title: Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor.
abstract: Hair cells are sensory receptors for the auditory and vestibular system in vertebrates. The transcription factor Atoh1 is both necessary and sufficient for the differentiation of hair cells, and is strongly upregulated during hair-cell regeneration in nonmammalian vertebrates. To identify genes involved in hair cell development and function, we performed RNA-seq profiling of purified Atoh1-expressing hair cells from the neonatal mouse cochlea. We identified >600 enriched transcripts in cochlear hair cells, of which 90% have not been previously shown to be expressed in hair cells. We identified 233 of these hair cell genes as candidates to be directly regulated by Atoh1 based on the presence of Atoh1 binding sites in their regulatory regions and by analyzing Atoh1 ChIP-seq datasets from the cerebellum and small intestine. We confirmed 10 of these genes as being direct Atoh1 targets in the cochlea by ChIP-PCR. The identification of candidate Atoh1 target genes is a first step in identifying gene regulatory networks for hair-cell development and may inform future studies on the potential role of Atoh1 in mammalian hair cell regeneration.
authors: Program in Developmental Biology.
authors: Tiantian
authors: T
authors: Cai
authors: Program in Developmental Biology.
authors: Hsin-I
authors: HI
authors: Jen
authors: Molecular and Human Genetics, and The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030.
authors: Hyojin
authors: H
authors: Kang
authors: Molecular and Human Genetics, and The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030.
authors: Tiemo J
authors: TJ
authors: Klisch
authors: Program in Developmental Biology, Departments of Neuroscience, Molecular and Human Genetics, and Howard Hughes Medical Institute, Baylor College of Medicine, Texas 77030, and The Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030.
authors: Huda Y
authors: HY
authors: Zoghbi
authors: Program in Developmental Biology, Departments of Neuroscience, Molecular and Human Genetics, and akgroves@bcm.edu.
authors: Andrew K
authors: AK
authors: Groves
mesh_terms: D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D005260:Female; D020869:Gene Expression Profiling; D063990:Gene Ontology; D006198:Hair Cells, Auditory / Q000378:metabolism*; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D008297:Male; D051379:Mice; D008822:Mice, Transgenic; D009154:Mutation / Q000235:genetics; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics*
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D008164:Luminescent Proteins; D009419:Nerve Tissue Proteins; D012333:RNA, Messenger; C500943:Atoh1 protein, mouse
keywords: Atoh1; cochlea; hair cells; inner ear