Details for: ATP6AP1 DT

Gene ID: 158960

Gene Type:  ncRNA (Non-coding RNA)  - A functional RNA molecule that is transcribed from DNA but not translated into a protein. Includes classes like miRNA and lncRNA.

Symbol: ATP6AP1 DT

Ensembl ID: ENSG00000197180

Description: ATP6AP1 divergent transcript

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • lung ciliated cell CL1000271
    CSI 7.6
    rCSI 8.78%
    PRS 98.21
  • ciliated columnar cell of tracheobronchial tree CL0002145
    CSI 7.13
    rCSI 16.24%
    PRS 97.41
  • deuterosomal cell CL4033044
    CSI 5.9
    rCSI 19.96%
    PRS 97.08
  • ciliated epithelial cell CL0000067
    CSI 5.74
    rCSI 5.04%
    PRS 97.58
  • ciliated cell CL0000064
    CSI 5.47
    rCSI 8.86%
    PRS 97.53
  • multi-ciliated epithelial cell CL0005012
    CSI 4.59
    rCSI 4.58%
    PRS 98.18
  • elicited macrophage CL0000861
    CSI 4.36
    rCSI 4%
    PRS 99.81
  • mononuclear phagocyte CL0000113
    CSI 2.62
    rCSI 5.78%
    PRS 99.57
  • Langerhans cell CL0000453
    CSI 2.52
    rCSI 3.85%
    PRS 99.94
  • alveolar macrophage CL0000583
    CSI 2.37
    rCSI 3.9%
    PRS 99.33
  • enteroendocrine cell CL0000164
    CSI 2.3
    rCSI 3.14%
    PRS 98.44
  • club cell CL0000158
    CSI 2.29
    rCSI 3.35%
    PRS 99.27
  • lung macrophage CL1001603
    CSI 2.03
    rCSI 4.54%
    PRS 99.81
  • retinal cone cell CL0000573
    CSI 1.89
    rCSI 3.05%
    PRS 97.4

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

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Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [ATP6AP1 DT](/details-gene/158960) is a non-coding RNA (ncRNA) classified as a divergent transcript, originating from the locus of the *ATP6AP1* gene on chromosome X. **Overall** expression data reveal a highly specific and significant role for this gene in ciliated cells. Its expression is most prominent in [lung ciliated cell](/details-cell/CL1000271)s, [ciliated columnar cell of tracheobronchial tree](/details-cell/CL0002145), and their developmental precursors, [deuterosomal cell](/details-cell/CL4033044)s. A secondary, but notable, expression signature is observed in various mononuclear phagocytes, including [elicited macrophage](/details-cell/CL0000861)s and [alveolar macrophage](/details-cell/CL0000583)s. This distinct expression landscape strongly suggests that [ATP6AP1 DT](/details-gene/158960) is involved in the biological processes of ciliogenesis, ciliary function, or the specialized cellular environments where these structures are prevalent. ## Cellular Roles and Expression Landscape The expression profile of [ATP6AP1 DT](/details-gene/158960) is dominated by a strong and consistent signal across multiple types of ciliated epithelial cells. It ranks as a top significant gene in [lung ciliated cell](/details-cell/CL1000271) (CSI: 7.60), [ciliated columnar cell of tracheobronchial tree](/details-cell/CL0002145) (CSI: 7.13), and the broader categories of [ciliated epithelial cell](/details-cell/CL0000067) (CSI: 5.74) and [ciliated cell](/details-cell/CL0000064) (CSI: 5.47). Its high significance in [deuterosomal cell](/details-cell/CL4033044)s (CSI: 5.90), which are specialized precursors responsible for basal body amplification during the formation of multi-ciliated cells, further implicates the gene in the developmental program of ciliogenesis. This makes [ATP6AP1 DT](/details-gene/158960) a robust marker for cells involved in mucociliary transport systems. Beyond its primary association with ciliated epithelium, [ATP6AP1 DT](/details-gene/158960) also shows significant expression in a subset of immune cells belonging to the mononuclear phagocyte system. This includes a high CSI in [elicited macrophage](/details-cell/CL0000861)s (CSI: 4.36), as well as notable expression in [Langerhans cell](/details-cell/CL0000453)s and tissue-resident macrophages like the [alveolar macrophage](/details-cell/CL0000583). The co-expression in lung-associated ciliated and phagocytic cells may suggest a potential role in epithelial-immune crosstalk within the respiratory mucosa. The highly restricted expression pattern implies that its function is likely specialized to these cell lineages. ## Pathways and Molecular Function As a non-coding divergent transcript, [ATP6AP1 DT](/details-gene/158960) does not code for a protein. Its function is presumed to be regulatory. Being transcribed from the promoter region of the protein-coding gene *ATP6AP1* but in the opposite direction, a primary hypothesized mechanism is the regulation of *ATP6AP1* expression in *cis*. The *ATP6AP1* gene encodes a subunit of the vacuolar-type H+-ATPase (V-ATPase), a proton pump essential for the acidification of various intracellular compartments. V-ATPase function is critical in a wide range of cellular processes, including endosomal trafficking and protein degradation, which are vital for both epithelial barrier function and macrophage activity. Therefore, [ATP6AP1 DT](/details-gene/158960) may act as a local epigenetic or transcriptional regulator, ensuring appropriate levels of *ATP6AP1* expression in cells with high metabolic or trafficking demands, such as ciliated cells and phagocytes. Alternatively, the [ATP6AP1 DT](/details-gene/158960) transcript itself may function *in trans*, acting as a molecular scaffold to assemble protein complexes or as a guide for chromatin-modifying enzymes to other target genes involved in ciliogenesis or immune cell activation. ## Research Directions The specific expression pattern of [ATP6AP1 DT](/details-gene/158960) points toward several compelling areas for future investigation, particularly concerning respiratory biology and ciliopathies. ### Testable Hypotheses 1. **Cis-regulatory control of ciliogenesis:** [ATP6AP1 DT](/details-gene/158960) functions as a cis-acting lncRNA that positively regulates transcription of the adjacent *ATP6AP1* gene. This coordinated expression is essential for V-ATPase activity required for the proper assembly and function of cilia in respiratory epithelial cells. 2. **Regulation of macrophage function:** In [alveolar macrophage](/details-cell/CL0000583)s, [ATP6AP1 DT](/details-gene/158960) expression modulates phagolysosomal acidification and inflammatory signaling, potentially by controlling the expression of *ATP6AP1* or other immune-related genes. ### Key Experiments To test the hypothesis that [ATP6AP1 DT](/details-gene/158960) is a cis-regulator essential for ciliogenesis (Hypothesis 1), a targeted knockdown approach could be employed. Specifically, CRISPR interference (CRISPRi) could be used to specifically repress the [ATP6AP1 DT](/details-gene/158960) promoter in primary human bronchial epithelial cells grown in an air-liquid interface (ALI) culture, a model that mimics the respiratory epithelium and supports differentiation into ciliated cells. The direct impact on local *ATP6AP1* mRNA and protein levels would be quantified by RT-qPCR and Western blotting. Functional consequences would be assessed by measuring changes in ciliogenesis (via immunofluorescence for acetylated tubulin) and ciliary beat frequency (via high-speed video microscopy). A concomitant decrease in *ATP6AP1* expression and impaired ciliary function upon [ATP6AP1 DT](/details-gene/158960) repression would provide strong support for this regulatory mechanism. ### Therapeutic Potential Given its highly specific expression in ciliated cells, [ATP6AP1 DT](/details-gene/158960) presents an attractive therapeutic target with a potentially wide therapeutic window. Diseases characterized by impaired mucociliary clearance, such as primary ciliary dyskinesia (PCD) or chronic obstructive pulmonary disease (COPD), could be addressed by modulating this lncRNA. If [ATP6AP1 DT](/details-gene/158960) is found to be a positive regulator of ciliary function, a therapeutic strategy would involve **activation** or supplementation. This could be achieved via inhaled delivery of synthetic [ATP6AP1 DT](/details-gene/158960) mimics or small molecules that enhance its transcription, offering a novel approach to restore airway cleaning mechanisms. Its nature as an RNA makes it a candidate for targeting with nucleic acid-based therapies like antisense oligonucleotides (ASOs).