Open AccessMultiomics analysis of the NAD+–PARP1 axis reveals a role for site-specific ADP-ribosylation in splicing in embryonic stem cells
Author(s) -
Aarin Jones,
W. Lee Kraus
Publication year - 2022
Publication title -
genes and development
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.136
H-Index - 438
eISSN - 1549-5477
pISSN - 0890-9369
DOI - 10.1101/gad.349335.121
Subject(s) - biology , parp1 , nad+ kinase , spliceosome , rna splicing , embryonic stem cell , microbiology and biotechnology , alternative splicing , transcriptome , proteome , induced pluripotent stem cell , cellular differentiation , adp ribosylation , genetics , gene expression , biochemistry , rna , gene isoform , gene , poly adp ribose polymerase , polymerase , enzyme
The differentiation of embryonic stem cells (ESCs) into a lineage-committed state is a dynamic process involving changes in cellular metabolism, epigenetic modifications, post-translational modifications, gene expression, and RNA processing. Here we integrated data from metabolomic, proteomic, and transcriptomic assays to characterize how alterations in NAD + metabolism during the differentiation of mouse ESCs lead to alteration of the PARP1-mediated ADP-ribosylated (ADPRylated) proteome and mRNA isoform specialization. Our metabolomic analyses indicate that mESCs use distinct NAD + biosynthetic pathways in different cell states: the de novo pathway in the pluripotent state, and the salvage and Preiss-Handler pathways as differentiation progresses. We observed a dramatic induction of PARP1 catalytic activity driven by enhanced nuclear NAD + biosynthesis during the early stages of mESC differentiation (e.g., within 12 h of LIF removal). PARP1-modified proteins in mESCs are enriched for biological processes related to stem cell maintenance, transcriptional regulation, and RNA processing. The PARP1 substrates include core spliceosome components, such as U2AF35 and U2AF65, whose splicing functions are modulated by PARP1-mediated site-specific ADP-ribosylation. Finally, we observed that splicing is dysregulated genome-wide in Parp1 knockout mESCs. Together, these results demonstrate a role for the NAD + -PARP1 axis in the maintenance of mESC state, specifically in the splicing program during differentiation.