Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells

Physiol Genomics. 2016 Feb;48(2):154-66. doi: 10.1152/physiolgenomics.00090.2015. Epub 2015 Oct 27.


The control of renal water excretion occurs in part by regulation of transcription in response to vasopressin in cells of the collecting duct. 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' nuclei. The goal of this article is to report comprehensive proteomic profiling of cellular fractions enriched in nuclear proteins from native inner medullary collecting duct (IMCD) cells of the rat. Multidimensional separation procedures and state-of-the art protein mass spectrometry produced 18 GB of spectral data that allowed the high-stringency identification of 5,048 proteins in nuclear pellet (NP) and nuclear extract (NE) fractions of biochemically isolated rat IMCD cells (URL: The analysis identified 369 transcription factor proteins out of the 1,371 transcription factors coded by the rat genome. The analysis added 1,511 proteins to the recognized proteome of rat IMCD cells, now amounting to 8,290 unique proteins. Analysis of samples treated with the vasopressin analog dDAVP (1 nM for 30 min) 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 seven distinct histone proteins, all of which showed decreased abundance in the NP fraction, consistent with a possible effect of vasopressin to induce chromatin remodeling. The results provide a data resource for future studies of vasopressin-mediated transcriptional regulation in the renal collecting duct.

Keywords: LC-MS/MS; aquaporin-2; chromatin; kidney; mRNA splicing; transcription; transcription factor.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Nucleus / metabolism
  • Chromatin / metabolism
  • Chromatin Assembly and Disassembly
  • Computational Biology
  • Gene Expression Profiling
  • Kidney / metabolism
  • Kidney Medulla / metabolism
  • Kidney Tubules, Collecting / metabolism*
  • Male
  • Mass Spectrometry
  • Proteome / metabolism*
  • Proteomics
  • RNA, Messenger / metabolism
  • Rats
  • Rats, Sprague-Dawley
  • Tandem Mass Spectrometry
  • Vasopressins / metabolism


  • Chromatin
  • Proteome
  • RNA, Messenger
  • Vasopressins