Gene expression profiling of sense and antisense transcripts in liver regeneration by microarray analysis

Chiba,Mitsuru; Yasue,Hiroshi; Ohkohchi,Nobuhiro

doi:10.3892/br.2013.80

Gene expression profiling of sense and antisense transcripts in liver regeneration by microarray analysis

Authors:
- Mitsuru Chiba
- Hiroshi Yasue
- Nobuhiro Ohkohchi
View Affiliations

Affiliations: Department of Surgery, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan, Animal Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-0901, Japan
Published online on: March 13, 2013 https://doi.org/10.3892/br.2013.80
Pages: 383-388

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Liver regeneration is a hyperplastic phenomenon induced by partial hepatectomy (PH) or hepatic damage. A large number of genes have been indicated to be involved in the process of liver regeneration. it was recently reported that natural antisense transcripts are involved in the regulation of gene expression. However, no antisense transcript expressions in liver regeneration have been reported thus far. Therefore, the present study aimed to comprehensively identify up- or downregulated sense and antisense transcripts in liver regeneration using PH mice and a sense/antisense custom‑microarray. The results showed that 97 genes were upregulated and 7 genes were downregulated for sense transcripts, whereas 15 genes were upregulated and 2 genes were downregulated for antisense transcripts in regenerating livers as compared to normal livers (P<0.05 and fold change >2.0). Sense and antisense transcripts of the genes, Apoa4, Hp, Fgb and Fgg, exhibited concordant upregulation during the course of liver regeneration. Apoa4, Hp and Fgb transcripts were further investigated by strand‑specific reverse transcription‑quantitative polymerase chain reaction (RT-qPCR), revealing results consistent with those of the microarray. In conclusion, the up- or downregulated sense and antisense transcripts identified in the present study are suggested to be involved in liver regeneration.

View Figures

View References

1	Clavien PA, Petrowsky H, DeOliveira ML and Graf R: Strategies for safer liver surgery and partial liver transplantation. N Engl J Med. 356:1545–1559. 2007. View Article : Google Scholar : PubMed/NCBI
2	Higgins GM and Anderson RM: Experimental pathology of the liver. Arch Pathol. 12:186–202. 1931.
3	Martins PN, Theruvath TP and Neuhaus P: Rodent models of partial hepatectomies. Liver Int. 28:3–11. 2008. View Article : Google Scholar
4	Fausto N, Campbell JS and Riehle KJ: Liver regeneration. Hepatology. 43:S45–S53. 2006. View Article : Google Scholar
5	Michalopoulos GK: Liver regeneration. J Cell Physiol. 213:286–300. 2007. View Article : Google Scholar : PubMed/NCBI
6	Taub R: Liver regeneration: from myth to mechanism. Nat Rev Mol Cell Biol. 5:836–847. 2004. View Article : Google Scholar : PubMed/NCBI
7	Cressman DE, Greenbaum LE, DeAngelis RA, et al: Liver failure and defective hepatocyte regeneration in interleukin-6-deficient mice. Science. 274:1379–1383. 1996. View Article : Google Scholar : PubMed/NCBI
8	Yamada Y, Kirillova I, Peschon JJ and Fausto N: Initiation of liver growth by tumor necrosis factor: deficient liver regeneration in mice lacking type I tumor necrosis factor receptor. Proc Natl Acad Sci USA. 94:1441–1446. 1997. View Article : Google Scholar : PubMed/NCBI
9	Togo S, Makino H, Kobayashi T, et al: Mechanism of liver regeneration after partial hepatectomy using mouse cDNA microarray. J Hepatol. 40:464–471. 2004. View Article : Google Scholar : PubMed/NCBI
10	Chiba M, Murata S, Myronovych A, et al: Elevation and characteristics of Rab30and S100a8/S100a9expression in an early phase of liver regeneration in the mouse. Int J Mol Med. 27:567–574. 2011.PubMed/NCBI
11	Katayama S, Tomaru Y, Kasukawa T, et al: Antisense transcription in the mammalian transcriptome. Science. 309:1564–1566. 2005. View Article : Google Scholar : PubMed/NCBI
12	Røsok Ø and Sioud M: Systematic identification of sense-antisense transcripts in mammalian cells. Nat Biotechnol. 22:104–108. 2004.PubMed/NCBI
13	Kiyosawa H, Yamanaka I, Osato N, Kondo S and Hayashizaki Y: Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res. 13:1324–1334. 2003. View Article : Google Scholar : PubMed/NCBI
14	Kiyosawa H, Mise N, Iwase S, Hayashizaki Y and Abe K: Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res. 15:463–474. 2005. View Article : Google Scholar : PubMed/NCBI
15	Lee JT, Davidow LS and Warshawsky D: Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet. 21:400–404. 1999. View Article : Google Scholar
16	Faghihi MA, Modarresi F, Khalil AM, et al: Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med. 14:723–730. 2008.
17	Kohno K, Chiba M, Murata S, et al: Identification of natural antisense transcripts involved in human colorectal cancer development. Int J Oncol. 37:1425–1432. 2010.PubMed/NCBI
18	Shteyer E, Liao Y, Muglia LJ, Hruz PW and Rudnick DA: Disruption of hepatic adipogenesis is associated with impaired liver regeneration in mice. Hepatology. 40:1322–1332. 2004. View Article : Google Scholar : PubMed/NCBI
19	White P, Brestelli JE, Kaestner KH and Greenbaum LE: Identification of transcriptional networks during liver regeneration. J Biol Chem. 280:3715–3722. 2005. View Article : Google Scholar : PubMed/NCBI
20	Jensen SA: Liver gene regulation in rats following both 70 or 90% hepatectomy and endotoxin treatment. J Gastroenterol Hepatol. 16:525–530. 2001.
21	Riehle KJ, Campbell JS, McMahan RS, et al: Regulation of liver regeneration and hepatocarcinogenesis by suppressor of cytokine signaling 3. J Exp Med. 205:91–103. 2008. View Article : Google Scholar : PubMed/NCBI
22	Grigoriadis A, Oliver GR, Tanney A, et al: Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues. BMC Genomics. 10:3242009. View Article : Google Scholar : PubMed/NCBI
23	Yu W, Gius D, Onyango P, et al: Epigenetic silencing of tumor suppressor gene p15 by its antisense RNA. Nature. 451:202–206. 2008. View Article : Google Scholar : PubMed/NCBI