Component

Human histone deacetylase 3

Human histone deacetylase 3. Species, exposure and limitations are retained in each linked claim.

4 recorded relationships. Experimental role, claim status and evidence remain attached to each record.

Read recorded mechanisms Open recursive mind map

How nutrients influence it

Every nutrient with a recorded effect on this component, credited to the nutrient that acted rather than the chapter that recorded it. Open a nutrient to see the findings and the conditions they were measured under.

How nutrients reach it in more than one step

Chains of two or more recorded steps that end here, grouped by the nutrient they start from. Each step is a separate finding, so a chain is a route a mechanism could take, not proof that it does.

Tracing routes…

What it does

Every recorded relationship this component is part of, grouped by its role. Plain wording comes first; the technical statement follows.

Recorded relationships

What acts on it

  1. HDAC3 inhibition and HDAC3 siRNA supported the HDAC3-dependent differentiation program induced by butyrate in human macrophages.

    Butyrate → Human histone deacetylase 3 source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary full text, Figure 5
    experimental_model
    Human donor macrophages; HDAC inhibitors and gene silencing.
    limitations
    Does not imply butyrate is selective for HDAC3 in every tissue.
    nutrient_topic
    Butyrate collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Butyrate
    plain_language
    A chromatin enzyme helped explain the antimicrobial program.
    primary_references
    The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. · 2019 · https://pubmed.ncbi.nlm.nih.gov/30683619/ · DOI 10.1016/j.immuni.2018.12.018

    Butyrate: microbial production, fuel use, signaling and nutrient interactions (2026-09-19) · lines 398–404

    AI-assisted research curation; primary-abstract references and experimental limitations individually identified. Not publisher full text. · supports · Human donor macrophages; HDAC inhibitors and gene silencing. · source_derived_draft · unverified_draft

    ## butyrate-macrophage-hdac3 A chromatin enzyme helped explain the antimicrobial program. HDAC3 inhibition and HDAC3 siRNA supported the HDAC3-dependent differentiation program induced by butyrate in human macrophages. Model: Human donor macrophages; HDAC inhibitors and gene silencing. Limitations: Does not imply butyrate is selective for HDAC3 in every tissue. Evidence access: Primary full text, Figure 5 The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. · 2019 · https://pubmed.ncbi.nlm.nih.gov/30683619/ · DOI 10.1016/j.immuni.2018.12.018
    Complete structured claim and evidence

  2. DIM promoted proteasomal depletion of HDAC3 in the colon-cancer study.

    3,3'-Diindolylmethane / DIM → Human histone deacetylase 3 source_derived_draftungraded
    Experimental context and source evidence
    evidence_span
    {"source_cache": "artifacts/dim-research/20068155.abstract.txt", "locator": "Primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "bbb7efbd817b44da2771c9dac2c27d0bf4fe3db97ad9452a93eefc97319ebab9", "start_char": 0, "end_char": 862, "text_sha256": "bbb7efbd817b44da2771c9dac2c27d0bf4fe3db97ad9452a93eefc97319ebab9"}
    experimental_model
    Protein degradation and cell-cycle studies
    exposure
    DIM; proteasome-mediated protein depletion
    limitations
    Preclinical concentration/model dependence. The mechanism is loss of HDAC protein, not established direct inhibition of every HDAC catalytic site.
    nutrient_topic
    Diindolylmethane (DIM) research collection; topical membership is not evidence of a direct dietary effect. · 3,3'-Diindolylmethane / DIM
    organism
    Human colon-cancer cells and xenografts
    plain_language
    This mechanism removes an epigenetic regulatory protein rather than merely blocking its active site.
    primary_references
    [dim-p20068155] Chemopreventive agent 3,3'-diindolylmethane selectively induces proteasomal degradation of class I histone deacetylases. (2010). https://pubmed.ncbi.nlm.nih.gov/20068155/ DOI: 10.1158/0008-5472.can-09-1924
    tissue_or_cell_type
    Class I HDAC regulation

    Diindolylmethane (DIM): formation, receptor signaling, metabolism and drug interactions (2026-09-17) · lines 1390–1401

    AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text. · supports · Protein degradation and cell-cycle studies · source_derived_draft · unverified_draft

    ### dim-hdac-hdac3 DIM promoted proteasomal depletion of HDAC3 in the colon-cancer study. Condition category: normal nutrient_topic: Diindolylmethane (DIM) research collection; topical membership is not evidence of a direct dietary effect. plain_language: This mechanism removes an epigenetic regulatory protein rather than merely blocking its active site. organism: Human colon-cancer cells and xenografts tissue_or_cell_type: Class I HDAC regulation experimental_model: Protein degradation and cell-cycle studies limitations: Preclinical concentration/model dependence. The mechanism is loss of HDAC protein, not established direct inhibition of every HDAC catalytic site. exposure: DIM; proteasome-mediated protein depletion evidence_span: {"source_cache": "artifacts/dim-research/20068155.abstract.txt", "locator": "Primary indexed abstract; zero-based, end-exclusive Unicode character offsets", "file_sha256": "bbb7efbd817b44da2771c9dac2c27d0bf4fe3db97ad9452a93eefc97319ebab9", "start_char": 0, "end_char": 862, "text_sha256": "bbb7efbd817b44da2771c9dac2c27d0bf4fe3db97ad9452a93eefc97319ebab9"} [dim-p20068155] Chemopreventive agent 3,3'-diindolylmethane selectively induces proteasomal degradation of class I histone deacetylases. (2010). https://pubmed.ncbi.nlm.nih.gov/20068155/ DOI: 10.1158/0008-5472.can-09-1924
    Complete structured claim and evidence

Where it participates (unsigned role)

  1. Butyrate inhibited histone decrotonylation in the study linking class-I HDAC activity to crotonylation; separate mouse microbiota depletion altered colonic crotonyl marks.

    Butyrate → Histone crotonylation in human cell and biochemical assays source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary abstract and full-text HCT116/HDAC assay results
    experimental_model
    Human cell/biochemical assays and separately analyzed mouse colon.
    limitations
    Crotonylation is a distinct modification from acetylation, butyrylation and beta-hydroxybutyrylation.
    nutrient_topic
    Butyrate collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Butyrate
    plain_language
    Its epigenetic effects extended beyond acetylation.
    primary_references
    Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. · 2018 · https://pubmed.ncbi.nlm.nih.gov/29317660/ · DOI 10.1038/s41467-017-02651-5

    Butyrate: microbial production, fuel use, signaling and nutrient interactions (2026-09-19) · lines 302–308

    AI-assisted research curation; primary-abstract references and experimental limitations individually identified. Not publisher full text. · supports · Human cell/biochemical assays and separately analyzed mouse colon. · source_derived_draft · unverified_draft

    ## butyrate-decrotonylation Its epigenetic effects extended beyond acetylation. Butyrate inhibited histone decrotonylation in the study linking class-I HDAC activity to crotonylation; separate mouse microbiota depletion altered colonic crotonyl marks. Model: Human cell/biochemical assays and separately analyzed mouse colon. Limitations: Crotonylation is a distinct modification from acetylation, butyrylation and beta-hydroxybutyrylation. Evidence access: Primary abstract and full-text HCT116/HDAC assay results Microbiota derived short chain fatty acids promote histone crotonylation in the colon through histone deacetylases. · 2018 · https://pubmed.ncbi.nlm.nih.gov/29317660/ · DOI 10.1038/s41467-017-02651-5
    Complete structured claim and evidence

  2. GPR109A/G-protein inhibition did not remove the tested human monocyte/macrophage anti-inflammatory response to butyrate; HDAC3-related mechanisms were implicated.

    Butyrate → Cytokine output of butyrate-treated human IBD biopsies source_derived_draftungraded
    Experimental context and source evidence
    evidence_access
    Primary abstract
    experimental_model
    Human monocytes and THP-1 macrophage experiments.
    limitations
    This does not negate the distinct mouse epithelial IL-18 dependency.
    nutrient_topic
    Butyrate collection; molecular form, preparation, species, exposure and manipulation remain explicit. · Butyrate
    plain_language
    A receptor important in some models was not required for this tested response.
    primary_references
    Butyrate suppresses mucosal inflammation in inflammatory bowel disease primarily through HDAC3 inhibition in monocytes and macrophages. · 2025 · https://pubmed.ncbi.nlm.nih.gov/41110099/ · DOI 10.1111/febs.70289

    Butyrate: microbial production, fuel use, signaling and nutrient interactions (2026-09-19) · lines 430–436

    AI-assisted research curation; primary-abstract references and experimental limitations individually identified. Not publisher full text. · supports · Human monocytes and THP-1 macrophage experiments. · source_derived_draft · unverified_draft

    ## butyrate-ibd-hcar2-not-required A receptor important in some models was not required for this tested response. GPR109A/G-protein inhibition did not remove the tested human monocyte/macrophage anti-inflammatory response to butyrate; HDAC3-related mechanisms were implicated. Model: Human monocytes and THP-1 macrophage experiments. Limitations: This does not negate the distinct mouse epithelial IL-18 dependency. Evidence access: Primary abstract Butyrate suppresses mucosal inflammation in inflammatory bowel disease primarily through HDAC3 inhibition in monocytes and macrophages. · 2025 · https://pubmed.ncbi.nlm.nih.gov/41110099/ · DOI 10.1111/febs.70289
    Complete structured claim and evidence

In the sources

Preserved passages that mention this component, quoted exactly. Open one to read it in context.

    This is a research prototype built from draft material. It is not medical advice, and its statements still await verification against the original studies.

    Evidence, AI assistance and curation standards