Premium
Mapping chromatin accessibility in mouse nephron segments
Author(s) -
Chen Lihe,
Chou ChungLin,
Knepper Mark A
Publication year - 2019
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.2019.33.1_supplement.571.4
Subject(s) - chromatin , nephron , biology , transcription factor , computational biology , microbiology and biotechnology , dna , distal convoluted tubule , enhancer , genetics , gene , kidney
Active DNA regulatory elements recruit transcription machinery to drive gene expression and generate nephron heterogeneity, which is crucial for renal physiology and pathophysiology. Such heterogeneity poses a significant challenge in the precise mapping of these DNA regulatory elements in each renal segment. Whole kidney chromatin accessibility analysis averages the signal from multiple cell types, thus it is necessary to carry out such analysis at the single‐tubule level. Here, we report single‐tubule ATAC‐seq, a method using hyperactive Tn5 transposase to simultaneously fragment and tag the regions of accessible chromatin with adapters for high‐throughput DNA sequencing. We adapted this method to the microdissected mouse proximal tubule S2 segment (PTS2), cortical thick ascending limb (cTAL), and cortical collecting duct (CCD). DNA libraries were sequenced to saturation and around 20M unique high‐quality reads were recovered for downstream analysis. Our data are consistent with the expected nucleosomal pattern and enrichment of reads in the transcription start site (UCSC, TSS, mm10), indicating the high quality and robust ATAC‐seq. Overall, we identified more than 95,000 narrow peaks for each segment (MACS2, ‐q 0.05 ‐‐nomodel). Coupled with single‐tubule RNA‐seq, for those transcripts uniquely expressed in these segments, our data revealed a high correlation of chromatin accessibility with gene expression. Initial analysis revealed unique chromatin openness in PTS2 including Slc22a7 , Aqp1 , Slc34a1 , Kap ; in cTAL including Hnf4a , Egf , Kcnj1 , Umod , Slc12a1 , Cldn16 ; and in CCD including Aqp2 , Aqp3 , Slc4a1 , Fxyd4 , and three ENaC subunits. Our results provide a comprehensive chromatin accessibility map for the nephron segments. The identification of these regulatory elements along the nephron will provide additional information beyond transcriptome and point to gene regulation in the kidney. Support or Funding Information The work was primarily funded by the Division of Intramural Research, National Heart, Lung, and Blood Institute (project ZIA‐HL001285 and ZIA‐HL006129, M.A.K.). This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .