No abstract

Severe coronavirus disease 2019 (COVID-19) is characterized by systemic inflammation and can result in protracted symptoms. Robust systemic inflammation may trigger persistent changes in hematopoietic cells and innate immune memory through epigenetic mechanisms. We reveal that rare circulating hematopoietic stem and progenitor cells (HSPC), enriched from human blood, match the diversity of HSPC in bone marrow, enabling investigation of hematopoiesis and HSPC epigenomics. Following COVID-19, HSPC retain epigenomic alterations that are conveyed, through differentiation, to progeny innate immune cells. Epigenomic changes vary with disease severity, persist for months to a year, and are associated with increased myeloid cell differentiation and inflammatory or antiviral programs. Epigenetic reprogramming of HSPC may underly altered immune function following infection and be broadly relevant, especially for millions of COVID-19 survivors.

115In vitro kinase assay and dot blot: Recombinant CHK1 kinase (Sigma) was incubated with kinase buffer (40mM 116 HEPES pH7.4, 20mM MgCl2), Magnesium/ATP cocktail (EMD) and histone tail peptides for overnight at 37C (Total 117 reaction 15ul, 2ug Peptide, Mg(4.5mM)/ATP(30uM) cocktail and 4ng Enzyme). The samples were then added with 118 5ul of 0.5%SDS followed by boiling for 5min at 95C. The samples were dropped on a dry nitrocellulose membrane 119 and probed with a-H3S31ph antibody. 121CRISPR targeting of H3.3: CRISPR targeting H3f3b and H3f3a was performed in RAW264.7 cells using methods 122 described in Ran et al. 2013 18 . Targeting was done consecutively first targeting H3f3b, then using H3f3b mutants 123 to target H3f3a. 124The gRNAs (Primers caccTAGAAATACCTGTAACGATG forward aaacCATCGTTACAGGTATTTCTA reverse for 125 H3f3a and caccGAAAGCCCCCCGCAAACAGC forward aaacGCTGTTTGCGGGGGGCTTTC reverse for H3f3b)