Epigenetic State

An epigenetic state is the τ-categorical pair (n, D_n) of refinement level and chromatin partition through which the SelfDesc evaluator reads the ω-germ code. It is the filter, not the code: same genome, different D_n, gives different transcriptional output. Epigenetic states are the categorical mechanism by which one ω-germ supports many cell types.

Categorical invariant. Pair (n, D_n) where n is refinement level in the development tower and D_n is the chromatin partition; the evaluator reads code(D)[ω] through the filter D_n, transcribing only genes in D_n⁻¹(+).

Primary registry anchor: VI.D79

Supporting items: VI.D09, VI.D12

1. I.K0 — Universe Postulate
2. VI.D15 — Life Sector
3. VI.D09 — Internal Evaluator — the carrier-internal decoder
4. VI.D12 — DecodeHorizon — the ω-germ code being filtered
5. VI.D79 — Epigenetic State — the (n, D_n) pair filtering evaluator access to code

Biomarker: DNA methylation (5-methylcytosine at CpG sites); histone post-translational modifications (H3K4me3 active, H3K27me3 repressed, H3K9me3 heterochromatin); chromatin accessibility (open vs closed); 3D chromatin organization (TADs, A/B compartments).

Measurable range: Mammalian methylome: ~28 million CpG sites; ~70-80% methylated in differentiated cells; ~200+ histone modification combinations characterised; ATAC-seq peaks per cell type ≈ 50,000-150,000 accessible regions.

Observation method: Whole-genome bisulfite sequencing (WGBS); ChIP-seq for histone marks; ATAC-seq for accessibility; Hi-C for 3D organization; single-cell ATAC-seq / methyl-seq for cell-type heterogeneity; CUT&RUN / CUT&Tag.

Calibration anchor: LG-Y02-kinetic-pseudoscalar-channel

Anchor chain:

1. VI.L18 chirality channel
2. DNA D-ribose backbone (handedness fixed by K_χ)
3. 5-methylcytosine modification preserves backbone chirality
4. epigenetic state as filter on the chirality-locked code

Manuscript reference: manuscript-sources/book-06/part06/ch35-cell-cycle.tex

Status: Not formalized

Related glossary entries

• LG-I01-genetic-code Genetic Code
• LG-Y02-kinetic-pseudoscalar-channel Kinetic Pseudoscalar Channel

Referenced by

• LG-I08-epigenetic-drift Epigenetic Drift