Integrative CUT&Tag-RNA-Seq analysis of histone variant
macroH2A1-dependent orchestration of human induced pluripotent
stem cell reprogramming

J 2023

Integrative CUT&Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming

LIORNI, Niccolo, Alessandro NAPOLI, Stefano CASTELLANA, Sebastiano GIALLONGO, Daniela HULÍNOVÁ et. al.

Basic information

Original name

Integrative CUT&Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming

Authors

LIORNI, Niccolo, Alessandro NAPOLI, Stefano CASTELLANA, Sebastiano GIALLONGO, Daniela HULÍNOVÁ (203 Czech Republic, belonging to the institution), Oriana LO RE, Irena KOUTNÁ (203 Czech Republic, belonging to the institution), Tommaso MAZZA and Manlio VINCIGUERRA

Edition

Epigenomics, Future Medicine Ltd, 2023, 1750-1911

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10601 Cell biology

Country of publisher

United Kingdom of Great Britain and Northern Ireland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.800 in 2022

RIV identification code

RIV/00216224:14110/23:00133308

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.2217/epi-2023-0267

UT WoS

001085184900001

Keywords in English

CUT&Tag; induced pluripotent stem cells; iPSCs; reprogramming; somatic cells

Abstract

V originále

Aim:Human induced pluripotent stem cells (iPSCs) are inefficiently derived from somatic cells by overexpression of defined transcription factors. Overexpression of H2A histone variant macroH2A1.1, but not macroH2A1.2, leads to increased iPSC reprogramming by unclear mechanisms. Materials & methods:Cleavage under targets and tagmentation (CUT&Tag) allows robust epigenomic profiling of a low cell number. We performed an integrative CUT&Tag-RNA-Seq analysis of macroH2A1-dependent orchestration of iPSCs reprogramming using human endothelial cells. Results:We demonstrate wider genome occupancy, predicted transcription factors binding, and gene expression regulated by macroH2A1.1 during reprogramming, compared to macroH2A1.2. MacroH2A1.1, previously associated with neurodegenerative pathologies, specifically activated ectoderm/neural processes. Conclusion:CUT&Tag and RNA-Seq data integration is a powerful tool to investigate the epigenetic mechanisms occurring during cell reprogramming.

Citovat

LIORNI, Niccolo, Alessandro NAPOLI, Stefano CASTELLANA, Sebastiano GIALLONGO, Daniela HULÍNOVÁ, Oriana LO RE, Irena KOUTNÁ, Tommaso MAZZA and Manlio VINCIGUERRA. Integrative CUT&Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming. Epigenomics. Future Medicine Ltd, 2023, vol. 15, No 17, p. 863-877. ISSN 1750-1911. Available from: https://dx.doi.org/10.2217/epi-2023-0267.

@article{2367478,
   author = {Liorni, Niccolo and Napoli, Alessandro and Castellana, Stefano and Giallongo, Sebastiano and Hulínová, Daniela and Lo Re, Oriana and Koutná, Irena and Mazza, Tommaso and Vinciguerra, Manlio},
   article_number = {17},
   doi = {http://dx.doi.org/10.2217/epi-2023-0267},
   keywords = {CUT&Tag; induced pluripotent stem cells; iPSCs; reprogramming; somatic cells},
   language = {eng},
   issn = {1750-1911},
   journal = {Epigenomics},
   title = {Integrative CUT&Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming},
   url = {https://www.futuremedicine.com/doi/10.2217/epi-2023-0267},
   volume = {15},
   year = {2023}
}

TY  - JOUR
ID  - 2367478
AU  - Liorni, Niccolo - Napoli, Alessandro - Castellana, Stefano - Giallongo, Sebastiano - Hulínová, Daniela - Lo Re, Oriana - Koutná, Irena - Mazza, Tommaso - Vinciguerra, Manlio
PY  - 2023
TI  - Integrative CUT&Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming
JF  - Epigenomics
VL  - 15
IS  - 17
SP  - 863-877
EP  - 863-877
PB  - Future Medicine Ltd
SN  - 17501911
KW  - CUT&Tag
KW  - induced pluripotent stem cells
KW  - iPSCs
KW  - reprogramming
KW  - somatic cells
UR  - https://www.futuremedicine.com/doi/10.2217/epi-2023-0267
N2  - Aim:Human induced pluripotent stem cells (iPSCs) are inefficiently derived from somatic cells by overexpression of defined transcription factors. Overexpression of H2A histone variant macroH2A1.1, but not macroH2A1.2, leads to increased iPSC reprogramming by unclear mechanisms. Materials & methods:Cleavage under targets and tagmentation (CUT&Tag) allows robust epigenomic profiling of a low cell number. We performed an integrative CUT&Tag-RNA-Seq analysis of macroH2A1-dependent orchestration of iPSCs reprogramming using human endothelial cells. Results:We demonstrate wider genome occupancy, predicted transcription factors binding, and gene expression regulated by macroH2A1.1 during reprogramming, compared to macroH2A1.2. MacroH2A1.1, previously associated with neurodegenerative pathologies, specifically activated ectoderm/neural processes. Conclusion:CUT&Tag and RNA-Seq data integration is a powerful tool to investigate the epigenetic mechanisms occurring during cell reprogramming.
ER  -

LIORNI, Niccolo, Alessandro NAPOLI, Stefano CASTELLANA, Sebastiano GIALLONGO, Daniela HULÍNOVÁ, Oriana LO RE, Irena KOUTNÁ, Tommaso MAZZA and Manlio VINCIGUERRA. Integrative CUT\&{}Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming. \textit{Epigenomics}. Future Medicine Ltd, 2023, vol.~15, No~17, p.~863-877. ISSN~1750-1911. Available from: https://dx.doi.org/10.2217/epi-2023-0267.

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