Fish Physiology and Biochemistry

, Volume 44, Issue 5, pp 1333–1347 | Cite as

Transcriptome analysis demonstrates that long noncoding RNA is involved in the hypoxic response in Larimichthys crocea

  • Wei Liu
  • Xiaoxu Liu
  • Changwen Wu
  • Lihua Jiang


The large yellow croaker (Larimichthys crocea) has low hypoxia tolerance compared with other fish species, and the mRNA levels of hypoxia-inducible factor (HIF)-1α in its brain do not change markedly under hypoxic conditions. In this study, we investigated noncoding transcription in the hypoxic response mechanism of L. crocea. We generated a catalog of long noncoding RNAs (lncRNAs) from the brain of L. crocea individuals under hypoxic stress, investigated lncRNA expression patterns, and analyzed the HIF signaling pathway by RNA sequencing. Prolyl hydroxylase domain 2 (PHD2) expression significantly increased after 6 and 12 h of hypoxia, and a lncRNA (Linc_06633.1) was found in the upstream, antisense region of PHD2. Linc_06633.1 may be an important regulator that promotes PDH2 expression under hypoxia in L. crocea, and we constructed a regulatory profile of L. crocea under hypoxic conditions. To the best of our knowledge, it is the first study that has been conducted on hypoxia signaling pathway regulation by lncRNAs in L. crocea and elucidates the role played by lncRNAs in the regulation of the hypoxia stress response in teleost fish.


Long noncoding RNA PHD2 HIF Larimichthys crocea Hypoxia 


Funding information

This study was supported by the Public Science and Technology Research Funds Projects of Ocean (no. 201505025) and the International Science and Technology Cooperation Program of China (no. 2015DFR30450).

Supplementary material

10695_2018_525_MOESM1_ESM.xls (9.9 mb)
ESM 1 (XLS 10176 kb)
10695_2018_525_MOESM2_ESM.xlsx (9.7 mb)
ESM 2 (XLSX 9961 kb)


  1. Ao J, Mu Y, Xiang LX, Fan DD, Feng MJ, Zhang S, Shi Q, Zhu LY, Li T, Ding Y (2015) Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation. PLoS Genet 11(4):e1005118CrossRefPubMedPubMedCentralGoogle Scholar
  2. Appelhoff RJ, Tian YM, Raval RR, Turley H, Harris AL, Pugh CW, Ratcliffe PJ, Gleadle JM (2004) Differential function of the prolyl hydroxylases PHD1, PHD2, and PHD3 in the regulation of hypoxia-inducible factor. J Biol Chem 279(37):38458–38465CrossRefPubMedGoogle Scholar
  3. Aprelikova O, Chandramouli GV, Wood M, Vasselli JR, Riss J, Maranchie JK, Linehan WM, Barrett JC (2004) Regulation of HIF prolyl hydroxylases by hypoxia-inducible factors. J Cell Biochem 92(3):491–501CrossRefPubMedGoogle Scholar
  4. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT (2000) Gene ontology: tool for the unification of biology. Nat Genet 25(1):25–29CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120CrossRefPubMedPubMedCentralGoogle Scholar
  6. Boquesastre R, Soler M, Oliveiramateos C, Portela A, Moutinho C, Sayols S, Villanueva A, Esteller M, Guil S (2015) Head-to-head antisense transcription and R-loop formation promotes transcriptional activation. Proc Natl Acad Sci U S A 112(18):5785–5790CrossRefGoogle Scholar
  7. Cazevieille C, Muller A, Meynier F, Bonne C (1993) Superoxide and nitric oxide cooperation in hypoxia/reoxygenation-induced neuron injury. Free Radic Biol Med 14(4):389–395CrossRefPubMedGoogle Scholar
  8. Chan PH (1996) Role of oxidants in ischemic brain damage. Stroke 27(6):1124–1129CrossRefPubMedGoogle Scholar
  9. Cioffi CL, Liu XQ, Kosinski PA, Garay M, Bowen BR (2003) Differential regulation of HIF-1 alpha prolyl-4-hydroxylase genes by hypoxia in human cardiovascular cells. Biochem Biophys Res Commun 303(3):947–953CrossRefPubMedGoogle Scholar
  10. Consortium GO (2001) Creating the gene ontology resource: design and implementation. Genome Res 11(8):1425–1433CrossRefPubMedCentralGoogle Scholar
  11. Courtnay R, Ngo DC, Malik N, Ververis K, Tortorella SM, Karagiannis TC (2015) Cancer metabolism and the Warburg effect: the role of HIF-1 and PI3K. Mol Biol Rep 42(4):841–851CrossRefPubMedGoogle Scholar
  12. Flügel D, Görlach A, Michiels C, Kietzmann T (2007) Glycogen synthase kinase 3 phosphorylates hypoxia-inducible factor 1α and mediates its destabilization in a VHL-independent manner. Mol Cell Biol 27(9):3253–3265CrossRefPubMedPubMedCentralGoogle Scholar
  13. Gao JL, Chen YG (2014) Natural compounds regulate glycolysis in hypoxic tumor microenvironment. Biomed Res Int 2015:8Google Scholar
  14. Genciana T, Simona R, Samuela C, Giovanni B, Rosalba G, Marco S (2008) Acute and chronic hypoxia affects HIF-1α mRNA levels in sea bass (Dicentrarchus labrax). Aquaculture 279(1):150–159Google Scholar
  15. Goff LA, Groff AF, Sauvageau M, Trayesgibson Z, Sanchezgomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalezceleiro M (2015) Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci 112(22):6855–6862CrossRefPubMedGoogle Scholar
  16. Gracey AY, Troll JV, Somero GN (2001) Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc Natl Acad Sci U S A 98(4):1993–1998CrossRefPubMedPubMedCentralGoogle Scholar
  17. Guennewig B, Cooper AA (2014) The central role of noncoding RNA in the brain. Int Rev Neurobiol 116:153–194CrossRefPubMedGoogle Scholar
  18. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Xian A, Fan L, Koziol MJ, Gnirke A, Nusbaum C (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28(5):503–510CrossRefPubMedPubMedCentralGoogle Scholar
  19. Hansen AJ (1985) Effect of anoxia on ion distribution in the brain. Physiol Rev 65(1):101–148CrossRefPubMedGoogle Scholar
  20. Herbert NA, Steffensen JF (2005) The response of Atlantic cod, Gadus morhua, to progressive hypoxia: fish swimming speed and physiological stress. Mar Biol 147(6):1403–1412CrossRefGoogle Scholar
  21. Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, Ohta K (2008) Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 456(7218):130–134CrossRefPubMedGoogle Scholar
  22. Huang LE, Gu J, Schau M, Bunn HF (1998) Regulation of hypoxia-inducible factor 1alpha is mediated by an O2-dependent degradation domain via the ubiquitin-proteasome pathway. Proc Natl Acad Sci U S A 95(14):7987–7992CrossRefPubMedPubMedCentralGoogle Scholar
  23. Huang DW, Sherman BT, Lempicki RA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57CrossRefGoogle Scholar
  24. Jingqun A, Yinnan M, Li-Xin X, Dingding F, Mingji F, Shicui Z, Qiong S, Lv-Yun Z, Ting L, Yang D (2015) Genome sequencing of the perciform fish Larimichthys crocea provides insights into molecular and genetic mechanisms of stress adaptation. Science Foundation in China 11(3):8–8Google Scholar
  25. Johnsson P, Ackley A, Vidarsdottir L, Lui WO, Corcoran M, Dan G, Morris KV (2013) A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol 20(4):1032–1035CrossRefGoogle Scholar
  26. Kaelin WG (2007) Von Hippel-Lindau disease. Annu Rev Pathol 2(2):527–532Google Scholar
  27. Kaelin WG, Ratcliffe PJ (2008) Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol Cell 30(4):393–402CrossRefPubMedGoogle Scholar
  28. Kallio PJ, Wilson WJ, O'Brien S, Makino Y, Poellinger L (1999) Regulation of the hypoxia-inducible transcription factor 1alpha by the ubiquitin-proteasome pathway. J Biol Chem 274(10):6519–6525CrossRefPubMedGoogle Scholar
  29. Kapahi P (2009) HIF-1 modulates dietary restriction-mediated lifespan extension via IRE-1 in Caenorhabditis elegans. PLoS Genet 5(5):e1000486CrossRefPubMedPubMedCentralGoogle Scholar
  30. Katayama Y, Kawamata T, Tamura T, Hovda DA, Becker DP, Tsubokawa T (1991) Calcium-dependent glutamate release concomitant with massive potassium flux during cerebral ischemia in vivo. Brain Res 558(1):136–140CrossRefPubMedGoogle Scholar
  31. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea MD, Thomas K, Presser A, Bernstein BE, Van OA (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106(28):11667–11672CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kiang JG, Tsen KT (2006) Biology of hypoxia. Chin J Physiol 49(5):223–233PubMedGoogle Scholar
  33. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):1CrossRefGoogle Scholar
  34. Kornienko AE, Guenzl PM, Barlow DP, Pauler FM (2013) Gene regulation by the act of long non-coding RNA transcription. BMC Biol 11(1):59CrossRefPubMedPubMedCentralGoogle Scholar
  35. KS NP, SS WR, HW LS, MK YR, YC KR (2006) Cloning and expression analysis of two distinct HIF-alpha isoforms – gcHIF-1alpha and gcHIF-4alpha – from the hypoxia-tolerant grass carp, Ctenopharyngodon idellus. BMC Mol Biol 7(1):1–13CrossRefGoogle Scholar
  36. Kwasek K, Rimoldi S, Cattaneo AG, Parker T, Dabrowski K, Terova G (2017) The expression of hypoxia-inducible factor-1α gene is not affected by low-oxygen conditions in yellow perch (Perca flavescens) juveniles. Fish Physiol Biochem 43(3):849–862CrossRefPubMedGoogle Scholar
  37. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):1–10CrossRefGoogle Scholar
  38. Lee DY, Moon J, Lee ST, Jung KH, Park DK, Yoo JS, Sunwoo JS, Byun JI, Lim JA, Kim TJ (2015) Dysregulation of long non-coding RNAs in mouse models of localization-related epilepsy. Biochem Biophys Res Commun 462(4):433–440CrossRefPubMedGoogle Scholar
  39. Li CH, Chen Y (2013) Targeting long non-coding RNAs in cancers: progress and prospects. Int J Biochem Cell Biol 45(8):1895–1910CrossRefPubMedGoogle Scholar
  40. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment-map format and SAMtools. Bioinformatics 25(16):2078–2079CrossRefPubMedPubMedCentralGoogle Scholar
  41. Lipovich L, Tarca AL, Cai J, Jia H, Chugani HT, Sterner KN, Grossman LI, Uddin M, Hof PR, Sherwood CC (2014) Developmental changes in the transcriptome of human cerebral cortex tissue: long noncoding RNA transcripts. Cereb Cortex 24(6):1451–1459CrossRefPubMedGoogle Scholar
  42. Lipton P (1999) Ischemic cell death in brain neurons. Physiol Rev 79(4):1431–1568CrossRefPubMedGoogle Scholar
  43. Liu P, Yu Y, Liu C (1991) Studies on the situation of pollution and countermeasures of control of the oceanic environment in Zhoushan fishing ground—the largest fishing ground in China ☆. Mar Pollut Bull 23(91):281–288CrossRefGoogle Scholar
  44. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(4):402–408CrossRefPubMedGoogle Scholar
  45. Lutz PL, Nilsson GE (1997) The brain without oxygen. Landes BioscienceGoogle Scholar
  46. Macmanus JP, Linnik MD (1997) Gene expression induced by cerebral ischemia: an apoptotic perspective. J Cereb Blood Flow Metab 17(8):815–832CrossRefPubMedGoogle Scholar
  47. Mcmahon S, Charbonneau M, Grandmont S, Richard DE, Dubois CM (2006) Transforming growth factor beta1 induces hypoxia-inducible factor-1 stabilization through selective inhibition of PHD2 expression. J Biol Chem 281(34):24171CrossRefPubMedGoogle Scholar
  48. Mehta R, Steinkraus KA, Sutphin GL, Ramos FJ, Shamieh LS, Huh A, Davis C, Chandler-Brown D, Kaeberlein M (2009) Proteasomal regulation of the hypoxic response modulates aging in C. elegans. Science 324(5931):1196–1198CrossRefPubMedPubMedCentralGoogle Scholar
  49. Metzen E, Stiehl DP, Doege K, Marxsen JH, Hellwig-Bürgel T, Jelkmann W (2005) Regulation of the prolyl hydroxylase domain protein 2 (phd2/egln-1) gene: identification of a functional hypoxia-responsive element. Biochem J 387(3):711–717CrossRefPubMedPubMedCentralGoogle Scholar
  50. Molyneaux B, Goff L, Brettler A, Chen HH, Brown J, Hrvatin S, Rinn J, Arlotta P (2015) DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron 85(2):275–288CrossRefPubMedGoogle Scholar
  51. Moran VA, Perera RJ, Khalil AM (2012) Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res 40(14):6391–6400CrossRefPubMedPubMedCentralGoogle Scholar
  52. Moulton J (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147(7):1537–1550CrossRefGoogle Scholar
  53. Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J (2015) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res 43(Database issue):D130–D137CrossRefPubMedGoogle Scholar
  54. Nowicki JP, Duval D, Poignet H, Scatton B (1991) Nitric oxide mediates neuronal death after focal cerebral ischemia in the mouse. Eur J Pharmacol 204(3):339–340CrossRefPubMedGoogle Scholar
  55. Numata K, Kiyosawa H (2012) Genome-wide impact of endogenous antisense transcripts in eukaryotes. Front Biosci 17(1):300CrossRefGoogle Scholar
  56. Pnueli L, Rudnizky S, Yosefzon Y, Melamed P (2015) RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin α-subunit gene. Proc Natl Acad Sci U S A 112(14):4369–4374CrossRefPubMedPubMedCentralGoogle Scholar
  57. Qiang L, Wu T, Zhang HW, Lu N, Hu R, Wang YJ, Zhao L, Chen FH, Wang XT, You QD (2012) HIF-1α is critical for hypoxia-mediated maintenance of glioblastoma stem cells by activating notch signaling pathway. Cell Death Differ 19(2):284–294CrossRefPubMedGoogle Scholar
  58. Qureshi IA, Mehler MF (2013) Long non-coding RNAs: novel targets for nervous system disease diagnosis and therapy. Neurotherapeutics 10(4):632–646CrossRefPubMedPubMedCentralGoogle Scholar
  59. Rahman MS, Thomas P (2007) Molecular cloning, characterization and expression of two hypoxia-inducible factor alpha subunits, HIF-1alpha and HIF-2alpha, in a hypoxia-tolerant marine teleost, Atlantic croaker (Micropogonias undulatus). Gene 396(2):273–282CrossRefPubMedGoogle Scholar
  60. Rimoldi S, Terova G, Ceccuzzi P, Marelli S, Antonini M, Saroglia M (2012) HIF-1α mRNA levels in Eurasian perch (Perca fluviatilis ) exposed to acute and chronic hypoxia. Mol Biol Rep 39(4):4009–4015CrossRefPubMedGoogle Scholar
  61. Rissanen E, Tranberg HK, Sollid J, Nilsson GE, Nikinmaa M (2006) Temperature regulates hypoxia-inducible factor-1 (HIF-1) in a poikilothermic vertebrate, crucian carp (Carassius carassius). J Exp Biol 209(6):994–1003CrossRefPubMedGoogle Scholar
  62. Salceda S, Caro J (1997) Hypoxia-inducible factor 1alpha (HIF-1alpha) protein is rapidly degraded by the ubiquitin-proteasome system under normoxic conditions. Its stabilization by hypoxia depends on redox-induced changes. J Biol Chem 272(36):22642–22647CrossRefPubMedGoogle Scholar
  63. Scarola M, Comisso E, Pascolo R, Chiaradia R, Marion RM, Schneider C, Blasco MA, Schoeftner S, Benetti R (2015) Epigenetic silencing of Oct4 by a complex containing SUV39H1 and Oct4 pseudogene lncRNA. Nat Commun 6:7631CrossRefPubMedPubMedCentralGoogle Scholar
  64. Schofield CJ, Ratcliffe PJ (2004) Oxygen sensing by HIF hydroxylases. Nat Rev Mol Cell Biol 5(5):343–354CrossRefPubMedGoogle Scholar
  65. Semenza GL (2004) Hydroxylation of HIF-1: oxygen sensing at the molecular level. Physiology 19(4):176–182CrossRefPubMedGoogle Scholar
  66. Shen RJ, Jiang XY, Pu JW, Zou SM (2010) HIF-1α and -2α genes in a hypoxia-sensitive teleost species Megalobrama amblycephala: cDNA cloning, expression and different responses to hypoxia. Comp Biochem Physiol B Biochem Mol Biol 157(3):273–280CrossRefPubMedGoogle Scholar
  67. Soitamo AJ, Rabergh CM, Gassmann M, Sistonen L, Nikinmaa M (2001) Characterization of a hypoxia-inducible factor (HIF-1alpha ) from rainbow trout. Accumulation of protein occurs at normal venous oxygen tension. J Biol Chem 276(23):19699–19705CrossRefPubMedGoogle Scholar
  68. Steinfeld I, Navon R, Creech ML, Yakhini Z, Tsalenko A (2015) ENViz: a Cytoscape app for integrated statistical analysis and visualization of sample-matched data with multiple data types. Bioinformatics 31(10):1683–1685CrossRefPubMedPubMedCentralGoogle Scholar
  69. Su WY, Li JT, Cui Y, Hong J, Du W, Wang YC, Lin YW, Xiong H, Wang JL, Kong X (2012) Bidirectional regulation between WDR83 and its natural antisense transcript DHPS in gastric cancer. Cell Res 22(9):1374–1389CrossRefPubMedPubMedCentralGoogle Scholar
  70. Sun J, Lin Y, Wu J (2013) Long non-coding RNA expression profiling of mouse testis during postnatal development. PLoS One 8(10):e75750CrossRefPubMedPubMedCentralGoogle Scholar
  71. Tan JY, Vance KW, Varela MA, Sirey T, Watson LM, Curtis HJ, Marinello M, Alves S, Steinkraus BR, Cooper S (2014) Cross-talking noncoding RNAs contribute to cell-specific neurodegeneration in SCA7. Nat Struct Mol Biol 21(11):955–961CrossRefPubMedPubMedCentralGoogle Scholar
  72. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105–1111CrossRefPubMedPubMedCentralGoogle Scholar
  73. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, Van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28(5):511–515CrossRefPubMedPubMedCentralGoogle Scholar
  74. Tsai MC, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329(5992):689–693CrossRefPubMedPubMedCentralGoogle Scholar
  75. Wang KC, Yang YW, Liu B, Sanyal A, Corceszimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472(7341):120–124CrossRefPubMedPubMedCentralGoogle Scholar
  76. Wang Y, He L, Du Y, Zhu P, Huang G, Luo J, Yan X, Ye B, Li C, Xia P (2015) The long noncoding RNA lncTCF7 promotes self-renewal of human liver cancer stem cells through activation of Wnt signaling. Cell Stem Cell 16(4):413–425CrossRefPubMedGoogle Scholar
  77. Wu P, Zuo X, Deng H, Liu X, Liu L, Ji A (2013) Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases. Brain Res Bull 97(8):69–80CrossRefPubMedGoogle Scholar
  78. Xu K, Liu Z (2007) The current stock of large yellow croaker Pseudosciaena crocea in the East China Sea with respects of its stock decline. Journal of Dalian Fisheries University 22(5):392–396Google Scholar
  79. Yang QL, Yao CL, Wang ZY (2012) Acute temperature and cadmium stress response characterization of small heat shock protein 27 in large yellow croaker, Larimichthys crocea. COMP BIOCHEM PHYS C 155(2):190–197Google Scholar
  80. Yin Y, Yan L, Jinlong S, Guang Z, Yangyang (2015) Opposing roles for the lncRNA haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation. Cell Stem Cell 16(5):504–516CrossRefPubMedGoogle Scholar
  81. Zhao F, Li YW, Pan HJ, Shi CB, Luo XC, Li AX, Wu SQ (2014) TAK1-binding proteins (TAB1 and TAB2) in grass carp (Ctenopharyngodon idella): identification, characterization, and expression analysis after infection with Ichthyophthirius multifiliis. Fish Shellfish Immun 38(2):389–399CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.National Engineering Research Center of Marine Facilities AquacultureZhejiang Ocean UniversityZhoushanPeople’s Republic of China

Personalised recommendations