CPSF6 / Cleavage and polyadenylation specificity factor subunit 6 · IHC design guide

Design Immunohistochemistry for CPSF6

Plan CPSF6 paraffin IHC around the nuclear staining observed across tissues (HPA tissue IHC). This guide covers fixation consistency, antibody selection, detection and nuclear scoring (standard IHC practice).

Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
Immunohistochemistry protocol sheet for CPSF6 (IHC for CPSF6): expected localisation Ubiquitous nuclear tissue staining (HPA tissue IHC), antibody A04551-1, validated IHC image, and IHC protocol steps
Printable CPSF6 IHC protocol sheet — expected localisation Ubiquitous nuclear tissue staining (HPA tissue IHC), antibody A04551-1, controls and protocol steps. Open the full CPSF6 IHC guide →

CPSF6 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 Ubiquitous nuclear tissue staining (HPA tissue IHC)
Staining pattern Nuclear staining across diverse cell types (HPA tissue IHC)
Antigen retrieval EDTA pH 8.0 HIER, heat-mediated (datasheet A04551-1)
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 consistent across sections (standard IHC practice; not target-specific)
Caveat Antibody staining and RNA show medium consistency (HPA tissue IHC)
Regulation Low tissue specificity (HPA tissue RNA)
Isoform / epitope 3 isoforms; epitope coverage is unknown (UniProt)
Section 1

Recommended CPSF6 IHC & IF Protocols

The catalog antibody’s IHC-P protocol (datasheet A04551-1) is presented alongside two published CPSF6 paraffin-section IHC protocols (PMC11234225; PMC5514498).

Recommended immunohistochemistry (IHC-P) protocol parameters
SampleParaffin-embedded human liver cancer tissue; fixative not specified (datasheet A04551-1)
FixationImage fixative and duration unreported (datasheet A04551-1); 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 A04551-1); 20 min, 95–100 °C (standard)
Peroxidase block3% H2O2, 10 min, room temperature (standard)
Blocking10% goat serum (datasheet A04551-1)
Primary antibodyRabbit anti-CPSF6, 2-5 μg/ml (datasheet A04551-1)
Primary incubationOvernight at 4 °C (datasheet A04551-1)
DetectionStreptavidin-biotin complex (SABC), DAB chromogen (datasheet A04551-1)
CounterstainHematoxylin, blue, dehydrate and mount (standard)
Expected resultCPSF6-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 for the catalog antibody (datasheet A04551-1). The breast cancer protocol used citrate pH 6.0 (PMC5514498).
Section 2

What Is the Expected CPSF6 Staining Pattern?

CPSF6 should stain predominantly in nuclei across many cell types, including adipocytes, hematopoietic cells and glandular cells reported as High by HPA (HPA tissue IHC: ubiquitous nuclear expression; High in these cells). Nucleoplasmic and speckled nuclear signal fits its known distribution; CPSF6 can also shuttle through the cytoplasm (UniProt Q16630: subcellular location). It has no transmembrane segment (UniProt Q16630: topology). HPA rates the tissue IHC pattern Supported, with medium agreement between staining and RNA data (HPA tissue IHC: reliability).

What am I looking at on my slide?
Nuclear chromogen appears in many cells, with clear signal in adipocytes or hematopoietic cells.This fits the broad nuclear pattern and reported High staining in those cells (HPA tissue IHC). Compare cells within the same section before scoring intensity; a High HPA call is a reference pattern, not a calibrated intensity threshold.
Cytoplasmic staining dominates while nuclei are faint or blank.Predominantly cytoplasmic IHC conflicts with the reported ubiquitous nuclear pattern (HPA tissue IHC). CPSF6 does shuttle between nucleus and cytoplasm (UniProt Q16630), so some cytoplasmic signal alone is inconclusive. Check nuclear preservation, background and control staining before calling the distribution biological.
Strong staining appears chiefly in a cell population while the expected High population is unstained.Review cell identification and possible cross-reactivity or endogenous detection activity (general IHC practice). HPA reports High staining in specified populations but supplies no negative cell populations here (HPA tissue IHC); an unlisted cell type cannot be declared CPSF6-negative from this record.
Chromogen coats tissue broadly, obscuring nuclear boundaries.A diffuse deposit cannot establish CPSF6 localization. Excess background may reflect nonspecific antibody binding, detection activity or inadequate washing (general IHC practice). Judge a positive result only where stained nuclei can be distinguished from surrounding tissue.
No nuclear signal is visible in bone marrow hematopoietic cells or adrenal glandular cells.Both are reported High by HPA, so absence warrants a run-level check (HPA tissue IHC). Review the positive control, antibody and detection reagents, and retrieval conditions (general IHC practice). A single blank section does not establish absent CPSF6 expression.
💡Expected CPSF6 appearanceCall the IHC result positive when distinct nuclear chromogen is visible across expected cell populations, including cells reported High by HPA; broad non-nuclear haze without discernible nuclei is a suspect positive (HPA tissue IHC; general IHC interpretation).
How each factor affects the staining
Nuclear distributionThe primary scoring compartment is the nucleus (HPA tissue IHC: ubiquitous nuclear expression). UniProt also places CPSF6 in nucleoplasm and nuclear speckles (UniProt Q16630); routine chromogenic sections may not resolve individual speckles (general microscopy practice).
Shuttling and cell-cycle distributionCPSF6 shuttles between nucleus and cytoplasm, and its speckle and paraspeckle distribution varies during the cell cycle (UniProt Q16630). Interpret modest compartment variation against the dominant tissue IHC pattern, without treating every cytoplasmic trace as failure (HPA tissue IHC).
Isoforms and epitope coverageThree isoforms are listed (UniProt Q16630). The supplied record gives no antibody epitope or isoform-specific IHC performance, so this evidence cannot predict which isoforms the catalog antibody detects or explain a negative section.
Antibody validationThe listed antibody HPA039973 is Supported for IHC and Enhanced for ICC (HPA antibodies). The tissue pattern has medium agreement with RNA expression (HPA tissue IHC); use the reported pattern as a reference, while evaluating the actual section and controls.
IF/ICC Q&AWhere should signal appear in IF/ICC? In nucleoplasm and nuclear speckles (HPA subcellular ICC-IF: both enhanced); UniProt also reports speckles and cytoplasmic shuttling (UniProt Q16630). This localization answer does not establish an IF/ICC protocol or dilution.
Why is my staining missing, weak or wrong?
SituationLikely causeNext action
Known High tissue gives no nuclear stain.The run may have failed at primary incubation, retrieval or detection (general IHC practice); HPA reports High staining in bone marrow hematopoietic cells (HPA tissue IHC).Check an on-run positive control and reagent sequence; review the catalog antibody's IHC-P instructions before adjusting retrieval or antibody concentration (general IHC practice).
Cytoplasm is stronger than nuclei throughout the section.This departs from the reported nuclear tissue pattern (HPA tissue IHC), although CPSF6 can shuttle (UniProt Q16630); diffuse background remains a possible explanation (general IHC practice).Inspect whether nuclei are intact and separately stained, then compare the positive and negative controls and reduce nonspecific background using standard IHC optimization (general IHC practice).
Brown deposit is diffuse or follows tissue edges.Nonspecific binding, drying or uneven reagent coverage can create misleading chromogen deposition (general IHC practice).Review section handling, blocking, wash coverage and development time; score only interpretable cellular staining with a nuclear location (general IHC practice; HPA tissue IHC: nuclear pattern).
Signal appears in the no-primary control.The primary antibody cannot account for that control's staining; endogenous detection activity or detection-reagent background is possible (general IHC practice).Check the detection chemistry and its appropriate endogenous-activity block, then repeat the control alongside the test section (general IHC practice).
Only an unlisted cell population stains strongly.Cell identification, cross-reactivity or local background may explain the mismatch (general IHC practice); the supplied HPA extract lists no negative populations (HPA tissue IHC).Confirm morphology and staining compartment, compare a reported High population on the same run, and avoid calling the unlisted cells false positive solely because they are unlisted.
Nuclear stain varies between adjacent cells.CPSF6 nuclear substructure distribution can vary with the cell cycle (UniProt Q16630); staining variation may also reflect section or detection variability (general IHC practice).Score the fraction of clearly stained nuclei and their intensity within each cell population, and compare technical controls before assigning biological meaning (general IHC practice).

Sample controls for CPSF6 IHC & IF

🧪Run appendix first and assess glandular cells for CPSF6 staining (HPA: High in appendix glandular cells). HPA detects CPSF6 in all 45 scored tissues, so there is no supported negative tissue; no internal cell population is validated as negative, and any cells lacking nuclear signal should be interpreted alongside the no-primary and isotype controls (HPA: no negative rows; UniProt Q16630: nuclear localization).
Positive control tissue: Adipose tissue (Adipocytes, HPA High)
Negative control tissue: None in HPA: CPSF6 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 CPSF6 in A-431, U-251MG, U2OS, HEK293, U2OS, siRNA 1 (10x), U2OS, siRNA 1 (40x), U2OS, siRNA 2 (10x), U2OS, siRNA 2 (40x), U2OS, scrambled (10x), U2OS, scrambled (40x), with annotated localisation: Nucleoplasm (enhanced), Nuclear speckles (enhanced) (HPA subcellular).
Technical controls: Include a no-primary, secondary-only slide and a rabbit IgG control matched to the primary antibody’s clonality and concentration; use a CPSF6 knockout sample processed in parallel as a biological specificity control (caption: rabbit anti-CPSF6 primary; standard IHC practice). Check endogenous peroxidase and biotin background in appendix before interpreting DAB signal from the biotin-based detection system (caption: biotinylated secondary, SABC and DAB; standard IHC practice).
⚠️Feasibility: No target-specific fixation window or fixation effect is reported, and the selected A04551-1 paraffin-section caption does not state a fixative (caption: fixative unreported). The caption uses heat-mediated retrieval in EDTA at pH 8.0, but does not establish that retrieval is required or compare retrieval conditions (caption: EDTA retrieval). The supplied evidence does not establish whether frozen sections or IF are easier; IF offers a localization readout in nucleoplasm and nuclear speckles, while endogenous peroxidase or biotin can complicate the appendix chromogenic readout (HPA: ICC-IF subcellular localization; caption: SABC/DAB; standard IHC practice).

HPA tissue IHC evidence for CPSF6

Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Supported — Medium 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: CPSF6 is detected in all 45 scored tissues. Use a no-primary (secondary-only) and an isotype control instead.
Section 3

Advanced CPSF6 IHC Tips

Use the documented paraffin-section conditions as a starting point, then assess nuclear staining, tissue controls, and background before interpreting CPSF6 signal.

How should I adjust retrieval when CPSF6 nuclear staining is weak or uneven?
Start with heat-mediated antigen retrieval in EDTA pH 8.0 for paraffin sections (datasheet A04551-1). The documented liver cancer section was then blocked with 10% goat serum and incubated with 2 μg/ml primary antibody overnight at 4°C (datasheet A04551-1). If nuclear staining is weak, compare retrieval duration across adjacent sections while keeping antibody concentration, detection, and development time constant (standard IHC practice). Check that improved signal remains predominantly nuclear, since CPSF6 is chiefly nucleoplasmic and associated with nuclear speckles (HPA subcellular; UniProt Q16630 localisation). Excessive retrieval can damage morphology, making nuclear scoring unreliable (standard IHC practice).
Could fixation explain weak CPSF6 staining in my paraffin sections?
Target-specific fixation sensitivity is unknown: the selected paraffin-section caption does not state a fixative (datasheet A04551-1). Record each specimen's fixative, fixation interval, and processing history, then compare sections processed together before attributing a signal difference to CPSF6 biology (standard IHC practice). Examine nuclear detail and section integrity alongside staining, because poor preservation can impair both antigen detection and compartment assignment (standard IHC practice). Keep the documented EDTA pH 8.0 retrieval and 2 μg/ml overnight primary incubation constant during that comparison (datasheet A04551-1). Do not infer fixation tolerance from the widespread nuclear tissue pattern (HPA tissue IHC).
How do I assess CPSF6 staining outside the nucleus?
Assess nuclear staining first: tissue IHC describes ubiquitous nuclear expression, and cell imaging places CPSF6 in the nucleoplasm and nuclear speckles (HPA tissue IHC; HPA subcellular). Cytoplasmic signal is biologically possible because CPSF6 shuttles between nucleus and cytoplasm (UniProt Q16630 localisation). For chromogenic sections, compare cytoplasmic color with nearby nuclei, a matched negative control, and the distribution of any diffuse background before assigning it to CPSF6 (standard IHC practice). Report nuclear and cytoplasmic compartments separately, since a change in their balance could reflect localisation or staining conditions (UniProt Q16630 localisation; standard IHC practice). Avoid calling individual nuclear speckles from diffuse DAB alone (standard IHC practice).
Can this stain distinguish CPSF6 isoforms or phosphorylation states?
CPSF6 has 3 annotated isoforms and an RNA recognition motif at residues 81–161 (UniProt Q16630 isoforms; UniProt Q16630 domains). The supplied antibody caption gives no epitope sequence or isoform-specific validation, so a positive chromogenic stain cannot identify which isoform was detected (datasheet A04551-1). Multiple modified residues are annotated, including phosphothreonines 157, 404, and 407 and phosphoserines 494 and 500 (UniProt Q16630 modified residues). Without phospho-specific validation, do not interpret changes in staining intensity as changes at any one of those sites (standard IHC interpretation). For a specific variant or site, obtain epitope documentation and use a separately validated assay (standard IHC practice).
How can IF help verify a puzzling CPSF6 IHC pattern?
Use IF on a separate section or preparation to compare CPSF6 with a marker for the cell population being scored, selecting that marker from the specimen's established cell identity (standard IF practice). Choose spectrally separated fluorophores and inspect an unstained specimen in each channel, since tissue autofluorescence can mimic a weak signal (standard IF practice). CPSF6 has no transmembrane segment and is principally nucleoplasmic, so permeabilisation must permit antibody access through the nuclear envelope to the intracellular epitope (UniProt Q16630 topology; HPA subcellular; standard IF practice). Compare nuclear overlap with the chromogenic pattern while interpreting puncta cautiously: CPSF6 localisation to nuclear speckles is supported by cell imaging (HPA subcellular).
What should I change if DAB appears throughout the section?
Compare the stained section with a no-primary control and inspect whether DAB follows nuclei or accumulates at edges, folds, and damaged areas (standard IHC practice). The documented detection used a biotinylated secondary, streptavidin-biotin complex, and DAB, so check secondary-only signal and the contribution of endogenous biotin where relevant (datasheet A04551-1; standard IHC practice). Include an endogenous peroxidase block and control DAB development time as general chromogenic workflow steps (standard IHC practice). If background persists, reassess blocking, washing, and the documented 2 μg/ml primary concentration one variable at a time (datasheet A04551-1; standard IHC practice). Widespread color without preferential nuclear staining is poor support for specific CPSF6 detection (HPA tissue IHC; standard IHC interpretation).
How should I quantify CPSF6 staining across heterogeneous specimens? ⚠ ANSWER MARKED FOR VERIFICATION
Define the cell population and compartment before scoring, and use the same section-selection and DAB thresholds for every specimen (standard IHC practice). For nuclear CPSF6, report the percentage of positive nuclei and an H-score based on nuclear intensity; if measuring positive-cell density, express it per mm² of viable tissue (HPA tissue IHC; standard IHC practice). Normalise counts to the number of evaluable nuclei, or density to the measured viable area, rather than to the whole image when empty or damaged regions vary (standard IHC practice). Record cytoplasmic signal separately because CPSF6 can shuttle between compartments (UniProt Q16630 localisation). Apply the same scoring rules to matched controls and specimens (standard IHC practice).
Which CPSF6 staining patterns warrant further validation?
A convincing positive pattern should emphasize nuclei in preserved cells, consistent with ubiquitous nuclear tissue expression and nucleoplasmic localisation (HPA tissue IHC; HPA subcellular). Strong color confined to tissue edges, folds, or necrotic areas should prompt review of section quality and the no-primary control (standard IHC practice). Diffuse cytoplasmic staining alone needs corroboration, although some cytoplasmic CPSF6 is possible through nucleocytoplasmic shuttling (UniProt Q16630 localisation). If the apparent signal follows endogenous peroxidase activity or the biotin-based detection system, repeat with appropriate controls before interpreting it as CPSF6 (datasheet A04551-1; standard IHC practice). Do not assign nuclear puncta or a cell-type-specific change from DAB appearance alone (HPA subcellular; standard IHC interpretation).
Boster reagents

Best CPSF6 / Cleavage and polyadenylation specificity factor subunit 6 IHC Antibodies

Anti-CPSF6 antibodies have IHC images from human paraffin sections (catalog IHC captions) and IF/ICC images from MCF-7 and U20S cells (catalog IF captions); both list human, monkey, mouse and rat reactivity (catalog applications/reactivity).

Real IHC data IHC analysis of CPSF6 using anti-CPSF6 antibody (A04551-1). CPSF6 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-CPSF6 Antibody (A04551-1) overnight at 4°C. Biotinylated goat anti-rabbit IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using Strepavidin-Biotin-Complex (SABC) (Catalog # SA1022) with DAB as the chromogen.
Anti-CPSF6 Antibody ®
Cat # A04551-1
Real IHC data IHC analysis of CPSF6 using anti-CPSF6 antibody (M04551). CPSF6 was detected in a paraffin-embedded section of human squamous cell carcinoma 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 mouse anti-CPSF6 Antibody (M04551) overnight at 4°C. Peroxidase Conjugated Goat Anti-mouse IgG was used as secondary antibody and incubated for 30 minutes at 37°C. The tissue section was developed using HRP Conjugated Mouse IgG Super Vision Assay Kit (Catalog # SV0001) with DAB as the chromogen.
Anti-CPSF6 Antibody ® (monoclonal, 3F11E1)
Cat # M04551

A04551-1 has IHC images from human liver cancer and appendiceal adenocarcinoma paraffin sections and an IF/ICC image from MCF-7 cells (A04551-1 image captions). M04551 has IHC images from human squamous cell carcinoma, cervical cancer, colorectal adenocarcinoma and ovarian cancer paraffin sections and an IF/ICC image from U20S cells (M04551 image captions).

Which to pick: For paraffin-section IHC, choose A04551-1 for its human liver cancer example or M04551 for its human squamous cell carcinoma example; each caption reports EDTA retrieval at pH 8.0, while neither reports the fixative (A04551-1 IHC caption; M04551 IHC caption). For IF/ICC, both have cell images at 5 μg/ml; A04551-1 is rabbit-hosted with an MCF-7 image, while M04551 is mouse-hosted clone 3F11E1 with a U20S image (catalog host/clone; A04551-1 IF caption; M04551 IF caption). For cross-species planning, both list human, mouse, rat and monkey reactivity, but their stated IHC-P dilutions cover human, mouse and rat, and their IF/ICC dilutions cover human (catalog reactivity; catalog dilution_raw).

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

References

  1. UniProt Consortium. UniProt entry Q16630 (CPSF6_HUMAN, Cleavage and polyadenylation specificity factor subunit 6).
  2. Human Protein Atlas. CPSF6 tissue IHC expression (reliability: Supported).
  3. Human Protein Atlas. CPSF6 subcellular location (ICC-IF): Localized to the nucleoplasm and nuclear speckles..
  4. Human Protein Atlas. CPSF6 antibody validation summary (1 antibodies).
  5. Negative Regulation of CPSF6 Suppresses the Warburg Effect and Angiogenesis Leading to Tumor Progression Via c-Myc Signaling Network: Potential Therapeutic Target for Liver Cancer Therapy. International journal of biological sciences 2024 — PMC11234225.
  6. CPSF6 is a Clinically Relevant Breast Cancer Vulnerability Target: Role of CPSF6 in Breast Cancer. EBioMedicine 2017 — PMC5514498.
  7. IGF2BP2 binding to CPSF6 facilitates m6A-mediated alternative polyadenylation of PUM2 and promotes malignant progression in ovarian cancer. Clinical and translational medicine 2025 — PMC12238680.
  8. SNW1 promotes lymphatic metastasis in bladder cancer by modulating SRPK1 splicing. iScience 2026 — PMC12907903.
  9. PubMed PMID:9659921 — UniProt-cited evidence.
  10. PubMed PMID:14702039 — UniProt-cited evidence.
  11. PubMed PMID:15489334 — UniProt-cited evidence.