Evidence map›Paper›PMID 40930103›Full record

ArticleCell genomics2025

Analog epigenetic memory revealed by targeted chromatin editing.

Sebastian Palacios, Simone Bruno, Ron Weiss, Elia Salibi, Isabella Goodchild-Michelman, Andrew Kane, Katherine Ilia, Domitilla Del Vecchio

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing 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

11 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Review
  5. Article
  6. Stochastic modeling of epigenetic memory.NPJ systems biology and applications · 2026
    Review
  7. Trainable computation in molecular networks.bioRxiv : the preprint server for biology · 2025
    Article
  8. Article
  9. Reversing transgene silencing via targeted chromatin editing.bioRxiv : the preprint server for biology · 2025
    Article
  10. Review
  11. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Sebastian PalaciosDepartment of Mechanical Engineering, MIT, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA.
Simone BrunoDepartment of Mechanical Engineering, MIT, Cambridge, MA, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA.
Ron WeissDepartment of Biological Engineering, MIT, Cambridge, MA, USA.
Elia SalibiDepartment of Mechanical Engineering, MIT, Cambridge, MA, USA.
Isabella Goodchild-MichelmanDepartment of Biological Engineering, MIT, Cambridge, MA, USA.
Andrew KaneDepartment of Biological Engineering, MIT, Cambridge, MA, USA.
Katherine IliaDepartment of Biological Engineering, MIT, Cambridge, MA, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA.
Domitilla Del VecchioDepartment of Mechanical Engineering, MIT, Cambridge, MA, USA; Department of Biological Engineering, MIT, Cambridge, MA, USA. Electronic address: ddv@mit.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Cells store information by means of chromatin modifications that persist through cell divisions and can hold gene expression silenced over generations. However, how these modifications may maintain other gene expression states has remained unclear. This study shows that chromatin modifications can maintain a wide range of gene expression levels over time, thus uncovering analog epigenetic memory. By engineering a genomic reporter and epigenetic effectors, we tracked the gene expression dynamics following targeted perturbations to the chromatin state. We found that distinct grades of DNA methylation led to corresponding, persistent gene expression levels. Altering the DNA methylation grade, in turn, resulted in permanent loss of gene expression memory. Consistent with experiments, our chromatin modification model indicates that analog memory arises when the positive feedback between DNA methylation and repressive histone modifications is lacking. This discovery will lead to a deeper understanding of epigenetic memory and to new tools for synthetic biology.

Indexed as

ChromatinEpigenesis, GeneticGene EditingDNA MethylationEpigenetic MemoryHistone CodeHistonesHumansChromatinHistonescomputational biologyepigeneticsgenome engineeringsynthetic biologysystems biology

Identifiers

PMID40930103
PMCPMC12648113

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.