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YME1L1 / ATP-dependent zinc metalloprotease YME1L1 · IHC design guide
Design Immunohistochemistry for YME1L1
Plan chromogenic YME1L1 staining in paraffin sections using the cytoplasmic tissue profile (HPA tissue IHC). The catalog antibody has IHC images from mouse and rat heart; compare staining by cell type when assessing results (datasheet A03012-1; HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
YME1L1 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Cytoplasmic in tissue (HPA tissue IHC); inner mitochondrial membrane (UniProt) | |
| Staining pattern | Cytoplasmic staining in most tissues (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A03012-1) | |
| Positive control | Adrenal gland+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A03012-1) | |
| Caveat | Staining and RNA have only medium consistency (HPA tissue IHC) | |
| Regulation | Expression regulation unreported (UniProt) | |
| Isoform / epitope | 3 isoforms; epitope differences unreported (UniProt) |
Section 1
Recommended YME1L1 IHC & IF Protocols
The catalog antibody’s IHC-P protocol (datasheet A03012-1) is accompanied by a published YME1L1 kidney-biopsy IHC protocol (PMC11809329).
| Sample | Paraffin-embedded mouse heart tissue; fixative not specified (datasheet A03012-1) |
| Fixation | Image fixative and duration unreported (datasheet A03012-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: EDTA pH 8.0 (datasheet A03012-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A03012-1) |
| Primary antibody | Rabbit anti-YME1L1, 1:50 recommended; image 1:100 (datasheet A03012-1) |
| Primary incubation | Overnight at 4 °C (datasheet A03012-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A03012-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | YME1L1-positive staining in glandular cells of adrenal gland (HPA tissue IHC: Medium). HPA tissue profile: Cytoplasmic expression in most tissues. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet A03012-1); the published kidney protocol reports antigen repair without specifying conditions (PMC11809329).
Section 2
What Is the Expected YME1L1 Staining Pattern?
YME1L1 is an inner mitochondrial membrane protein with one transmembrane segment; its amino terminus faces the matrix and its carboxyl terminus faces the intermembrane space (UniProt Q96TA2 topology). In paraffin section IHC, expect cytoplasmic staining in many tissues, including medium staining in several glandular cell populations and respiratory epithelial cells (HPA: tissue IHC). The HPA tissue profile is Approved, with medium consistency between antibody staining and RNA data (HPA: reliability).
| Cytoplasmic chromogen is visible in glandular cells of appendix, breast, or duodenum, while nuclei remain comparatively clear. | This matches the reported medium staining in those cell populations (HPA: tissue IHC) and the mitochondrial location of YME1L1 (UniProt Q96TA2; HPA: supported mitochondrial ICC-IF). Judge the cell population and compartment together; chromogenic IHC need not resolve individual mitochondria (general IHC practice). |
| Strong, predominantly nuclear or cell surface staining replaces the expected cytoplasmic pattern. | Treat this as a compartment mismatch requiring control review: the established locations are mitochondrial (UniProt Q96TA2; HPA: supported mitochondrial ICC-IF). HPA also reports nuclear bodies in ICC-IF, but labels that additional location uncertain; it does not establish broad nuclear staining as an expected paraffin section result (HPA: subcellular ICC-IF). |
| A cell population listed as not detected stains as strongly as a listed medium population. | Check whether the stained cells were identified correctly and whether staining persists in detection controls (general IHC practice). HPA reports adipocytes and bone marrow hematopoietic cells as not detected (HPA: tissue IHC). Unexpected staining can reflect nonspecific antibody binding or endogenous detection activity; one discrepant slide cannot establish either cause (general IHC practice). |
| Color spreads evenly across tissue, lumina, and areas without recognizable cells. | A uniform deposit lacks the cell and cytoplasmic distribution used to interpret the HPA pattern (HPA: cytoplasmic expression in most tissues). Review reagent controls, blocking, washing, and chromogen development for background (general IHC practice). |
| A glandular population reported as medium shows no convincing cytoplasmic signal. | First verify the sampled cell type and run a known staining reference in the same batch (general IHC practice). HPA reports medium staining in appendix, breast, and duodenal glandular cells (HPA: tissue IHC). An absent signal alone cannot distinguish technical failure from sample variation, especially given medium antibody–RNA consistency (HPA: reliability). |
💡Expected YME1L1 appearanceA credible positive is cell associated, mainly cytoplasmic chromogen of approximately medium intensity in a listed medium population such as appendix glandular cells (HPA: tissue IHC), consistent with mitochondrial YME1L1 (UniProt Q96TA2); diffuse deposit or dominant broad nuclear staining warrants investigation (general IHC practice; HPA: subcellular ICC-IF).
| Cell type and tissue selection | HPA reports cytoplasmic expression in most tissues but low tissue specificity by RNA (HPA: tissue IHC). Its listed medium and not detected calls apply to the named cell populations, not every cell in those organs (HPA: tissue IHC). Use cell level comparisons when selecting reference sections (general IHC practice). |
| Mitochondrial topology | YME1L1 spans the inner mitochondrial membrane at residues 296–316; residues 1–295 face the matrix and 317–773 face the intermembrane space (UniProt Q96TA2 topology). This supports a mitochondrial expectation, but the record does not identify the antibody epitope or predict its antigen retrieval requirements. |
| Isoforms and antibody interpretation | UniProt lists 3 isoforms (UniProt Q96TA2). The supplied record gives no isoform specific IHC pattern or antibody epitope, so staining cannot be assigned to an individual isoform from location or intensity alone (UniProt Q96TA2; HPA: antibody validation). |
| Strength of antibody evidence | The listed antibody, HPA066953, is Approved for IHC and Supported for ICC (HPA: antibody validation). The tissue profile's medium antibody–RNA consistency calls for cautious interpretation of isolated discrepancies (HPA: reliability). These designations do not establish the cause of unexpected staining in a particular section. |
| Does IF/ICC predict the IHC result? | ICC-IF supports mitochondria as the main location and marks additional nuclear body localisation uncertain (HPA: subcellular ICC-IF). Use that evidence to assess compartment plausibility; score paraffin section staining against the HPA tissue IHC cell populations (HPA: tissue IHC). IF/ICC has a separate guide. |
| Situation | Likely cause | Next action |
|---|---|---|
| No staining in an appendix, breast, or duodenal glandular reference. | The wrong cell population may have been sampled, or the IHC run may have failed; these glandular populations are reported at medium level (HPA: tissue IHC). | Confirm cell identity and section integrity, then review retrieval, primary antibody use, detection reagents, and a same run reference (general IHC practice). Do not infer a YME1L1 specific retrieval requirement from the supplied record. |
| Only adipocytes or bone marrow hematopoietic cells appear positive. | Both named populations are reported as not detected (HPA: tissue IHC); unexpected color could arise from background, detection activity, or cell identification error (general IHC practice). | Recheck morphology and compare with a listed medium population. Inspect a no primary control and the detection chemistry before assigning biological positivity (general IHC practice). |
| Predominantly nuclear staining is scored as positive. | The supported subcellular location is mitochondrial, while nuclear bodies are an uncertain additional ICC-IF finding (HPA: subcellular ICC-IF). Broad nuclear chromogen therefore needs separate validation. | Reassess cytoplasmic signal at cell level and compare a no primary control (general IHC practice). Do not use the uncertain nuclear body annotation to validate widespread nuclear IHC staining (HPA: subcellular ICC-IF). |
| Diffuse brown background obscures cellular boundaries. | Excess reagent binding, incomplete washing, or endogenous chromogenic detection activity can obscure specific staining (general IHC practice). HPA provides no target specific cause for this appearance. | Review blocking and wash steps; compare no primary and detection controls, and assess whether development was excessive (general IHC practice). Interpret YME1L1 only where cell associated cytoplasmic staining remains discernible (HPA: tissue IHC). |
| Staining intensity differs between named tissues or neighboring cell types. | HPA assigns medium, low, and not detected levels to different specified populations, and reports medium antibody–RNA consistency (HPA: tissue IHC; HPA: reliability). | Record the precise cell population, compartment, and intensity for each section. Compare like populations within the same staining run before treating an intensity difference as a technical failure (general IHC practice). |
| ICC-IF shows nuclear puncta, but paraffin section IHC does not. | HPA labels nuclear bodies an uncertain additional ICC-IF location; mitochondria are the supported main location (HPA: subcellular ICC-IF). The two applications offer different readouts (general IHC/IF practice). | Base the IHC call on the reported cytoplasmic tissue pattern and an appropriate cell population (HPA: tissue IHC). Consult the separate IF/ICC guide for fluorescence interpretation. |
Experiment evidence
IHC & IF images showing YME1L1 staining
A03012-1 · IHCIHC analysis of YME1L1 using anti-YME1L1 antibody (A03012-1). YME1L1 was detected in a paraffin-embedded section of mouse heart tissue. Heat
A03012-1 · IHCIHC analysis of YME1L1 using anti-YME1L1 antibody (A03012-1). YME1L1 was detected in a paraffin-embedded section of rat heart tissue. Heat m
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000136758-YME1L1/tissue/cerebral+cortex#imid_18661884
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000136758-YME1L1/tissue/colon#imid_18661810
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000136758-YME1L1/tissue/liver#imid_18661827
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000136758-YME1L1/tissue/kidney#imid_18661812
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA066953; green = YME1L1, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA066953; green = YME1L1, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for YME1L1 IHC & IF
🧪Run breast first: glandular cells should stain (HPA: Medium in breast glandular cells); use cervix glandular cells as the negative tissue comparator (HPA: Not detected in cervix glandular cells). On the breast slide, assess non-glandular cells for background staining without assuming they are true YME1L1-negative cells (HPA: breast result specifies glandular cells only).
Positive control tissue: Adrenal gland (Glandular cells, HPA Medium)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show YME1L1 in A-431, Rh30, U2OS, with annotated localisation: Mitochondria (supported) (HPA subcellular).
Technical controls: Include no-primary/secondary-only and host- and isotype-matched rabbit IgG controls, and confirm specificity with a matched YME1L1 knockout specimen (selected tissue-IHC caption: rabbit primary; standard IHC practice). Quench endogenous peroxidase and check blood-containing areas for DAB background when using HRP detection (selected tissue-IHC caption: HRP/DAB; standard IHC practice).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected A03012-1 paraffin-section caption does not state a fixative (selected tissue-IHC caption). Heat-mediated EDTA retrieval at pH 8.0 preceded 1:100 antibody incubation overnight at 4°C in the mouse-heart example; whether retrieval is necessary in breast is unreported (selected tissue-IHC caption). The evidence does not establish whether frozen sections or IF are easier; IF/ICC images support mitochondrial localization in A-431, Rh30 and U2OS, while blood-associated peroxidase background remains a practical concern when scoring breast HRP/DAB sections (HPA subcellular; standard IHC practice).
HPA tissue IHC evidence for YME1L1
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Approved — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
| Appendix | Glandular cells | Medium | Protein (IHC) | HPA → |
| Breast | Glandular cells | Medium | Protein (IHC) | HPA → |
| Bronchus | Respiratory epithelial cells | Medium | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Bone marrow | Hematopoietic cells | Not detected | Protein (IHC) | HPA → |
| Cervix | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Liver | Cholangiocytes | Not detected | Protein (IHC) | HPA → |
| Ovary | Ovarian stroma cells | Not detected | Protein (IHC) | HPA → |
Section 3
Advanced YME1L1 IHC Tips
Use compartment, tissue pattern, and matched controls to troubleshoot chromogenic YME1L1 staining in paraffin sections.
How should I optimize retrieval when YME1L1 staining is weak?
Start with heat-mediated retrieval in EDTA pH 8.0 for paraffin sections (datasheet A03012-1). The selected mouse-heart image used this retrieval with 1:100 primary antibody overnight at 4°C (caption A03012-1). If staining is weak, compare heating durations on serial sections while holding the antibody dilution, cooling, and detection steps constant (standard IHC practice). Include a no-primary control because stronger retrieval may also increase background (standard IHC practice). Assess whether improvement produces a plausible cytoplasmic pattern, consistent with the reported tissue staining and mitochondrial location (HPA tissue IHC; HPA subcellular).
Can I change fixation to improve YME1L1 staining?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (caption A03012-1). Record fixative, fixation duration, and tissue thickness for each specimen, then compare otherwise matched sections before attributing weak staining to fixation (standard IHC practice). Keep heat retrieval at EDTA pH 8.0 and the primary at 1:100 during that comparison (caption A03012-1). Assess morphology alongside staining, since poor preservation can make compartment-level interpretation unreliable (standard IHC practice). Do not infer a YME1L1-specific fixation effect from its reported mitochondrial topology or tissue staining pattern (UniProt Q96TA2 topology; HPA tissue IHC).
Where should convincing YME1L1 staining appear in tissue?
Expect cytoplasmic staining at the light-microscopy level: YME1L1 resides in the mitochondrial inner membrane, and tissue IHC is described as cytoplasmic in most tissues (UniProt Q96TA2 subcellular; HPA tissue IHC). Its 296–316 transmembrane segment separates a matrix-facing 1–295 region from an intermembrane-space-facing 317–773 region (UniProt Q96TA2 topology). Look for a reproducible cytoplasmic pattern in intact cells, using serial sections and a no-primary control to check ambiguous staining (standard IHC practice). Treat isolated nuclear staining cautiously; nuclear bodies are an uncertain additional IF location, whereas mitochondria are the supported main location (HPA subcellular).
Could epitope position explain different staining across sections?
YME1L1 has 3 listed isoforms, but the supplied tissue-image evidence does not identify this antibody's epitope or establish isoform selectivity (UniProt Q96TA2 isoforms; caption A03012-1). Its single membrane span lies at residues 296–316, with residues 1–295 on the matrix side and 317–773 on the intermembrane side (UniProt Q96TA2 topology). Because the recognized sequence is unspecified, do not assign staining differences to a particular isoform or membrane-facing domain (UniProt Q96TA2 isoforms; caption A03012-1). Compare matched sections with the documented EDTA pH 8.0 retrieval before investigating epitope accessibility further (datasheet A03012-1; standard IHC practice).
How can IF help resolve an ambiguous IHC pattern?
On a separate IF preparation, multiplex YME1L1 with a marker for the cell type under examination and a mitochondrial marker to assess cell identity and compartment (HPA subcellular; standard IF practice). Choose fluorophores whose emissions are distinguishable from the specimen's measured autofluorescence, and include single-stain and no-primary controls (standard IF practice). Permeabilisation may need optimization for antibody access because the unknown epitope could lie on either side of the 296–316 inner-membrane span (UniProt Q96TA2 topology; caption A03012-1). Interpret nuclear-body overlap cautiously: mitochondria are the supported main IF location, while the additional nuclear-body assignment is uncertain (HPA subcellular).
What should I check when DAB staining is diffuse?
First compare the stained section with a no-primary control and inspect whether signal follows tissue edges, damaged areas, or endogenous pigment (standard IHC practice). Apply an endogenous peroxidase block before HRP detection and keep DAB development matched across slides (standard IHC practice). The selected image used 10% goat serum blocking and 1:100 primary antibody overnight at 4°C; these are documented conditions, not proof they suit every specimen (caption A03012-1). If controls remain clean but staining spreads diffusely, titrate the primary and revisit retrieval while checking whether intact-cell cytoplasm retains a plausible mitochondrial pattern (standard IHC practice; HPA subcellular).
How should I score YME1L1 across tissue samples? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and analysis area before scoring, then use the same staining and imaging settings across sections (standard IHC practice). For chromogenic IHC, report an H-score from staining intensity and percentage of positive cells, or report positive-cell percentage with an explicit threshold (standard IHC practice). If using positive-cell density per mm², normalize to viable tissue area and report the number of evaluable cells or sampled regions (standard IHC practice). Score cytoplasmic staining separately from ambiguous nuclear or edge signal, since the reported tissue pattern is cytoplasmic and the supported main compartment is mitochondrial (HPA tissue IHC; HPA subcellular).
When is an apparent YME1L1-positive cell likely an artefact?
Favor reproducible staining in intact-cell cytoplasm over signal confined to nuclei, section edges, or necrotic areas (HPA tissue IHC; HPA subcellular; standard IHC practice). Check the no-primary and peroxidase-block controls when brown signal persists in tissue compartments prone to endogenous enzyme activity (standard IHC practice). Cell identity matters: HPA reports medium glandular-cell staining in appendix but no detected signal in adipocytes, so interpret each population against its own reference pattern (HPA tissue IHC). A clean control and plausible location strengthen an IHC call, while neither alone proves target specificity; seek concordant evidence when a finding changes the biological conclusion (standard IHC practice).
Boster reagents
Best YME1L1 / ATP-dependent zinc metalloprotease YME1L1 IHC Antibodies
A03012-1 has IHC images from paraffin-embedded mouse and rat heart sections (catalog image captions). IF and ICC are listed applications, but no IF image is supplied (catalog applications; IF image alts).
Real IHC data
Anti-YME1L1 Antibody
Cat # A03012-1
A03012-1 will render with its mouse heart paraffin-section IHC figure (catalog card caption). Its catalog also shows rat heart paraffin-section IHC and lists Human, Mouse and Rat reactivity plus IF and ICC applications (catalog image captions; catalog applications and reactivity).
Which to pick: Choose A03012-1 for paraffin-section tissue IHC: its mouse and rat heart captions describe EDTA retrieval at pH 8.0 and primary antibody at 1:100 (catalog image captions). The sections’ fixative is unreported (catalog image captions). For IF/ICC or work across the listed Human, Mouse and Rat species, A03012-1 is the available rabbit polyclonal option; IF/ICC support comes from the application list, with no IF image supplied (catalog dilution_raw; catalog applications and reactivity; IF image alts).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q96TA2 (YMEL1_HUMAN, ATP-dependent zinc metalloprotease YME1L1).
- Human Protein Atlas. YME1L1 tissue IHC expression (reliability: Approved).
- Human Protein Atlas. YME1L1 subcellular location (ICC-IF): Mainly localized to the mitochondria. In addition localized to the nuclear bodies..
- Human Protein Atlas. YME1L1 antibody validation summary (1 antibodies).
- SREBP1c-Mediated Transcriptional Repression of YME1L1 Contributes to Acute Kidney Injury by Inducing Mitochondrial Dysfunction in Tubular Epithelial Cells. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2025 — PMC11809329.
- Targeted Sirtuin 3 Activation by Biomimetic Black Phosphorus Nanosheets Mitigates Sepsis-Induced Acute Kidney Injury through Yeast Mitochondrial Escape 1-Like 1 Deacetylation. Biomaterials research 2026 — PMC13311258.
- Canopy Homolog 2 as a Novel Molecular Target in Hepatocarcinogenesis. Cancers 2021 — PMC8306219.
- Sirt3 mitigates LPS-induced mitochondrial damage in renal tubular epithelial cells by deacetylating YME1L1. Cell proliferation 2023 — PMC9890524.
- PubMed PMID:10843804 — UniProt-cited evidence.
- PubMed PMID:12975309 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for YME1L1 (ATP-dependent zinc metalloprotease YME1L1). Expected localisation Cytoplasmic in tissue (HPA tissue IHC); inner mitochondrial membrane (UniProt). Antigen retrieval: EDTA pH 8.0 HIER, heat-mediated (datasheet A03012-1). Validated IHC antibody: A03012-1 at 1:50 recommended; image 1:100 (the product's own IHC validation image is shown). Controls (HPA): positive Adrenal gland (Glandular cells); negative Adipose tissue. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded mouse heart tissue; fixative not specified (datasheet A03012-1); 2. Fixation: Image fixative and duration unreported (datasheet A03012-1); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat retrieval: EDTA pH 8.0 (datasheet A03012-1); 20 min, 95–100 °C (standard); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet A03012-1); 8. Primary antibody: Rabbit anti-YME1L1, 1:50 recommended; image 1:100 (datasheet A03012-1); 9. Primary incubation: Overnight at 4 °C (datasheet A03012-1). Watch for: Fixation: Matched tissue-IHC evidence does not establish the fixation claim. Validate the specimen-specific method before use. (selected-SKU IHC image A03012-1); Caveat: Staining and RNA have only medium consistency (HPA tissue IHC); Isoform / epitope: 3 isoforms; epitope differences unreported (UniProt); Regulation: Expression regulation unreported (UniProt). Evidence: UniProt Q96TA2, HPA tissue IHC · Approved, HPA ICC-IF · Mainly localized to the mitochondria. In addition localized to the…, Datasheet A03012-1, PMC11809329. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/YME1L1/immunohistochemistry-ihc-guide.