Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue
S. A. Lehnert A B , Y. H. Wang A and K. A. Byrne AA The Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Biosciences Precinct, 306 Carmody Road, St Lucia, Qld 4067, Australia.
B Corresponding author. Email: sigrid.lehnert@csiro.au
Australian Journal of Experimental Agriculture 44(11) 1127-1133 https://doi.org/10.1071/EA03238
Submitted: 16 November 2003 Accepted: 5 April 2004 Published: 14 December 2004
Abstract
In order to gain new knowledge of the genetic control of biochemical and developmental processes that contribute to beef quality, we constructed a bovine microarray of 9600 elements comprising about 2000 expressed sequence tags (ESTs) and 7300 anonymous cDNA clones from muscle and fat-derived cDNA libraries. The microarray was used in 2 animal experiments aimed at uncovering gene expression differences associated with adipogenesis and protein turnover. The results obtained so far show that expression profiling of bovine muscle using the microarray can reliably identify differentially expressed genes and confirm existing hypotheses. Moreover, the technique can provide new evidence on the detailed involvement of well-characterised genes and can identify genes that have not previously been described as having a role in these processes.
Acknowledgments
The authors thank Wes Barris, Sean McWilliam and Toni Reverter for bioinformatics support; Leanne Dierens and Siok Hwee Tan for assistance with cDNA library construction and phage picking; Tony Vuocolo with cDNA library construction and semi-multiplex diagnostic PCR development; Bill Barendse, Cynthia Bottema, Greg Harper and Ross Tellam for input into candidate gene selection; Greg Nattrass for myogenic regulatory gene probes and our many collaborators in the CRC for Cattle and Beef Quality (Peter Allingham, Heather Bruce, Drewe Ferguson, Masaaki Taniguchi, Soichi Tsuji) for their cooperation with obtaining tissue samples.
Altschul SF,
Gish W,
Miller W,
Myers EW, Lipman DJ
(1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403–410.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Bai Q,
McGillivray C,
daCosta N,
Dornan S,
Evans G,
Stear MJ, Chang K-C
(2003) Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles. BMC Genomics [Epub.] 4, 8.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Barendse W,
Bunch R,
Thomas M,
Armitage S,
Baud S, Donaldson N
(2004) The TG5 thyroglobulin gene test for a marbling quantitative tratit loci evaluated in feedlot cattle. Australian Journal of Experimental Agriculture 44, 669–674.
| Crossref | GoogleScholarGoogle Scholar |
Benson DA,
Karsch-Mizrachi I,
Lipman DJ,
Ostell J,
Rapp BA, Wheeler DL
(2002) GenBank. Nucleic Acids Research 30, 17–20.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Byrne KA,
Wang YH,
Lehnert SA,
Harper GS,
McWilliam SM,
Bruce HL, Reverter A
(2005) Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction. Journal of Animal Science in press 83,
| PubMed |
Campanaro S,
Romualdi C,
Fanin M,
Celegato B, Pacchioni B , et al.
(2002) Gene expression profiling in dysferlinopathies using a dedicated muscle microarray. Human Molecular Genetics 11, 3283–3298.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Kayo T,
Allison DB,
Weindruch R, Prolla TA
(2001) Influences of aging and caloric restriction on the transcriptional profile of skeletal muscle from rhesus monkeys. Proceedings of the National Academy of Sciences of the United States of America 98, 5093–5098.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Pacchioni B,
Trevisan S,
Gomirato S,
Toppo S,
Valle G, Lanfranchi G
(1996) Semi-multiplex PCR technique for screening of abundant transcripts during systematic sequencing of cDNA libraries. BioTechniques 21, 644–649.
| PubMed |
Reverter A,
Byrne KA,
Bruce HL,
Wang YH,
Dalrymple B, Lehnert SA
(2003) A mixture model-based cluster analysis of cDNA microarray gene expression data on Brahman and Brahman composite steers fed high, medium and low quality diets. Journal of Animal Science 81, 1900–1910.
| PubMed |
Smith TPL,
Grosse WM,
Freking BA,
Roberts AJ, Stone RT , et al.
(2001) Sequence evaluation of four pooled-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Research 11, 626–630.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Sreekumar R,
Unnikrishnan J,
Fu A,
Nygren J,
Short KR,
Schimke J,
Barazzoni R, Nair KS
(2002) Effects of caloric restriction on mitochondrial function and gene transcripts in rat muscle. American Journal of Physiology. Endocrinology and Metabolism 283, 38–43.
Suchyta SP,
Sipkovsky S,
Kruska R,
Jeffers A, McNulty A , et al.
(2003) Development and testing of a high-density cDNA Microarray resource for cattle. Physiological Genomics 15, 158–164.
| PubMed |
Sudre K,
Leroux C,
Pietu G,
Cassar-Malek I,
Petit E,
Listrat A,
Auffray C,
Picard B,
Martin P, Hocquette J-F
(2003) Transcriptome analysis of two bovine muscles during ontogenesis. Journal of Biochemistry 133, 745–756.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Wang YH,
Byrne KA,
Reverter A,
Harper GS,
Taniguchi M,
McWilliam SM,
Mannen H,
Oyama K, Lehnert SA
(2005) Comparison of gene expression profiles of muscle tissue in Japanese Black and Holstein cattle. Mammalian Genome in press ,
| PubMed |
Wang YH,
McWilliam SM,
Barendse W,
Kata SR,
Womack JE,
Moore SS, Lehnert SA
(2001) Mapping of 12 bovine ribosomal protein genes using a bovine radiation hybrid panel. Animal Genetics 322, 69–73.
Weindruch R,
Kayo T,
Lee CK, Prolla TA
(2001) Microarray profiling of gene expression in aging and its alteration by caloric restriction in mice. The Journal of Nutrition 131, 918–923.
Yao J,
Coussens PM,
Saama P,
Suchyta S, Ernst CW
(2002) Generation of expressed sequence tags from a normalized porcine skeletal muscle cDNA library. Animal Biotechnology 13, 211–222.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
Zembayashi M,
Nishimura K,
Lunt DK, Smith SB
(1995) Effect of breed type and sex on the fatty acid composition of subcutaneous and intramuscular lipids of finishing steers and heifers. Journal of Animal Science 73, 3325–3332.
| PubMed |
