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| Heat-response-related Genes Screened in Skeletal Muscle of Mongolian Sheep (Ovis aries) and Dorper Sheep by RNA-sequence |
| CAO Yu,ZHANG Dong,LU Yang,ZHANG Yan-Ru,ZHOU Huan-Min* |
| College of Life Sciences, Inner Mongolia Agricultural University, Hohhot 010018, China |
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Abstract Mongolian sheep (Ovis aries) and Dorper sheep, as excellent sheep breeds in China and South Africa, have good performance in stress resistance and mutton quality, but that little is known about the regulation of their heat response. In this study, By Illumina HiSeq system, the skeletal muscles of Mongolian sheep and Dorper sheep were sampled and RNA-sequence (RNA-seq) under heat condition (＞30 ℃), and further detected 252 differentially expressed protein-coding genes (including 109 annotated genes) and 60 long non-coding RNA genes. Based on gene functional enrichment, pathway enrichment analysed and previous studied for differentially expressed genes, 19 heat-response-related protein-coding genes were screened out. Immediate early response 5 (IER5), arly growth response 1 (EGR1), sprouty related EVH1 domain containing 1 (SPRED1), testis expressed 15, meiosis and synapsis associated (TEX15), etc 15 genes were involved in heat-response of skeletal muscle in Mongolian sheep. Angiopoietin like 7 (ANGPTL7), circadian associated repressor of transcription (CIART), ATP binding cassette subfamily A member 12 (ABCA12), calcium and integrin binding family member 2 (CIB2) were involved in heat-response of skeletal muscle in Dorper sheep. The biological functions of above 19 protein-coding genes contained cellular heat response, heat shock protein binding, calcium ion binding, folding-competent state maintaining of denatured protein and DNA repair etc. Heat-response-related BCL2 associated athanogene 3 (BAG3), DnaJ heat shock protein family (Hsp40) member A4 (DNAJA4), heat shock protein family A (Hsp70) member 1 like (HSPA1L), EGR1, IER5, DNAJB1 and myosin light chain 10 (MYL10) were trans-regulated by lncRNA transcripts of long non-coding RNA genes XLOC_1944721, XLOC_3483583, XLOC_775492, etc. Above heat-response protein-coding genes and long non-coding RNA genes can make people comprehend heat regulation in sheep, while the genes also provide molecular theoretical basis for livestock breeding on targeting heat-resistant.
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Received: 22 March 2019
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Corresponding Authors:
zhouhuanminim@163.com
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1 崔艳军. 2016. 热应激和氧化应激对肥育猪骨骼肌代谢的影响及硫辛酸的调控作用[D]. 博士学位论文, 中国农业科学院,导师: 顾宪红. pp. 14-32.
(Cui Y J.2016. Effects of heat stress and oxidative stress on metabolism of skeletal muscle and protection of lipoic acid in finishing pigs[D]. Thesis for Ph. D., Chinese Academy of Agricultural Sciences, Supervisor: Gu X H, pp. 14-32)
2 顾重建, 金建钰, 上官福根, 等. 2016. 温度驯化对红耳滑龟幼龟选择体温、热耐受性和抗氧化酶活性的影响[J]. 生态学报, 36(6): 1737-1745.
(Gu C J, Jin J Y, Shangguan F G, et al.2016. The influence of temperature acclimation on selected body temperature, thermal tolerance and the activity of antioxidant enzymes of juvenile red-eared slider turtles, Trachemys scripta elegans[J]. Acta Ecologica Sinica, 36(6): 1737-1745.)
3 侯成林. 2014. 蒙古羊全基因组测序及基于转录组分析的抗寒性状遗传基础研究[D]. 博士学位论文,内蒙古农业大学,导师: 周欢敏. pp. 1.
(Hou C L.2014. Genome sequencing of Mongolia sheep and genetic basis of cold resistance traits based on transcriptome analysis[D]. Thesis for Ph. D., Inner Mongolia Agricultural University, Supervisor: Zhou H M, pp. 1)
4 李灿雯, 王康才, 罗庆云, 等. 2012. 外源Ca2+处理对高温胁迫下半夏植株保护效应及主要成分积累规律的影响[J]. 中国中药杂志, 37(19): 2875-2878.
(Li C W, Wang K C, Luo Q Y, et al.2012. Effect of exogenous Ca2+ on protective infection of Pinellia ternata and accumulation of major components under high temperature stress[J]. China Journal of Chinese Materia Medica, 37(19): 2875-2878.)
5 Bateman A, Birney E, Cerruti L, et al.2002. The Pfam protein families database[J]. Nucleic Acids Research, 30(1): 276-280.
6 Beladjal L, Gheysens T, Clegg J S, et al.2018. Life from the ashes: Survival of dry bacterial spores after very high temperature exposure[J]. Extremophiles, 22(5): 1-9.
7 Briggs P.2018. Weather & Climate-South Africa[G]. SAFARIBOOKINGS.
8 Cao Y, Ohwatari N, Matsumoto T, et al.1999. TGF-β1 mediates 70-kDa heat shock protein induction due to ultraviolet irradiation in human skin fibroblasts[J]. Pflügers Archiv-European Journal of Physiology, 438(3):239-244.
9 Chu Y, Corey D R.2012. RNA sequencing: Platform selection, experimental design, and data interpretation[J]. Nucleic Acid Therapeutics, 22(4): 271-274.
10 De Maio A.1999. Heat shock proteins: Facts, thoughts, and dreams[J]. Shock, 11(1): 1-12.
11 Dias E Silva T P, Costa Torreão J N, Torreão Marques C A, et al.2016. Effect of multiple stress factors (thermal, nutritional and pregnancy type) on adaptive capability of native ewes under semi-arid environment[J]. Journal of Thermal Biology, 59: 39-46.
12 Fernandez J, Soto T S J, Cansado J, et al.1997. Heat-shock response in Schizosaccharomyces pombe cells lacking cyclic AMP-dependent phosphorylation[J]. Current Genetics, 31(2): 112-118.
13 Huang H, Bogstie J N, Vogel H J.2012. Biophysical and structural studies of the human calcium- and integrin-binding protein family: Understanding their functional similarities and differences[J]. Biochemistry and Cell Biology, 90(5): 646-656.
14 Iue K, Oboznyi A I.2012. Participation of the active oxygen forms in the induction of ascorbate peroxidase and guaiacol peroxidase under heat hardening of wheat seedlings[J]. Ukrainskyi Biokhimichnyi Zhurnal, 84(6): 131-138.
15 Kim D, Pertea G, Trapnell C, et al.2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions[J]. Genome Biology, 14(4): R36.
16 Kong L, Zhang Y, Ye Z Q, et al.2007. CPC: Assess the protein-coding potential of transcripts using sequence features and support vector machine[J]. Nucleic Acids Research, 35(Web Server issue): W345-W349.
17 Laplante A F, Moulin V, Auger F A, et al.1998. Expression of heat shock proteins in mouse skin during wound healing[J]. The Journal of Histochemistry and Cytochemistry, 46(11): 1291-1301.
18 Liang S, Luo H, Bu D, et al.2013. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts[J]. Nucleic Acids Research, 41(17): e166.
19 Lin M F, Jungreis I, Kellis M.2011. PhyloCSF: A comparative genomics method to distinguish protein coding and non-coding regions[J]. Bioinformatics, 27(13): i275-i282. h
20 Liu Y, Li D, Li H, et al.2011. A novel SNP of the ATP1A1 gene is associated with heat tolerance traits in dairy cows[J]. Molecular Biology Reports, 38(1): 83-88.
21 Lu N, Zang X, Zhang X, et al.2012. Gene cloning, expression and activity analysis of manganese superoxide dismutase from two strains of Gracilaria lemaneiformis (Gracilariaceae, Rhodophyta) under heat stress[J]. Molecules, 17(4): 4522-4532.
22 Lu Y, Wu Z, Song Z, et al.2016. Insight into the heat resistance of fish via blood: Effects of heat stress on metabolism, oxidative stress and antioxidant response of olive flounder Paralichthys olivaceus and turbot Scophthalmus maximus[J]. Fish Shellfish Immunology, 58: 125-135.
23 Ma L, Bajic V B, Zhang Z.2013. On the classification of long non-coding RNAs[J]. RNA Biology, 10(6): 924-933.
24 Mahjoubi E, Yazdi M H, Aghaziarati N, et al.2015. The effect of cyclical and severe heat stress on growth performance and metabolism in Afshari lambs[J]. Journal of Animal Science, 93(4): 1632-1640.
25 Mao X, Cai T, Olyarchuk J G, et al.2005. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary[J]. Bioinformatics, 21(19): 3787-3793.
26 Matz J M, Blake M J, Tatelman H M, et al.1995. Characterization and regulation of cold-induced heat shock protein expression in mouse brown adipose tissue[J]. The American Journal of Physiology, 269(1 Pt 2): R38-R47.
27 Orsburn B, Sucre K, Popham D L, et al.2009. The SpmA/B and DacF proteins of Clostridium perfringens play important roles in spore heat resistance[J]. FEMS Microbiol Lett, 291(2): 188-194.
28 Perkel J M.2013. Visiting “noncodarnia”[J]. Biotechniques, 54(6): 301-304.
29 Punta M, Coggill P C, Eberhardt R Y, et al.2011. The Pfam protein families database[J]. Nucleic Acids Research, 40(D1): D290-D301. h
30 Rathwa S D, Vasava A A, Pathan M M, et al.2017. Effect of season on physiological, biochemical, hormonal, and oxidative stress parameters of indigenous sheep[J]. Veterinary World, 10(6): 650-654.
31 Ritossa F.1962. A new puffing pattern induced by temperature shock and DNP in drosophila[J]. Experientia, 18(12): 571-573.
32 Salo D C, Donovan C M, Davies K J A.1991. HSP70 and other possible heat shock or oxidative stress proteins are induced in skeletal muscle, heart, and liver during exercise[J]. Free Radical Biology and Medicine, 11(3): 239-246.
33 Sprake P M, Hubertus C, Bissett W T, et al.2013. Neurological disease in lambs associated with exposure to high environmental temperature and humidity[J]. Journal of Veterinary Internal Medicine, 27(5): 1242-1247.
34 Trapnell C, Williams B A, Pertea G, et al.2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation[J]. Nature Biotechnology, 28(5): 511-515.
35 Wang Z, Gerstein M, Snyder M.2009. RNA-Seq: A revolutionary tool for transcriptomics[J]. Nature Reviews Genetics, 10(1): 57-63.
36 Wang Z, Wang G, Huang J, et al.2011. Novel SNPs in the ATP1B2 gene and their associations with milk yield, milk composition and heat-resistance traits in Chinese Holstein cows[J]. Molecular Biology Reports, 38(3): 1749-1755.
37 Wu C.1995. Heat shock transcription factors: Structure and regulation[J]. Annual Review of Cell and Developmental Biology, 11: 441-469.
38 Young M D, Wakefield M J, Smyth G K, et al.2010. Gene ontology analysis for RNA-seq: Accounting for selection bias[J]. Genome Biology, 11(2): R14. |
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