Pith Number

pith:R3IYBPZY

pith:2026:R3IYBPZYZPYYZLPZNMWNG47VVQ

not attested not anchored not stored refs resolved

Autonomous Reshaping of Expression Landscapes by DNA Methylation

Kaifeng Wang, Ming Han

DNA methylation feedback can reshape gene expression landscapes over time rather than only stabilizing them.

arxiv:2605.14562 v1 · 2026-05-14 · q-bio.MN · cond-mat.soft

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\usepackage{pith}
\pithnumber{R3IYBPZYZPYYZLPZNMWNG47VVQ}

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Record completeness

1 Bitcoin timestamp

2 Internet Archive

3 Author claim open · sign in to claim

4 Citations open

5 Replications open

✓ Portable graph bundle live · download bundle · merged state

The bundle contains the canonical record plus signed events. A mirror can host it anywhere and recompute the same current state with the deterministic merge algorithm.

Claims

C1strongest claim

this feedback does more than preserve a past state: it autonomously reshapes the expression landscape. In a methylation-coupled toggle, the preferred expression state can move continuously through single-well drift, allowing commitment without first entering a multiwell regime.

C2weakest assumption

The assumption of clear time-scale separation between fast expression dynamics and slow methylation flow, which permits the decomposition into conditioned fast dynamics and expression-written slow methylation; if methylation rates are comparable to expression timescales, the autonomous reshaping may not emerge.

C3one line summary

DNA methylation functions as a slow dynamical coordinate that autonomously reshapes expression landscapes in gene regulatory models through reciprocal feedback with transcription factor occupancy.

References

36 extracted · 36 resolved · 0 Pith anchors

[1] Bird, Genes & Development16, 6 (2002) 2002

[2] E. Li and Y. Zhang, Cold Spring Harbor perspectives in biology6, a019133 (2014) 2014

[3] S. B. Baylin, Nature clinical practice Oncology2, S4 (2005) 2005

[4] S. Fan, L. Ma, C. Song, X. Han, B. Zhong, and Y. Lin, Cell Systems15, 808 (2024) 2024

[5] M. Brandeis, D. Frank, I. Keshet, Z. Siegfried, M. Mendelsohn, A. Nemes, V. Temper, A. Razin, and H. Cedar, Nature371, 435 (1994) 1994

Formal links

2 machine-checked theorem links

Receipt and verification

First computed	2026-05-17T23:39:05.580346Z
Builder	pith-number-builder-2026-05-17-v1
Signature	Pith Ed25519 (`pith-v1-2026-05`) · public key
Schema	pith-number/v1.0

Canonical hash

8ed180bf38cbf18cadf96b2cd373f5ac1089eaa6c671ac18e4b5ab420e8df907

Aliases

arxiv: 2605.14562 · arxiv_version: 2605.14562v1 · doi: 10.48550/arxiv.2605.14562 · pith_short_12: R3IYBPZYZPYY · pith_short_16: R3IYBPZYZPYYZLPZ · pith_short_8: R3IYBPZY

Agent API

Resolver JSON Graph JSON Events JSON Schema Signing key

Verify this Pith Number yourself

curl -sH 'Accept: application/ld+json' https://pith.science/pith/R3IYBPZYZPYYZLPZNMWNG47VVQ \
  | jq -c '.canonical_record' \
  | python3 -c "import sys,json,hashlib; b=json.dumps(json.loads(sys.stdin.read()), sort_keys=True, separators=(',',':'), ensure_ascii=False).encode(); print(hashlib.sha256(b).hexdigest())"
# expect: 8ed180bf38cbf18cadf96b2cd373f5ac1089eaa6c671ac18e4b5ab420e8df907

Canonical record JSON

{
  "metadata": {
    "abstract_canon_sha256": "975764d09d8281e1a14c897b447741d5d0419c95f36589ced48de598d006f74f",
    "cross_cats_sorted": [
      "cond-mat.soft"
    ],
    "license": "http://arxiv.org/licenses/nonexclusive-distrib/1.0/",
    "primary_cat": "q-bio.MN",
    "submitted_at": "2026-05-14T08:34:57Z",
    "title_canon_sha256": "b3e6eef5fc927135a0b73809336c785641c7e419bdbbee6df64f52e5c7e00bce"
  },
  "schema_version": "1.0",
  "source": {
    "id": "2605.14562",
    "kind": "arxiv",
    "version": 1
  }
}