title: ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells.
abstract: Biobanking is a widespread practice for storing biological samples for future studies ranging from genotyping to RNA analysis. However, methods that probe the status of the epigenome are lacking. Here, the framework for applying the Assay for Transposase Accessible Sequencing (ATAC-seq) to biobanked specimens is described and was used to examine the accessibility landscape of naïve B cells from Systemic Lupus Erythematosus (SLE) patients undergoing disease flares. An SLE specific chromatin accessibility signature was identified. Changes in accessibility occurred at loci surrounding genes involved in B cell activation and contained motifs for transcription factors that regulate B cell activation and differentiation. These data provide evidence for an altered epigenetic programming in SLE B cells and identify loci and transcription factor networks that potentially impact disease. The ability to determine the chromatin accessibility landscape and identify cis-regulatory elements has broad application to studies using biorepositories and offers significant advantages to improve the molecular information obtained from biobanked samples.
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Scharer
authors.affiliation: Department of Rheumatology, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Emily L
authors.initials: EL
authors.lastname: Blalock
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Benjamin G
authors.initials: BG
authors.lastname: Barwick
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Robert R
authors.initials: RR
authors.lastname: Haines
authors.affiliation: Department of Rheumatology, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Chungwen
authors.initials: C
authors.lastname: Wei
authors.affiliation: Department of Rheumatology, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Sanz
authors.affiliation: Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA.
authors.forename: Jeremy M
authors.initials: JM
authors.lastname: Boss
mesh_terms: D001402:B-Lymphocytes / Q000166:cytology / Q000187:drug effects / Q000276:immunology / Q000378:metabolism*; D001681:Biological Assay; D001771:Blood Banks; D002843:Chromatin / Q000737:chemistry* / Q000378:metabolism; D002874:Chromosome Mapping; D015925:Cryopreservation / Q000379:methods*; D003451:Cryoprotective Agents / Q000494:pharmacology; D004251:DNA Transposable Elements; D004121:Dimethyl Sulfoxide / Q000494:pharmacology; D044127:Epigenesis, Genetic; D056426:Genetic Loci; D005838:Genotype; D006801:Humans; D008180:Lupus Erythematosus, Systemic / Q000235:genetics* / Q000473:pathology; D017422:Sequence Analysis, DNA; D019895:Transposases / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; D003451:Cryoprotective Agents; D004251:DNA Transposable Elements; D019895:Transposases; D004121:Dimethyl Sulfoxide