key: cord-0285197-4kec8re4 authors: Miao, Zhen; Balzer, Michael S.; Ma, Ziyuan; Liu, Hongbo; Wu, Junnan; Shrestha, Rojesh; Aranyi, Tamas; Kwan, Amy; Kondo, Ayano; Pontoglio, Marco; Kim, Junhyong; Li, Mingyao; Kaestner, Klaus H.; Susztak, Katalin title: Single cell resolution regulatory landscape of the mouse kidney highlights cellular differentiation programs and renal disease targets date: 2020-05-28 journal: bioRxiv DOI: 10.1101/2020.05.24.113910 sha: 32dfbde4cf73ea2ca3b878854229b87c084b3b11 doc_id: 285197 cord_uid: 4kec8re4 The kidney has a very limited capacity to repair. Defining cellular differentiation during development therefore could aid the understanding of homeostatic and maladaptive regeneration. Here, we profiled open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We define key cell type-specific transcription factors and major gene-regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrated that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells followed a more complex differentiation, where Hfn4a was associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease identified critical cell types, developmental stages, genes, and regulatory mechanisms. We provide a global single cell resolution view of chromatin accessibility of kidney development. The dataset is available via an interactive public website. Together with regulon analysis, as implemented in SCENIC, we have identified several TFs as 541 well as their target genes that are important for kidney development. Leveraging this newly 542 identified cell type-specific regulatory network will be essential for future studies of cellular 543 reprogramming of precursors into specific kidney cell types and for better understanding 544 homeostatic and maladaptive regeneration. 545 546 Our studies revealed dynamic chromatin accessibility that tracks with renal cell differentiation. 547 These states may reveal mechanisms governing the establishment of cell fate during development, 548 in particular those underlying the emergence of specific cell types. We found a consistent and 549 coherent pattern between gene expression and open chromatin information, where the nephron 550 progenitors differentiated into two branches representing podocytes and tubule cells 52 . We found 551 that podocytes commitment occurred earlier, while tubule differentiation and segmentation 552 appeared to be more complex. This podocyte specification correlated with the maintenance of 553 expression of Foxc2 and Foxl1 expression in podocytes. While Foxc2 has been known to play a 554 role in nephron progenitors and podocytes, this is the first description of Foxl1 in kidney and 555 podocyte development. Our studies are consistent with recent observations from organoid models 556 that recapitulated podocyte differentiation better than tubule cell differentiation 53 . Our study also 557 sheds light on tubule differentiation and segmentation. We confirmed the key role of Hnf4a in 558 proximal tubules. We have identified a large number of new transcriptional regulators such as 559 Tfap2a that seem to be critical for the distal portion of the nephron. Our data indicate that distal Furthermore, we showed that the GWAS variants map only to those regions where chromatin is 588 open exclusively in nephron progenitors, whereas chromatin becomes inaccessible as 589 differentiation progresses during later stages, such as Shroom3 and Uncx. This is an interesting 590 and important novel mechanism, indicating that the altered expression of this gene might play a 591 role in the development rewiring of the kidney. This mechanism is similar to genes associated with 592 autism that are known to be expressed in the fetal but not in the adult stages 58 of proximal tubule, the same marker genes as in snATAC-seq data were used (Slc5a2 and Slc22a30 1143 for proximal tubule S1 and S3, respectively). 1144 (G) Correlation between snATAC-seq gene activity scores and gene expression values in P0 data. 1145 The correlation of the adult dataset is shown in Figure S1p . Open chromatin and co-accessibility view at alternative scales to those shown in Figure 6 . Mapping eGFR loci to the renal transcriptome and phenome in the 1046 VA Million Veteran Program Genetic associations at 53 loci highlight cell types and biological 1049 pathways relevant for kidney function Intronic locus determines SHROOM3 expression and potentiates 1052 renal allograft fibrosis Developmental Origins for Kidney Disease Due to Shroom3 Deficiency Renal compartment-specific genetic variation analyses identify new 1056 pathways in chronic kidney disease Six2 defines and regulates a multipotent self-renewing nephron 1059 progenitor population throughout mammalian kidney development Single cell census of human kidney organoids shows 1062 reproducibility and diminished off-target cells after transplantation PGC-1alpha Protects from Notch-Induced Kidney Fibrosis 1065 From genome-wide associations to candidate 1067 causal variants by statistical fine-mapping The cis-regulatory dynamics of embryonic development at 1070 single-cell resolution Inferring Relevant Cell Types for Complex Traits by Using Single-1072 Integrative functional genomic analyses implicate specific 1075 molecular pathways and circuits in autism An ultra high-throughput method for single-cell joint analysis of open 1078 chromatin and transcriptome High-throughput sequencing of the transcriptome and 1081 chromatin accessibility in the same cell ATAC-seq: A Method for 1084 An improved ATAC-seq protocol reduces background and enables 1087 interrogation of frozen tissues Assessment of computational methods for the analysis of single-cell 1090 Differential regulation of mouse and human nephron progenitors by 1092 the Six family of transcriptional regulators Epigenetic memory at embryonic enhancers identified in DNA 1095 methylation maps from adult mouse tissues GREAT improves functional interpretation of cis-regulatory 1098 regions deepTools2: a next generation web server for deep-sequencing data 1100 analysis Software for Computing and Annotating Genomic Ranges Comprehensive Integration of Single-Cell Data The single-cell transcriptional landscape of mammalian organogenesis SCENIC: single-cell regulatory network inference and clustering 2-(Tetra-zol-1-yl)acetato-kappaO]tris-(tri-1110 phenyl-phosphine-kappaP)silver(I) mono-hydrate Foxl1-expressing mesenchymal cells constitute the intestinal stem cell 1113 niche Proteomics. Tissue-based map of the human proteome