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Identification of HSF1 Target Genes Involved in Thermal Stress in the Pacific Oyster Crassostrea gigas by ChIP-seq

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Abstract

The Pacific oyster Crassostrea gigas, a commercially important species inhabiting the intertidal zone, facing enormous temperature fluctuations. Therefore, it is important to identify candidate genes and key regulatory relationships associated with thermal tolerance, which can aid the molecular breeding of oysters. Heat shock transcription factor 1 (HSF1) plays an important role in the thermal stress resistance. However, the regulatory relationship between the expansion of heat shock protein (HSP) HSP 70 and HSF1 is not yet clear in C. gigas. In this study, we analyzed genes regulated by HSF1 in response to heat shock by chromatin immunoprecipitation followed by sequencing (ChIP-seq), determined the expression patterns of target genes by qRT-PCR, and validated the regulatory relationship between one HSP70 and HSF1. We found 916 peaks corresponding to HSF1 binding sites, and these peaks were annotated to the nearest genes. In Gene Ontology analysis, HSF1 target genes were related to signal transduction, energy production, and response to biotic stimulus. Four HSP70 genes, two HSP40 genes, and one small HSP gene exhibited binding to HSF1. One HSP70 with a binding site in the promoter region was validated to be regulated by HSF1 under heat shock. These results provide a basis for future studies aimed at determining the mechanisms underlying thermal tolerance and provide insights into gene regulation in the Pacific oyster.

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References

  • Baird NA, Douglas PM, Simic MS, Grant AR, Moresco JJ, Wolff SC, Manning G, Dillin A (2014) HSF-1-mediated cytoskeletal integrity determines thermotolerance and life span. Science 346:360–363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baird NA, Turnbull DW, Johnson EA (2006) Induction of the heat shock pathway during hypoxia requires regulation of heat shock factor by hypoxia-inducible factor-1. J Biol Chem 281:38675–38681

    Article  CAS  PubMed  Google Scholar 

  • Beck MW, Brumbaugh RD, Airoldi L, Carranza A, Coen LD, Crawford C, Defeo O, Edgar GJ, Hancock B, Kay MC, Lenihan HS, Luckenbach MW, Toropova CL, Zhang G, Guo X (2011) Oyster reefs at risk and recommendations for conservation, restoration, and management. Bioscience 61:107–116

    Article  Google Scholar 

  • Bedulina DS, Evgen'ev MB, Timofeyev MA, Protopopova MV, Garbuz DG, Pavlichenko VV, Luckenbach T, Shatilina ZM, Axenov-Gribanov DV, Gurkov AN, Sokolova IM, Zatsepina OG (2013) Expression patterns and organization of the hsp70 genes correlate with thermotolerance in two congener endemic amphipod species (Eulimnogammarus cyaneus and E. verrucosus) from Lake Baikal. Mol Ecol 22:1416–1430

    Article  CAS  PubMed  Google Scholar 

  • Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR (2007) Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res 17:910–916

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bozinovic F, Calosi P, Spicer JI (2011) Physiological correlates of geographic range in animals. Annu Rev Ecol Evol S 42:155–179

    Article  Google Scholar 

  • Brunquell J, Morris S, Lu Y, Cheng F, Westerheide SD (2016) The genome-wide role of HSF-1 in the regulation of gene expression in Caenorhabditis elegans. BMC Genomics 17:1–18

    Article  CAS  Google Scholar 

  • Chen M, Yang H, Delaporte M, Zhao S (2007) Immune condition of Chlamys farreri in response to acute temperature challenge. Aquaculture 271:479–487

    Article  Google Scholar 

  • Cheng J, Xun XG, Kong YF, Wang SY, Yang ZH, Li YJ, Kong DX, Wang S, Zhang LL, Hu XL, Bao ZM (2016) Hsp70 gene expansions in the scallop Patinopecten yessoensis and their expression regulation after exposure to the toxic dinoflagellate Alexandrium catenella. Fish Shellfish Immunol 58:266–273

  • Franzolin E, Pontarin G, Rampazzo C, Miazzi C, Ferraro P, Palumbo E, Reichard P, Bianchi V (2013) The deoxynucleotide triphosphohydrolase SAMHD1 is a major regulator of DNA precursor pools in mammalian cells. Proc Natl Acad Sci 110:14272–14277

    Article  PubMed  Google Scholar 

  • Frydman J (2001) Folding of newly translated proteins in vivo: the role of molecular chaperones. Annu Rev Biochem 70:603–647

    Article  CAS  PubMed  Google Scholar 

  • Guertin MJ, Lis JT (2010) Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet 6:e1001114

  • Guo X, He Y, Zhang L, Lelong C, Jouaux A (2015) Immune and stress responses in oysters with insights on adaptation. Fish Shellfish Immunol 46:107–119

  • Hégaret H, Wikfors GH, Soudant P, Delaporte M, Alix JH, Smith BC, Dixon MS, Quére C, Le Coz JR, Paillard C, Moal J, Samain JF (2004) Immunological competence of eastern oysters, Crassostrea virginica, fed different microalgal diets and challenged with a temperature elevation. Aquaculture 234:541–560

    Article  Google Scholar 

  • Hahn J-S, Hu Z, Thiele DJ, Iyer VR (2004) Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol 24:5249–5256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hartl FU, Hayer-Hartl M (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295:1852

    Article  CAS  PubMed  Google Scholar 

  • Jaeger AM, Makley LN, Gestwicki JE, Thiele DJ (2014) Genomic heat shock element sequences drive cooperative human heat shock factor 1 DNA binding and selectivity. J Biol Chem 289:30459–30469

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jedlicka P, Mortin MA, Wu C (1997) Multiple functions of Drosophila heat shock transcription factor in vivo. EMBO J 16:2452–2462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502

    Article  CAS  PubMed  Google Scholar 

  • Kawabe S, Yokoyama Y (2011) Novel isoforms of heat shock transcription factor 1 are induced by hypoxia in the Pacific oyster Crassostrea gigas. J Exp Zool A Ecol Genet Physiol 315:394–407

    Article  CAS  PubMed  Google Scholar 

  • Lang RP, Bayne CJ, Camara MD, Cunningham C, Jenny MJ, Langdon CJ (2009) Transcriptome profiling of selectively bred Pacific oyster Crassostrea gigas families that differ in tolerance of heat shock. Mar Biotechnol 11:650–668

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li A, Li L, Wang W, Zhang G (2019) Evolutionary trade-offs between baseline and plastic gene expression in two congeneric oyster species. Biol Lett, 15: 20190202

  • Lim H-J, Kim B-M, Hwang IJ, Lee J-S, Choi I-Y, Kim Y-J, Rhee J-S (2016) Thermal stress induces a distinct transcriptome profile in the Pacific oyster Crassostrea gigas. Comp Biochem Physiol Part D Genomics Proteomics 19:62–70

  • Liu AY, Mathur R, Mei N, Langhammer CG, Babiarz B, Firestein BL (2011) Neuroprotective drug riluzole amplifies the heat shock factor 1 (HSF1)- and glutamate transporter 1 (GLT1)-dependent cytoprotective mechanisms for neuronal survival. J Biol Chem 286:2785–2794

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Li L, Huang B, Wang W, Zhang G (2019) RNAi based transcriptome suggests genes potentially regulated by HSF1 in the Pacific oyster Crassostrea gigas under thermal stress. BMC Genomics 20:639

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mahat DB, Salamanca HH, Duarte FM, Danko CG, Lis JT (2016) Mammalian heat shock response and mechanisms underlying its genome-wide transcriptional regulation. Mol Cell 62:63–78

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mann R, Burreson EM, Baker PK (1991) The decline of the Virginia oyster fishery in Chesapeake Bay considerations for introduction of a non-endemic species, Crassostrea gigas (Thunberg, 1793). J Shellfish Res 10:379

    Google Scholar 

  • Meistertzheim AL, Tanguy A, Moraga D, Thebault MT (2007) Identification of differentially expressed genes of the Pacific oyster Crassostrea gigas exposed to prolonged thermal stress. FEBS J 274:6392–6402

    Article  CAS  PubMed  Google Scholar 

  • Mishra BB, Gundra UM, Teale JM (2008) Expression and distribution of toll-like receptors 11–13 in the brain during murine neurocysticercosis. J Neuroinflammation 5:53

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Morimoto RI (1993) Cells in stress: transcriptional activation of heat shock genes. Science 259:1409–1410

    Article  CAS  PubMed  Google Scholar 

  • Morimoto RI (1998) Regulation of the heat shock transcriptional response: cross talk between a family of heat shock factors, molecular chaperones, and negative regulators. Genes Dev 12:3788–3796

    Article  CAS  PubMed  Google Scholar 

  • Ortner V, Ludwig A, Riegel E, Dunzinger S, Czerny T (2015) An artificial HSE promoter for efficient and selective detection of heat shock pathway activity. Cell Stress Chaperones 20:277–288

    Article  CAS  PubMed  Google Scholar 

  • Ouyang Z, Zhou Q, Wong WH (2009) ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci 106:21521–21526

    Article  PubMed  Google Scholar 

  • Pistevos JCA, Calosi P, Widdicombe S, Bishop JDD (2011) Will variation among genetic individuals influence species responses to global climate change? Oikos 120:675–689

    Article  Google Scholar 

  • Samain J-F (2011) Review and perspectives of physiological mechanisms underlying genetically-based resistance of the Pacific oyster Crassostrea gigas to summer mortality. Aquat Living Resour 24:227–236

    Article  CAS  Google Scholar 

  • Samain JF, Dégremont L, Soletchnik P, Haure J, Bédier E, Ropert M, Moal J, Huvet A, Bacca H, Van Wormhoudt A, Delaporte M, Costil K, Pouvreau S, Lambert C, Boulo V, Soudant P, Nicolas JL, Le Roux F, Renault T, Gagnaire B, Geret F, Boutet I, Burgeot T, Boudry P (2007) Genetically based resistance to summer mortality in the Pacific oyster (Crassostrea gigas) and its relationship with physiological, immunological characteristics and infection processes. Aquaculture 268:227–243

    Article  Google Scholar 

  • Sarge KD, Murphy S, Morimoto R (1993) Activation of heat shock gene transcription by heat shock factor 1 involves oligomerization, acquisition of DNA-binding activity, and nuclear localization and can occur in the absence of stress. Mol Cell Biol 13:1392–1407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schödel J, Oikonomopoulos S, Ragoussis J, Pugh CW, Ratcliffe PJ, Mole DR (2011) High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq. Blood 117:e207

  • Sokolova IM, Portner HO (2001) Temperature effects on key metabolic enzymes in Littorina saxatilis and L-obtusata from different latitudes and shore levels. Mar Biol 139:113–126

    Article  CAS  Google Scholar 

  • Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein DNA interactions in vivo with formaldehyde - evidence that histone-H4 is retained on a highly transcribed gene. Cell 53:937–947

    Article  CAS  PubMed  Google Scholar 

  • Sorensen JG, Kristensen TN, Loeschcke V (2003) The evolutionary and ecological role of heat shock proteins. Ecol Lett 6:1025–1037

    Article  Google Scholar 

  • Sorger PK, Pelham HRB (1988) Yeast heat shock factor is an essential DNA-binding protein that exhibits temperature-dependent phosphorylation. Cell 54:855–864

    Article  CAS  PubMed  Google Scholar 

  • Ugalde SC, Preston J, Ogier E, Crawford C (2018) Analysis of farm management strategies following herpesvirus (OsHV-1) disease outbreaks in Pacific oysters in Tasmania, Australia. Aquaculture 495:179–186

    Article  Google Scholar 

  • Viña J (2002) Biochemical adaptation: mechanism and process in physiological evolution. Biochem Mol Biol Educ 30:215–216

    Article  Google Scholar 

  • Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854–858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Westerheide SD, Morimoto RI (2005) Heat shock response modulators as therapeutic tools for diseases of protein conformation. J Biol Chem 280:33097–33100

    Article  CAS  PubMed  Google Scholar 

  • Wu C (1995) Heat shock transcription factors: structure and regulation. Annu Rev Cell Dev Biol 11:441–469

  • Xiao H, Perisic O, Lis JT (1991) Cooperative binding of drosophila heat shock factor to arrays of a conserved 5 bp unit. Cell 64:585–593

    Article  CAS  PubMed  Google Scholar 

  • Young JC, Agashe VR, Siegers K, Hartl FU (2004) Pathways of chaperone-mediated protein folding in the cytosol. Nat Rev Mol Cell Biol 5:781–791

    Article  CAS  PubMed  Google Scholar 

  • Zhan W, Wang W, Shi W (2015) Development of a ChIP-seq method in Crassostrea gigas. Oceanol Limnol Sin 46:1557–1562

  • Zhang G, Li L, Meng J, Qi H, Qu T, Xu F, Zhang L (2016) Molecular basis for adaptation of oysters to stressful marine intertidal environments. Annu Rev Anim Biosci 4:357–381

  • Zhang GF, Fang XD, Guo XM, Li L, Luo RB, Xu F, Yang PC, Zhang LL, Wang XT, Qi HG, Xiong ZQ, Que HY, Xie YL, Holland PWH, Paps J, Zhu YB, Wu FC, Chen YX, Wang JF, Peng CF, Meng J, Yang L, Liu J, Wen B, Zhang N, Huang ZY, Zhu QH, Feng Y, Mount A, Hedgecock D, Xu Z, Liu YJ, Domazet-Loso T, Du YS, Sun XQ, Zhang SD, Liu BH, Cheng PZ, Jiang XT, Li J, Fan DD, Wang W, Fu WJ, Wang T, Wang B, Zhang JB, Peng ZY, Li YX, Li N, Wang JP, Chen MS, He Y, Tan FJ, Song XR, Zheng QM, Huang RL, Yang HL, Du XD, Chen L, Yang M, Gaffney PM, Wang S, Luo LH, She ZC, Ming Y, Huang W, Zhang S, Huang BY, Zhang Y, Qu T, Ni PX, Miao GY, Wang JY, Wang Q, Steinberg CEW, Wang HY, Li N, Qian LM, Zhang GJ, Li YR, Yang HM, Liu X, Wang J, Yin Y, Wang J (2012a) The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490:49–54

    Article  CAS  PubMed  Google Scholar 

  • Zhang H, Wang H, Chen H, Wang M, Zhou Z, Qiu L, Wang L, Song L (2019) The transcriptional response of the Pacific oyster Crassostrea gigas under simultaneous bacterial and heat stresses. Dev Comp Immunol 94:1–10

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Hou R, Su H, Hu X, Wang S, Bao Z (2012b) Network analysis of oyster transcriptome revealed a cascade of cellular responses during recovery after heat shock. PLoS One 7:e35484

  • Zhang L, Li L, Guo X, Litman GW, Dishaw LJ, Zhang G (2015) Massive expansion and functional divergence of innate immune genes in a protostome. Sci Rep 5

  • Zhu C, Gao W, Zhao K, Qin X, Zhang Y, Peng X, Zhang L, Dong Y, Zhang W, Li P, Wei W, Gong Y, Yu X-F (2013) Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase. Nat Commun 4:2722–2729

    Article  CAS  PubMed  Google Scholar 

  • Zhu Q, Zhang L, Li L, Que H, Zhang G (2016) Expression characterization of stress genes under high and low temperature stresses in the Pacific oyster, Crassostrea gigas. Mar Biotechnol (NY) 18:176–188

    Article  CAS  Google Scholar 

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Acknowledgments

We thank all members of the laboratory for helping with oyster sampling and valuable discussion. We thank Dr. Sheng Liu for the suggestions on the article writing.

Funding

The authors thank the National Key R&D Program of China (2018YFD0900304), Strategic Priority Research Program of Chinese Academy of Science (XDA24030105), and the Earmarked Fund for Modern Agro-industry Technology Research System (CARS-49) for supporting this research.

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Contributions

LL conceived the project. YLL, QHZ, LL, and GFZ participated in the design of the study and discussed the results. QHZ prepared the samples for ChIP-seq. RNA extraction, content measurement of HSF1, and validation of the results were conducted by YLL. YLL and QHZ carried out bioinformatics analyses. YLL, QHZ, and LL wrote and polished the manuscript. WW collected the experimental materials. All authors have read and approved the final manuscript.

Corresponding author

Correspondence to Li Li.

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No specific permission was required for the collection of oysters, and all experiments were conducted with the approval of the Experimental Animal Ethics Committee, Institute of Oceanology, Chinese Academy of Sciences, China. No endangered or protected species were involved.

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The authors declare that they have no conflict of interests.

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Liu, Y., Zhu, Q., Li, L. et al. Identification of HSF1 Target Genes Involved in Thermal Stress in the Pacific Oyster Crassostrea gigas by ChIP-seq. Mar Biotechnol 22, 167–179 (2020). https://doi.org/10.1007/s10126-019-09942-6

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