SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination

• Published in: Cell reports (Cambridge) 2017-03, Vol.18 (13), p.3117-3128
• Main Authors: Xiao, Shu, Lu, Jia, Sridhar, Bharat, Cao, Xiaoyi, Yu, Pengfei, Zhao, Tianyi, Chen, Chieh-Chun, McDee, Darina, Sloofman, Laura, Wang, Yang, Rivas-Astroza, Marcelo, Telugu, Bhanu Prakash V.L., Levasseur, Dana, Zhang, Kang, Liang, Han, Zhao, Jing Crystal, Tanaka, Tetsuya S., Stormo, Gary, Zhong, Sheng
• Format: Article
• Language: English
• Subjects: Animals; Base Sequence; Binding Sites; Cells, Cultured; ChIP-seq; Chromatin - metabolism; Citrullination; DNA Helicases; Embryo, Mammalian - metabolism; Embryonic Development; Embryonic Stem Cells - metabolism; Epigenesis, Genetic; Female; Gene Knockdown Techniques; Genome; histone modification; Histones - metabolism; Lysine - metabolism; Male; Methylation; Mice; naive state; Nuclear Proteins - metabolism; Phenotype; pluripotency; Pluripotent Stem Cells - metabolism; protein array; Protein Binding; Protein Processing, Post-Translational; SMARCAD1; stem cells; Transcriptome - genetics
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2017.02.070

Histone citrullination regulates diverse cellular processes. Here, we report that SMARCAD1 preferentially associates with H3 arginine 26 citrullination (H3R26Cit) peptides present on arrays composed of 384 histone peptides harboring distinct post-transcriptional modifications. Among ten histone modifications assayed by ChIP-seq, H3R26Cit exhibited the most extensive genomewide co-localization with SMARCAD1 binding. Increased Smarcad1 expression correlated with naive pluripotency in pre-implantation embryos. In the presence of LIF, Smarcad1 knockdown (KD) embryonic stem cells lost naive state phenotypes but remained pluripotent, as suggested by morphology, gene expression, histone modifications, alkaline phosphatase activity, energy metabolism, embryoid bodies, teratoma, and chimeras. The majority of H3R26Cit ChIP-seq peaks occupied by SMARCAD1 were associated with increased levels of H3K9me3 in Smarcad1 KD cells. Inhibition of H3Cit induced H3K9me3 at the overlapping regions of H3R26Cit peaks and SMARCAD1 peaks. These data suggest a model in which SMARCAD1 regulates naive pluripotency by interacting with H3R26Cit and suppressing heterochromatin formation. [Display omitted] •SMARCAD1 preferentially binds histone peptides carrying the H3R26Cit modification•Smarcad1 KD embryonic stem cells lose naive state features but remain pluripotent•Suppression of Smarcad1 induces H3K9me3 at SMARCAD1-binding regions•Inhibition of H3Cit induces H3K9me3 at SMARCAD1-binding regions Xiao et al. identify SMARCAD1 as a candidate reader protein of the H3R26Cit histone modification. Knockdown of Smarcad1 causes mouse ESCs to exit the naive pluripotent state and leads to increased H3K9me3 at SMARCAD1-binding regions. This suggests a model whereby SMARCAD1 guards naive pluripotency by interacting with H3R26Cit and suppressing H3K9me3.