Sequences analyses and expression profiles in tissues and embryos of Japanese flounder (Paralichthys olivaceus) PRDM1

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• 作者：Conghui Liu ; Wei Liu ; Lin Fan ; Jinxiang Liu ; Peizhen Li…
• 关键词：prdm1 ; Real ; time quantitative polymerase chain reaction amplification (RT ; qPCR) ; In situ hybridization (ISH) ; Promoter analysis
• 刊名：Fish Physiology and Biochemistry
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：42
• 期：2
• 页码：467-482
• 全文大小：5,288 KB
• 参考文献：Ancelin K, Lange UC, Hajkova P, Schneider R, Bannister AJ, Kouzarides T, Surani MA (2006) Blimp1 associates with Prmt5 and directs histone arginine methylation in mouse germ cells. Nat Cell Biol 8:623–630CrossRef PubMed
  Baxendale S, Davison C, Muxworthy C, Wolff C, Ingham PW, Roy S (2004) The B-cell maturation factor Blimp-1 specifies vertebrate slow-twitch muscle fiber identity in response to Hedgehog signaling. Nat Genet 36:88–93CrossRef PubMed
  Beermann ML, Ardelt M, Girgenrath M, Miller JB (2010) Prdm1 (Blimp-1) and the expression of fast and slow myosin heavy chain isoforms during avian myogenesis in vitro. PLoS One 5:e9951CrossRef PubMed PubMedCentral
  Bikoff EK, Morgan MA, Robertson EJ (2009) An expanding job description for Blimp-1/PRDM1. Curr Opin Genet Dev 19:379–385CrossRef PubMed
  Brzezinski JAT, Lamba DA, Reh TA (2010) Blimp1 controls photoreceptor versus bipolar cell fate choice during retinal development. Development 137:619–629CrossRef PubMed PubMedCentral
  Cartharius K, Frech K, Grote K, Klocke B, Haltmeier M, Klingenhoff A, Frisch M, Bayerlein M, Werner T (2005) MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 21:2933–2942CrossRef PubMed
  Chan YS, Goke J, Lu X, Venkatesan N, Feng B, Su IH, Ng HH (2012) A PRC2-dependent repressive role of PRDM14 in human embryonic stem cells and induced pluripotent stem cell reprogramming. Stem Cells 31:682–692CrossRef
  Chang DH, Calame KL (2002) The dynamic expression pattern of B lymphocyte induced maturation protein-1 (Blimp-1) during mouse embryonic development. Mech Dev 17:305–309CrossRef
  Derunes C, Briknarova K, Geng L, Li S, Gessner CR, Hewitt K, Wu S, Huang S, Woods VI Jr, Ely KR (2005) Characterization of the PR domain of RIZ1 histone methyltransferase. Biochem Biophys Res Commun 333:925–934CrossRef PubMed
  Eom GH, Kim K, Kim SM, Kee HJ, Kim JY, Jin HM, Kim JR, Kim JH, Choe N, Kim KB et al (2009) Histone methyltransferase PRDM8 regulates mouse testis steroidogenesis. Biochem Biophys Res Commun 388:131–136CrossRef PubMed
  Fog CK, Galli GG, Lund AH (2012) PRDM proteins: important players in differentiation and disease. Bioessays 34:50–60CrossRef PubMed
  Gao J, Wang J, Jiang J, Fan L, Wang W, Liu J, Zhang Q, Wang X (2013) Identification and characterization of a nanog homolog in Japanese flounder (Paralichthys olivaceus). Gene 531:411–421
  Gewies A, Castineiras-Vilarino M, Ferch U, Jahrling N, Heinrich K, Hoeckendorf U, Przemeck GK, Munding M, Gross O, Schroeder T et al (2013) Prdm6 is essential for cardiovascular development in vivo. PLoS One 8:e81833CrossRef PubMed PubMedCentral
  Gong D, Malek TR (2006) Cytokine-dependent Blimp-1 expression in activated T cells inhibits IL-2 production. J Immunol 178:242–252CrossRef
  Gyory I, Wu J, Fejer G, Seto E, Wright KL (2004) PRDI-BF1 recruits the histone H3 methyltransferase G9a in transcriptional silencing. Nat Immunol 5:299–308CrossRef PubMed
  Ha AS, Riddle RD (2003) cBlimp-1 expression in chick limb bud development. Gene Expr Patterns 3:297–300CrossRef PubMed
  Hahn S, Buratowski S, Sharp PA, Guarente L (1989) Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences. Proc Natl Acad Sci 86:5718–5722CrossRef PubMed PubMedCentral
  Harper J, Mould A, Andrews RM, Bikoff EK, Robertson EJ (2011) The transcriptional repressor Blimp1/Prdm1 regulates postnatal reprogramming of intestinal enterocytes. Proc Natl Acad Sci USA 108:10585–10590CrossRef PubMed PubMedCentral
  Hayashi K, de Sousa Lopes SM, Surani MA (2007) Germ cell specification in mice. Science 316:394–396CrossRef PubMed
  Hernandez-Lagunas L, Choi IF, Kaji T, Simpson P, Hershey C, Zhou Y, Zon L, Mercola M, Artinger KB (2005) Zebrafish narrowminded disrupts the transcription factor prdm1 and is required for neural crest and sensory neuron specification. Dev Biol 278:347–357CrossRef PubMed PubMedCentral
  Hohenauer T, Moore AW (2012) The Prdm family: expanding roles in stem cells and development. Development 139:2267–2282CrossRef PubMed
  Huang S (2002) Histone methyltransferases, diet nutrients and tumour suppressors. Nat Rev Cancer 2:469–476CrossRef PubMed
  Huang S, Shao G, Liu L (1998) The PR domain of the Rb-binding zinc finger protein RIZ1 Is a protein binding interface and is related to the SET domain functioning in chromatin-mediated gene expression. J Biol Chem 273:15933–15939CrossRef PubMed
  Huang L, Li G, Mo Z, Xiao P, Li J, Huang J (2015) De Novo assembly of the Japanese flounder (Paralichthys olivaceus) spleen transcriptome to identify putative genes involved in immunity. PLoS One 10:e0117642CrossRef PubMed PubMedCentral
  John SA, Garrett-Sinha LA (2009) Blimp1: a conserved transcriptional repressor critical for differentiation of many tissues. Exp Cell Res 315:1077–1084CrossRef PubMed
  Kallies A, Hawkins ED, Belz GT, Metcalf D, Hommel M, Corcoran LM, Hodgkin PD, Nutt SL (2006) Transcriptional repressor Blimp-1 is essential for T cell homeostasis and self-tolerance. Nat Immunol 7:466–474CrossRef PubMed
  Katoh K, Omori Y, Onishi A, Sato S, Kondo M, Furukawa T (2010) Blimp1 suppresses Chx10 expression in differentiating retinal photoreceptor precursors to ensure proper photoreceptor development. J Neurosci 30:6515–6526CrossRef PubMed
  Keller AD, Maniatis T (1991) Identification and characterization of a novel repressor of beta-interferon gene expression. Genes Dev 5:868–879CrossRef PubMed
  Keller A, Maniatis T (1992) Only two of the five zinc fingers of the eukaryotic transcriptional repressor PRDI-BF1 are required for sequence-specific DNA binding. Mol Cell Biol 12:1940–1949CrossRef PubMed PubMedCentral
  Kim J, Nikolov D, Burley S (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520–527CrossRef PubMed
  Koh-Stenta X, Joy J, Poulsen A, Li R, Tan Y, Shim Y, Min JH, Wu L, Ngo A, Peng J et al (2014) Characterisation of the histone methyltransferase PRDM9 utilising biochemical, biophysical and chemical biology techniques. Biochem J 461:323–334CrossRef PubMed
  Kuo TC, Calame KL (2004) B lymphocyte-induced maturation protein (Blimp)-1, IFN regulatory factor (IRF)-1, and IRF-2 can bind to the same regulatory sites. J Immunol 173:5556–5563CrossRef PubMed
  Kurimoto K, Yabuta Y, Ohinata Y, Shigeta M, Yamanaka K, Saitou M (2008) Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice. Genes Dev 22:1617–1635CrossRef PubMed PubMedCentral
  Lee BC, Roy S (2006) Blimp-1 is an essential component of the genetic program controlling development of the pectoral limb bud. Dev Biol 300:623–634CrossRef PubMed
  Letunic I, Doerks T, Bork P (2012) SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res 40:D302–D305CrossRef PubMed PubMedCentral
  Lo K, Smale S (1996) Generality of a functional initiator consensus sequence. Gene 182:13–22CrossRef PubMed
  Magnusdottir E, Kalachikov S, Mizukoshi K, Savitsky D, Ishida-Yamamoto A, Panteleyev AA, Calame K (2007) Epidermal terminal differentiation depends on B lymphocyte-induced maturation protein-1. Proc Natl Acad Sci USA 104:14988–14993CrossRef PubMed PubMedCentral
  Martins GA, Cimmino L, Shapiro-Shelef M, Szabolcs M, Herron A, Magnusdottir E, Calame K (2006) Transcriptional repressor Blimp-1 regulates T cell homeostasis and function. Nat Immunol 7:457–465CrossRef PubMed
  Muncan V, Heijmans J, Krasinski SD, Buller NV, Wildenberg ME, Meisner S, Radonjic M, Stapleton KA, Lamers WH, Biemond I et al (2011) Blimp1 regulates the transition of neonatal to adult intestinal epithelium. Nat Commun 2:452CrossRef PubMed PubMedCentral
  Nishikawa K, Nakashima T, Hayashi M, Fukunaga T, Kato S, Kodama T, Takahashi S, Calame K, Takayanagi H (2010) Blimp1-mediated repression of negative regulators is required for osteoclast differentiation. Proc Natl Acad Sci USA 107:3117–3122CrossRef PubMed PubMedCentral
  Ohinata Y, Payer B, O’Carroll D, Ancelin K, Ono Y, Sano M, Barton SC, Obukhanych T, Nussenzweig M, Tarakhovsky A et al (2005) Blimp1 is a critical determinant of the germ cell lineage in mice. Nature 436:207–213CrossRef PubMed
  Ohtani M, Miyadai T (2011) Functional analysis of fish BCL-6 and Blimp-1 in vitro: transcriptional repressors for B-cell terminal differentiation in fugu (Takifugu rubripes). Mol Immunol 48:818–825CrossRef PubMed
  Ohtani M, Miyadai T, Hiroishi S (2006) B-lymphocyte-induced maturation protein-1 (Blimp-1) gene of torafugu (Takifugu rubripes). Fish Shellfish Immunol 20:409–413CrossRef PubMed
  Pinheiro I, Margueron R, Shukeir N, Eisold M, Fritzsch C, Richter FM, Mittler G, Genoud C, Goyama S, Kurokawa M et al (2012) Prdm3 and Prdm16 are H3K9me1 methyltransferases required for mammalian heterochromatin integrity. Cell 150:948–960CrossRef PubMed
  Pulendran B, Katsikis PD, Schoenberger SP (2011) Crossroads between innate and adaptive immunity III. Nat Immunol 13:85–100
  Robertson EJ, Charatsi I, Joyner CJ, Koonce CH, Morgan M, Islam A, Paterson C, Lejsek E, Arnold SJ, Kallies A et al (2007) Blimp1 regulates development of the posterior forelimb, caudal pharyngeal arches, heart and sensory vibrissae in mice. Development 134:4335–4345CrossRef PubMed
  Roy S, Ng T (2004) Blimp-1 specifies neural crest and sensory neuron progenitors in the zebrafish embryo. Curr Biol CB14:1772–1777CrossRef
  Saitou M (2009) Germ cell specification in mice. Curr Opin Genet Dev 19:386–395CrossRef PubMed
  Saitou M, Barton SC, Surani MA (2002) A molecular programme for the specification of germ cell fate in mice. Nature 418:293–300CrossRef PubMed
  Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory Press, New York
  Schultz J, Milpetz F, Bork P, Ponting CP (1998) SMART, a simple modular architecture research tool: identification of signaling domains. PNAS 95:5857–5864CrossRef PubMed PubMedCentral
  Seikai T (2002) Flounder culture and its challenges in Asia. Rev Fish Sci 10:421–432CrossRef
  Seki Y, Hayashi K, Itoh K, Mizugaki M, Saitou M, Matsui Y (2005) Extensive and orderly reprogramming of genome-wide chromatin modifications associated with specification and early development of germ cells in mice. Dev Bio 278:440–458CrossRef
  Seki Y, Yamaji M, Yabuta Y, Sano M, Shigeta M, Matsui Y, Saga Y, Tachibana M, Shinkai Y, Saitou M (2007) Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice. Development 134:2627–2638CrossRef PubMed
  Shapiro-Shelef M, Lin KI, McHeyzer-Williams LJ, Liao J, McHeyzer-Williams MG, Calame K (2003) Blimp-1 is required for the formation of immunoglobulin secreting plasma cells and pre-plasma memory B cells. Immunity 19:607–620CrossRef PubMed
  Singer V, Wobbe C, Struhl K (1990) A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation. Genes Dev 4:636–645CrossRef PubMed
  Sun XJ, Xu PF, Zhou T, Hu M, Fu CT, Zhang Y, Jin Y, Chen Y, Chen SJ, Huang QH et al (2008) Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PLoS One 3:e1499CrossRef PubMed PubMedCentral
  Tsunoda T, Takagi T (1990) Estimating transcription factor bindability on DNA. Bioinformatics 15:622–630CrossRef
  Turner CA Jr, Mack DH, Davis MM (1994) Blimp-l, a novel zinc finger-containing protein that can drive the maturation of B lymphocytes into immunoglobulin-secreting cells. Cell 77:297–306CrossRef PubMed
  Vincent SD, Dunn NR, Sciammas R, Shapiro-Shalef M, Davis MM, Calame K, Bikoff EK, Robertson EJ (2005) The zinc finger transcriptional repressor Blimp1/Prdm1 is dispensable for early axis formation but is required for specification of primordial germ cells in the mouse. Development 132:1315–1325CrossRef PubMed
  Vincent SD, Mayeuf-Louchart A, Watanabe Y, Brzezinski JAt, Miyagawa-Tomita S, Kelly RG, Buckingham M (2014) Prdm1 functions in the mesoderm of the second heart field, where it interacts genetically with Tbx1, during outflow tract morphogenesis in the mouse embryo. Human Mol Genet 23:5087–5101
  Wilm TP, Solnica-Krezel L (2005) Essential roles of a zebrafish prdm1/blimp1 homolog in embryo patterning and organogenesis. Development 132:393–404CrossRef PubMed
  Wu Y, Ferguson JE 3rd, Wang H, Kelley R, Ren R, McDonough H, Meeker J, Charles PC, Wang H, Patterson C (2008) PRDM6 is enriched in vascular precursors during development and inhibits endothelial cell proliferation, survival, and differentiation. J Mol Cell Cardiol 44:47–58CrossRef PubMed PubMedCentral
  Yabuta Y, Kurimoto K, Ohinata Y, Seki Y, Saitou M (2006) Gene expression dynamics during germline specification in mice identified by quantitative single-cell gene expression profiling. Biol Reprod 75:705–716CrossRef PubMed
  Yamaji M, Seki Y, Kurimoto K, Yabuta Y, Yuasa M, Shigeta M, Yamanaka K, Ohinata Y, Saitou M (2008) Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat Genet 40:1016–1022CrossRef PubMed
  Yamaji M, Ueda J, Hayashi K, Ohta H, Yabuta Y, Kurimoto K, Nakato R, Yamada Y, Shirahige K, Saitou M (2013) PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells. Cell Stem Cell 12:368–382CrossRef PubMed
  Zenzie-Gregory B, Khachi A, Garraway I, Smale S (1993) Mechanism of initiator-mediated transcription: evidence for a functional interaction between the TATA-binding protein and DNA in the absence of a specific recognition sequence. Mol Cell Biol 13:3841–3849CrossRef PubMed PubMedCentral
  Zhao H, Zhang X, Cheng N, Duan J, Wang J, Nagahama Y, Zhong X, Zhou Q, Wang Y (2013) Identification and expression profiles of prdm1 in medaka Oryzias latipes. Mol Biol Rep 41:617–626
  Zheng WJ, Sun L (2011) Evaluation of housekeeping genes as references for quantitative real time RT-PCR analysis of gene expression in Japanese flounder (Paralichthys olivaceus). Fish Shellfish Immunol 30:638–645CrossRef PubMed
  Zhong Q, Zhang Q, Wang Z, Qi J, Chen Y, Li S, Sun Y, Li C, Lan X (2008) Expression profiling and validation of potential reference genes during Paralichthys olivaceus embryogenesis. Mar Biotechnol (NY) 10:310–318CrossRef
  Zwollo P (2011) Dissecting teleost B cell differentiation using transcription factors. Dev Comp Immunol 35:898–905CrossRef PubMed PubMedCentral
  
• 作者单位：Conghui Liu (1)
  Wei Liu (1)
  Lin Fan (1)
  Jinxiang Liu (1)
  Peizhen Li (1)
  Wei Zhang (1)
  Jinning Gao (1)
  Zan Li (1)
  Quanqi Zhang (1)
  Xubo Wang (1) (2)
  
  1. Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China
  2. College of Marine Life Science, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Hydrobiology
  Animal Physiology
  Animal Anatomy, Morphology and Histology
  Animal Biochemistry
  Zoology
  
• 出版者：Springer Netherlands
• ISSN：1573-5168

文摘

PRDM1 (PRDI-BF1-RIZ1 homologous domain containing 1) appears to be a pleiotropic regulatory factor in various processes. It contains a PR (PRDI-BF1-RIZ1 homologous) domain protein and five zinc fingers. In the present study, a gene coding the homolog of prdm1 and the 5′ regulatory region of prdm1 was identified from the Paralichthys olivaceus (denoted Po-prdm1). Results of real-time quantitative polymerase chain reaction amplification (RT-qPCR) and in situ hybridization (ISH) in embryos revealed that Po-prdm1 was highly expressed between the early gastrula and tail bud stages, with its expression peaking in the mid-gastrula stage, whereas the results of RT-qPCR and ISH in tissues demonstrated that Po-prdm1 transcripts were ubiquitously detected in all tissues, which indicates its pleiotropic function in multiple processes. ISH of gonadal tissues revealed that the transcripts were located in the nucleus and cytoplasm of the oocytes in the ovaries but only in the spermatogonia and not in the spermatocytes in the testes. The Po-prdm1 transcription factor binding sites and their conserved binding region among vertebrates were analyzed in this study. The combined results suggest that Po-PRDM1 has a conserved function in teleosts and mammals.