A Method for Exploring Adult Neurogenesis in the Songbird Brain

Asik, Kemal; Rao, Jiang Liu; Kirn, John R.

doi:10.1101/pdb.prot084590

Cited by 3 publications

(3 citation statements)

References 16 publications

(14 reference statements)

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“…In the past few decades, songbirds became a widely used model system in the behavioral neurobiology of learning 1 , evolutionary genetics 2 , neuroendocrinology 3 – particularly the sexual differentiation of the brain – and adult neurogenesis 4 . Songbirds evolved the ability to learn vocalizations by copying a singing adult.…”

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confidence: 99%

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

Steyaert

Diddens

Galle

et al. 2016

Sci Rep

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Learning and memory formation are known to require dynamic CpG (de)methylation and gene expression changes. Here, we aimed at establishing a genome-wide DNA methylation map of the zebra finch genome, a model organism in neuroscience, as well as identifying putatively epigenetically regulated genes. RNA- and MethylCap-seq experiments were performed on two zebra finch cell lines in presence or absence of 5-aza-2′-deoxycytidine induced demethylation. First, the MethylCap-seq methodology was validated in zebra finch by comparison with RRBS-generated data. To assess the influence of (variable) methylation on gene expression, RNA-seq experiments were performed as well. Comparison of RNA-seq and MethylCap-seq results showed that at least 357 of the 3,457 AZA-upregulated genes are putatively regulated by methylation in the promoter region, for which a pathway analysis showed remarkable enrichment for neurological networks. A subset of genes was validated using Exon Arrays, quantitative RT-PCR and CpG pyrosequencing on bisulfite-treated samples. To our knowledge, this study provides the first genome-wide DNA methylation map of the zebra finch genome as well as a comprehensive set of genes of which transcription is under putative methylation control.

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confidence: 99%

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

Steyaert

Diddens

Galle

et al. 2016

Sci Rep

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“…The accompanying papers describe Husbandry and Breeding Guidelines for the Zebra Finch, Taeniopygia guttata (Olson et al 2014), An optimized protocol for high-throughput in situ hybridization of zebra finch brain (Carleton et al 2014), A Method for exploring adult neurogenesis in the songbird brain (Asik et al 2014), a protocol for In vivo detection of fluctuating brain steroid levels (Ikeda et al 2014), a method for In vivo recording of single-unit activity during singing in zebra finches (Okubo et al 2014), and a protocol for the Generation of transgenic zebra finches with replication-deficient lentiviruses (Velho and Lois 2014). …”

Section: Technical Approachesmentioning

confidence: 99%

The Zebra Finch,Taeniopygia guttata: An Avian Model for Investigating the Neurobiological Basis of Vocal Learning

Mello

2014

Cold Spring Harb Protoc

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Songbirds are capable of learning their vocalizations by copying a singing adult. This vocal learning ability requires juveniles to hear and memorize the sound of the adult song, and later to imitate that song through a process involving sensorimotor integration. Vocal learning is a trait that songbirds share with humans, where it forms the basis of spoken language acquisition, with other avian groups (parrots and hummingbirds), and with a few other mammals (cetaceans, bats). It is however absent in traditional model organisms like rodents and non-human primates. Zebra finches, a songbird species from Australia, are popular pets, as they have attractive plumage and social behaviors and are easy to breed. They also sing a relatively simple and stereotyped song that is very amenable to quantitative analysis. Zebra finches have thus emerged as a choice model organism for investigating the neurobiological basis of vocal learning. A number of tools and methodologies have been developed to characterize the bioacoustics properties of their song, analyze the degree of accurate copying during vocal learning, map the brain circuits that control singing and song learning, and investigate the physiology of these circuits. Such studies have led to a large base of knowledge on song production and learning, and their underlying neural substrate. Several molecular resources have recently become available, including brain cDNA/EST databases, microarrays, BAC libraries, a molecular brain atlas, a complete genome assembly, and the ability to perform transgenesis. The recent availability of many other avian genomes provides unique opportunities for comparative analysis in the search of features unique to vocal learning organisms.

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“…The nature of autoradiography allows for the calculation of a precise threshold for number of silver grains denoting a newly formed cell. Unfortunately, this procedure runs the risk of obfuscating fluorescent neuronal markers (Asik et al, 2014). Fortunately, when injected subcutaneously, nonradioactive thymidine analogs such as bromodeoxyuridine (BrdU) function well as cell birth date markers.…”

Section: Identifying New Neuronsmentioning

confidence: 99%

Singing in the Brain: Investigating the Role of Adult Neurogenesis in Long-Term Memory Preservation

Junkins¹

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A Method for Exploring Adult Neurogenesis in the Songbird Brain

Cited by 3 publications

References 16 publications

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq

The Zebra Finch,Taeniopygia guttata: An Avian Model for Investigating the Neurobiological Basis of Vocal Learning

Singing in the Brain: Investigating the Role of Adult Neurogenesis in Long-Term Memory Preservation

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