DNMT1 / DNA (cytosine-5)-methyltransferase 1 · IHC design guide

Design Immunohistochemistry for DNMT1

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).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for DNMT1 (IHC for DNMT1): expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody A00172-1, validated IHC image, and IHC protocol steps
Printable DNMT1 IHC protocol sheet — expected localisation Nuclear staining in tissue (HPA tissue IHC), antibody A00172-1, controls and protocol steps. Open the full DNMT1 IHC guide →

DNMT1 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 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
Important caveats
Reasons your staining may differ from the expected pattern.
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)
Section 1

Recommended DNMT1 IHC & IF Protocols

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).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human breast cancer tissue; fixative not specified (datasheet A00172-1)
FixationImage fixative and duration unreported (datasheet A00172-1); 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 A00172-1); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A00172-1)
Primary antibodyRabbit anti-DNMT1, 2-5μg/ml (datasheet A00172-1)
Primary incubationOvernight at 4 °C (datasheet A00172-1)
DetectionHRP-conjugated secondary, DAB chromogen (datasheet A00172-1)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultDNMT1-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.
💡Decision noteStart with heat-mediated EDTA at pH 8.0 for the catalog antibody (datasheet A00172-1). When reproducing a published method, use that article’s stated retrieval conditions.
Section 2

What Is the Expected DNMT1 Staining Pattern?

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).

What am I looking at on my slide?
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.
💡Expected DNMT1 appearanceCall a result positive when chromogenic signal is clearly nuclear and strongest in the named high-staining populations (HPA: tissue IHC profile and High cell populations); broad cytoplasmic or cell-border color is a localisation mismatch (UniProt P26358: nuclear and chromosome location).
How each factor affects the staining
Cell population and proliferative contextHPA 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 distributionDNMT1 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 validationThe 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 coverageUniProt 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.
Why is my staining missing, weak or wrong?
SituationLikely causeNext 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).

Sample controls for DNMT1 IHC & IF

🧪Run tonsil first and expect nuclear staining in germinal center cells (HPA: High in tonsil germinal center cells; UniProt P26358: nucleus). Use adrenal gland glandular cells as the negative tissue (HPA: Not detected in adrenal gland glandular cells); on the tonsil slide, cells outside germinal centers with absent nuclear staining can provide an internal comparison if present (HPA: High is specified for germinal center cells only).
Positive control tissue: Bone marrow (Hematopoietic cells, HPA High)
Negative control tissue: Adipose tissue (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show DNMT1 in A-431, U-251MG, U2OS, with annotated localisation: Nucleoplasm (supported) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only control, a species-matched isotype control, and DNMT1 knockout material or immunogen-peptide competition if available (standard IHC practice). For chromogenic tonsil IHC, quench endogenous peroxidase and check for residual background before interpreting nuclear DAB signal (standard IHC practice; HPA: High in tonsil germinal center cells).
⚠️Feasibility: The selected A00172-1 paraffin-section caption reports heat-mediated retrieval in EDTA at pH 8.0, but does not report a fixative; a DNMT1-specific fixation window or fixation effect is unreported (A00172-1 tissue-IHC caption). Retrieval is part of that documented IHC workflow, while the supplied evidence does not establish whether frozen sections or IF are easier (A00172-1 tissue-IHC caption). In tonsil, evaluate nuclear signal against the hematoxylin counterstain and peroxidase-control slide so background in immune cells is not scored as DNMT1 (HPA: High in tonsil germinal center cells; standard IHC practice).

HPA tissue IHC evidence for DNMT1

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.

Positive expression · recommended positive controls

TissueCell typeLevelEvidenceSource
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 →

Undetected expression · recommended negative controls

TissueCell typeLevelEvidenceSource
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 →
Section 3

Advanced DNMT1 IHC Tips

Troubleshoot DNMT1 staining by checking nuclear localisation, the documented paraffin-section workflow, and cell-specific controls before interpreting signal intensity.

How should I adjust retrieval when DNMT1 nuclear staining is weak?
Start with heat-mediated retrieval in EDTA at pH 8.0 (datasheet A00172-1). The selected paraffin-section example used that condition before nuclear staining with the catalog antibody (datasheet A00172-1; UniProt P26358 localisation). If signal remains weak, vary heating duration on adjacent sections while holding antibody concentration and detection constant, and inspect tissue morphology after each condition (standard IHC practice). Use a proliferative reference population, such as tonsillar germinal center cells, to distinguish poor retrieval from low expression in the test cells (HPA tissue IHC: High in tonsillar germinal center cells). Record background alongside nuclear signal because excessive retrieval can impair interpretation (standard IHC practice).
Could fixation explain weak or uneven DNMT1 staining in paraffin sections?
The selected tissue caption identifies a paraffin-embedded section but does not state its fixative, so DNMT1-specific fixation sensitivity remains unknown (datasheet A00172-1). Compare sections with documented fixation histories and run the same EDTA pH 8.0 retrieval and detection workflow on each (datasheet A00172-1; standard IHC practice). Inspect preserved nuclear detail and staining at section edges before attributing intensity differences to DNMT1 abundance (standard IHC practice). Include a consistently processed positive reference, such as lymph-node germinal center cells, in each staining run (HPA tissue IHC: High in lymph-node germinal center cells; standard IHC practice). Do not infer a fixation effect from tissue expression patterns (HPA tissue IHC).
What should I make of cytoplasmic or patchy DNMT1 staining?
Score DNMT1 primarily in nuclei because UniProt places it in the nucleus and on chromosomes, while HPA reports distinct nuclear tissue staining (UniProt P26358 localisation; HPA tissue IHC). Nucleoplasmic staining is supported, and perinucleolar localisation and replication-foci association can make nuclear signal uneven (HPA subcellular; UniProt P26358 localisation). Compare suspicious cytoplasmic colour with a no-primary control and assess whether it follows tissue damage or section edges (standard IHC practice). DNMT1 has no transmembrane segment, so a crisp membrane-only pattern warrants antibody and detection troubleshooting (UniProt P26358 topology; standard IHC practice). Record the fraction of evaluable nuclei rather than treating diffuse cytoplasmic colour as positive nuclear staining (standard IHC practice).
Can the antibody distinguish DNMT1 isoforms or modified epitopes in tissue?
Do not assign isoforms from this stain without an antibody epitope map or isoform-specific validation (UniProt P26358 isoforms; standard IHC practice). UniProt lists 3 DNMT1 isoforms, with isoform 2 less expressed than isoform 1 (UniProt P26358 isoforms and tissue specificity). Its RFTS domain spans residues 400–533, and the catalytic domain spans 1139–1599; epitope placement determines which forms an antibody could recognise (UniProt P26358 domains; standard IHC practice). Document the immunogen and test orthogonal expression evidence before interpreting a missing stain as isoform absence (standard IHC practice). DNMT1 also has reported modified residues, so unexplained condition-dependent staining needs epitope validation rather than an assumed modification effect (UniProt P26358 modified residues; standard IHC practice).
How can I check DNMT1 localisation by multiplex IF?
Use IF as a separate validation experiment and expect predominantly nucleoplasmic DNMT1 signal (HPA subcellular: supported nucleoplasm). Pair DNMT1 with a marker that identifies the expected proliferative cell population, and include a nuclear counterstain to assign signals to individual cells (HPA tissue IHC: mainly highly proliferative cells; standard IF practice). Choose a fluorophore channel with low background in the specimen and inspect unstained tissue for autofluorescence before interpreting overlap (standard IF practice). Permeabilise sufficiently for an intracellular nuclear epitope, because DNMT1 is nuclear and has no transmembrane segment (UniProt P26358 localisation and topology; standard IF practice). Check single-stain controls for bleed-through during multiplex acquisition (standard IF practice).
How do I reduce diffuse brown staining without losing DNMT1 signal?
First compare no-primary and positive-reference sections to separate detection background from weak DNMT1 staining (standard IHC practice). The selected paraffin-section workflow used 10% goat serum, 2 μg/ml primary antibody overnight at 4°C, and an HRP/DAB detection sequence (datasheet A00172-1). If background rises with primary antibody, optimise its concentration and washing while keeping retrieval at EDTA pH 8.0 initially (datasheet A00172-1; standard IHC practice). Apply a peroxidase block as a general precaution for HRP detection, and compare its no-primary control with the stained section (standard IHC practice). Assess brown deposits outside nuclei cautiously because DNMT1 tissue expression is described as distinctly nuclear (HPA tissue IHC).
How should I quantify DNMT1 across heterogeneous tissue regions? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and region before scoring, then count evaluable nuclei within comparable tissue areas (standard IHC practice). Report the percentage of DNMT1-positive nuclei and, when intensity is reproducible, an H-score from 0–300 based on the proportions at intensity grades 0–3 (standard IHC practice). Normalise cell counts to the number of evaluable target cells, or report positive-cell density per mm² of viable tissue (standard IHC practice). Analyse proliferative compartments separately from neighbouring low-signal cells because HPA describes DNMT1 expression mainly in highly proliferative cells (HPA tissue IHC). Keep exposure, counterstain assessment, thresholds, and exclusion rules consistent across slides (standard IHC practice).
Which findings support true DNMT1 positivity rather than staining artefact?
A convincing positive pattern is nuclear staining in an appropriate cell population, particularly a proliferative compartment (UniProt P26358 localisation; HPA tissue IHC). High staining in tonsillar or lymph-node germinal center cells can provide a biological reference, while absent staining in breast adipocytes is an expected comparison (HPA tissue IHC). Treat membrane-only or diffuse cytoplasmic colour, edge accentuation, and signal in necrotic areas as reasons to inspect controls and morphology (UniProt P26358 topology and localisation; standard IHC practice). Check a no-primary section for endogenous peroxidase or nonspecific DAB deposition before assigning brown colour to DNMT1 (standard IHC practice). Interpret differences in intensity alongside the percentage of viable, evaluable nuclei (standard IHC practice).
Boster reagents

Best DNMT1 / DNA (cytosine-5)-methyltransferase 1 IHC Antibodies

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).

Real IHC data IHC analysis of DNMT1 using anti-DNMT1 antibody (A00172-1). DNMT1 was detected in a paraffin-embedded section of human breast 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-DNMT1 Antibody (A00172-1) 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-Dnmt1 Antibody ®
Cat # A00172-1
Real IHC data Immunohistochemical analysis of paraffin-embedded Rat spleen, using the Antibody at 1:100 dilution.
Anti-Dnmt1 Rabbit Monoclonal Antibody
Cat # M00172
Real IHC data Human tonsil was stained with anti-Dnmt1 rabbit antibody
Anti-Dnmt1 Rabbit Monoclonal Antibody
Cat # M00172-3

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).

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

References

  1. UniProt Consortium. UniProt entry P26358 (DNMT1_HUMAN, DNA (cytosine-5)-methyltransferase 1).
  2. Human Protein Atlas. DNMT1 tissue IHC expression (reliability: Enhanced).
  3. Human Protein Atlas. DNMT1 subcellular location (ICC-IF): Localized to the nucleoplasm..
  4. Human Protein Atlas. DNMT1 antibody validation summary (2 antibodies).
  5. Pancreatic cancer DNMT1 expression and sensitivity to DNMT1 inhibitors. Cancer biology & therapy 2010 — PMC2920347.
  6. Investigation of the expression patterns and correlation of DNA methyltransferases and class I histone deacetylases in ovarian cancer tissues. Oncology letters 2013 — PMC3573157.
  7. A higher degree of expression of DNA methyl transferase 1 in cervical cancer is associated with poor survival outcome. International journal of women's health 2017 — PMC5476577.
  8. Reduced 5-methylcytosine level as a potential progression predictor in patients with T1 or non-invasive urothelial carcinoma. International journal of molecular sciences 2014 — PMC4307268.
  9. PubMed PMID:1594447 — UniProt-cited evidence.
  10. PubMed PMID:8940105 — UniProt-cited evidence.
  11. PubMed PMID:15057824 — UniProt-cited evidence.