Evidence map›Paper›PMID 39094565›Full record

ArticleDevelopmental cell2024

Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation.

Ajay Larkin, Colin Kunze, Melissa Seman, Alexander Levashkevich, Justin Curran, Dionysus Morris-Evans, Sophia Lemieux, Ahmad S Khalil, Kaushik Ragunathan

Abstract read
In one paragraph

Article in Developmental cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. Article
  5. Article
  6. Loss ofmicroPublication biology · 2025
    Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Ajay LarkinDepartment of Biology, Brandeis University, Waltham, MA 02453, USA.
Colin KunzeBiological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
Melissa SemanDepartment of Biology, Brandeis University, Waltham, MA 02453, USA.
Alexander LevashkevichDepartment of Biology, Brandeis University, Waltham, MA 02453, USA.
Justin CurranDepartment of Biology, Brandeis University, Waltham, MA 02453, USA.
Dionysus Morris-EvansDepartment of Biology, Brandeis University, Waltham, MA 02453, USA.
Sophia LemieuxDepartment of Biology, Brandeis University, Waltham, MA 02453, USA.
Ahmad S KhalilBiological Design Center, Boston University, Boston, MA 02215, USA; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA. Electronic address: khalil@bu.edu.
Kaushik RagunathanDepartment of Biology, Brandeis University, Waltham, MA 02453, USA. Electronic address: kaushikr@brandeis.edu.

Funding

Center for Genomic Editing and Recording: Development and Application of Next-Generation Genome and Epigenome Editing Methods to Advance the Study and Treatment of Human DiseaseRM1HG009490 · NHGRI · WHITEHEAD INSTITUTE FOR BIOMEDICAL RES · PI Brittany S. Adamson, Martin Joseph Ankrah Aryee · 2017 to 2026
$22.7M
CELLULAR AND MOLECULAR BIOLOGY AT MICHIGANT32GM007315 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI PUTHENVEEDU, MANOJKUMAR A · 1985 to 2021
$12.8M
PREDOCTORAL TRAINING IN GENETICST32GM007544 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI MORAN, JOHN V. · 1985 to 2022
$11.3M
ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potentialR01EB027793 · NIBIB · BROAD INSTITUTE, INC. · PI Ahmad Samir Khalil, DAVID R LIU · 2019 to 2026
$6.1M
Synthetic toolkit for precision gene expression control and signal processing in mammalian cellsR01EB029483 · NIBIB · HARVARD UNIVERSITY · PI Ahmad Samir Khalil · 2020 to 2026
$5.0M
Programmable benchtop bioreactors for scalable eco-evolutionary dynamics of the human microbiomeR01AI171100 · NIAID · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · PI KHALIL, AHMAD SAMIR, RAKOFF-NAHOUM, SETH · 2022 to 2025
$4.1M
Heterochromatin dynamics during inheritance and adaptationR35GM137832 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Kaushik Ragunathan · 2020 to 2026
$3.2M
NHGRI NIH HHS RM1 HG009490NIAID NIH HHS R01 AI171100NIBIB NIH HHS R01 EB027793NIBIB NIH HHS R01 EB029483NIGMS NIH HHS R35 GM137832NIGMS NIH HHS T32 GM007315NIGMS NIH HHS T32 GM007544
6 · The paper itself

Abstract

Epigenetic mechanisms enable cells to develop novel adaptive phenotypes without altering their genetic blueprint. Recent studies show histone modifications, such as heterochromatin-defining H3K9 methylation (H3K9me), can be redistributed to establish adaptive phenotypes. We developed a precision-engineered genetic approach to trigger heterochromatin misregulation on-demand in fission yeast. This enabled us to trace genome-scale RNA and H3K9me changes over time in long-term, continuous cultures. Adaptive H3K9me establishes over remarkably slow timescales relative to the initiating stress. We captured dynamic H3K9me redistribution events which depend on an RNA binding complex MTREC, ultimately leading to cells converging on an optimal adaptive solution. Upon stress removal, cells relax to new transcriptional and chromatin states, establishing memory that is tunable and primed for future adaptive epigenetic responses. Collectively, we identify the slow kinetics of epigenetic adaptation that allow cells to discover and heritably encode novel adaptive solutions, with implications for drug resistance and response to infection.

Indexed as

Epigenesis, GeneticHeterochromatinHistonesSchizosaccharomycesAdaptation, PhysiologicalGene Expression Regulation, FungalMethylationSchizosaccharomyces pombe ProteinsHeterochromatinHistonesSchizosaccharomyces pombe Proteinsadaptationbet-hedgingClr4epigeneticsgene silencingheterochromatinhistone methylationhysteresismemory

Identifiers

PMID39094565
PMCPMC11338711

What Socratic holds

Textmetadata
LicenceTDM
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 Socratic graph.