Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animals and Tissue Collection
2.3. PEDV Examination by Quantitative Real-Time PCR (qRT-PCR)
2.4. Histopathological Analysis
2.5. RNA-Seq Library Preparation and Sequencing
2.6. RNA-Seq Data Analysis
2.7. Functional Annotation of Differentially Expressed Genes
2.8. Validation of RNA-Seq Data by qRT-PCR
2.9. Transcription Factor Annotation and Motif Occurrences Analysis
2.10. ChIP-Seq Analysis
3. Results
3.1. PEDV Detection and Histopathological Analysis
3.2. Overview of the RNA-Seq Data
3.3. Differential Gene Expression Analysis
3.4. Annotation of Differentially Expressed Transcription Factors
3.5. Alterations in H3K4me3 Patterns in the PEDV-Infected Jejunum
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
- Song, D.; Park, B. Porcine epidemic diarrhoea virus: A comprehensive review of molecular epidemiology, diagnosis, and vaccines. Virus Genes 2012, 44, 167–175. [Google Scholar] [CrossRef] [PubMed]
- Stevenson, G.W.; Hoang, H.; Schwartz, K.J.; Burrough, E.R.; Sun, D.; Madson, D.; Cooper, V.L.; Pillatzki, A.; Gauger, P.; Schmitt, B.J.; et al. Emergence of porcine epidemic diarrhea virus in the United States: Clinical signs, lesions, and viral genomic sequences. J. Vet. Diag. Investig. 2013, 25, 649–654. [Google Scholar] [CrossRef] [PubMed]
- Perlman, S.; Netland, J. Coronaviruses post-sars: Update on replication and pathogenesis. Nat. Rev. Microbiol. 2009, 7, 439–450. [Google Scholar] [CrossRef] [PubMed]
- Yang, X.; Huo, J.Y.; Chen, L.; Zheng, F.M.; Chang, H.T.; Zhao, J.; Wang, X.W.; Wang, C.Q. Genetic variation analysis of reemerging porcine epidemic diarrhea virus prevailing in central China from 2010 to 2011. Virus Genes 2013, 46, 337–344. [Google Scholar] [CrossRef]
- Sun, D.; Wang, X.; Wei, S.; Chen, J.; Feng, L. Epidemiology and vaccine of porcine epidemic diarrhea virus in china: A mini-review. J. Vet. Med. Sci. 2016, 78, 355–363. [Google Scholar] [CrossRef]
- Zhang, Q.; Liu, X.; Fang, Y.; Zhou, P.; Wang, Y.; Zhang, Y. Detection and phylogenetic analyses of spike genes in porcine epidemic diarrhea virus strains circulating in china in 2016–2017. Virol. J. 2017, 14, 194. [Google Scholar] [CrossRef]
- Pearce, S.C.; Schweer, W.P.; Schwartz, K.J.; Yoon, K.J.; Lonergan, S.M.; Gabler, N.K. Pig jejunum protein profile changes in response to a porcine epidemic diarrhea virus challenge. J. Anim. Sci. 2016, 94, 412–415. [Google Scholar] [CrossRef]
- Zhonghua, L.; Fangzhou, C.; Shiyi, Y.; Xiaozhen, G.; Atta, M.M.; Meizhou, W.; Qigai, H. Comparative proteome analysis of porcine jejunum tissues in response to a virulent strain of porcine epidemic diarrhea virus and its attenuated strain. Viruses 2016, 8, 323. [Google Scholar]
- Lin, H.; Li, B.; Chen, L.; Ma, Z.; He, K.; Fan, H. Differential protein analysis of IPEC-J2 cells infected with porcine epidemic diarrhea virus pandemic and classical strains elucidates the pathogenesis of infection. J. Proteome Res. 2017, 16, 2113–2120. [Google Scholar] [CrossRef]
- Kim, O.; Chae, C. In situ hybridization for the detection and localization of porcine epidemic diarrhea virus in the intestinal tissues from naturally infected piglets. Vet. Pathol. 2000, 37, 62–67. [Google Scholar] [CrossRef]
- Kim, D.; Pertea, G.; Trapnell, C.; Pimentel, H.; Kelley, R.; Salzberg, S.L. Tophat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013, 14, R36. [Google Scholar] [CrossRef] [PubMed]
- Anders, S.; Pyl, P.T.; Huber, W. Htseq—A python framework to work with high-throughput sequencing data. Bioinformatics 2015, 31, 166–169. [Google Scholar] [CrossRef] [PubMed]
- Anders, S.; Huber, W. Differential Expression of RNA-Seq Data at the Gene Level—The DESeq Package; European Molecular Biology Laboratory: Heidelberg, Germany, 2012. [Google Scholar]
- Young, M.D.; Wakefield, M.J.; Smyth, G.K.; Oshlack, A. Gene ontology analysis for RNA-seq: Accounting for selection bias. Genome Biol. 2010, 11, R14. [Google Scholar] [CrossRef] [PubMed]
- Mao, X.; Cai, T.; Olyarchuk, J.G.; Wei, L. Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 2005, 21, 3787–3793. [Google Scholar] [CrossRef] [PubMed]
- Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 2001, 25, 402–408. [Google Scholar] [CrossRef] [PubMed]
- Zhang, H.M.; Liu, T.; Liu, C.J.; Song, S.; Zhang, X.; Liu, W.; Jia, H.; Xue, Y.; Guo, A.Y. AnimalTFDB 2.0: A resource for expression, prediction and functional study of animal transcription factors. Nucleic Acids Res. 2014, 43, D76–D81. [Google Scholar] [CrossRef] [PubMed]
- Grant, C.E.; Bailey, T.L.; Noble, W.S. FIMO: Scanning for occurrences of a given motif. Bioinformatics 2011, 27, 1017–1018. [Google Scholar] [CrossRef] [PubMed]
- Jiang, H.; Lei, R.; Ding, S.W.; Zhu, S. Skewer: A fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinform. 2014, 15, 182. [Google Scholar] [CrossRef]
- Li, H.; Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 2009, 25, 1754–1760. [Google Scholar] [CrossRef]
- Zhang, Y.; Liu, T.; Meyer, C.A.; Eeckhoute, J.; Johnson, D.S.; Bernstein, B.E.; Nusbaum, C.; Myers, R.M.; Brown, M.; Li, W.; et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008, 9, R137. [Google Scholar] [CrossRef]
- Bertolini, F.; Harding, J.C.S.; Mote, B.; Ladinig, A.; Plastow, G.S.; Rothschild, M.F. Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks. Anim. Genet. 2017, 48, 228–232. [Google Scholar] [CrossRef] [PubMed]
- Yan, B.; Yang, X.; Lee, T.L.; Friedman, J.; Tang, J.; Van Waes, C.; Chen, Z. Genome-wide identification of novel expression signatures reveal distinct patterns and prevalence of binding motifs for p53, nuclear factor-κB and other signal transcription factors in head and neck squamous cell carcinoma. Genome Biol. 2007, 8, R78. [Google Scholar] [CrossRef] [PubMed]
- Kobayashi, T.; Matsuoka, K.; Sheikh, S.Z.; Elloumi, H.Z.; Kamada, N.; Hisamatsu, T.; Hansen, J.J.; Doty, K.S.; Smale, S.T.; Hibi, T.; et al. NFIL3 is a regulator of IL-12 p40 in macrophages and mucosal immunity. J. Immunol. 2011, 186, 4649–4655. [Google Scholar] [CrossRef] [PubMed]
- Lv, D.W.; Zhang, K.; Li, R. Interferon regulatory factor 8 regulates aspase-1 expression to facilitate Epstein-Barr virus reactivation in response to B cell receptor stimulation and chemical induction. PLoS Pathog. 2018, 14, e1006868. [Google Scholar] [CrossRef] [PubMed]
- Sahu, S.K.; Kumar, M.; Chakraborty, S.; Banerjee, S.K.; Kumar, R.; Gupta, P.; Jana, K.; Gupta, U.D.; Ghosh, Z.; Kundu, M.; et al. MicroRNA 26a (miR-26a)/KLF4 and CREB-C/EBPβ regulate innate immune signaling, the polarization of macrophages and the trafficking of Mycobacterium tuberculosis to lysosomes during infection. PloS Pathog. 2017, 13, e1006410. [Google Scholar] [CrossRef] [PubMed]
- Liu, C.; Tang, J.; Ma, Y.; Liang, X.; Yang, Y.; Peng, G.; Qi, Q.; Jing, S.; Li, J.; Du, L.; et al. Receptor usage and cell entry of porcine epidemic diarrhea coronavirus. J. Virol. 2015, 89, 6121–6125. [Google Scholar] [CrossRef] [PubMed]
- Donovan, A.; Lima, C.A.; Pinkus, J.L.; Pinkus, G.S.; Zon, L.I.; Robine, S.; Andrews, N.C. The iron exporter ferroportin/Slc40a1 is essential for iron homeostasis. Cell Metab. 2005, 1, 191–200. [Google Scholar] [CrossRef] [Green Version]
- Pallesi-Pocachard, E.; Bazellieres, E.; Viallat-Lieutaud, A.; Delgrossi, M.H.; Barthelemy-Requin, M.; Le Bivic, A.; Massey-Harroche, D. Hook2, a microtubule-binding protein, interacts with Par6α and controls centrosome orientation during polarized cell migration. Sci. Rep. 2016, 6, 33259. [Google Scholar] [CrossRef]
- Hentze, M.W.; Muckenthaler, M.U.; Andrews, N.C. Balancing acts: Molecular control of mammalian iron metabolism. Cell 2004, 117, 285–297. [Google Scholar] [CrossRef]
- Moeser, A.J.; Blikslager, A.T. Mechanisms of porcine diarrheal disease. J. Am. Vet. Med. Assoc. 2007, 231, 56–67. [Google Scholar] [CrossRef]
- Misinzo, G.; Delputte, P.L.; Nauwynck, H.J. Inhibition of endosome-lysosome system acidification enhances porcine circovirus 2 infection of porcine epithelial cells. J. Virol. 2008, 82, 1128–1135. [Google Scholar] [CrossRef] [PubMed]
- Schoggins, J.W.; Wilson, S.J.; Panis, M.; Murphy, M.Y.; Jones, C.T.; Bieniasz, P.; Rice, C.M. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 2011, 472, 481–485. [Google Scholar] [CrossRef] [PubMed]
- Zhu, J.; Zhang, Y.; Ghosh, A.; Cuevas, R.A.; Forero, A.; Dhar, J.; Ibsen, M.S.; Schmid-Burgk, J.L.; Schmidt, T.; Ganapathiraju, M.K.; et al. Antiviral activity of human OASL protein is mediated by enhancing signaling of the RIG-I RNA sensor. Immunity 2014, 40, 936–948. [Google Scholar] [CrossRef] [PubMed]
- Ishibashi, M.; Wakita, T.; Esumi, M. 2′,5′-Oligoadenylate synthetase-like gene highly induced by hepatitis C virus infection in human liver is inhibitory to viral replication in vitro. Biochem. Biophys. Res. Commun. 2010, 392, 397–402. [Google Scholar] [CrossRef] [PubMed]
- Yakub, I.; Lillibridge, K.M.; Moran, A.; Gonzalez, O.Y.; Belmont, J.; Gibbs, R.A.; Tweardy, D.J. Single nucleotide polymorphisms in genes for 2′-5′-oligoadenylate synthetase and RNase L in patients hospitalized with West Nile virus infection. J. Infect. Dis. 2005, 192, 1741–1748. [Google Scholar] [CrossRef] [PubMed]
- Li, Y.; Zhou, H.; Wen, Z.; Wu, S.; Huang, C.; Jia, G.; Chen, H.; Jin, M. Transcription analysis on response of swine lung to H1N1 swine influenza virus. BMC Genom. 2011, 12, 398. [Google Scholar] [CrossRef] [PubMed]
- Cai, B.; Bai, Q.; Chi, X.; Goraya, M.U.; Wang, L.; Wang, S.; Chen, B.; Chen, J.L. Infection with classical swine fever virus induces expression of type III interferons and activates innate immune signaling. Front. Microbiol. 2017, 8, 2558. [Google Scholar] [CrossRef]
- Lenschow, D.J.; Lai, C.; Frias-Staheli, N.; Giannakopoulos, N.V.; Lutz, A.; Wolff, T.; Osiak, A.; Levine, B.; Schmidt, R.E.; García-Sastre, A.; et al. IFN-stimulated gene 15 functions as a critical antiviral molecule against influenza, herpes, and Sindbis viruses. Proc. Natl. Acad. Sci. USA 2007, 104, 1371–1376. [Google Scholar] [CrossRef] [Green Version]
- Park, S.W.; Zhen, G.; Verhaeghe, C.; Nakagami, Y.; Nguyenvu, L.T.; Barczak, A.J.; Killeen, N.; Erle, D.J. The protein disulfide isomerase AGR2 is essential for production of intestinal mucus. Proc. Natl. Acad. Sci. USA 2009, 106, 6950–6955. [Google Scholar] [CrossRef] [Green Version]
- Guo, L.; Luo, X.; Li, R.; Xu, Y.; Zhang, J.; Ge, J.; Bu, Z.; Feng, L.; Wang, Y. Porcine epidemic diarrhea virus infection inhibits interferon signaling by targeted degradation of STAT1. J. Virol. 2016, 90, 8281–8292. [Google Scholar] [CrossRef]
- Honda, K.; Taniguchi, T. IRFs: Master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nat. Rev. Immunol. 2006, 6, 644–658. [Google Scholar] [CrossRef] [PubMed]
- Sun, L.; Leger, A.J.S.; Yu, C.R.; He, C.; Mahdi, R.M.; Chan, C.C.; Wang, H.; Morse, H.C.; Egwuagu, C.E. Interferon regulator factor 8 (IRF8) limits ocular pathology during HSV-1 infection by restraining the activation and expansion of CD8+ T Cells. PLoS ONE 2016, 11, e0155420. [Google Scholar] [CrossRef] [PubMed]
- Yan, M.; Wang, H.; Sun, J.; Liao, W.; Li, P.; Zhu, Y.; Xu, C.; Joo, J.; Sun, Y.; Abbasi, S.; et al. Cutting edge: Expression of IRF8 in gastric epithelial cells confers protective innate immunity against Helicobacter pylori infection. J. Immunol. 2016, 196, 1999–2003. [Google Scholar] [CrossRef] [PubMed]
- Luda, K.M.; Joeris, T.; Persson, E.K.; Rivollier, A.; Demiri, M.; Sitnik, K.M.; Pool, L.; Holm, J.B.; Richter, L.; Lambrecht, B.N.; et al. IRF8 transcription-factor-dependent classical dendritic cells are essential for intestinal T cell homeostasis. Immunity 2016, 44, 860–874. [Google Scholar] [CrossRef] [PubMed]
- Matulova, M.; Varmuzova, K.; Sisak, F.; Havlickova, H.; Babak, V.; Stejskal, K.; Zdynekl, Z.; Rychlik, I. Chicken innate immune response to oral infection with Salmonella enterica serovar Enteritidis. Vet. Res. 2013, 44, 37. [Google Scholar] [CrossRef] [PubMed]
- Cho, H.; Proll, S.C.; Szretter, K.J.; Katze, M.G.; Gale, M., Jr.; Diamond, M.S. Differential innate immune response programs in neuronal subtypes determine susceptibility to infection in the brain by positive-stranded RNA viruses. Nat. Med. 2013, 19, 458. [Google Scholar] [CrossRef]
- Luo, W.W.; Lian, H.; Zhong, B.; Shu, H.B.; Li, S. Krüppel-like factor 4 negatively regulates cellular antiviral immune response. Cell Mol. Immunol. 2014, 13, 65–72. [Google Scholar] [CrossRef] [PubMed]
- Nawandar, D.M.; Wang, A.; Makielski, K.; Lee, D.; Ma, S.; Barlow, E.; Reusch, J.; Jiang, R.; Wille, C.K.; Greenspan, D.; et al. Differentiation-dependent KLF4 expression promotes lytic Epstein-Barr virus infection in epithelial cells. PLoS Pathog. 2015, 11, e1005195. [Google Scholar] [CrossRef]
- Karlić, R.; Chung, H.R.; Lasserre, J.; Vlahovićek, K.; Vingron, M. Histone modification levels are predictive for gene expression. Proc. Natl. Acad. Sci. USA 2010, 107, 2926–2931. [Google Scholar] [CrossRef] [Green Version]
- Menachery, V.D.; Eisfeld, A.J.; Schäfer, A.; Josset, L.; Sims, A.C.; Proll, S.; Fan, S.; Li, C.; Neumann, G.; Tilton, S.C.; et al. Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. mBio 2014, 5, e01174-14. [Google Scholar] [CrossRef]
- Sadler, A.J.; Williams, B.R. Interferon-inducible antiviral effectors. Nat. Rev. Immunol. 2008, 8, 559–568. [Google Scholar] [CrossRef] [PubMed]
- Klein, K.; Frank-Bertoncelj, M.; Karouzakis, E.; Gay, R.E.; Kolling, C.; Ciurea, A.; Bostanci, N.; Belibasakis, G.N.; Lin, L.L.; Distler, O.; et al. The epigenetic architecture at gene promoters determines cell type-specific LPS tolerance. J. Autoimmun. 2017, 83, 122–133. [Google Scholar] [CrossRef] [PubMed]
- Gu, X.; Boldrup, L.; Coates, P.J.; Fahraeus, R.; Nylander, E.; Loizou, C.; Olofsson, K.; Norberg-Spaak, L.; Nylander, K. Epigenetic regulation of OAS2 shows disease-specific DNA methylation profiles at individual CpG sites. Sci. Rep. 2016, 6, 32579. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Gene Symbol | Log2 (Fold Change) | Ratio (Infected/Control) |
---|---|---|
APOC3 | −4.4897 | 0.2225 a |
OASL | 3.6703 | 3.8880 a/2.256 b |
APOA1 | −3.2846 | 0.4873 a |
ANXA4 | 2.6891 | 1.8863 a |
HK2 | 2.6892 | 2.7343 a |
ISG15 | 2.3519 | 2.4863 a |
PNP | 3.1261 | 2.1248 a |
GCNT3 | 2.2081 | 2.0617 a |
GPD1 | −3.0855 | 1.8292 a |
ENTPD5 | −2.0974 | 0.7424 a |
CYP2J34 | −1.9876 | 0.7187 a |
ABCD3 | −2.2627 | 1.2734 a |
EPHX1 | −3.1905 | 0.5197 a |
CAT | −1.8051 | 0.9870 a |
NPM3 | 1.8512 | 2.6182 a |
EHHADH | −1.8011 | 1.3862 a/1.399 b |
GDPD2 | −3.7889 | 0.735 b |
UPP1 | 2.6795 | 1.348 b |
AGR2 | 1.8933 | 1.334 b |
Transcription Factor Family | Gene Symbol |
---|---|
zf-C2H2 | KLF4, PRDM16, ZNF852, ZKSCAN7 |
TF-bZIP | NFIL3, DBP |
THR-like | NR1I3 |
IRF | IRF8 |
ETS | ETV4 |
Homeobox | HOXD1 |
Transcription cofactors | HELZ2, IL31RA, ADRB2, YWHAB, CDK2, MAPK9, RBM39, PPARGC1, WNT5A, ASB4, LOC100514979, SCAND1, NPM1, MAP3K10, USP27X |
Chromatin remodeling factors | JAK2, NPM2 |
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Wang, H.; Yang, L.; Qu, H.; Feng, H.; Wu, S.; Bao, W. Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs. Animals 2019, 9, 523. https://doi.org/10.3390/ani9080523
Wang H, Yang L, Qu H, Feng H, Wu S, Bao W. Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs. Animals. 2019; 9(8):523. https://doi.org/10.3390/ani9080523
Chicago/Turabian StyleWang, Haifei, Li Yang, Huan Qu, Haiyue Feng, Shenglong Wu, and Wenbin Bao. 2019. "Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in Pigs" Animals 9, no. 8: 523. https://doi.org/10.3390/ani9080523