Catalyzes the citrullination/deimination of arginine residues of proteins such as histones, thereby playing a key role in histone code and regulation of stem cell maintenance (PubMed:15339660, PubMed:15345777, PubMed:16567635, PubMed:19153223, PubMed:21245532, PubMed:25622091). Citrullinates histone H1 at 'Arg-54' (to form H1R54ci), histone H3 at 'Arg-2', 'Arg-8', 'Arg-17' and/or 'Arg-26' (to form H3R2ci, H3R8ci, H3R17ci, H3R26ci, respectively) and histone H4 at 'Arg-3' (to form H4R3ci) (PubMed:15339660, PubMed:15345777, PubMed:16567635, PubMed:21245532). Acts as a key regulator of stem cell maintenance by mediating citrullination of histone H1: citrullination of 'Arg-54' of histone H1 (H1R54ci) results in H1 displacement from chromatin and global chromatin decondensation, thereby promoting pluripotency and stem cell maintenance (PubMed:15339660, PubMed:15345777, PubMed:16567635, PubMed:21245532). Promotes profound chromatin decondensation during the innate immune response to infection in neutrophils by mediating formation of H1R54ci (PubMed:18209087). Citrullination of histone H3 prevents their methylation by CARM1 and HRMT1L2/PRMT1 and represses transcription (PubMed:15345777). Involved for the formation of neutrophil extracellular traps (NETs) by mediating citrullination of histone H3 and initiating decondensation of chromatin and nuclear membrane rupture (PubMed:19153223, PubMed:25622091, PubMed:28574339, PubMed:32170015). NETs are mainly composed of DNA fibers and are released by neutrophils to trap pathogens during inflammation (PubMed:19153223). Citrullinates EP300/P300 at 'Arg-2142', which favors its interaction with NCOA2/GRIP1 (PubMed:15731352). {ECO:0000269|PubMed:15339660, ECO:0000269|PubMed:15345777, ECO:0000269|PubMed:15731352, ECO:0000269|PubMed:16567635, ECO:0000269|PubMed:18209087, ECO:0000269|PubMed:19153223, ECO:0000269|PubMed:21245532, ECO:0000269|PubMed:25622091, ECO:0000269|PubMed:28574339, ECO:0000269|PubMed:32170015}. This is the function of Ensembl gene identifier ENSG00000159339 (PADI4, peptidyl arginine deiminase 4).