior and/or vocal learning.

Expression of the GABA(A) receptor gamma4-subunit gene in discrete nuclei within the zebra finch song system

The acquisition, production and maintenance of song by oscine birds is a form of audition-dependent learning that, in many ways, resembles the process by which humans learn to speak. In songbirds, the generation of structured song is determined by the activity of two interconnected neuronal pathways (the anterior forebrain pathway and the vocal motor pathway), each of which contains a number of discrete nuclei that together form the song system. It is becoming increasingly evident that inhibitory GABAergic mechanisms are indispensable in counterbalancing the excitatory actions of glutamate and, thus, likely shape the neuronal firing patterns of neurons within this network. Furthermore, there is compelling evidence for the involvement of GABA(A) receptors, although the molecular composition of these has, to date, remained elusive. Here we describe the isolation of a complementary DNA for the zebra finch GABA(A) receptor gamma4 subunit, and map the expression pattern of the corresponding gene within the zebra finch (Taeniopygia guttata) brain. Our findings show, remarkably, that the gamma4-subunit transcript is highly enriched in the major nuclei of the song system, including the lateral magnocellular nucleus of the anterior nidopallium (LMAN), the medial magnocellular nucleus of the anterior nidopallium (MMAN), Area X, the robust nucleus of the arcopallium (RA) and the HVC (used as the proper name), as well as Field L, which innervates the area surrounding HVC. In summary, we have demonstrated the presence of the mRNA for the gamma4 subunit of the GABA(A) receptor, the major inhibitory receptor in brain, in most of the nuclei of the two neural circuits that mediate song production in the zebra finch. This not only marks the beginning of the characterization of the GABA(A) receptor subtype(s) that mediates the actions of GABA in the song system but it also provides a robust molecular marker with which to distinguish song system-specific brain structures.

Reversal of the expression pattern of Aldolase C mRNA in Purkinje cells and Ube 1x mRNA in Golgi cells by a dopamine D1 receptor agonist injections in the methamphetamine sensitized-rat cerebellum

The cerebellum has a parasagittal modular structure, in which Zebrin (Aldolase) positive and negative bands expressed in Purkinje cell layers alternate, and is involved in amphetamine psychosis. Administration of SKF38393, a D1 receptor agonist, reversed the behavioral sensitization of methamphetamine. In the vermis, there were the binding sites of SKF38393. In methamphetamine-sensitized rats the expression of the Aldolase mRNA positive bands move laterally in the rat vermis. We provide here the evidence that the D1 agonist injections also reversed the expression pattern of both the Aldolase mRNA in Purkinje cells and Ube (ubiquitin activating enzyme) 1x mRNA in Golgi interneurons of the sensitized rats. Thus the reverse changes in gene expression pattern in the vermis may be involved in the mechanisms of the behavioral plasticity and suggests the new treatment of drug abuse.