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

Design Immunohistochemistry for DNMT1

Plan chromogenic DNMT1 IHC in paraffin sections around the nuclear staining seen mainly in proliferative cells (HPA tissue IHC). Use high-staining cell populations as reference points and assess 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 proliferative cells (HPA tissue IHC), antibody A00172-1, validated IHC image, and IHC protocol steps
Printable DNMT1 IHC protocol sheet — expected localisation Nuclear staining in proliferative cells (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 proliferative cells (HPA tissue IHC)
Staining pattern Distinct nuclear signal, mainly in 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 Cell-type mix can obscure positive nuclei (HPA tissue IHC)
Regulation Higher in proliferative cells (HPA tissue IHC)
Isoform / epitope 3 isoforms; isoform 2 is less expressed than 1 (UniProt)
Section 1

Recommended DNMT1 IHC & IF Protocols

The catalog antibody uses heat retrieval with EDTA pH 8.0 (datasheet A00172-1). The published DNMT1 IHC protocols below cover pancreatic and cervical cancer tissue (PMC2920347; PMC5476577).

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 EDTA pH 8.0 heat retrieval for the catalog antibody (datasheet A00172-1); citrate pH 6.0 is a published alternative (PMC5476577).
Section 2

What Is the Expected DNMT1 Staining Pattern?

DNMT1 should appear chiefly in nuclei, with the clearest IHC staining in proliferative cell populations (UniProt P26358: nucleus and chromosome; HPA tissue IHC: distinct nuclear expression, mainly in highly proliferative cells). HPA rates its tissue staining evidence “Enhanced,” citing consistency between antibody staining and RNA expression (HPA tissue IHC: reliability). DNMT1 has no transmembrane segment, so a membrane pattern would be unexpected (UniProt P26358: topology).

What am I looking at on my slide?
Distinct nuclear staining in bone marrow hematopoietic cells, lymph node or tonsil germinal center cells, placental cytotrophoblasts, or testicular spermatogonia (HPA tissue IHC: High).This matches the reported compartment and several cell populations with High staining (HPA tissue IHC: nuclear profile and High entries). Compare nuclei within the relevant population; an entire tissue section need not stain uniformly because the HPA observations name specific cells (HPA tissue IHC: cell level entries).
Predominantly membrane or cytoplasmic chromogen, with little convincing nuclear signal (UniProt P26358: nuclear location and no transmembrane segment).The compartment conflicts with the expected DNMT1 pattern (UniProt P26358: subcellular location; HPA tissue IHC: nuclear profile). Treat it as possible nonspecific staining or detection artefact; compartment alone cannot identify the cause (general IHC interpretation). Check whether the signal survives appropriate negative controls (general IHC practice).
Strong staining in adipocytes or another cell population listed as Not detected, while expected positive nuclei are weak (HPA tissue IHC: adipocytes Not detected).The cell level distribution raises concern for cross-reactivity or endogenous detection activity; it does not prove either mechanism (general IHC interpretation). HPA’s Not detected designation applies to its listed cell population and observations, so review matched morphology and controls before calling the whole tissue DNMT1 negative (HPA tissue IHC: cell level entries).
A diffuse brown haze spans nuclei, cytoplasm, and extracellular areas without a clear cell pattern (general chromogenic IHC observation).This obscures the distinct nuclear pattern reported by HPA (HPA tissue IHC: nuclear profile). Consider nonspecific antibody binding, inadequate blocking or washing, or chromogen background as general IHC possibilities; assess a negative detection control and compare with intact tissue morphology (general IHC practice).
No nuclear staining in an intact expected positive population, such as tonsil germinal center cells or placental cytotrophoblasts (HPA tissue IHC: High).A negative run in those cells calls for a technical check before interpreting the test specimen (general IHC practice). Confirm section quality, retrieval and detection controls, and the antibody’s IHC-P instructions; the supplied HPA and UniProt data do not specify a DNMT1 fixation sensitivity or an optimal retrieval condition.
💡Expected DNMT1 appearanceCall a positive result when discrete nuclear chromogen is evident in expected cell populations, especially those reported High by HPA; isolated strong membrane staining or diffuse staining without nuclear definition is suspicious rather than a convincing DNMT1 pattern (HPA tissue IHC: nuclear profile and High entries; UniProt P26358: nuclear location and topology).
How each factor affects the staining
Cell population and proliferation contextHPA describes nuclear staining mainly in highly proliferative cells and rates bone marrow hematopoietic cells, germinal center cells, cytotrophoblasts, and spermatogonia High (HPA tissue IHC). Choose and score the named populations instead of assuming every cell in a positive tissue has equal intensity (HPA tissue IHC: cell level entries).
Nuclear distributionDNMT1 associates with chromosomes and replication foci during S phase and can localize near the nucleolus (UniProt P26358: subcellular location). Nuclear staining may therefore vary within or between nuclei; HPA’s tissue IHC profile supports a nuclear call, but does not establish a required punctate IHC pattern (HPA tissue IHC: profile).
Antibody validationBoth listed rabbit antibodies, HPA002694 and CAB005876, have Enhanced IHC validation; HPA describes Enhanced as agreement from independent antibodies or orthogonal data (HPA antibodies: IHC validation). This supports the reported pattern, but does not validate an unlisted antibody, a particular dilution, or a retrieval method (HPA antibodies: scope of supplied data).
Isoform and epitope coverageUniProt lists 3 DNMT1 isoforms and reports isoform 2 at lower expression than isoform 1 (UniProt P26358: isoforms and tissue specificity). The payload gives no antibody epitope or isoform recognition data; do not assign an unusual staining pattern to isoform selectivity without antibody specific evidence.
IF/ICC Q&A: where should signal appear?Answer: HPA reports supported nucleoplasmic localization in ICC-IF, consistent with UniProt’s nuclear assignment (HPA subcellular ICC-IF: Nucleoplasm; UniProt P26358: nucleus). That observation is a localization cross-check for this IHC guide; it does not provide an IF/ICC protocol or transfer an IHC staining intensity to cultured cells.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Expected positive nuclei are blank.A failed or weak IHC workflow is possible; no target specific fixation or retrieval effect is established by the supplied sources.Run a named High population alongside the specimen, then verify section integrity, the catalog antibody’s IHC-P instructions, retrieval, and detection controls (HPA tissue IHC: High entries; general IHC practice).
Chromogen is mostly membranous or cytoplasmic.The distribution conflicts with DNMT1’s nuclear localization and lack of a transmembrane segment (UniProt P26358: location and topology).Compare with expected positive nuclei and an appropriate negative detection control; check staining specificity before scoring those cells as positive (HPA tissue IHC: nuclear profile; general IHC practice).
Adipocytes stain strongly.HPA lists adipocytes as Not detected; cross-reactivity or endogenous detection activity is possible, but the image alone cannot distinguish them (HPA tissue IHC: adipocytes; general IHC interpretation).Check the cell identity and a negative detection control, then reassess whether nuclear staining in a named High population remains convincing (HPA tissue IHC: High entries; general IHC practice).
Diffuse background hides nuclear detail.Nonspecific binding, incomplete washing, or detection background can obscure compartment calls (general chromogenic IHC practice).Review blocking and washing steps and the negative detection control; adjust the workflow according to the catalog antibody’s IHC-P instructions, then reassess nuclear definition (general IHC practice).
Only a subset of otherwise similar cells stains.DNMT1 associates with replication foci during S phase, and HPA reports staining mainly in proliferative cells (UniProt P26358: subcellular note; HPA tissue IHC: profile).Score the cell population and compartment, compare intact neighboring cells, and avoid treating uneven intensity alone as assay failure (HPA tissue IHC: cell level pattern; general IHC interpretation).
Weak staining appears in a low or Not detected HPA population.HPA’s categories describe observed cell level staining, not a universal threshold for every specimen or antibody (HPA tissue IHC: low and Not detected entries).Check morphology, background, and controls before calling it positive; report the observed compartment and intensity rather than extrapolating from a whole tissue label (general IHC practice; HPA tissue IHC: cell level entries).

Sample controls for DNMT1 IHC & IF

🧪Run tonsil first: germinal center cells should show nuclear DNMT1 staining (HPA: High in tonsil germinal center cells; UniProt P26358: nucleus). Use adipose tissue as the negative comparator, scoring adipocytes, where DNMT1 is not detected; on the tonsil slide, neighboring cells without nuclear staining provide an internal background reference (HPA: Not detected in adipocytes; standard IHC practice).
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 slide; a concentration-matched rabbit IgG isotype control; and, if available, DNMT1 knockout material as a biological negative (caption: rabbit anti-DNMT1; standard IHC practice). Block endogenous peroxidase before DAB detection because tonsillar leukocytes can produce peroxidase background (caption: DAB detection; standard IHC practice).
⚠️Feasibility: No DNMT1-specific fixation window or fixation effect is reported, and the selected A00172-1 paraffin-section caption leaves the fixative unreported (caption: fixative not stated). Heat-mediated retrieval with EDTA at pH 8.0 is documented for that antibody, but the caption does not establish that retrieval is required (caption: EDTA retrieval). The evidence does not establish whether frozen sections or IF are easier; HPA supports nucleoplasmic ICC-IF localization, while endogenous peroxidase in tonsillar leukocytes may complicate chromogenic scoring (HPA: supported nucleoplasm localization; 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 in paraffin-section IHC by checking nuclear localisation, tissue context, processing, and controls before interpreting signal intensity.

What should I adjust when DNMT1 nuclear staining is weak after retrieval?
Begin with heat-mediated retrieval in EDTA at pH 8.0 for paraffin sections (datasheet A00172-1). The selected tissue image used that condition with 2 μg/ml antibody incubated overnight at 4°C (datasheet A00172-1). If nuclei stain weakly, check deparaffinisation, heating consistency, and tissue retention before changing retrieval conditions (standard IHC practice). Compare a limited retrieval-time series on adjacent sections while keeping antibody concentration and detection constant, then judge nuclear signal alongside morphology and background; excessive retrieval can damage sections (standard IHC practice; UniProt P26358: nuclear localisation).
Could fixation explain variable DNMT1 staining between paraffin sections?
DNMT1-specific fixation sensitivity is unknown because the selected paraffin-section caption does not state a fixative (datasheet A00172-1). Record fixative, fixation duration, tissue thickness, and delay before fixation when investigating variation between specimens (standard IHC practice). On matched sections, keep EDTA retrieval at pH 8.0 and antibody concentration at 2 μg/ml while comparing processing histories (datasheet A00172-1; standard IHC practice). Assess nuclear signal together with morphology and staining uniformity, since uneven fixation can complicate antigen access in paraffin-section IHC (standard IHC practice). Neither nuclear localisation nor the tissue expression profile establishes a DNMT1-specific fixation effect (UniProt P26358: nucleus; HPA: tissue IHC profile).
How should I troubleshoot cytoplasmic or uneven DNMT1 staining?
Expect predominantly nuclear staining: DNMT1 localises to the nucleus and chromosomes, with reported perinucleolar localisation (UniProt P26358: subcellular location). Distinct nuclear expression, mainly in highly proliferative cells, is also reported in tissue IHC (HPA: tissue IHC profile). If cytoplasm stains strongly, compare it with a no-primary control and inspect whether the signal follows tissue edges or damaged areas (standard IHC practice). Review deparaffinisation, blocking, washes, and detection exposure before accepting a compartment shift (standard IHC practice). Replication-foci association during S phase can make nuclear staining heterogeneous, so evaluate intact nuclei across comparable cell populations (UniProt P26358: S-phase localisation; standard IHC practice).
Can this antibody distinguish DNMT1 isoforms or modified epitopes in sections?
DNMT1 has 3 listed isoforms, and isoform 2 is less expressed than isoform 1 (UniProt P26358: isoforms and tissue specificity). The supplied tissue caption does not identify the antibody epitope or establish isoform selectivity (datasheet A00172-1). Do not assign a staining difference to one isoform without epitope mapping and independent validation in the relevant sections (standard IHC practice). DNMT1 also has numerous reported modified residues, including phosphorylation near residues 127–141, but the caption does not establish modification-specific recognition (UniProt P26358: modified residues; datasheet A00172-1). Compare nuclear staining under matched processing conditions before interpreting biological differences (standard IHC practice).
How can IF help investigate an ambiguous DNMT1 IHC pattern?
Use IF as a separate confirmation experiment, recognising that the supplied antibody evidence documents paraffin-section chromogenic IHC, not an IF validation (datasheet A00172-1). Multiplex DNMT1 with a proliferation marker such as Ki-67 and a nuclear counterstain to examine the expected nuclear signal in proliferative cells (HPA: nuclear expression mainly in highly proliferative cells; standard IF practice). Select spectrally separated fluorophores, favouring a far-red channel when tissue autofluorescence obscures shorter wavelengths (standard IF practice). DNMT1 lacks a transmembrane segment and is nuclear, so permeabilisation must permit access to intracellular nuclear epitopes (UniProt P26358: topology and subcellular location; standard IF practice). Compare single-stain and no-primary controls before interpreting overlap (standard IF practice).
What controls identify nonspecific DNMT1 colour or diffuse background?
Run a no-primary control through the same secondary, peroxidase, and DAB steps to assess detection-related colour (standard IHC practice). The selected procedure used 10% goat serum blocking, a peroxidase-conjugated secondary, and DAB development (datasheet A00172-1). If background persists, review serum blocking, secondary compatibility, wash stringency, and whether endogenous peroxidase was adequately quenched (standard IHC practice). Compare the colour with intact nuclear staining rather than total brown area, because DNMT1 is nuclear and tissue staining is concentrated in proliferative cells (UniProt P26358: nucleus; HPA: tissue IHC profile). Exclude folds, damaged edges, and necrotic regions from interpretation (standard IHC practice).
How should I quantify DNMT1 across sections with different cell composition? ⚠ ANSWER MARKED FOR VERIFICATION
Score nuclear staining within a defined cell population using percentage-positive nuclei and intensity, or combine them as an H-score (standard IHC practice; UniProt P26358: nuclear localisation). Keep the positivity threshold, magnification, sampled area, and staining batch consistent across comparisons (standard IHC practice). Normalise positive counts to the number of eligible intact nuclei, or report positive-cell density per mm² when tissue area is the endpoint (standard IHC practice). Record proliferative compartments separately because tissue IHC shows stronger DNMT1 expression mainly in highly proliferative cells (HPA: tissue IHC profile). Exclude damaged tissue and document the scoring region before comparing specimens (standard IHC practice).
When is a DNMT1-positive pattern biologically credible rather than artefactual?
A credible pattern is nuclear in intact cells and consistent across comparable regions, since DNMT1 localises to nuclei and chromosomes (UniProt P26358: subcellular location; standard IHC practice). Stronger staining in proliferative populations fits the reported tissue IHC profile; germinal center cells and spermatogonia show high expression (HPA: tissue IHC profile). Question predominantly cytoplasmic colour or signal confined to section edges, folds, or necrotic areas (UniProt P26358: nuclear localisation; standard IHC practice). Check no-primary controls and peroxidase blocking when widespread brown colour suggests detection artefact (standard IHC practice). Interpret any intensity difference alongside cell composition and processing records before attributing it to DNMT1 biology (standard IHC practice).
Boster reagents

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

The catalog lists human-reactive DNMT1 antibodies with IHC images from human tissue, rat spleen and mouse lung; A00172-1 also has an IF image from U2OS cells (catalog applications, reactivity and image captions).

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 IHC in paraffin-embedded human breast and pancreas cancer sections and IF in U2OS cells (A00172-1 image captions). M00172 shows IHC in paraffin-embedded rat spleen, human lung cancer and glioblastoma, and mouse lung; M00172-3 shows IHC staining of human tonsil (M00172 and M00172-3 image captions).

Which to pick: For human tissue IHC, choose A00172-1 when its documented paraffin-section workflow is useful; M00172-3 offers a human tonsil IHC example, but its caption does not report section processing (A00172-1 and M00172-3 IHC image captions). For IF/ICC, A00172-1 has a documented U2OS IF example and lists both applications (A00172-1 IF image caption and applications). For cross-species tissue IHC, M00172 lists human, mouse and rat reactivity and shows paraffin-section images from each; the fixative is unreported in its captions (M00172 reactivity and IHC image 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.