{
  "abstract": "Tracing molecular cell state transitions through development, homeostasis and disease is still beyond reach at single-cell resolution. We present scReMeMber-Seq, a methylation-based cell-memory recorder connecting past transcriptional states with present transcriptome and DNA methylome in individual cells. scReMeMber-Seq leverages pulse induction of DCM-Polr2b (TimeMachine) and single-cell methylome-transcriptome (scMT) sequencing for endpoint readout. In mouse neural stem cells (NSCs) and pancreatic organoids, single-cell DCM methylation profiles (scDCMome) accurately discriminate cell types. Over time, scDCMome also record NSC quiescence-activation state changes across multiple cell divisions. In zebrafish embryos, scDCMome resolve individual transcriptional trajectories from progenitor to neuron. Together, scReMeMber-Seq enables real time reconstruction of cellular trajectories, connecting past and present molecular states in single cells, at genome scale, across experimental systems, in vitro and in vivo.",
  "abstract_shown": true,
  "affiliations": [
    "Institut Pasteur and CNRS UMR3738, Paris, France"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 23,
  "authors": [
    {
      "name": "Z. AYDIN"
    },
    {
      "name": "S. OVCHINNIKOVA"
    },
    {
      "name": "I. A. UNTERWEGER"
    },
    {
      "name": "S. CERRIZUELA"
    },
    {
      "name": "N. PONT"
    },
    {
      "name": "V. WUST"
    },
    {
      "name": "R. BOERS"
    },
    {
      "name": "K. ZIRNGIBL"
    },
    {
      "name": "O. CAN"
    },
    {
      "name": "M. SPATUZZI"
    },
    {
      "name": "T. TRABOULSI"
    },
    {
      "name": "X. SUN"
    },
    {
      "name": "A. KORKMAZ"
    },
    {
      "name": "S. ORTICA"
    },
    {
      "name": "T. FOLEY"
    },
    {
      "name": "K. VOLK"
    },
    {
      "name": "S. KLEBER"
    },
    {
      "name": "A. SANZ-MOREJON"
    },
    {
      "name": "M. Hasan"
    },
    {
      "name": "J. Gribnau"
    },
    {
      "name": "S. ANDERS"
    },
    {
      "name": "A. MARTIN-VILLALBA"
    },
    {
      "affs": [
        0
      ],
      "name": "L. BALLY-CUIF"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/btcr2e7fnfc11.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.28.755048",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.28.755048v1.full",
  "id": "btcr2e7fnfc11",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.28.755048v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "neuroscience"
    ],
    [
      "openalex",
      "1312|Single-cell and spatial transcriptomics"
    ]
  ],
  "openalex": "W7214929657",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.28.755048v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-28",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/btcr2e7fnfc11.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:25:23Z",
      "native_id": "10.64898/2026.09.28.755048",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.28.755048v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:neuroscience",
      "subfield": "neuroscience"
    }
  ],
  "title": "Joint recording of past and present transcriptomes reconstructs single-cell trajectories",
  "title_text": "Joint recording of past and present transcriptomes reconstructs single-cell trajectories",
  "type": "preprint",
  "updated_at": "2026-10-30T12:25:23Z",
  "url": "https://research.draconitic.com/paper/btcr2e7fnfc11",
  "venue": "bioRxiv",
  "versions": []
}