NEAT-seq: simultaneous profiling of intra-nuclear proteins, chromatin accessibility and gene expression in single cells.
Amy F ChenBenjamin E ParksArwa S KathiriaBenjamin Ober-ReynoldsJorg J GoronzyWilliam J GreenleafPublished in: Nature methods (2022)
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.
Keyphrases
- genome wide
- transcription factor
- dna methylation
- gene expression
- single cell
- induced apoptosis
- rna seq
- dna binding
- copy number
- cell cycle arrest
- genome wide identification
- genome wide association study
- dna damage
- endoplasmic reticulum stress
- oxidative stress
- working memory
- big data
- cell death
- pi k akt
- small molecule
- cell proliferation
- artificial intelligence
- data analysis