ALYREF / THO complex subunit 4 · IHC design guide

Design Immunohistochemistry for ALYREF

This guide uses the catalog antibody’s 1:50 dilution and HRP/DAB detection for paraffin-section IHC (datasheet M03580). Assess the nuclear pattern against the reported ubiquitous tissue staining, including high staining in bone marrow hematopoietic cells (HPA tissue IHC).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for ALYREF (IHC for ALYREF): expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody M03580, validated IHC image, and IHC protocol steps
Printable ALYREF IHC protocol sheet — expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody M03580, controls and protocol steps. Open the full ALYREF IHC guide →

ALYREF 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 Nuclear staining in tissue (HPA tissue IHC)
Staining pattern Ubiquitous nuclear staining across tissue cell types (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet M03580)
Positive control ⓘ Adipose tissue+4 more · see all
Negative control ⓘ None in HPA (detected in all 45 tissues); use no-primary + isotype controls
Important caveats
Reasons your staining may differ from the expected pattern.
Fixation Keep fixation conditions consistent across sections. (standard IHC practice; not target-specific)
Caveat Marrow peroxidase can mimic DAB staining (HPA tissue IHC; standard IHC practice)
Regulation No staining-linked regulator listed (UniProt)
Isoform / epitope No isoforms listed; no extracellular domain (UniProt)
Section 1

Recommended ALYREF IHC & IF Protocols

The catalog antibody protocol uses EDTA pH 8.0 retrieval (datasheet: M03580). The options below summarize three published paraffin-section IHC protocols (PMC9079359; PMC12618602; PMC12439426).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human lung cancer tissue; fixative not specified (datasheet M03580)
FixationImage fixative and duration unreported (datasheet M03580); verify before use.
Sectioning4–5 µm sections on charged slides (standard)
DeparaffinisationXylene, graded ethanol series to water (standard)
Antigen retrievalHeat retrieval: EDTA pH 8.0 (datasheet M03580); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet M03580)
Primary antibodyRabbit monoclonal (clone 22A24) anti-ALYREF, 1:50 (datasheet M03580)
Primary incubationOvernight at 4 °C (datasheet M03580)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet M03580)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultALYREF-positive staining in adipocytes of adipose tissue (HPA tissue IHC: High). HPA tissue profile: Ubiquitous nuclear expression. No signal in the no-primary control.
💡Decision noteStart with heat-mediated EDTA pH 8.0 retrieval (datasheet: M03580); citrate pH 6.0 is a published alternative for retinoblastoma sections (PMC12439426).
Section 2

What Is the Expected ALYREF Staining Pattern?

ALYREF is expected mainly in nuclei across tissue cell types, with high staining reported in several cell populations including bone marrow hematopoietic cells (HPA: ubiquitous nuclear expression; High in hematopoietic cells). Nuclear speckles are a documented location; cytoplasmic transit is also described (UniProt Q86V81: subcellular location). Its lack of a transmembrane segment gives no basis for a membrane pattern (UniProt Q86V81: topology). HPA rates the tissue IHC pattern Supported (HPA: tissue IHC reliability).

What am I looking at on my slide?
Many nuclei stain in the section, including nuclei of the chosen HPA high control population (HPA: ubiquitous nuclear expression; High in bone marrow hematopoietic cells).This fits the reported IHC distribution. Compare cells within the same section and a matched negative control before judging intensity; HPA's High labels describe observed cell populations, not a required intensity in every specimen (HPA: tissue IHC profile and levels; standard IHC practice).
The dominant signal outlines membranes or fills cytoplasm while nuclei are unstained.A dominant membrane pattern conflicts with the reported nuclear IHC pattern and lack of a transmembrane segment (HPA: ubiquitous nuclear expression; UniProt Q86V81: topology). UniProt describes cytoplasmic transit, so limited cytoplasmic signal alone is inconclusive; review the nuclear signal and controls before calling an artefact (UniProt Q86V81: subcellular location; standard IHC practice).
Only an unexpected cell population stains while neighboring nuclei and the chosen high control population remain blank.Check cross-reactivity or endogenous chromogen activity against the negative control (standard IHC practice). HPA reports ubiquitous nuclear expression and supplies no negative cell population here, so an unlisted cell type cannot be declared ALYREF-negative from these data (HPA: tissue IHC profile; supplied positive/negative lists).
Brown color spreads between cells or coats much of the section without distinct nuclear boundaries.Diffuse background does not establish ALYREF localization. Review reagent-only and tissue controls, wash quality, antibody concentration and chromogen development under the local IHC workflow (standard IHC practice); do not score indistinct color as positive nuclei (HPA: ubiquitous nuclear expression).
The chosen known-positive control has no discernible nuclear signal, including its listed high population.The run is uninterpretable until detection and tissue handling are checked (standard IHC practice). Bone marrow hematopoietic cells are one reported high IHC example, but HPA's rating does not guarantee a signal with every antibody or run condition (HPA: High in hematopoietic cells; tissue IHC reliability).
💡Expected ALYREF appearanceCall a section positive when identifiable nuclei stain in the expected cells, with a clearly visible signal in an HPA high control population; do not score isolated membrane color or diffuse noncellular brown deposit as ALYREF (HPA: ubiquitous nuclear expression; High in listed populations; UniProt Q86V81: topology; standard IHC practice).
How each factor affects the staining
Which compartment should drive the IHC score?Nuclear localization is the tissue-level anchor (HPA: ubiquitous nuclear expression). UniProt also reports cytoplasmic travel with mRNA, so minor cytoplasmic color is interpreted with controls rather than used alone as proof of specificity (UniProt Q86V81: subcellular location; standard IHC practice).
How much weight should the HPA antibody record carry?HPA lists tissue IHC as Supported and two antibodies with Supported IHC entries, HPA019799 and CAB016281 (HPA: tissue IHC reliability; antibody validation list). Those labels support the reported pattern; they do not validate an unlisted antibody or establish a universal dilution (HPA: antibody validation list).
Can processing or isoforms explain a different compartment?The supplied record lists no signal peptide, propeptide, transmembrane segment or isoforms, and describes a chain spanning residues 2–257 (UniProt Q86V81: processing, topology, isoforms). It provides no basis to predict a secreted or membrane-specific IHC pattern (UniProt Q86V81: processing and topology).
Can an epitope or retrieval setting be chosen from this record?The RRM spans residues 106–182 and modified residues are listed, but no antibody epitope or target-specific retrieval response is supplied (UniProt Q86V81: domain and modified residues; supplied antibody data). Select retrieval conditions from the IHC-validated antibody's instructions and local controls (standard IHC practice).
IF/ICC Q&A: what pattern should fluorescence show?HPA approves nucleoplasm and nuclear speckles as main locations in ICC-IF (HPA: subcellular summary). Speckles can help interpret fluorescence images; their visibility is not a requirement for chromogenic paraffin IHC (HPA: ICC-IF location; standard IHC practice).
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
No nuclear stain in the positive control.An unsuccessful IHC run is possible; the pattern alone cannot identify whether tissue handling, retrieval, primary antibody or detection caused it (standard IHC practice).Confirm the control contains an HPA high population, then check the catalog antibody's IHC-P instructions and each detection step (HPA: High in listed populations; standard IHC practice).
Weak nuclear color in the sample, but the control stains.HPA's high examples and ubiquitous profile do not specify the intensity of every specimen or cell (HPA: tissue IHC profile and positive list).Compare matched sections and scoring thresholds within the run; report weak nuclear signal as observed rather than forcing a high call (standard IHC practice).
Predominantly cytoplasmic or membrane color.Dominant extranuclear color is discordant with tissue IHC; limited cytoplasmic transit is documented, but a membrane location is unsupported (HPA: ubiquitous nuclear expression; UniProt Q86V81: subcellular location and topology).Inspect the negative control and nuclear counterstain; optimize the IHC workflow before assigning specificity to the extranuclear color (standard IHC practice).
Only one unexpected cell population appears positive.Cross-reactivity or endogenous detection activity is possible; the supplied HPA list contains no confirmed negative cell type (standard IHC practice; HPA: supplied positive/negative lists).Compare a primary-antibody omission control and an HPA high population in the same run; describe the finding as unresolved if controls cannot distinguish it (HPA: positive list; standard IHC practice).
Diffuse brown background obscures nuclei.Excess chromogen, insufficient washing or nonspecific detection can obscure a compartment-specific result (standard IHC practice).Review the negative control, wash and development conditions, then rescore only nuclei with clear cell boundaries (standard IHC practice; HPA: ubiquitous nuclear expression).
The investigator expects visible nuclear speckles in a chromogenic section.Speckles are an approved ICC-IF location, while the tissue IHC summary reports ubiquitous nuclear expression without a speckle-resolution requirement (HPA: subcellular summary; tissue IHC profile).Judge paraffin IHC by interpretable nuclear staining and tissue controls; use the separate IF/ICC guide when speckle localization itself is the question (HPA: tissue IHC profile; ICC-IF location; standard IHC practice).

Sample controls for ALYREF IHC & IF

🧪Run bone marrow first and expect nuclear staining in hematopoietic cells (HPA: High in bone marrow hematopoietic cells). HPA detects ALYREF in all 45 scored tissues, so there is no supported negative tissue; no-primary and isotype controls carry the negative comparison, while mature anucleate erythrocytes on the positive slide should lack nuclear staining (HPA: no negative tissue rows; standard IHC practice).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: ALYREF is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show ALYREF in A-431, U-251MG, U2OS, HEK293, U2OS, siRNA 2 (10x), U2OS, siRNA 2 (40x), U2OS, scrambled (10x), U2OS, scrambled (40x), with annotated localisation: Nucleoplasm (approved), Nuclear speckles (approved) (HPA subcellular).
Technical controls: Include a secondary-only slide with no primary antibody and a control antibody matched to the primary antibody’s host species, immunoglobulin class, clonality and concentration; if available, use ALYREF knockout material as a biological specificity control (standard IHC practice). In bone marrow, quench endogenous peroxidase and assess background in the secondary-only slide before interpreting DAB staining (standard IHC practice).
⚠️Feasibility: Nuclear staining is a practical readout for paraffin-section IHC (UniProt Q86V81: nucleus and nuclear speckles; HPA: approved nucleoplasm and nuclear speckle localization). The selected M03580 tissue-IHC caption reports heat retrieval in EDTA at pH 8.0, but its fixative is unreported and the supplied evidence reports no target-specific fixation window or fixation effect (M03580 caption). IF/ICC images are available in the listed HPA cell lines, but the supplied evidence does not establish that IF or frozen sections are easier; in bone marrow, endogenous peroxidase can complicate chromogenic interpretation (HPA: ICC-IF cell-line list; standard IHC practice).

HPA tissue IHC evidence for ALYREF

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — High 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

TissueCell typeLevelEvidenceSource
Adipose tissue Adipocytes High Protein (IHC) HPA →
Adrenal gland Glandular cells High Protein (IHC) HPA →
Appendix Glandular cells High Protein (IHC) HPA →
Bone marrow Hematopoietic cells High Protein (IHC) HPA →
Breast Adipocytes High Protein (IHC) HPA →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
None in HPA: ALYREF is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced ALYREF IHC Tips

Troubleshoot ALYREF staining in paraffin sections by checking retrieval, nuclear localisation, controls and scoring before interpreting changes in expression.

Which retrieval condition should I try first for ALYREF in paraffin sections?
Start with heat-mediated EDTA retrieval at pH 8.0 for this catalog antibody (datasheet M03580). The selected paraffin-section example used that condition before incubation with antibody at 1:50 overnight at 4°C (datasheet M03580). If staining is weak, compare retrieval duration across matched sections while keeping the detection method and exposure to DAB consistent (standard IHC practice). Score whether nuclear staining improves without diffuse background or damaged morphology, using the same positive-control tissue in each run (HPA: ubiquitous nuclear expression; standard IHC practice). The caption does not report a fixative, so its retrieval result cannot establish performance for every fixation condition (datasheet M03580).
Could fixation explain weak or uneven ALYREF staining?
Target-specific fixation sensitivity is unknown from the supplied evidence; the selected image describes a paraffin-embedded section but does not state its fixative (datasheet M03580). Record the fixative, fixation duration and section processing for each specimen before comparing staining intensity (standard IHC practice). Compare sections processed alike and run a positive-control section through the same EDTA pH 8.0 retrieval and detection sequence (datasheet M03580; standard IHC practice). If signal varies with processing history, repeat the comparison on matched material before assigning the difference to ALYREF expression (standard IHC practice). Neither its nuclear localisation nor its listed modifications establish a particular fixation effect (UniProt Q86V81).
Where should convincing ALYREF signal appear in a tissue section?
Expect predominantly nuclear staining: tissue IHC reports ubiquitous nuclear expression, while subcellular imaging places ALYREF in the nucleoplasm and nuclear speckles (HPA: tissue IHC and subcellular localisation). UniProt also places ALYREF around speckles and reports that it can travel to the cytoplasm with an mRNA-bound exon junction complex (UniProt Q86V81). At chromogenic resolution, assess whether DAB is concentrated within intact nuclei rather than claiming individual speckles from a brown deposit (standard IHC practice; HPA: nuclear speckles). Compare suspect cytoplasmic signal with adjacent nuclei, morphology and a no-primary control before interpreting redistribution (standard IHC practice; UniProt Q86V81).
How do I investigate an unexpected ALYREF staining pattern without a mapped epitope?
The supplied record lists 0 isoforms and an RNA recognition motif at residues 106–182, but it does not map this antibody’s epitope (UniProt Q86V81; datasheet M03580). Therefore, a changed staining pattern cannot be assigned to isoform selection or epitope masking from these data alone (UniProt Q86V81; datasheet M03580). ALYREF has listed modified residues, including methylated arginine and phosphorylated serine, but no supplied evidence shows that they alter this antibody’s binding (UniProt Q86V81; datasheet M03580). Compare retrieval and staining controls first, then seek an independently validated reagent or orthogonal expression measurement if specificity remains uncertain (standard IHC practice).
How should I assess ALYREF by multiplex IF alongside a cell-type marker?
Use IF as a separate validation workflow: the selected antibody example establishes paraffin-section chromogenic staining, while HPA subcellular imaging supports nucleoplasm and nuclear-speckle localisation (datasheet M03580; HPA: subcellular localisation). For bronchus, pair ALYREF with a respiratory epithelial marker such as pan-cytokeratin and a nuclear counterstain to assign signal to the expected cells (HPA: high in bronchus respiratory epithelial cells; standard IF practice). Choose a spectrally separated, preferably far-red fluorophore after checking tissue autofluorescence and single-color controls (standard IF practice). Because ALYREF has no transmembrane segment and is mainly nuclear, permeabilise sufficiently to admit antibody to the nucleus, then verify that morphology and nuclear staining remain intact (UniProt Q86V81; standard IF practice).
What should I change if brown staining obscures ALYREF-positive nuclei?
First compare the slide with a no-primary control and inspect whether the brown deposit follows nuclei or spreads through extracellular material (standard IHC practice; HPA: ubiquitous nuclear expression). The selected example used 10% goat-serum blocking, 1:50 primary antibody overnight at 4°C, and DAB detection (datasheet M03580). Check washing, antibody concentration and chromogen development on matched sections if staining is diffuse (standard IHC practice). Include an endogenous-peroxidase block and inspect sections for intrinsic pigment before attributing all brown signal to ALYREF (standard chromogenic IHC practice). Preserve the expected nuclear signal while adjusting one workflow variable at a time (HPA: tissue IHC; standard IHC practice).
How can I score ALYREF staining across sections reproducibly? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and nuclear scoring rule before viewing group labels, because the reported tissue pattern is broadly nuclear (HPA: ubiquitous nuclear expression; standard IHC practice). For comparable sections, record the percentage of positive nuclei and intensity categories 0–3; an H-score then spans 0–300 (standard IHC practice). Normalise positive counts to intact nuclei in the specified compartment, or report positive-cell density per mm² of viable tissue when cell density itself matters (standard IHC practice). Keep retrieval, DAB development, imaging and threshold settings consistent, and exclude folds and necrotic regions using predefined rules (standard IHC practice).
How do I distinguish true ALYREF staining from tissue artefact?
Prioritise staining in intact nuclei across the relevant cell population, consistent with the supported ubiquitous nuclear tissue pattern and nucleoplasm localisation (HPA: tissue IHC and subcellular localisation). A predominantly extracellular, edge-restricted or necrotic deposit should trigger a morphology and control review before it is called ALYREF (standard IHC practice). Cytoplasmic signal needs careful context: UniProt reports cytoplasmic travel with mRNA-bound complexes, but that observation alone does not validate diffuse cytoplasmic DAB staining in a section (UniProt Q86V81; standard IHC practice). Compare no-primary and peroxidase-block controls, and verify the cell identity and nuclear denominator before interpreting a group difference (standard IHC practice).
Boster reagents

Best ALYREF / THO complex subunit 4 IHC Antibodies

Both catalog antibodies have IHC images from human paraffin sections (IHC captions: M03580, A03580-3); A03580-3 also has an IF image from A431 cells (IF caption: A03580-3).

Real IHC data IHC analysis of ALY using anti-ALY antibody (M03580). ALY was detected in a paraffin-embedded section of human lung cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 1:50 rabbit anti-ALY Antibody (M03580) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-Aly Rabbit Monoclonal Antibody
Cat # M03580
Real IHC data IHC analysis of ALYREF using anti-ALYREF antibody (A03580-3). ALYREF was detected in a paraffin-embedded section of human liver cancer tissue. Heat mediated antigen retrieval was performed in EDTA buffer (pH 8.0, epitope retrieval solution). The tissue section was blocked with 10% goat serum. The tissue section was then incubated with 2 μg/ml rabbit anti-ALYREF Antibody (A03580-3) overnight at 4°C. Peroxidase Conjugated Goat Anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Rabbit IgG Super Vision Assay Kit (Catalog # SV0002) with DAB as the chromogen.
Anti-ALYREF Antibody ®
Cat # A03580-3

M03580 has IHC images from human lung cancer, lymphoma, glioma, and testis cancer paraffin sections (M03580 IHC captions). A03580-3 has IHC images from human liver cancer and liver paraffin sections and an IF image from A431 cells (A03580-3 IHC and IF captions).

Which to pick: For tissue IHC, choose M03580 if a monoclonal antibody and its 1:50 starting dilution suit the experiment (catalog: clone 22A24; M03580 IHC caption: human paraffin section, EDTA pH 8.0 retrieval); its fixative is unreported (M03580 IHC caption). For IF/ICC, A03580-3 has a documented A431-cell IF example at 5 μg/mL (A03580-3 IF caption). Both list Human, Mouse, and Rat reactivity (catalog: M03580, A03580-3), but their IHC images document human sections only, and neither IHC caption reports the fixative (M03580 and A03580-3 IHC captions).

Each figure is that product's own IHC / IF validation image from its datasheet.

References

  1. UniProt Consortium. UniProt entry Q86V81 (THOC4_HUMAN, THO complex subunit 4).
  2. Human Protein Atlas. ALYREF tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. ALYREF subcellular location (ICC-IF): Localized to the nucleoplasm and nuclear speckles..
  4. Human Protein Atlas. ALYREF antibody validation summary (3 antibodies).
  5. ALYREF associated with immune infiltration is a prognostic biomarker in hepatocellular carcinoma. Translational oncology 2022 — PMC9079359.
  6. Comprehensive analysis of ALYREF gene expression and its correlation with immunotherapy efficacy and circulating tumor cells in bladder cancer. Scientific reports 2025 — PMC12618602.
  7. ALYREF/THOC4 expression and cell growth modulation in retinoblastoma. Pathology, research and practice 2024 — PMC12439426.
  8. Drosophila Ref1/ALYREF regulates transcription and toxicity associated with ALS/FTD disease etiologies. Acta neuropathologica communications 2019 — PMC6487524.
  9. PubMed PMID:16625196 — UniProt-cited evidence.
  10. PubMed PMID:15489334 — UniProt-cited evidence.
  11. PubMed PMID:9952027 — UniProt-cited evidence.