基于异源cDNA基因芯片杂交的鳜鱼肌肉组织基因表达谱初步分析
GENE EXPRESSI ON PROFI LES OF THEM USCLE TISSUES OF THEMANDARIN FISH,SIN IPERCA CHUATSI L. W ITH ZEBRAFISH cDNA M ICROARRAY
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摘要: cDNA基因芯片技术已广泛应用于生物物种间功能基因组和表达谱学研究.然而,鱼类基因芯片开发和应用相对落后.为了筛选与肉质性状相关功能基因,本研究首次试用异源斑马鱼基因cDNA芯片,对两种肉质性状明显差异的鳜鱼和鲢鱼肌肉组织中基因表达进行了比较分析.从两种鱼肌肉组织中提取总RNA,经Biotin荧光标记与拥有15617个cDNA片段的斑马鱼基因芯片(Affymetrix)杂交后,检测出375个表达基因.与鲢鱼比较,鳜鱼肌肉组织锁定的基因中有180个上调表达基因和195个下调表达基因.在鳜鱼肌肉组织180个上调基因中,49个为已知功能基因,131个为未知功能基因.根据基因文库同源功能基因分析,我们将49个已知上调基因按功能大约分为七大类,其中与肌肉结构相关基因包括肌球蛋白重链基因(MYH)、肌纤维间连接基因和细胞骨架结构基因等.同时,我们对与肉质结构性状密切相关的功能基因进行了分析,并结合与鳜鱼优良肉质结构和功能基因表达关系进行了讨论.Abstract: The mandarin fish has been recently becoming one of the most important aquaculture fish species in China be-cause of its good meat quality and protein composition1I mproving the production of these fish is a continuing goal of the aq-uaculture industry, and a better understanding of the molecular control of the muscle structure and development in this commercially important species could prove beneficial for more economic rearing and quality of production1Therefore,we intended to investigate what genes control the development of large amount of high-quality white muscle in this species, which may provide foundation for the understanding of itsmyogensis and information to refine musculature for aquaculture1 cDNA microarray is a powerful tool for the assaying of an organism’ s gemone and expression profiles1However, it is relatively behind in fish because limited arrays available1In order to obtain the gene expression profile and screen differ-entially expressed genes in muscle tissues in themandarin fish,we applied theAffymetrix zebrafish cDNA microarray heter-olously hybridized to both themadarin fish, Siniperca chuatsi and the silver carp, H1molitrix1Total RNAswere isolated from the muscle tissues of the two species of fish and labeled with biotin, and hybridized to Zebrafish cDNA gene chips1Hybridized microarray chips were scanned with Affymetrix 418 Array Scanner1All expression signals from the hy-bridization to 156.7 genes in zebrafish cDNA array were analyzed by R/Bioconductor software (http://www1bioconductor1org) 1Background correction and normalization were done by the methods of Robust multi-Array Aver-age known as gcRMA in R/Bioconductor1Out of 15617 genes in Zebrafish cDNA chips, total of 375 geneswere identified to be significantly expressed in themuscle tissuesof the two fishes1Compared to the silver carp, 180 genes are up-regulated and 195 are down-regulated in the madarine fish’ smuscle tissues1Among the 180 up-regulated genes, 49 genes are func-tionally known and 131 are unknown1The 49 known genes could be categorized into seven functional groups and several of them are considered aspotential candidates related to the fish’ smuscle structure and development1Several genes related to the muscle structure and meat textureswere identified, including myosin heavy chain gene (MYH),myofiber linker gene (plectin) and cytoskeletal structure genes (tubulin and actin) 1In themandarin fish,myosin heavy chain gene is expressed extremely higher at 3-% than that in the silver carp (Tab1-) and this large amount ofmyosin heavy chain protein expres-sion may reflect to the large abundance of high-qualitywhite muscle in this fish1Plactin identified from mammalian muscle tissue is another gene directly related to muscle structure and it functions as a cytolinker to cytoskeletal proteins and signal transductor1Plactin was expressed 16.5% higher in the mandarin fish than that in silver carp (log-ratio at 3195/3130). Titin gene was also highly expressed in both of the two fish1These results indicated that the muscle tissue of the mandarin fish was highly endurant and elastic1A cluster of genes functioning in cytoskeleton and dynamics including tubulin iso-forms, actin and microtubule-associated protein genes were quite abundantly expressed in the muscle of the mandarin fish1This group of genes played important roles in muscle cell structure, cell division and material transportation1In com-parison to the silver carp, both alpha-and beta-tubulin were expressed at 21% and 17% higher in themandarin fish,which suggested that high amount of tubulin protein in muscle cells of the mandarin fish may be directly related to itsmuscle e-lastic feature1 This is the first study using zebrafish cDNA microarray to heterogonous hybridization of other evolutionally far from fish species, and this information can be used to help select strains of high quality ofmuscular species for aquaculture industry and to provide a better understanding of gene expression profiles in relation to their biological functions in muscle tissue of different fish species.
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Keywords:
- Siniperca chuatsi /
- H1molitrix /
- Muscle /
- Gene express /
- cDNA microarray
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