Genomic Resources for Birdsong Research
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE6412
PROVIDER: PRJNA99653 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Vocal learning and neuronal replacement have been studied extensively in the songbird brain, but until recently, few molecular and genomic tools have been available for this work. Here we describe new molecular/genomic resources for songbird research. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11000 clones were sequenced from these libraries, representing 5870 unique gene transcripts. A web-based database has been established for sequence analysis and functional annotations. The cDNA libraries were not normalized. Sequence analysis revealed that a cDNA library made from brains at post-hatching day 30-50, when the song system goes through rapid development and birds learn to sing, shows the highest gene discovery rate. We grouped genes into functional categories according to the Gene Ontology classification and found that expression of the functional categories changed as the brain developed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the HVC of both adult male zebra finches and canaries (Serinus canaria). Statistical Analysis of Microarrays (SAM) was used for data analysis. A subset of the differentially regulated genes was validated by in situ hybridization. The bioinformatic tools EASE and Ingenuity Pathway Analysis were used to identify over-represented functional groups and gene networks among the regulated genes. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis. Keywords: HVC, songbird, cDNA microarray, gene expression
2006-12-06 | GSE6412 | GEO
Project description:A defining feature of our species is the ability to manipulate our environment through the fine control of our hands and to communicate with others through the rapid and complex motor orchestration of human speech. The courtship song of songbirds shares a number of neural and behavioral similarities with human speech and other learned motor skills, providing a powerful model for understanding how enhanced motor skills develop at molecular and cellular levels. Birdsong is controlled by a specialized neural circuit whose properties enable high precision and speed. In particular, glutamatergic neurons in the birdsong motor region RA (Glut-RA) have higher spike rates and narrower action potentials than projection neurons in an adjacent motor region that does not control song, the dorsal intermediate arcopallium (Glut-AId). To identify candidate gene regulatory networks that establish the specialized properties of Glut-RA neurons, we performed single-nucleus profiling of gene expression and chromatin accessibility across song and non-song motor regions. We found that Glut-RA projection neurons and fast spiking interneurons (FSIs), a GABAergic type also characterized by high spike rates and narrow action potentials, share several transcriptional similarities. In particular, the transcription factor MAFB, which is essential for the development and fast-spiking physiology of FSIs in mice, is expressed in Glut-RA but no other projection neuron type. We found that MAFB transcription factor binding sites have enhanced chromatin accessibility specifically in glutamatergic neurons in RA relative to AId. Furthermore, gene regulatory network inference and in silico knockdown of MAFB expression reveal common MAFB targets in Glut-RA neurons and FSIs, and suggest that the transcription factor is necessary to specialize song Glut-RA neurons from non-song Glut-AId neurons. These data support a model in which birdsong projection neurons co-opt an interneuron gene regulatory program to enable the rapid physiological properties required for fast and precise birdsong performance.
2026-03-02 | GSE316538 | GEO
Project description:Genomic Postmortem Research Project study
| PRJNA1030496 | ENA
Project description:Genomic Postmortem Research Project study
| PRJNA1030497 | ENA
Project description:Analysis of the effects of deafening on gene expression in birdsong neural circuitry
2022-04-15 | GSE200663 | GEO
Project description:Analysis of the effects of unilateral LMAN lesioning on gene expression in birdsong neural circuitry
2022-04-15 | GSE200664 | GEO
Project description:A defining feature of our species is the ability to manipulate our environment through the fine control of our hands and to communicate with others through the rapid and complex motor orchestration of human speech. The courtship song of songbirds shares a number of neural and behavioral similarities with human speech and other learned motor skills, providing a powerful model for understanding how enhanced motor skills develop at molecular and cellular levels. Birdsong is controlled by a specialized neural circuit whose properties enable high precision and speed. In particular, glutamatergic neurons in the birdsong motor region RA (Glut-RA) have higher spike rates and narrower action potentials than projection neurons in an adjacent motor region that does not control song, the dorsal intermediate arcopallium (Glut-AId). To identify candidate gene regulatory networks that establish the specialized properties of Glut-RA neurons, we performed single-nucleus profiling of gene expression and chromatin accessibility across song and non-song motor regions. We found that Glut-RA projection neurons and fast spiking interneurons (FSIs), a GABAergic type also characterized by high spike rates and narrow action potentials, share several transcriptional similarities. In particular, the transcription factor MAFB, which is essential for the development and fast-spiking physiology of FSIs in mice, is expressed in Glut-RA but no other projection neuron type. We found that MAFB transcription factor binding sites have enhanced chromatin accessibility specifically in glutamatergic neurons in RA relative to AId. Furthermore, gene regulatory network inference and in silico knockdown of MAFB expression reveal common MAFB targets in Glut-RA neurons and FSIs, and suggest that the transcription factor is necessary to specialize song Glut-RA neurons from non-song Glut-AId neurons. These data support a model in which birdsong projection neurons co-opt an interneuron gene regulatory program to enable the rapid physiological properties required for fast and precise birdsong performance.
2026-03-02 | GSE316539 | GEO
Project description:Gene regulatory co-option drives birdsong neural circuit specialization
| PRJNA1403281 | ENA
Project description:Black Representation in Genomic Research Whole Blood eQTL Study
| PRJNA852853 | ENA
Project description:Black Representation in Genomic Research Whole Blood eQTL Study
| PRJNA852854 | ENA