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Transcriptional and functional motifs defining renal function revealed by single nuclear sequencing

ABSTRACT: Transcriptional and functional motifs defining renal function revealed by single nuclear sequencing

PROVIDER: PRJNA836597 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19146922_1.fastq.gz	Fastqsanger.gz
	SRR19146922_2.fastq.gz	Fastqsanger.gz
	SRR19146923_1.fastq.gz	Fastqsanger.gz
	SRR19146923_2.fastq.gz	Fastqsanger.gz
	SRR19146924_1.fastq.gz	Fastqsanger.gz

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Transcriptional and functional motifs defining renal function revealed by single nuclear sequencing

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2022-05-11 | GSE202575 | GEO

Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing.

Project description:Recent advances in single-cell sequencing provide a unique opportunity to gain novel insights into the diversity, lineage, and functions of cell types constituting a tissue/organ. Here, we performed a single-nucleus study of the adult Drosophila renal system, consisting of Malpighian tubules and nephrocytes, which shares similarities with the mammalian kidney. We identified 11 distinct clusters representing renal stem cells, stellate cells, regionally specific principal cells, garland nephrocyte cells, and pericardial nephrocytes. Characterization of the transcription factors specific to each cluster identified fruitless (fru) as playing a role in stem cell regeneration and Hepatocyte nuclear factor 4 (Hnf4) in regulating glycogen and triglyceride metabolism. In addition, we identified a number of genes, including Rho guanine nucleotide exchange factor at 64C (RhoGEF64c), Frequenin 2 (Frq2), Prip, and CG1093 that are involved in regulating the unusual star shape of stellate cells. Importantly, the single-nucleus dataset allows visualization of the expression at the organ level of genes involved in ion transport and junctional permeability, providing a systems-level view of the organization and physiological roles of the tubules. Finally, a cross-species analysis allowed us to match the fly kidney cell types to mouse kidney cell types and planarian protonephridia, knowledge that will help the generation of kidney disease models. Altogether, our study provides a comprehensive resource for studying the fly kidney.

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Comprehensive Proteomic Profiling of Nuclear Fractions from Native Renal Inner Medullary Collecting Duct Cells

Project description:Regulation of renal water excretion is dependent on control of the molecular water channel aquaporin‐2 by the peptide hormone vasopressin in renal collecting duct cells. The control is in part due to the regulation of transcription of the Aqp2 gene and other genes by vasopressin. A systems biology‐based approach to understanding transcriptional control in renal collecting duct cells depends on knowledge of what transcription factors and other regulatory proteins are present in the cells' nucleus. The goal of this paper is to report comprehensive proteomic profiling of nuclear proteins in native inner medullary collecting duct (IMCD) cells of the rat. Multi‐dimensional separation procedures and state‐of‐the art protein mass spectrometry allowed the high stringency identification of a total of 5105 proteins in nuclear pellet (NP) and nuclear extract (NE) fractions of biochemically isolated rat IMCD cells (URL: https://helixweb.nih.gov/ESBL/Database/IMCD_Nucleus/)*. The analysis identified 369 transcription factor proteins out of the 1371 transcription factors coded by the rat genome. The analysis added 1898 proteins to the recognized proteome of rat IMCD cells, now amounting to 7003 unique proteins. Analysis of samples treated with the vasopressin analog dDAVP (1 nM for 30min) or its vehicle revealed 99 proteins in the NP fraction and 88 proteins in the NE fraction with significant changes in spectral counts (Fisher Exact Test, P<0.005). Among those altered by vasopressin were 7 distinct histone proteins all of which showed decreased abundance in the NP fraction, consistent with a possible effect of vasopressin to induce chromatin remodeling.

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