Gene expression variance based on random sequencing in rat remnant kidney

Naoshi Horiba, Satohiro Masuda, Ayako Takeuchi, Hideyuki Saito, Masahiro Okuda, Ken Ichi Inui

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Background. Several examinations have been performed to identify the genes involved in chronic renal failure using 5/6 nephrectomized rats. Recently, many systematic techniques for examining molecular expression have been developed. They might also be effective in elucidating the molecular mechanism of progressive renal failure. In this study, digital expression pro filing was carried out to construct a subtractive mRNA expression database for the 5/6 nephrectomized kidney. Methods. One thousand clones were randomly sequenced from 5/6 nephrectomized and sham-operated rat kidney cDNA libraries, respectively, and defined by BLAST search. In silico subtractive analysis was performed to search for genes up- or down-regulated in the 5/6 nephrectomized kidney. Results. The growth factor-related mRNAs and the mRNAs encoding cytoskeletal or membrane proteins were up-regulated, but the transporter-related mRNAs were down-regulated in the 5/6 nephrectomized kidney database. In silico subtraction revealed that 63 mRNAs were increased and 59 were decreased in the 5/6 nephrectomized kidney. To confirm whether the in silico subtractive database reflected the actual expression of mRNA or protein, 12 known genes were examined by Northern blotting or immunoblotting, respectively. The actual expression of the 12 genes was comparable with the results of in silico subtraction. In addition, we successfully isolated five unknown genes, two up-regulated and three down-regulated in the 5/6 nephrectomized kidney. Conclusion. We constructed a subtractive mRNA expression database for 5/6 nephrectomized kidney, which reflects the actual alterations in mRNA expression after subtotal nephrectomy. This database may be useful for elucidation of the molecular mechanism of progressive renal failure.

Original languageEnglish
Pages (from-to)29-45
Number of pages17
JournalKidney International
Volume66
Issue number1
DOIs
Publication statusPublished - Jul 2004

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Kidney
Gene Expression
Messenger RNA
Computer Simulation
Databases
Genes
Renal Insufficiency
Cytoskeletal Proteins
Nephrectomy
Gene Library
Immunoblotting
Northern Blotting
Chronic Kidney Failure
Intercellular Signaling Peptides and Proteins
Membrane Proteins
Clone Cells
Proteins

All Science Journal Classification (ASJC) codes

  • Nephrology

Cite this

Horiba, N., Masuda, S., Takeuchi, A., Saito, H., Okuda, M., & Inui, K. I. (2004). Gene expression variance based on random sequencing in rat remnant kidney. Kidney International, 66(1), 29-45. https://doi.org/10.1111/j.1523-1755.2004.00704.x

Gene expression variance based on random sequencing in rat remnant kidney. / Horiba, Naoshi; Masuda, Satohiro; Takeuchi, Ayako; Saito, Hideyuki; Okuda, Masahiro; Inui, Ken Ichi.

In: Kidney International, Vol. 66, No. 1, 07.2004, p. 29-45.

Research output: Contribution to journalArticle

Horiba, N, Masuda, S, Takeuchi, A, Saito, H, Okuda, M & Inui, KI 2004, 'Gene expression variance based on random sequencing in rat remnant kidney', Kidney International, vol. 66, no. 1, pp. 29-45. https://doi.org/10.1111/j.1523-1755.2004.00704.x
Horiba, Naoshi ; Masuda, Satohiro ; Takeuchi, Ayako ; Saito, Hideyuki ; Okuda, Masahiro ; Inui, Ken Ichi. / Gene expression variance based on random sequencing in rat remnant kidney. In: Kidney International. 2004 ; Vol. 66, No. 1. pp. 29-45.
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