Evidence map›Paper›PMID 42685696›Full record

ArticleCell systems2026

Genome-wide chromatin recording resolves dynamic cell state changes.

Yodai Takei, Jordan A Lay, James M Linton, Duncan M Chadly, Yoshiki Ochiai, Ron Hadas, Andrew A Perez, Mario R Blanco, Paola Laurino, Mitchell Guttman and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell systems, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Yodai TakeiDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Biohub, New York, NY, USA.
Jordan A LayDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
James M LintonDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Duncan M ChadlyDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Yoshiki OchiaiProtein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.
Ron HadasDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Andrew A PerezDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Mario R BlancoDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Paola LaurinoProtein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan; Institute for Protein Research, Osaka University, Suita-shi, Osaka, Japan.
Mitchell GuttmanDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Michael B ElowitzDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA. Electronic address: melowitz@caltech.edu.

Funding

A spatial view of hematopoietic regeneration dynamics in the bone marrowR01DK143671 · NIDDK · UNIVERSITY OF SOUTHERN CALIFORNIA · PI MICHAEL B ELOWITZ, Rong Lu · 2024 to 2026
$8.1M
Dynamics of chromosome organization and chromatin states in single cellsU01DK127420 · NIDDK · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, ELOWITZ, MICHAEL B · 2020 to 2024
$5.7M
Using spatial, single-cell genomic recording to investigate age-associated clonal hematopoiesisR01AG080982 · NIA · UNIVERSITY OF SOUTHERN CALIFORNIA · PI MICHAEL B ELOWITZ, CARLOS LOIS · 2023 to 2026
$2.1M
Howard Hughes Medical InstituteNIA NIH HHS R01 AG080982NIDDK NIH HHS R01 DK143671NIDDK NIH HHS U01 DK127420
6 · The paper itself

Abstract

Understanding how the chromatin state of a cell influences its future behavior is a major challenge throughout biology. However, most chromatin profiling methods are limited to endpoint assays. Here, we present LagTag, a method for recovery of earlier and endpoint chromatin states in the same mammalian cells. In this approach, transient activity of bacterial adenine methyltransferase fusions records the DNA-binding profiles of chromatin-associated proteins of interest at earlier time points. Subsequent tagmentation and sequencing recover the earlier chromatin profile from adenine methylation profiles, alongside endpoint profiles of endogenous chromatin-associated proteins. We verified that LagTag profiles aligned with those from established methods in mouse and human cells. We then applied LagTag to record and recover dynamic chromatin state transitions during mouse embryonic stem cell differentiation, capturing transcriptional signatures from pre- and post-differentiation time points within the same cell population. LagTag thus provides a foundation for temporally resolved chromatin profiling. A record of this paper's transparent peer review process is included in the supplemental information.

Indexed as

chromatin organizationchromatin recordinggene regulationgenomicssynthetic biology

Identifiers

PMID42685696
PMCPMC13540299

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.