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Related Concept Videos

Hair Cells01:22

Hair Cells

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Hair cells are the sensory receptors of the auditory system—they transduce mechanical sound waves into electrical energy that the nervous system can understand. Hair cells are located in the organ of Corti within the cochlea of the inner ear, between the basilar and tectorial membranes. The actual sensory receptors are called inner hair cells. The outer hair cells serve other functions, such as sound amplification in the cochlea, and are not discussed in detail here.
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The Cochlea01:13

The Cochlea

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The cochlea is a coiled structure in the inner ear that contains hair cells—the sensory receptors of the auditory system. Sound waves are transmitted to the cochlea by small bones attached to the eardrum called the ossicles, which vibrate the oval window that leads to the inner ear. This causes fluid in the chambers of the cochlea to move, vibrating the basilar membrane.
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Chromatin Structure Regulates pre-mRNA Processing02:41

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In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...
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Auditory Pathway01:15

Auditory Pathway

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Auditory pathways constitute the complex neural circuits responsible for transmitting and interpreting auditory information from the peripheral auditory system to the brain. Sound waves are initially captured by the outer ear, funneled through the ear canal, and reach the tympanic membrane (eardrum). These vibrations are transmitted via the middle ear's ossicles to the inner ear's cochlea.
When viewed cross-sectionally, the cochlea reveals the scala vestibuli and scala tympani flanking...
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Position-effect Variegation02:32

Position-effect Variegation

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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Related Experiment Video

Updated: Sep 8, 2025

Author Spotlight: Advancements in Cultivating Mouse Hair Cells for Auditory Research
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Author Spotlight: Advancements in Cultivating Mouse Hair Cells for Auditory Research

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Differential Chromatin Accessibility, Gene Expression, and mRNA Splicing Between Developing Cochlear Inner and Outer

Chuan Zhi Foo1,2, Anne Duggan1, Elizabeth T Bartom3

  • 1Department of Anesthesiology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.

Journal of the Association for Research in Otolaryngology : JARO
|September 5, 2025
PubMed
Summary
This summary is machine-generated.

Developing inner and outer hair cells in the cochlea show distinct gene expression and splicing patterns, regulated by chromatin accessibility. This research offers insights into the molecular basis of hearing and deafness.

Keywords:
ATAC-seqAlternative mRNA splicingInner hair cell (IHC)Novel promotersOuter hair cell (OHC)RNA-seq

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Area of Science:

  • Genomics
  • Epigenetics
  • Developmental Biology

Background:

  • Mammalian cochlear hair cells, inner (IHC) and outer (OHC), are crucial for hearing.
  • Dysfunction or loss of these cells leads to congenital and acquired deafness.
  • IHCs and OHCs possess distinct transcriptomes during development.

Purpose of the Study:

  • Investigate chromatin-level regulation of differential gene expression in developing IHCs and OHCs.
  • Explore differences in mRNA splicing between developing IHCs and OHCs.
  • Determine if chromatin accessibility differences explain differential gene expression.

Main Methods:

  • Bulk RNA-sequencing of developing mouse IHCs and OHCs to analyze transcriptomes.
  • Bulk ATAC-sequencing of developing mouse IHCs and OHCs to map chromatin accessibility.
  • Comparative analysis of RNA-seq and ATAC-seq data to link gene expression to chromatin states.

Main Results:

  • Differential chromatin accessibility was observed in promoters of many differentially expressed genes in developing IHCs and OHCs.
  • Both transient developmental genes and genes with sustained adult expression showed distinct chromatin accessibility.
  • Alternative mRNA splicing and transcription start sites contribute to transcriptomic diversity.
  • Cochlear hair cells exhibit unique promoters and mRNA isoforms not found in other cell types.

Conclusions:

  • Differential gene expression in developing hair cell types is controlled by pre- and post-transcriptional mechanisms.
  • Unique promoters and mRNA isoforms in cochlear hair cells underscore the significance of studying rare cell type transcriptomes and epigenomes.
  • A publicly accessible resource for visualizing gene promoters and mRNA isoforms in neonatal hair cells is provided.