Evidence map›Paper›PMID 39222083›Full record

ArticleCellular and molecular life sciences : CMLS2024

Tracking induced pluripotent stem cell differentiation with a fluorescent genetically encoded epigenetic probe.

Afanasii I Stepanov, Alexandra A Shuvaeva, Lidia V Putlyaeva, Daniil K Lukyanov, Adelya A Galiakberova, Dmitry A Gorbachev, Dmitry I Maltsev, Valeriya Pronina, Dmitry V Dylov, Alexey V Terskikh and 2 more

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In one paragraph

Article in Cellular and molecular life sciences : CMLS, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

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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

12 authors.

Afanasii I Stepanov *Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
Alexandra A Shuvaeva *Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
Lidia V PutlyaevaSkolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
Daniil K LukyanovSkolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
Adelya A GaliakberovaPirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia.
Dmitry A GorbachevShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
Dmitry I MaltsevShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
Valeriya ProninaSkolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
Dmitry V DylovSkolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
Alexey V TerskikhThe Scintillon Research Institute, 6404 Nancy Ridge Dr., San Diego, CA, 92121, USA.
Konstantin A LukyanovShemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
Nadya G GurskayaSkolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia. gurskayanadya@gmail.com.ORCID http://orcid.org/0000-0002-8028-8176

Funding

Russian Science Foundation 22-14-00141
6 · The paper itself

Abstract

Epigenetic modifications (methylation, acetylation, etc.) of core histones play a key role in regulation of gene expression. Thus, the epigenome changes strongly during various biological processes such as cell differentiation and dedifferentiation. Classical methods of analysis of epigenetic modifications such as mass-spectrometry and chromatin immuno-precipitation, work with fixed cells only. Here we present a genetically encoded fluorescent probe, MPP8-Green, for detecting H3K9me3, a histone modification associated with inactive chromatin. This probe, based on the chromodomain of MPP8, allows for visualization of H3K9me3 epigenetic landscapes in single living cells. We used this probe to track changes in H3K9me3 landscapes during the differentiation of induced pluripotent stem cells (iPSCs) into induced neurons. Our findings revealed two major waves of global H3K9me3 reorganization during 4-day differentiation, namely on the first and third days, whereas nearly no changes occurred on the second and fourth days. The proposed method LiveMIEL (Live-cell Microscopic Imaging of Epigenetic Landscapes), which combines genetically encoded epigenetic probes and machine learning approaches, enables classification of multiparametric epigenetic signatures of single cells during stem cell differentiation and potentially in other biological models.

Indexed as

Cell DifferentiationEpigenesis, GeneticFluorescent DyesHistonesInduced Pluripotent Stem CellsAnimalsHumansMiceNeuronsFluorescent DyesHistonesEpigeneticsFluorescent proteinsGenetically encoded sensorH3K9me3Histone modificationMachine learning

Identifiers

PMID39222083
PMCPMC11368889

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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.