A Comprehensive Map of mRNAs and Their Isoforms across All 14 Renal Tubule Segments of Mouse

Abstract

Significance Statement There are at least 14 different renal tubule segments, each with characteristic cell types with distinct functions. Although the advent of RNA sequencing (RNA-seq) has greatly improved our understanding of gene expression in these renal epithelial cell types, detailed mapping of transcripts has been limited by methods that tend to be biased toward transcript ends. Coupling full-length RNA-seq analysis with renal tubule microdissection characterized gene expression along the mouse renal tubule, including mapping of transcript abundance and alternative exon usage. The data provide a comprehensive view of gene expression along the nephron and collecting duct, made available to scientists via a user-friendly web resource. Background The repertoire of protein expression along the renal tubule depends both on regulation of transcription and regulation of alternative splicing that can generate multiple proteins from a single gene. Methods A full-length, small-sample RNA-seq protocol profiled transcriptomes for all 14 renal tubule segments microdissected from mouse kidneys. Results This study identified >34,000 transcripts, including 3709 that were expressed in a segment-specific manner. All data are provided as an online resource (https://esbl.nhlbi.nih.gov/MRECA/Nephron/). Many of the genes expressed in unique patterns along the renal tubule were solute carriers, transcription factors, or G protein–coupled receptors that account for segment-specific function. Mapping the distribution of transcripts associated with Wnk-SPAK-PKA signaling, renin-angiotensin-aldosterone signaling, and cystic diseases of the kidney illustrated the applications of the online resource. The method allowed full-length mapping of RNA-seq reads, which facilitated comprehensive, unbiased characterization of alternative exon usage along the renal tubule, including known isoforms of Cldn10 , Kcnj1 (ROMK), Slc12a1 (NKCC2), Wnk1 , Stk39 (SPAK), and Slc14a2 (UT-A urea transporter). It also identified many novel isoforms with segment-specific distribution. These included variants associated with altered protein structure ( Slc9a8 , Khk , Tsc22d1 , and Scoc ), and variants that may affect untranslated, regulatory regions of transcripts ( Pth1r , Pkar1a , and Dab2 ). Conclusions Full-length, unbiased sequencing of transcripts identified gene-expression patterns along the mouse renal tubule. The data, provided as an online resource, include both quantitative and qualitative differences in transcripts. Identification of alternative splicing along the renal tubule may prove critical to understanding renal physiology and pathophysiology.

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