Integrative transcriptome and chromatin landscape analysis reveals distinct epigenetic regulations in human memory B cells

Memory B cells (MBCs) are long-lived and produce high-affinity, generally, class-switched antibodies. Here, we use a multiparameter approach involving CD27 to segregate naïve B cells (NBC), IgD+ unswitched (unsw)MBCs and IgG+ or IgA+ class-switched (sw)MBCs from humans of different age, sex and race. Conserved antibody variable gene expression indicates that MBCs emerge through unbiased selection from NBCs. Integrative analyses of mRNAs, miRNAs, lncRNAs, chromatin accessibility and cis-regulatory elements uncover a core mRNA-ncRNA transcriptional signature shared by IgG+ and IgA+ swMBCs and distinct from NBCs, while unswMBCs display a transitional transcriptome. Some swMBC transcriptional signature loci are accessible but not expressed in NBCs. Profiling miRNAs reveals downregulated MIR181, and concomitantly upregulated MIR181 target genes such as RASSF6, TOX, TRERF1, TRPV3 and RORα, in swMBCs. Finally, lncRNAs differentially expressed in swMBCs cluster proximal to the IgH chain locus on chromosome 14. Our findings thus provide new insights into MBC transcriptional programs and epigenetic regulation, opening new investigative avenues on these critical cell elements in human health and disease.

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All studies must disclose on these points even when the disclosure is negative. All sequencing data that support the findings of this study have been made publicly available. Raw and processed data files for the RNA-Seq, smRNA-Seq and ATAC-Seq have been deposited in the NCBI Gene Expression Omnibus under accession number GSE156904 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi? acc=GSE156904). Raw data files for recombined VHDJH-CH amplicons the have been deposited in the NCBI BioProject database under accession number PRJNA658698 (https://www.ncbi.nlm.nih.gov/bioproject/658698 ). No custom or modified scripts were used in association with this study. All other relevant data are available from the corresponding author on request. The samples analyzed in this study were randomly chosen.
Blinding was not performed as the results are directly derived from the sequencing analysis of sorted B cell populations, therefore each exact sample needed to be accounted for and paired with its intra-subject comparator.

October 2018
We require information from authors about some types of materials, experimental systems and methods used in many studies. Here, indicate whether each material, system or method listed is relevant to your study. If you are not sure if a list item applies to your research, read the appropriate section before selecting a response. Note that full information on the approval of the study protocol must also be provided in the manuscript. These cell lines were not tested for mycoplasma contamination.
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Blood donors were seven human subjects (20 and 39 years of age; 4 males and 3 females ) healthy and non-immunocompromised.
Buffy coats were obtained from the South Texas Blood and Tissue Center, San Antonio, TX. No self-selection bias or other biases were known to be present as human subjects were chosen based on buffy coat availability, which is determined by South Texas Blood and Tissue Center.
Blood collection was covered by an IRB protocol of the South Texas Blood and Tissue Center, San Antonio, TX. All experiments involving human samples were approved by the Institutional Review Board (IRB) of UTHSCSA, protocol #HSC20140234H (please see attached IRB approval)