Details for: WDFY3 AS2

Gene ID: 404201

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: WDFY3 AS2

Ensembl ID: ENSG00000180769

Description: WDFY3 antisense RNA 2

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Significant Cells

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

  • Mueller cell CL0000636
    CSI 4.14
    rCSI 9.45%
    PRS 99.32
  • kidney loop of Henle thin descending limb epithelial cell CL1001111
    CSI 3.98
    rCSI 5.64%
    PRS 99.65
  • epithelial cell of proximal tubule CL0002306
    CSI 2.67
    rCSI 6.51%
    PRS 98.96
  • astrocyte of the cerebral cortex CL0002605
    CSI 2.29
    rCSI 5.13%
    PRS 99.17

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

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  • Node Color (Target Cell CSI, relative to current network):
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    • High
    • Medium
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    • 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 [WDFY3 AS2](/details-gene/404201) is a long non-coding RNA located on chromosome 4q21.23. As an antisense transcript to the protein-coding gene `WDFY3`, its primary function is likely related to the regulation of `WDFY3` expression. The sense gene, `WDFY3`, is a critical component of the selective autophagy machinery, a fundamental process for cellular homeostasis. The expression profile of [WDFY3 AS2](/details-gene/404201) shows high significance in specialized, metabolically active cell types, including retinal [Mueller cell](/details-cell/CL0000636)s, distinct epithelial cells of the kidney, and [astrocyte of the cerebral cortex](/details-cell/CL0002605)s, suggesting a role in modulating autophagy in these specific cellular contexts. ## Cellular Roles and Expression Landscape The **Overall** expression pattern of [WDFY3 AS2](/details-gene/404201) highlights its importance in a specific subset of glial and epithelial cells, rather than broad expression across multiple lineages. Its most significant cellular contexts are: * **Retinal Glia:** It shows the highest significance in [Mueller cell](/details-cell/CL0000636)s (CSI: 4.14), which are essential for maintaining the structural and metabolic integrity of the retina. * **Renal Epithelia:** High significance is also observed in [kidney loop of Henle thin descending limb epithelial cell](/details-cell/CL1001111)s (CSI: 3.98) and [epithelial cell of proximal tubule](/details-cell/CL0002306)s (CSI: 2.67). These cells are characterized by high rates of transport and metabolic activity, requiring robust homeostatic mechanisms. * **Central Nervous System Glia:** The gene is also a significant marker in [astrocyte of the cerebral cortex](/details-cell/CL0002605)s (CSI: 2.29), which provide critical support for neuronal function and brain homeostasis. The common feature among these cell types is their intense metabolic activity and reliance on quality control pathways like autophagy to manage cellular stress and turnover of organelles and proteins. The specific expression of [WDFY3 AS2](/details-gene/404201) in these cells suggests it may be a key regulator fine-tuning the autophagic capacity necessary for their specialized functions. ## Pathways and Molecular Function Direct functional annotation data for [WDFY3 AS2](/details-gene/404201) is limited. However, as an antisense RNA, its function can be inferred from its regulatory relationship with its sense transcript, `WDFY3`. The `WDFY3` protein, also known as ALFY (Autophagy-Linked FYVE protein), acts as a large scaffolding protein that facilitates the targeted degradation of cellular components via selective autophagy. Therefore, the primary molecular function of [WDFY3 AS2](/details-gene/404201) is likely the modulation of autophagy through transcriptional or post-transcriptional regulation of `WDFY3` levels. This regulatory action would be particularly important in the cell types where it is highly expressed, allowing for precise control over this critical homeostatic pathway. ## Research Directions The specific expression of [WDFY3 AS2](/details-gene/404201) in cells highly dependent on autophagy presents several compelling avenues for future research. **Proposed Hypotheses:** 1. [WDFY3 AS2](/details-gene/404201) functions as a negative regulator of `WDFY3` expression in [Mueller cell](/details-cell/CL0000636)s. Downregulation of this lncRNA could therefore enhance autophagic flux, offering a potential protective mechanism against retinal stress or degeneration. 2. In kidney [epithelial cell of proximal tubule](/details-cell/CL0002306)s, the expression of [WDFY3 AS2](/details-gene/404201) is dynamically altered in response to nephrotoxic or ischemic injury, serving as a rheostat to control the level of protective autophagy needed for cell survival and recovery. **Suggested Experimental Approach:** To test the hypothesis that [WDFY3 AS2](/details-gene/404201) regulates `WDFY3` and autophagy in the retina, one could utilize an in vitro model of human immortalized [Mueller cell](/details-cell/CL0000636)s. A loss-of-function study could be performed by transfecting these cells with antisense oligonucleotides (ASOs) or a CRISPR interference (CRISPRi) system targeting [WDFY3 AS2](/details-gene/404201). The direct impact on its sense transcript would be measured by quantifying `WDFY3` mRNA and protein levels via RT-qPCR and western blotting, respectively. The functional consequences on autophagy would then be assessed by monitoring autophagy markers, such as the conversion of LC3-I to LC3-II and the degradation of the autophagy receptor p62/SQSTM1, under both basal and stress-induced conditions (e.g., nutrient deprivation or oxidative stress). **Therapeutic Potential:** Given that dysregulation of autophagy is a hallmark of numerous pathologies, including neurodegenerative diseases (e.g., age-related macular degeneration) and acute kidney injury, [WDFY3 AS2](/details-gene/404201) emerges as a potential therapeutic target. As a non-coding RNA, it is amenable to targeting with nucleic acid-based therapeutics like ASOs. Its restricted expression pattern in specific glial and epithelial cells is highly advantageous, as it may allow for targeted intervention while minimizing off-target effects in other tissues. Depending on the disease context, therapeutic strategies could involve either inhibition of [WDFY3 AS2](/details-gene/404201) to boost protective autophagy or overexpression to suppress excessive or detrimental autophagic activity.