A synthetic lethality screen reveals ING5 as a genetic dependency of catalytically dead Set1A/COMPASS in mouse embryonic stem cells

Bercin K. Cenik, Christie C. Sze, Caila A. Ryan, Siddhartha Das, Kaixiang Cao, Delphine Douillet, Emily J. Rendleman, Didi Zha, Nabiha Haleema Khan, Elizabeth Bartom, Ali Shilatifard

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

Embryonic stem cells (ESCs) are defined by their ability to self-renew and the potential to differentiate into all tissues of the developing organism. We previously demonstrated that deleting the catalytic SET domain of the Set1A/complex of proteins associated with SET1 histone methyltransferase (Set1A/COMPASS) in mouse ESCs does not impair their viability or ability to self-renew; however, it leads to defects in differentiation. The precise mechanisms by which Set1A executes these functions remain to be elucidated. In this study, we demonstrate that mice lacking the SET domain of Set1A are embryonic lethal at a stage that is unique from null alleles. To gain insight into Set1A function in regulating pluripotency, we conducted a CRISPR/Cas9-mediated dropout screen and identified the MOZ/MORF (monocytic leukaemia zinc finger protein/monocytic leukaemia zinc finger protein-related factor) and HBO1 (HAT bound to ORC1) acetyltransferase complex member ING5 as a synthetic perturbation to Set1A. The loss of Ing5 in Set1AΔSET mouse ESCs decreases the fitness of these cells, and the simultaneous loss of ING5 and in Set1AΔSET leads to up-regulation of differentiation-associated genes. Taken together, our results point toward Set1A/COMPASS and ING5 as potential coregulators of the self-renewal and differentiation status of ESCs.

Original languageEnglish (US)
Article numbere2118385119
JournalProceedings of the National Academy of Sciences of the United States of America
Volume119
Issue number19
DOIs
StatePublished - May 10 2022

Funding

ACKNOWLEDGMENTS. Research in the A.S. laboratory is supported by NIH grant R35CA197569 to A.S. C.C.S. was supported by the NIH/National Cancer Institute (NCI) Predoctoral to Postdoctoral Transition Award (Grant 5F99CA234945-02). K.C. was supported by the NIH Pathway to Independence Award from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (Grant K99HD094906). We thank Dr. Lihua Zou for the initial analysis of the CRISPR screen data and designing the parameters for differential dependency score calculation. We would also like to thank Oliver Vickman for technical assistance. We would additionally like to thank Stacy Marshall for the preparation and running of NGS samples. Proteomics services were performed by the Northwestern Proteomics Core Facility, generously supported by NCI CCSG P30 CA060553 awarded to the Robert H. Lurie Comprehensive Cancer Center, instrumentation award (S10OD025194) from NIH Office of Director, and the National Resource for Translational and Developmental Proteomics supported by P41 GM108569. We would additionally like to thank Drs. Jeannie Camarillo and Neil Kelleher for their assistance in the design and analysis of the mass spectrometry experiments. The genetically engineered mice were generated with the assistance of Northwestern University TTML. The Northwestern University TTML is partially supported by NIH grant CA60553 to the Robert H. Lurie Comprehensive Cancer Center at Northwestern University. We thank Nicole Ethen for providing the illustrations in Figs. 2A and 3A and Brianna Monroe for providing the illustrations in Fig. 6. Finally, we would like to acknowledge Drs. Marc Morgan and Edwin Smith and all the members of the A.S. laboratory for their insights and suggestions on improving our study and manuscript.

ASJC Scopus subject areas

  • General

Fingerprint

Dive into the research topics of 'A synthetic lethality screen reveals ING5 as a genetic dependency of catalytically dead Set1A/COMPASS in mouse embryonic stem cells'. Together they form a unique fingerprint.

Cite this