NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells.

Amy F Chen, Benjamin Parks, Arwa S Kathiria, Benjamin Ober-Reynolds, Jorg J Goronzy, William J Greenleaf

Nature methods 2022 May

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In this work, we describe NEAT-seq (sequencing of nuclear protein epitope abundance, chromatin accessibility and the transcriptome in single cells), enabling interrogation of regulatory mechanisms spanning the central dogma. We apply this technique to profile CD4 memory T cells using a panel of master transcription factors (TFs) that drive T cell subsets and identify examples of TFs with regulatory activity gated by transcription, translation and regulation of chromatin binding. We also link a noncoding genome-wide association study single-nucleotide polymorphism (SNP) within a GATA motif to a putative target gene, using NEAT-seq data to internally validate SNP impact on GATA3 regulation. © 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

Citation

Amy F Chen, Benjamin Parks, Arwa S Kathiria, Benjamin Ober-Reynolds, Jorg J Goronzy, William J Greenleaf. NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells. Nature methods. 2022 May;19(5):547-553