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- Table of Contents
Plan DNMT1 paraffin IHC around nuclear staining in proliferative cells (HPA tissue IHC). Use bone marrow hematopoietic cells as a positive reference and adipose tissue adipocytes as a negative reference, then score nuclear signal by cell type (HPA tissue IHC).
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
| Expected localisation | Nuclear staining in tissue (HPA tissue IHC) | |
| Staining pattern | Nuclear staining, mainly in highly proliferative cells (HPA tissue IHC) | |
| Antigen retrieval | EDTA pH 8.0 HIER, heat-mediated (datasheet A00172-1) | |
| Positive control | Bone marrow+4 more · see all | |
| Negative control | Adipose tissue+4 more · see all |
| Fixation | Keep paraffin-section fixation consistent across samples (standard IHC practice; not target-specific) | |
| Caveat | Signal varies by cell type within tissues (HPA tissue IHC) | |
| Regulation | Enriched in highly proliferative cells (HPA tissue IHC) | |
| Isoform / epitope | 3 isoforms; check epitope coverage before isoform claims (UniProt) |
The catalog antibody’s IHC-P protocol (datasheet A00172-1) is accompanied by published DNMT1 IHC methods for pancreatic, ovarian, cervical, and urothelial carcinoma specimens (PMC2920347; PMC3573157; PMC5476577; PMC4307268).
| Sample | Paraffin-embedded human breast cancer tissue; fixative not specified (datasheet A00172-1) |
| Fixation | Image fixative and duration unreported (datasheet A00172-1); 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 A00172-1); 20 min, 95–100 °C (standard) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% goat serum (datasheet A00172-1) |
| Primary antibody | Rabbit anti-DNMT1, 2-5μg/ml (datasheet A00172-1) |
| Primary incubation | Overnight at 4 °C (datasheet A00172-1) |
| Detection | HRP-conjugated secondary, DAB chromogen (datasheet A00172-1) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | DNMT1-positive staining in hematopoietic cells of bone marrow (HPA tissue IHC: High). HPA tissue profile: Distinct nuclear expression in several different cell types, mainly in highly proliferative cells. No signal in the no-primary control. |
DNMT1 should stain nuclei, particularly in highly proliferative cells (HPA: distinct nuclear expression; Enhanced tissue IHC reliability). UniProt places DNMT1 in the nucleus and on chromosomes, with no transmembrane segment (UniProt P26358: subcellular location and topology). Expect strong staining in germinal center cells, bone marrow hematopoietic cells, placental cytotrophoblasts, and testicular spermatogonia (HPA: High in each listed cell population).
| Distinct chromogenic staining is concentrated in nuclei of germinal center cells, with much less signal in surrounding cells. | This fits the reported positive pattern in lymph node and tonsil (HPA: High in germinal center cells). Score the named cell population and its nuclear signal; DNMT1 expression is not expected to be uniform across every cell in a positive tissue (HPA: distinct nuclear expression, mainly in highly proliferative cells). |
| Strong staining lies mainly in cytoplasm or along cell borders, while nuclei are pale. | Treat this as a localisation mismatch requiring investigation: DNMT1 is nuclear and chromosome associated (UniProt P26358: subcellular location), and tissue IHC shows distinct nuclear expression (HPA: tissue IHC profile). Review counterstain alignment, detection conditions, and an appropriate negative control before interpreting the signal as DNMT1. |
| Adipocytes show convincing staining, or signal appears in another cell population reported as not detected. | Adipocytes in adipose tissue and breast are reported as Not detected (HPA: adipose tissue and breast). Such staining raises concern for cross-reactivity or endogenous detection activity; check a negative control and the location of the deposit. Do not extend a cell-specific HPA negative call to every cell in that tissue. |
| Color is spread across nuclei, cytoplasm, and the spaces between cells without clear cellular boundaries. | Diffuse background cannot establish a DNMT1-positive cell. The expected tissue pattern is distinct and nuclear (HPA: tissue IHC profile; UniProt P26358: subcellular location). Inspect the negative control, blocking, washing, and chromogen development, then compare any remaining nuclear signal with the positive cell populations. |
| No nuclear signal appears in germinal center cells or another documented high-staining population. | An entirely blank expected-positive population warrants an assay check before a biological negative call (HPA: High in lymph node or tonsil germinal center cells; High in bone marrow hematopoietic cells). Verify the section contains the named cells, then review antibody use, antigen retrieval, detection reagents, and a concurrently stained positive control. |
| Cell population and proliferative context | HPA reports distinct nuclear expression mainly in highly proliferative cells (HPA: tissue IHC profile). High calls apply to specific populations, including placental cytotrophoblasts and testicular spermatogonia (HPA: High in each); low respiratory epithelial or enterocyte staining should not be scored against those high examples (HPA: Low in nasopharynx, bronchus, and duodenum). |
| Cell cycle and nuclear distribution | DNMT1 associates with replication foci during S phase and also associates with chromatin during G2 and M phases (UniProt P26358: subcellular location and function). Nuclear staining can therefore vary within a field; this biology does not justify scoring predominantly cytoplasmic deposition as a correct pattern (UniProt P26358: nuclear and chromosome location). |
| Antibody validation | The reported tissue pattern has Enhanced reliability, described as high consistency between antibody staining and RNA expression (HPA: tissue IHC reliability). HPA lists HPA002694 and CAB005876 as Enhanced for IHC (HPA: antibody validation). These summaries support comparison with the documented pattern; they do not validate every antibody or detection setup. |
| Isoforms and epitope coverage | UniProt lists three DNMT1 isoforms and notes that isoform 2 is less expressed than isoform 1 (UniProt P26358: isoforms and tissue specificity). An antibody's ability to detect each isoform depends on its epitope; no epitope mapping is supplied here, so do not infer isoform-specific staining from a tissue IHC result. |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected-positive germinal center cells are unstained. | The result conflicts with a documented High cell population (HPA: lymph node and tonsil germinal center cells); the cause cannot be assigned from HPA staining data alone. | Confirm germinal center cells are present. Check the catalog antibody's IHC-P instructions, retrieval and detection steps, and a concurrently processed positive section before calling the specimen negative. |
| Signal is chiefly cytoplasmic or membranous. | The compartment conflicts with nuclear and chromosome localisation (UniProt P26358: subcellular location) and distinct nuclear tissue staining (HPA: tissue IHC profile). | Compare the deposit with nuclear counterstain and a negative control. Review antibody concentration and detection conditions; retain only clearly localised nuclear signal for interpretation. |
| Adipocytes or another HPA-negative cell population stains. | This differs from the cell-specific Not detected report (HPA: adipocytes in adipose tissue and breast). Cross-reactivity or endogenous detection activity is possible, but the image alone cannot distinguish them. | Inspect controls for primary-antibody-independent color, review blocking and detection, and compare the suspect cells with a documented positive population on a suitable section. |
| Every cell and extracellular area carries faint color. | Diffuse color obscures the distinct nuclear pattern reported for DNMT1 (HPA: tissue IHC profile). It may reflect the staining workflow rather than interpretable cell-specific signal. | Check the negative control; review washing, blocking, and chromogen development. Reassess only where nuclear boundaries and signal can be distinguished. |
| A low-staining population looks weaker than the positive control. | HPA reports Low staining in respiratory epithelial cells of nasopharynx and bronchus and in duodenal enterocytes, versus High staining in several named proliferative populations (HPA: tissue IHC cell levels). | Compare the same named cell types across sections. Confirm nuclear localisation, but do not require a Low population to match a High population's intensity. |
| IF/ICC Q: What localisation should be expected? | The separate ICC-IF evidence reports supported nucleoplasmic localisation; this is a localisation reference, not an IHC-P protocol (HPA: subcellular summary). | For IF/ICC interpretation, look for nucleoplasmic signal and consult its dedicated guide (HPA: supported nucleoplasm). For this chromogenic IHC-P guide, assess the documented tissue-specific nuclear pattern (HPA: tissue IHC profile). |
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — 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.
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Bone marrow | Hematopoietic cells | High | Protein (IHC) | HPA → |
| Lymph node | Germinal center cells | High | Protein (IHC) | HPA → |
| Placenta | Cytotrophoblasts | High | Protein (IHC) | HPA → |
| Testis | Spermatogonia cells | High | Protein (IHC) | HPA → |
| Tonsil | Germinal center cells | High | Protein (IHC) | HPA → |
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Adipose tissue | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Adrenal gland | Glandular cells | Not detected | Protein (IHC) | HPA → |
| Breast | Adipocytes | Not detected | Protein (IHC) | HPA → |
| Caudate | Glial cells | Not detected | Protein (IHC) | HPA → |
| Cerebellum | Cells in granular layer | Not detected | Protein (IHC) | HPA → |
Troubleshoot DNMT1 staining by checking nuclear localisation, the documented paraffin-section workflow, and cell-specific controls before interpreting signal intensity.
The catalog shows IHC images from human breast cancer, rat spleen and human tonsil (catalog IHC captions), plus IF data from U2OS cells (A00172-1 IF caption).
A00172-1 shows human breast cancer paraffin-section IHC and U2OS-cell IF (A00172-1 image captions); M00172 shows rat spleen paraffin-section IHC (M00172 IHC caption). M00172-3 shows human tonsil IHC, with section processing unspecified (M00172-3 IHC caption).
Which to pick: For human paraffin-section IHC, choose A00172-1: its own caption documents that sample and heat retrieval in EDTA at pH 8.0; the fixative is unreported (A00172-1 IHC caption). For IF/ICC, A00172-1 has a U2OS-cell IF image at 5 μg/mL, while M00172 and M00172-3 list IF without an IF image in this payload (A00172-1 IF caption; M00172 and M00172-3 catalog applications and image captions). For cross-species IHC, M00172 is a rabbit monoclonal with human, mouse and rat reactivity and a rat spleen paraffin-section image; M00172-3 is also a rabbit monoclonal with those species listed, but its human tonsil caption gives no section processing details; neither IHC caption reports a fixative (M00172 and M00172-3 catalog entries and IHC captions).