Introduction
ADP-ribosylation (ADPr) is a clinically important posttranslational modification (PTM) that controls many cellular processes, including DNA repair, transcription, translation, and chromatin remodeling (Gupte et al., 2017, Posavec Marjanović et al., 2017, Palazzo et al., 2017, Cohen and Chang, 2018). The ADPr reaction consists of the enzymatic transfer of ADPr from positively charged nicotinamide adenine dinucleotide (NAD+) onto an acceptor molecule with the simultaneous release of nicotinamide (Gupte et al., 2017, Pascal and Ellenberger, 2015). Poly(ADPr) polymerases (PARPs) are the major family of enzymes that perform ADPr, and 17 PARP family members are encoded in the human genome (Barkauskaite et al., 2015). PARP1 and PARP2 are the most studied members of the family and are particularly known for their key roles in the DNA damage response (DDR) (Martin-Hernandez et al., 2017, Pascal and Ellenberger, 2015).
PARPs modify proteins at specific residues, and several amino acids, most commonly glutamate (Glu) and aspartate (Asp) but also arginine (Arg), lysine (Lys), and cysteine (Cys), have been reported to be ADPr (Vyas et al., 2014, Vivelo and Leung, 2015, Crawford et al., 2018). Recently, we identified serine ADPr (Ser-ADPr) as an elusive type of histone PTMs that target specific Ser residues (Leidecker et al., 2016) and revealed the basic molecular mechanisms underlying Ser-ADPr conjugation and its reversal. Specifically, we established Ser as a target of PARP1/2-mediated ADPr (Bonfiglio et al., 2017b) and described histone PARylation factor 1 (HPF1/C4orf27) as the PARP1/2-interacting protein (Gibbs-Seymour et al., 2016) required for conferring specificity toward Ser (Bonfiglio et al., 2017b). We also characterized ADPr 3 (ARH3, or ADPRHL2) as the hydrolase responsible for Ser-ADPr removal (Fontana et al., 2017). Further studies identified hundreds of DNA damage-induced Ser-ADPr sites in proteins involved in DNA repair, transcription, and chromatin organization (Bonfiglio et al., 2017b, Abplanalp et al., 2017) and revealed that Ser-ADPr is the major type of ADPr in the regulation of the DDR (Palazzo et al., 2018).
Ser-ADPr core histone marks are localized on N-terminal tails (Leidecker et al., 2016), which are heavily decorated with a plethora of dynamic, covalent modifications, including phosphorylation, acetylation, methylation, and ubiquitylation (Huang et al., 2015). Specific combinations of these marks act together to regulate a host of important nuclear functions, such as chromatin compaction and dynamics, transcription, replication, and DNA repair (Lawrence et al., 2016, Tan et al., 2011, Huang et al., 2015). Many studies have already been conducted on various histone modifications, yet all of them have overlooked Ser-ADPr because this PTM remained elusive until recently (Leidecker et al., 2016). Conversely, despite their focus on histones, studies centered on Ser-ADPr have so far investigated this PTM independent of other histone marks (Leidecker et al., 2016, Bonfiglio et al., 2017b, Fontana et al., 2017, Bilan et al., 2017).
In this paper, we provide insights into the interplay between Ser-ADPr and canonical histone marks. Furthermore, by characterizing the PARP/HPF1-catalyzed ADPr consensus motif, we determine the relative significance of the preceding basic residue and discover tyrosine as an acceptor for ADPr. The resulting interplay analysis examines the effect of surrounding histone PTMs and shows that certain specific acetylation and phosphorylation marks can inhibit Ser-ADPr and vice versa. To broaden and improve studies of histone marks interplay, we introduce a method for visualization of modified as well as unmodified counterpart peptides.