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  • Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney.

Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney.

Nature communications (2021-04-15)
Yoshiharu Muto, Parker C Wilson, Nicolas Ledru, Haojia Wu, Henrik Dimke, Sushrut S Waikar, Benjamin D Humphreys
ABSTRACT

The integration of single cell transcriptome and chromatin accessibility datasets enables a deeper understanding of cell heterogeneity. We performed single nucleus ATAC (snATAC-seq) and RNA (snRNA-seq) sequencing to generate paired, cell-type-specific chromatin accessibility and transcriptional profiles of the adult human kidney. We demonstrate that snATAC-seq is comparable to snRNA-seq in the assignment of cell identity and can further refine our understanding of functional heterogeneity in the nephron. The majority of differentially accessible chromatin regions are localized to promoters and a significant proportion are closely associated with differentially expressed genes. Cell-type-specific enrichment of transcription factor binding motifs implicates the activation of NF-κB that promotes VCAM1 expression and drives transition between a subpopulation of proximal tubule epithelial cells. Our multi-omics approach improves the ability to detect unique cell states within the kidney and redefines cellular heterogeneity in the proximal tubule and thick ascending limb.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Magna ChIP® A/G Chromatin Immunoprecipitation Kit, Single day chromatin immunoprecipitation (ChIP) kit containing all necessary reagents to perform 22 individual chromatin immunoprecipitation (ChIP) reactions using magnetic A/G beads.
Sigma-Aldrich
ChIPAb+ NFκB p65 (RelA) - ChIP Validated Antibody and Primer Set, from mouse