This website uses cookies to ensure you get the best experience on our website.
- Table of Contents
HDAC3 / Histone deacetylase 3 · IHC design guide
Design Immunohistochemistry for HDAC3
Plan HDAC3 paraffin-section IHC around general nuclear staining (HPA tissue IHC). Compare nuclear signal in high-staining cerebellar granular-layer cells with lower-staining parathyroid glandular cells (HPA tissue IHC).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
HDAC3 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 | General nuclear tissue staining (HPA tissue IHC); cytoplasmic location is also annotated (UniProt) | |
| Staining pattern | General nuclear staining across tissue cell types (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6 HIER, heat-mediated (datasheet PA1600-1) | |
| Positive control | Cerebellum+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 consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Staining intensity varies by cell type (HPA tissue IHC) | |
| Regulation | Low tissue specificity (HPA tissue RNA) | |
| Isoform / epitope | 2 isoforms; epitope coverage is unclear (UniProt) |
Section 1
Recommended HDAC3 IHC & IF Protocols
Use the catalog antibody’s IHC-P protocol (datasheet: PA1600-1) alongside these three published HDAC3 staining methods (PMC4270766; PMC7670781; PMC6015978).
| Sample | Paraffin-embedded human intestinal cancer tissues; fixative not specified (datasheet PA1600-1) |
| Fixation | Image fixative and duration unreported (datasheet PA1600-1); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat retrieval: Citrate pH 6, 20 min (datasheet PA1600-1) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet PA1600-1) |
| Primary antibody | Rabbit anti-HDAC3, 0.5-1μg/ml (datasheet PA1600-1) |
| Primary incubation | Overnight at 4 °C (datasheet PA1600-1) |
| Detection | Streptavidin-biotin complex (SABC), DAB chromogen (datasheet PA1600-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | HDAC3-positive staining in cells in granular layer of cerebellum (HPA tissue IHC: High). HPA tissue profile: General nuclear expression. No signal in the no-primary control. |
💡Decision noteStart with heat-mediated citrate pH 6 retrieval (datasheet: PA1600-1); the published high-temperature, high-pressure method specifies 3 min but no buffer (PMC7670781).
Section 2
What Is the Expected HDAC3 Staining Pattern?
HDAC3 is predominantly nuclear and has no transmembrane segment (UniProt O15379: subcellular location, topology). In paraffin sections, expect nuclear staining across multiple tissues, with prominent signal in the specific cells HPA rates High; HPA describes the tissue pattern as general nuclear expression and rates its reliability Supported because antibody staining agrees with RNA expression (HPA: tissue IHC).
| Distinct nuclear chromogen in cerebellar granular-layer cells, cortical neurons, epididymal glandular cells, or bladder urothelial cells. | This fits the expected compartment and HPA's High staining in those cell populations (HPA: tissue IHC). Compare nuclei with neighboring cells and the counterstain before scoring; a High designation describes the reported cells, not every cell in the section (HPA: tissue IHC; standard IHC interpretation). |
| Cytoplasmic staining dominates while nuclei are faint or unstained in an otherwise positive tissue. | Treat this as an uncertain IHC result: HPA describes general nuclear tissue staining, although UniProt also lists cytoplasm and HPA ICC-IF reports additional cytosol and Golgi localization (HPA: tissue IHC and subcellular; UniProt O15379: subcellular location). Check controls before calling the cytoplasmic signal HDAC3. |
| Strong chromogen appears in a cell population outside the HPA-described pattern, especially with little nuclear staining. | Cross-reactivity or endogenous detection activity is possible; the appearance alone cannot distinguish them (HPA: tissue IHC; standard IHC practice). Check whether signal persists when the primary antibody is omitted, and compare its location with a validated positive cell population (standard IHC practice). |
| Weak, diffuse color covers nuclei, cytoplasm, and surrounding tissue without clear cell boundaries. | The lack of a discernible nuclear pattern limits interpretation against HPA's general nuclear profile (HPA: tissue IHC). Nonspecific antibody binding, residual detection activity, or excessive chromogen development can produce background; use a primary-omission control and review blocking and development conditions (standard IHC practice). |
| No nuclear signal is visible in a section containing an HPA High cell population. | A negative experimental result conflicts with the reported pattern for those cells, but does not establish HDAC3 absence (HPA: tissue IHC). Inspect tissue identity and preservation, then check the antibody and detection controls; HPA supplies no target-specific fixation-sensitivity claim here (standard IHC practice; HPA: tissue IHC). |
💡Expected HDAC3 appearanceCall the stain consistent with HDAC3 when nuclear chromogen is discernible in an HPA-reported cell population, particularly one rated High; isolated diffuse color or cytoplasm-dominant staining without matching nuclei is an uncertain positive (HPA: tissue IHC; UniProt O15379: subcellular location).
| Cell population and tissue | HPA rates cerebellar granular-layer cells, cortical neurons, epididymal glandular cells, and bladder urothelial cells High, but lists several other populations as Low; compare the same cell type rather than treating all tissues as equally intense (HPA: tissue IHC). |
| Compartment | HPA's tissue profile is generally nuclear; UniProt also lists cytoplasm, while HPA ICC-IF supports nucleoplasm and cytosol and approves an additional Golgi location. Those sources do not make diffuse cytoplasmic chromogen the expected IHC result (HPA: tissue IHC and subcellular; UniProt O15379: subcellular location). |
| Antibody validation | HPA lists IHC as Supported for HPA052052, CAB005583, and CAB072336, and rates the tissue profile Supported. These are validation summaries for those antibodies; they do not establish the performance of a different catalog antibody (HPA: antibodies; HPA: tissue IHC). |
| Isoforms and epitope coverage | UniProt lists two HDAC3 isoforms and no annotated domain, but the supplied record gives no antibody epitope or isoform coverage. An isoform-specific interpretation therefore requires evidence for the actual antibody; the tissue staining pattern alone cannot provide it (UniProt O15379: isoforms, domains; HPA: tissue IHC). |
| Retrieval and detection controls | Antigen retrieval and blocking are general paraffin-IHC workflow variables; the supplied sources give no HDAC3-specific retrieval setting or fixation effect (standard IHC practice; HPA: tissue IHC). With enzyme-based chromogenic detection, a primary-omission control helps assess endogenous activity and background (standard IHC practice). |
| Situation | Likely cause | Next action |
|---|---|---|
| No stain in an HPA High cell population. | Tissue or detection failure is possible; HPA reports High staining in defined cells, but supplies no HDAC3-specific fixation sensitivity (HPA: tissue IHC). | Verify the expected cells are present, inspect the counterstain, and run a known-positive section alongside the test; review the antibody's IHC-P instructions for retrieval and detection (standard IHC practice). |
| Nuclei and surrounding tissue share a diffuse brown haze. | Background from antibody binding, detection chemistry, or overdevelopment may obscure the general nuclear pattern (HPA: tissue IHC; standard IHC practice). | Compare a primary-omission control, review blocking and washes, and shorten chromogen development if controls show excess background (standard IHC practice). |
| Cytoplasm is stronger than nuclei. | The result conflicts with HPA's general nuclear IHC profile, although cytoplasmic HDAC3 is reported by UniProt and HPA ICC-IF (HPA: tissue IHC and subcellular; UniProt O15379). | Check a known-positive nuclear pattern and omission control, then review antibody concentration and detection background before assigning the cytoplasmic signal to HDAC3 (standard IHC practice). |
| An unexpected cell type stains strongly. | Cross-reactivity or endogenous enzyme activity may be contributing; HPA's reported staining levels apply to specified cell populations (HPA: tissue IHC; standard IHC practice). | Compare adjacent cells and a primary-omission control; if the unexpected signal persists or lacks a nuclear pattern, avoid scoring it as confirmed HDAC3 (standard IHC practice; HPA: tissue IHC). |
| Signal varies sharply across a section. | Uneven section handling or detection can create a gradient that complicates comparison with HPA's cell-specific ratings (standard IHC practice; HPA: tissue IHC). | Check section integrity and reagent coverage, then compare the same cell population in an evenly stained area or a repeat section (standard IHC practice). |
| What should an IF/ICC image show? | HPA reports mainly nucleoplasmic HDAC3, with additional cytosol and Golgi localization in ICC-IF; those observations have a different application context from tissue IHC (HPA: subcellular; HPA: tissue IHC). | Use the IF/ICC guide for that assay. Interpret the image against HPA's supported nucleoplasm and cytosol and approved Golgi annotations; do not transfer an IF/ICC pattern directly into an IHC score (HPA: subcellular; standard assay interpretation). |
Experiment evidence
IHC & IF images showing HDAC3 staining
PA1600-1 · IHCIHC analysis of HDAC3 using anti-HDAC3 antibody (PA1600-1). HDAC3 was detected in paraffin-embedded section of human intestinal cancer tissu
PA1600-1 · IHCIHC analysis of HDAC3 using anti-HDAC3 antibody (PA1600-1). HDAC3 was detected in paraffin-embedded section of human lung cancer tissues. He
PA1600-1 · IFIF analysis of HDAC3 using anti-HDAC3 antibody (PA1600-1). HDAC3 was detected in immunocytochemical section of U20S cell. Enzyme antigen ret
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000171720-HDAC3/tissue/cerebral+cortex#imid_2063424
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000171720-HDAC3/tissue/colon#imid_2063366
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000171720-HDAC3/tissue/liver#imid_2063367
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000171720-HDAC3/tissue/kidney#imid_2063360
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA052052; green = HDAC3, blue = nucleus, red = microtubules.
HPA · ICC-IF A-431Human Protein Atlas immunofluorescence, A-431, antibody HPA052052; green = HDAC3, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for HDAC3 IHC & IF
🧪Run cerebellum first and look for staining in granular-layer cells (HPA: High in cells in the granular layer). HPA detects HDAC3 in all 45 scored tissues, so use no-primary and isotype controls for the negative comparison; any cells without nuclear chromogen on the positive slide should show counterstain alone, but should not be designated HDAC3-negative cells (HPA: no negative tissue rows; UniProt O15379: nuclear localization).
Positive control tissue: Cerebellum (Cells in granular layer, HPA High)
Negative control tissue: None in HPA: HDAC3 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 HDAC3 in A-431, U-251MG, U2OS, NIH 3T3, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Run a secondary-only slide and a host-species- and clonality-matched isotype control; use HDAC3 knockout material or a peptide-blocked primary, if available, to assess target specificity (selected IHC caption: rabbit primary antibody; standard IHC controls). Quench endogenous peroxidase and check for endogenous biotin background in cerebellum when using the caption’s biotin–streptavidin/DAB detection (selected IHC caption: biotinylated secondary, SABC and DAB).
⚠️Feasibility: A target-specific fixation window or fixation effect is unreported, and the selected PA1600-1 tissue-IHC caption does not state the fixative (selected IHC caption: fixative unreported). That paraffin-section example used heat retrieval in citrate buffer at pH 6 for 20 minutes; retrieval dependence beyond that example is unreported (selected IHC caption). Frozen sections and IF are not established as easier by the supplied evidence; for cerebellar DAB scoring, assess pigment-like background against the no-primary slide (selected IHC caption: DAB detection; standard IHC practice).
HPA tissue IHC evidence for HDAC3
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
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebellum | Cells in granular layer | High | Protein (IHC) | HPA → |
| Cerebral cortex | Neuronal cells | High | Protein (IHC) | HPA → |
| Epididymis | Glandular cells | High | Protein (IHC) | HPA → |
| Urinary bladder | Urothelial cells | High | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Medium | Protein (IHC) | HPA → |
Undetected expression · recommended negative controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| None in HPA: HDAC3 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead. | ||||
Section 3
Advanced HDAC3 IHC Tips
Troubleshoot HDAC3 staining in paraffin sections by checking retrieval, nuclear signal, background, and scoring against documented tissue patterns.
What retrieval should I try first if HDAC3 staining is weak?
Start with heat-mediated retrieval in citrate buffer at pH 6 for 20 minutes (datasheet PA1600-1). The catalog antibody produced HDAC3 staining in a paraffin section of human intestinal cancer using that retrieval, followed by 1 μg/ml primary antibody overnight at 4°C (datasheet PA1600-1). If nuclear staining remains weak, compare a modestly longer heating step on adjacent sections while keeping antibody concentration and detection constant; inspect tissue morphology for heat damage (general IHC practice). Judge improvement by nuclear signal relative to surrounding background, since general nuclear expression is the supported tissue pattern (HPA tissue IHC).
Could fixation explain absent or uneven HDAC3 staining?
Target-specific sensitivity of HDAC3 staining to fixation is unknown from the supplied evidence; the selected paraffin-section caption does not state a fixative (datasheet PA1600-1). Record the fixative, time in fixative, and processing history for each specimen before comparing staining intensity across sections (general IHC practice). For a weak specimen, stain a concurrently processed control section and repeat the documented citrate pH 6, 20-minute retrieval to separate processing variation from retrieval variation (datasheet PA1600-1; general IHC practice). Compare intact central tissue with section edges and avoid assigning a fixation mechanism solely from an uneven stain (general IHC practice).
How should I assess cytoplasmic HDAC3 staining in tissue sections?
Expect predominantly nuclear staining in tissue IHC, because the documented tissue profile is general nuclear expression (HPA tissue IHC). Cytoplasmic HDAC3 is biologically plausible: the protein is annotated in nucleus, chromosome, cytoplasm, and cytosol, and cytoplasmic colocalization with XBP1 and AKT1 is reported (UniProt O15379 subcellular location). Score nuclear and cytoplasmic signal separately in intact cells, using the same detection exposure and counterstain across comparison sections (general IHC practice). If cytoplasmic color is diffuse across several cell types or follows damaged tissue, review background controls before calling redistribution; the supported nucleoplasmic IF location can guide compartment review but does not validate a particular tissue stain (HPA subcellular; general IHC practice).
Can this stain distinguish HDAC3 isoforms or a modified epitope?
HDAC3 has 2 annotated isoforms and a reported phosphoserine at residue 424 (UniProt O15379 isoforms; UniProt O15379 modified residues). The supplied antibody caption gives no epitope sequence or isoform selectivity, so its chromogenic signal cannot be assigned to either isoform or to that phosphorylation state (datasheet PA1600-1). Check the antibody's documented immunogen or epitope before making an isoform claim, and use an independently validated isoform-specific reagent if that distinction is essential (general IHC practice). Compare matched sections under the same citrate pH 6 retrieval conditions, because changes in accessibility can alter staining without establishing a change in HDAC3 isoform abundance (datasheet PA1600-1; general IHC practice).
How can IF help verify an unexpected HDAC3 IHC pattern?
Use IF on a separately optimized specimen to compare HDAC3 with a validated marker of the expected cell type and a nuclear counterstain; tissue IHC shows general nuclear expression (HPA tissue IHC; general IF practice). Choose spectrally separated fluorophores and check an unstained specimen for tissue autofluorescence before interpreting colocalization (general IF practice). HDAC3 has no transmembrane segment and is annotated in nuclear and cytosolic compartments, so permeabilization must allow antibody access to the intracellular epitope while preserving cell structure (UniProt O15379 topology; UniProt O15379 subcellular location; general IF practice). Optimize fixation and permeabilization for IF independently; the paraffin-section IHC caption does not report its fixative (datasheet PA1600-1).
What should I change when DAB appears outside HDAC3-positive nuclei?
First compare a section processed without primary antibody with the test section to locate detection-system or tissue-derived color (general IHC practice). The documented workflow used 10% goat serum block, biotinylated goat anti-rabbit secondary, a streptavidin–biotin complex, and DAB, so evaluate each detection component when background persists (datasheet PA1600-1). Include a peroxidase-blocking step and assess endogenous biotin where relevant to that detection system; these are general chromogenic controls, not demonstrated HDAC3-specific requirements (general IHC practice). Reduce excessive primary incubation or detection development only after checking that nuclear signal remains distinguishable, using the documented 1 μg/ml overnight primary condition as a reference (datasheet PA1600-1; general IHC practice).
How should I quantify HDAC3 across differently stained tissue sections? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and analysis regions before scoring, then report the percentage of cells with nuclear DAB signal and an intensity-weighted nuclear H-score (general IHC practice). Normalize cell counts to the number of evaluable nuclei, or report positive-cell density per mm² of viable tissue when tissue area is the relevant denominator (general IHC practice). Keep retrieval, primary concentration, chromogen development, imaging, and threshold settings consistent across the comparison set; the documented starting conditions are citrate pH 6 for 20 minutes and 1 μg/ml primary antibody (datasheet PA1600-1; general IHC practice). Report cytoplasmic staining separately because general nuclear expression is the supported tissue pattern (HPA tissue IHC; general IHC practice).
How do I distinguish true HDAC3 signal from a staining artefact?
Give the greatest weight to crisp signal within intact nuclei of the cell population being evaluated, consistent with general nuclear HDAC3 expression in tissue IHC (HPA tissue IHC; general IHC practice). HDAC3 can also occur in the cytosol, so a reproducible cytoplasmic pattern merits separate review rather than automatic rejection (UniProt O15379 subcellular location). Treat staining concentrated at section edges, in necrotic areas, or in unrelated tissue structures as suspect until it survives matched control and morphology checks (general IHC practice). A no-primary control helps reveal endogenous enzyme or detection-system color, while comparison with the documented citrate pH 6 retrieval provides a reproducible starting condition (datasheet PA1600-1; general IHC practice).
Boster reagents
Best HDAC3 / Histone deacetylase 3 IHC Antibodies
PA1600-1 has IHC images from human intestinal and lung cancer tissue, rat intestine and mouse brain, plus IF images from U20S and Hela cells (catalog image captions).
Real IHC data
Anti-Histone deacetylase 3 HDAC3 Antibody ®
Cat # PA1600-1
PA1600-1 is the rendered SKU; its IHC images show paraffin sections of human intestinal and lung cancer tissue and rat intestine, plus frozen mouse brain (PA1600-1 IHC image captions). Its IF images show U20S and Hela cells (PA1600-1 IF image captions).
Which to pick: For tissue IHC, pick PA1600-1 for its paraffin section examples; the fixative is unreported (PA1600-1 IHC image captions). For IF/ICC, PA1600-1 has cell images, while M00839 is a rabbit monoclonal listed for IF/ICC without supplied image captions (PA1600-1 IF image captions; M00839 catalog). For cross-species work, both list human, mouse and rat reactivity, and PA1600-1 has IHC images from all three species (catalog reactivity; PA1600-1 IHC image captions).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry O15379 (HDAC3_HUMAN, Histone deacetylase 3).
- Human Protein Atlas. HDAC3 tissue IHC expression (reliability: Supported).
- Human Protein Atlas. HDAC3 subcellular location (ICC-IF): Mainly localized to the nucleoplasm. In addition localized to the Golgi apparatus and cytosol..
- Human Protein Atlas. HDAC3 antibody validation summary (3 antibodies).
- Aberrant HDAC3 expression correlates with brain metastasis in breast cancer patients. Thoracic cancer 2020 — PMC7471029.
- Ginsenoside Rg3 inhibits melanoma cell proliferation through down-regulation of histone deacetylase 3 (HDAC3) and increase of p53 acetylation. PloS one 2014 — PMC4270766.
- HDAC3 deteriorates colorectal cancer progression via microRNA-296-3p/TGIF1/TGFβ axis. Journal of experimental & clinical cancer research : CR 2020 — PMC7670781.
- Histone Deacetylase-3 Modification of MicroRNA-31 Promotes Cell Proliferation and Aerobic Glycolysis in Breast Cancer and Is Predictive of Poor Prognosis. Journal of breast cancer 2018 — PMC6015978.
- PubMed PMID:9464271 — UniProt-cited evidence.
- PubMed PMID:9346952 — UniProt-cited evidence.
- PubMed PMID:9501169 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for HDAC3 (Histone deacetylase 3). Expected localisation General nuclear tissue staining (HPA tissue IHC); cytoplasmic location is also annotated (UniProt). Antigen retrieval: Citrate pH 6 HIER, heat-mediated (datasheet PA1600-1). Validated IHC antibody: PA1600-1 at 0.5-1μg/ml (the product's own IHC validation image is shown). Controls (HPA): positive Cerebellum (Cells in granular layer); negative None in HPA (detected in all 45 tissues); use no-primary + isotype controls. IHC-P workflow on paraffin sections; fixative unspecified. Protocol steps: 1. Sample: Paraffin-embedded human intestinal cancer tissues; fixative not specified (datasheet PA1600-1); 2. Fixation: Image fixative and duration unreported (datasheet PA1600-1); 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: Citrate pH 6 , 20 min (datasheet PA1600-1); 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% goat serum (datasheet PA1600-1); 8. Primary antibody: Rabbit anti-HDAC3, 0.5-1μg/ml (datasheet PA1600-1); 9. Primary incubation: Overnight at 4 °C (datasheet PA1600-1). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Staining intensity varies by cell type (HPA tissue IHC); Isoform / epitope: 2 isoforms; epitope coverage is unclear (UniProt); Regulation: Low tissue specificity (HPA tissue RNA). Evidence: UniProt O15379, HPA tissue IHC · Supported, HPA ICC-IF · Mainly localized to the nucleoplasm. In addition localized to the…, Datasheet PA1600-1, PMC4270766, PMC7670781. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/HDAC3/immunohistochemistry-ihc-guide.