Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

Shiran Bar; Dan Vershkov; Gal Keshet; Elyad Lezmi; Naama Meller; Atilgan Yilmaz; Ofra Yanuka; Malka Nissim-Rafinia; Eran Meshorer; Talia Eldar-Geva; Nissim Benvenisty

doi:10.1038/s41467-021-26949-7

Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

Shiran Bar, Dan Vershkov, Gal Keshet, Elyad Lezmi, Naama Meller, Atilgan Yilmaz, Ofra Yanuka, Malka Nissim-Rafinia, Eran Meshorer, Talia Eldar-Geva, Nissim Benvenisty^*

^*Corresponding author for this work

Department of Genetics

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity.

Original language	American English
Article number	6718
Journal	Nature Communications
Volume	12
Issue number	1
DOIs	https://doi.org/10.1038/s41467-021-26949-7
State	Published - 18 Nov 2021

Bibliographical note

Funding Information:
We thank all members of The Azrieli Center for Stem Cells and Genetic Research for critical reading of the manuscript. This work was partially supported by the Israel Science Foundation (494/17), the Israel Precision Medicine Program, the Rosetrees Trust, and Azrieli Foundation. S.B. is a Clore fellow. N.B. is the Herbert Cohn Chair in Cancer Research.

Publisher Copyright:
© 2021, The Author(s).

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title = "Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells",

abstract = "In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity.",

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AU - Yilmaz, Atilgan

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AU - Nissim-Rafinia, Malka

AU - Meshorer, Eran

AU - Eldar-Geva, Talia

AU - Benvenisty, Nissim

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N2 - In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity.

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Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells

Abstract

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