EpiTyping: analysis of epigenetic aberrations in parental imprinting and X-chromosome inactivation using RNA-seq.
Journal
Nature protocols
ISSN: 1750-2799
Titre abrégé: Nat Protoc
Pays: England
ID NLM: 101284307
Informations de publication
Date de publication:
Dec 2023
Dec 2023
Historique:
received:
09
06
2022
accepted:
28
07
2023
medline:
7
12
2023
pubmed:
2
11
2023
entrez:
2
11
2023
Statut:
ppublish
Résumé
Human pluripotent stem cells (hPSCs) hold a central role in studying human development, in disease modeling and in regenerative medicine. These cells not only acquire genetic modifications when kept in culture, but they may also harbor epigenetic aberrations, mainly involving parental imprinting and X-chromosome inactivation. Here we present a detailed bioinformatic protocol for detecting such aberrations using RNA sequencing data. We provide a pipeline designed to process and analyze RNA sequencing data for the identification of abnormal biallelic expression of imprinted genes, and thus detect loss of imprinting. Furthermore, we show how to differentiate among X-chromosome inactivation, full activation and aberrant erosion of X chromosome in female hPSCs. In addition to providing bioinformatic tools, we discuss the impact of such epigenetic variations in hPSCs on their utility for various purposes. This pipeline can be used by any user with basic understanding of the Linux command line. It is available on GitHub as a software container ( https://github.com/Gal-Keshet/EpiTyping ) and produces reliable results in 1-4 d.
Identifiants
pubmed: 37914783
doi: 10.1038/s41596-023-00898-5
pii: 10.1038/s41596-023-00898-5
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
3881-3917Subventions
Organisme : United States-Israel Binational Science Foundation (BSF)
ID : 2021278
Organisme : Israel Science Foundation (ISF)
ID : 2054/22
Organisme : Israel Science Foundation (ISF)
ID : 3605/21
Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 101056712
Informations de copyright
© 2023. Springer Nature Limited.
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