鸡胚心脏组织转录组数据鉴定雪域白鸡高原低氧适应性关键基因

doi:10.11843/j.issn.0366-6964.2023.10.014

Abstract

Abstract: The aim of this study was to identify candidate genes for hypoxia adaptation in chicken embryos by analyzing the gene expression changes in embryonic heart tissues of White Leghorn (WL) and Xueyu White (XYW) chickens incubated under hypoxic conditions. The eggs were incubated at high altitude. The heart tissues were collected from embryos at day 16 of incubation, and the RNAs were extracted for RNA sequencing (RNA-seq). Differently expressed genes (DEGs) were screened, which were validated using fluorescence quantitative PCR (qRT-PCR). The functional enrichment analysis and a transcription factor-target gene regulatory network was constructed to further screen candidate genes related to hypoxia adaptation in XYW. The 253 DEGs were screened in heart tissues between XYW and WL, and 5 DEGs were randomly selected for qRT-PCR validation. Their expression trend was consistent with the sequencing results. Enrichment analysis showed that DEGs were mainly enriched in biological processes and signaling pathways related to cardiovascular development and cardiac function. Comparing DEGs with known chicken transcription factors, FOXP2 and HOXA2 were screened, which regulated angiogenesis, myocardial contraction and other functions, and played a key role in hypoxia adaptation in XYW embryos. Through the analysis of transcriptomic data, TENM2, NOG, SMOC1, CCBE1 and other candidate genes were identified for plateau hypoxia adaptation in chicken embryos, which provide a theoretical basis for analyzing the molecular mechanism of plateau hypoxia adaptation in XYW.

Key words: Xueyu White chicken, White Leghorn chicken, hypoxia adaptation, heart, transcriptome

CLC Number:

S831.2

CHEN Xuejiao, LIU Huijie, ZANG Lei, FENG Jing, PENG Da, ZHANG Hao. Transcriptome Data from Chicken Embryo Heart Tissue Identified Key Genes for Altitude Hypoxia Adaptation in Xueyu White Chickens[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4154-4163.

References 36

[1]	单增群佩.拉萨白鸡选育历程的回顾[J].西藏农业科技, 2001, 23(3):57-58.DAN Z Q P.A review of the selection and breeding process of Lhasa white chicken[J].Tibet Journal of Agricultural Sciences, 2001, 23(3):57-58.(in Chinese)
[2]	NECHAEVA M V.Physiological responses to acute changes in temperature and oxygenation in bird and reptile embryos[J].Respir Physiol Neurobiol, 2011, 178(1):108-117.
[3]	张浩, 吴常信, 强巴央宗, 等.氧气对低地鸡蛋胚胎死亡和孵化率的影响[J].畜牧兽医学报, 2006, 37(2):112-116.ZHANG H, WU C X, QIANGBA Y Z, et al.Influences of oxygen on embryonic mortality and hatchability of chicken eggs[J].Acta Veterinaria et Zootechnica Sinica, 2006, 37(2):112-116.(in Chinese)
[4]	冯静, 袁经纬, 臧蕾, 等.高海拔环境下不同品种鸡种蛋孵化效果研究[J].畜牧与饲料科学, 2018, 39(8):13-15.FENG J, YUAN J W, ZANG L, et al.Study on the hatching effect of different species of chicken eggs in high altitude area[J].Animal Husbandry and Feed Science, 2018, 39(8):13-15.(in Chinese)
[5]	ZHANG H, BURGGREN W W.Hypoxic level and duration differentially affect embryonic organ system development of the chicken (Gallus gallus)[J].Poult Sci, 2012, 91(12):3191-3201.
[6]	苟文钰.鸡胚胎低氧适应表型及心脏组织差异表达基因鉴定[D].北京:中国农业大学, 2015.GOU W Y.Identification of hypoxic adaptation phenotypes and the differential expression genes of myocardial tissue in chicken[D].Beijing:China Agricultural University, 2015.(in Chinese)
[7]	PERTEA M, PERTEA G M, ANTONESCU C M, et al.StringTie enables improved reconstruction of a transcriptome from RNA-seq reads[J].Nat Biotechnol, 2015, 33(3):290-295.
[8]	LOVE M I, HUBER W, ANDERS S.Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2[J].Genome Biol, 2014, 15(12):550.
[9]	YU B Q, WANG X, SONG Y T, et al.The role of hypoxia-inducible factors in cardiovascular diseases[J].Pharmacol Ther, 2022, 238:108186.
[10]	PENA E, EL ALAM S, SIQUES P, et al.Oxidative stress and diseases associated with high-altitude exposure[J].Antioxidants (Basel), 2022, 11(2):267.
[11]	LI Y, ZHAO L, LI X F.Hypoxia and the tumor microenvironment[J].Technol Cancer Res Treat, 2021, 20, doi:10.1177/15330338211036304.
[12]	SIMONSON T S, YANG Y Z, HUFF C D, et al.Genetic evidence for high-altitude adaptation in tibet[J].Science, 2010, 329(5987):72-75.
[13]	QI X B, ZHANG Q, HE Y X, et al.The transcriptomic landscape of yaks reveals molecular pathways for high altitude adaptation[J].Genome Biol Evol, 2019, 11(1):72-85.
[14]	GIUSSANI D A.Breath of life:heart disease link to developmental hypoxia[J].Circulation, 2021, 144(17):1429-1443.
[15]	SMITH K L M, SWIDERSKA A, LOCK M C, et al.Chronic developmental hypoxia alters mitochondrial oxidative capacity and reactive oxygen species production in the fetal rat heart in a sex-dependent manner[J].J Pineal Res, 2022, 73(3):e12821.
[16]	MENENDEZ-MONTES I, ESCOBAR B, GOMEZ M J, et al.Activation of amino acid metabolic program in cardiac HIF1-alpha-deficient mice[J].iScience, 2021, 24(2):102124.
[17]	PATTERSON A J, ZHANG L.Hypoxia and fetal heart development[J].Curr Mol Med, 2010, 10(7):653-666.
[18]	AYALEW W, CHU M, LIANG C N, et al.Adaptation mechanisms of yak (Bos grunniens) to high-altitude environmental stress[J].Animals (Basel), 2021, 11(8):2344.
[19]	ZHANG Q, GOU W Y, WANG X T, et al.Genome resequencing identifies unique adaptations of Tibetan chickens to hypoxia and high-dose ultraviolet radiation in high-altitude environments[J].Genome Biol Evol, 2016, 8(3):765-776.
[20]	RADHAKRISHNAN K, LAMANNA J C, CABRERA M E.A quantitative study of oxygen as a metabolic regulator[M]//DUNN J F, SWARTZ H M.Oxygen Transport to Tissue XXIV.Boston:Springer, 2003:547-554.
[21]	MARKERT C L.Lactate dehydrogenase.Biochemistry and function of lactate dehydrogenase[J].Cell Biochem Funct, 1984, 2(3):131-134.
[22]	WILSON D F, MATSCHINSKY F M.Metabolic homeostasis:oxidative phosphorylation and the metabolic requirements of higher plants and animals[J].J Appl Physiol, 2018, 125(4):1183-1192.
[23]	LAMBERT S A, JOLMA A, CAMPITELLI L F, et al.The human transcription factors[J].Cell, 2018, 172(4):650-665.
[24]	TOGNON M, GIUGNO R, PINELLO L.A survey on algorithms to characterize transcription factor binding sites[J].Brief Bioinform, 2023, 24(3):bbad156.
[25]	DE MATTOS K, VIGER R S, TREMBLAY J J.Transcription factors in the regulation of leydig cell gene expression and function[J].Front Endocrinol (Lausanne), 2022, 13:881309.
[26]	XU R F, WANG F, YANG H Q, et al.Action sites and clinical application of HIF-1α inhibitors[J].Molecules, 2022, 27(11):3426.
[27]	PENG X F, GAO H, XU R, et al.The interplay between HIF-1α and noncoding RNAs in cancer[J].J Exp Clin Cancer Res, 2020, 39(1):27.
[28]	WU F, TONG D D, NI L, et al.HIF-1α suppresses myeloma progression by targeting Mcl-1[J].Int J Clin Exp Pathol, 2020, 13(7):1483-1491.
[29]	TANG K C, BREEN E C, WAGNER H, et al.HIF and VEGF relationships in response to hypoxia and sciatic nerve stimulation in rat gastrocnemius[J].Respir Physiol Neurobiol, 2004, 144(1):71-80.
[30]	SADEGHI F, KARDAR G A, BOLOURI M R, et al.Overexpression of bHLH domain of HIF-1 failed to inhibit the HIF-1 transcriptional activity in hypoxia[J].Biol Res, 2020, 53(1):25.
[31]	ZENG W, SU J, WU L, et al.CD147 promotes melanoma progression through hypoxia-induced MMP2 activation[J].Curr Mol Med, 2014, 14(1):163-173.
[32]	RAFFETTO J D, KHALIL R A.Matrix metalloproteinases and their inhibitors in vascular remodeling and vascular disease[J]. Biochem Pharmacol, 2008, 75(2):346-359.
[33]	SIEFERT S A, SARKAR R.Matrix metalloproteinases in vascular physiology and disease[J].Vascular, 2012, 20(4):210-216.
[34]	WANG X, KHALIL R A.Matrix metalloproteinases, vascular remodeling, and vascular disease[J].Adv Pharmacol, 2018, 81:241-330.
[35]	YUAN S M.α-smooth muscle actin and ACTA2 gene expressions in vasculopathies[J].Braz J Cardiovasc Surg, 2015, 30(6):644-649.
[36]	KAW A, KAW K, HOSTETLER E M, et al.Expanding ACTA2 genotypes with corresponding phenotypes overlapping with smooth muscle dysfunction syndrome[J].Am J Med Genet Part A, 2022, 188(8):2389-2396.

Transcriptome Data from Chicken Embryo Heart Tissue Identified Key Genes for Altitude Hypoxia Adaptation in Xueyu White Chickens

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 36

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LIU Yili, TANG Jiao, MIN Qi, YANG Lu, WANG Zening, HU Lian, ZHAO Di, JIANG Mingfeng. Mining Key Candidate Genes of Development and Metabolism in Yak Abomasum Based on Transcriptome Data [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 153-168.
[2]	HU Ting, ZHANG Yonghong, HOU Xiaolin, YAO Hua, CUI Defeng, PAN Zaozao, ZHANG Lingyu, ZHANG Jiaxi, WU Qiong. The Effects of Bisphenol A on Inflammation and Amino Acid Metabolism Pathways in Porcine Testis Sertoli Cells Based on Transcriptome Analysis [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2858-2871.
[3]	LIU Hang, WANG Huanhuan, GE Ying, ZHANG Lei, ZHANG Weiwu, WEI Yinghui, LI Qinghai, FAN Jinghui, ZHANG Xuedong. Screening of Candidate Genes of Skin Color of Black-Bone Chicken Based on Transcriptome and Proteome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2320-2329.
[4]	BAI Lu, WANG Mengjie, MA Xiaochun, HE Zhengxiao, KONG Fuli, LIU Dawei, YING Fan, ZHU Dan, ZHAO Guiping, WEN Jie, LIU Ranran. Study of the Alteration of Wooden Breast Histological and Molecular Regulatory Pathways in Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1915-1926.
[5]	WANG Meihui, ZHONG Zhenyu, BAI Jiade, SHAN Yunfang, CHENG Zhibin, ZHANG Qingxun, MENG Yuping, DONG Yulan, GUO Qingyun. Transcriptomic Analysis of Key Genes and Pathways in Deer Gut Infected by Clostridium perfringens Type C [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 2147-2157.
[6]	SUN Meijie, CAO Liwen, ZHENG Wenjin, SHEN Junshi, ZHU Weiyun. Effect of Dietary Urea Supplementation on Liver Ammonia Metabolism in Fattening Hu Lambs Based on Transcriptome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1148-1159.
[7]	LIU Yuanyi, LI Xinyu, Bayinnamula, CUI Fang, MANG Lai, DU Ming. Single-Cell Transcriptome Sequencing Technology and its Application in Animal Reproduction [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 421-433.
[8]	YU Zuhua, JIA Yanyan, HE Lei, LIAO Chengshui, LI Jing, WEI Ying, CHEN Jian, CHEN Songbiao, SHANG Ke, DING Ke. Effects of gga-miR-155 on MDCC-MSB1 Cell Transcriptomes [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 663-672.
[9]	HAN Haoyuan, LI Shikai, YANG Ruiqiao, LI Manman, LI Jun, HA Si, ZHAO Jinyan, WEI Hongfang, QUAN Kai. Mining Key Candidate Genes for High Reproduction Performance of Huai Goats Based on Transcriptome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5077-5090.
[10]	WANG Wenxiang, DU Lili, HU Junwei, ZHANG Yanxiang, MA Minghao, DUAN Rui, QIAN Cong, WANG Xinyue, LI Sanlu, ZHANG Changqing, ZHANG Lupei, GAO Xue, XU Lingyang, LI Junya, GAO Huijiang. Mining Candidate Genes Related to Meat Quality Traits of Longissimus Lumborum in Pingliang Red Steer Based on Transcriptome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4589-4604.
[11]	ZHANG Qian, CUI Yan, YU Sijiu, HE Junfeng, PAN Yangyang, WANG Meng. Transcriptome Analysis of the Cerebral Cortex in Newborn and Adult Yaks (Bos grunniens) [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4605-4614.
[12]	CHEN Lu, CHANG Xinyu, SHEN Jiachen, SHEN Ruiting, ZHAO Zhenhua, HOU Xiaolin. Transcriptome Sequencing and Analysis of HD11 Cells Infected by Avian Infectious Bronchitis Virus [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4860-4865.
[13]	GUO Yulong, ZHI Yihao, LI Xinyan, DONG Jiajia, LI Zhuanjian, TIAN Yadong, LI Hong, LIU Xiaojun. Study on Genome-wide Methylation Difference and Its Effect on Liver Transcriptome in Chickens During Pre-laying and Peak-laying Periods [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 2888-2899.
[14]	LI Xiaobo, LIU Zhanfa, LIU Yue, CHEN Qian, MA Yuehui, ZHAO Qianjun, YE Shaohui. Mining Genes Related to Wool Bending of Zhongwei Goat Based on WGCNA and GSEA [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 2930-2943.
[15]	MAO Yanni, CHANG Jiawei, LI Na, WANG Xin, KANG Xinyun, MA Qiang, MA Liang, WANG Guiqin. Transcriptome Differential Expression Analysis of Staphylococcus aureus in Biofilm State and Planktonic State [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2697-2707.