Screening for Protein-DNA Interactions by Automatable DNA-Protein Interaction ELISA

DNA-binding proteins (DBPs), such as transcription factors, constitute about 10% of the protein-coding genes in eukaryotic genomes and play pivotal roles in the regulation of chromatin structure and gene expression by binding to short stretches of DNA. Despite their number and importance, only for a minor portion of DBPs the binding sequence had been disclosed. Methods that allow the de novo identification of DNA-binding motifs of known DBPs, such as protein binding microarray technology or SELEX, are not yet suited for high-throughput and automation. To close this gap, we report an automatable DNA-protein-interaction (DPI)-ELISA screen of an optimized double-stranded DNA (dsDNA) probe library that allows the high-throughput identification of hexanucleotide DNA-binding motifs. In contrast to other methods, this DPI-ELISA screen can be performed manually or with standard laboratory automation. Furthermore, output evaluation does not require extensive computational analysis to derive a binding consensus. We could show that the DPI-ELISA screen disclosed the full spectrum of binding preferences for a given DBP. As an example, AtWRKY11 was used to demonstrate that the automated DPI-ELISA screen revealed the entire range of in vitro binding preferences. In addition, protein extracts of AtbZIP63 and the DNA-binding domain of AtWRKY33 were analyzed, which led to a refinement of their known DNA-binding consensi. Finally, we performed a DPI-ELISA screen to disclose the DNA-binding consensus of a yet uncharacterized putative DBP, AtTIFY1. A palindromic TGATCA-consensus was uncovered and we could show that the GATC-core is compulsory for AtTIFY1 binding. This specific interaction between AtTIFY1 and its DNA-binding motif was confirmed by in vivo plant one-hybrid assays in protoplasts. Thus, the value and applicability of the DPI-ELISA screen for de novo binding site identification of DBPs, also under automatized conditions, is a promising approach for a deeper understanding of gene regulation in any organism of choice.

[1]  Joseph C. Pearson,et al.  Twine: display and analysis of cis-regulatory modules , 2013, Bioinform..

[2]  K. Shinozaki,et al.  DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. , 2013, Trends in plant science.

[3]  D. Swigon,et al.  Interplay of Protein and DNA Structure Revealed in Simulations of the lac Operon , 2013, PloS one.

[4]  L. Maher,et al.  Single-molecule FRET analysis of DNA binding and bending by yeast HMGB protein Nhp6A , 2012, Nucleic acids research.

[5]  Fangping Mu,et al.  Improved predictions of transcription factor binding sites using physicochemical features of DNA , 2012, Nucleic acids research.

[6]  J. Reece-Hoyes,et al.  Yeast one-hybrid assays: a historical and technical perspective. , 2012, Methods.

[7]  K. Harter,et al.  Screening for in planta protein-protein interactions combining bimolecular fluorescence complementation with flow cytometry , 2012, Plant Methods.

[8]  James Taylor,et al.  Genomic approaches towards finding cis-regulatory modules in animals , 2012, Nature Reviews Genetics.

[9]  Hans-Peter Klenk,et al.  Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics , 2012, PloS one.

[10]  Vibha Rani,et al.  DNA–protein interactions: methods for detection and analysis , 2012, Molecular and Cellular Biochemistry.

[11]  Rainer P Birkenbihl,et al.  Arabidopsis WRKY33 Is a Key Transcriptional Regulator of Hormonal and Metabolic Responses toward Botrytis cinerea Infection1[W] , 2012, Plant Physiology.

[12]  Philip Bradley,et al.  The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target , 2012, Science.

[13]  J. Browse,et al.  Social Network: JAZ Protein Interactions Expand Our Knowledge of Jasmonate Signaling , 2012, Front. Plant Sci..

[14]  M. Biggin,et al.  High-throughput SELEX determination of DNA sequences bound by transcription factors in vitro. , 2012, Methods in molecular biology.

[15]  Neville E Sanjana,et al.  A transcription activator-like effector toolbox for genome engineering , 2012, Nature Protocols.

[16]  Klaus Harter,et al.  Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription , 2012, BMC Plant Biology.

[17]  D. Trono,et al.  In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions , 2011, Molecular cell.

[18]  M. Vázquez,et al.  DNA Recognition by Synthetic Constructs , 2011, Chembiochem : a European journal of chemical biology.

[19]  C. Matiolli,et al.  The Arabidopsis bZIP Gene AtbZIP63 Is a Sensitive Integrator of Transient Abscisic Acid and Glucose Signals1[W][OA] , 2011, Plant Physiology.

[20]  Timothy L. Bailey,et al.  Gene expression Advance Access publication May 4, 2011 DREME: motif discovery in transcription factor ChIP-seq data , 2011 .

[21]  J. Franco-Zorrilla,et al.  Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors. , 2011, The Plant journal : for cell and molecular biology.

[22]  Abraham P. Fong,et al.  Genome-wide transcription factor binding: beyond direct target regulation. , 2011, Trends in genetics : TIG.

[23]  Yumei Zheng,et al.  Chromatin immunoprecipitation to verify or to identify in vivo protein-DNA interactions. , 2011, Methods in molecular biology.

[24]  E. Grotewold,et al.  SELEX (Systematic Evolution of Ligands by EXponential Enrichment), as a powerful tool for deciphering the protein-DNA interaction space. , 2011, Methods in molecular biology.

[25]  Andreas Zell,et al.  Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors , 2010, PloS one.

[26]  Luise H. Brand,et al.  DPI-ELISA: a fast and versatile method to specify the binding of plant transcription factors to DNA in vitro , 2010, Plant Methods.

[27]  Jens Boch,et al.  Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors , 2010, Proceedings of the National Academy of Sciences.

[28]  William Stafford Noble,et al.  High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions , 2010, PLoS Comput. Biol..

[29]  Jörg D. Hoheisel,et al.  Analysis of DNA–protein interactions: from nitrocellulose filter binding assays to microarray studies , 2010, Analytical and bioanalytical chemistry.

[30]  A. Bogdanove,et al.  TAL effectors: finding plant genes for disease and defense. , 2010, Current opinion in plant biology.

[31]  B. Mueller‐Roeber,et al.  Genome-Wide Phylogenetic Comparative Analysis of Plant Transcriptional Regulation: A Timeline of Loss, Gain, Expansion, and Correlation with Complexity , 2010, Genome biology and evolution.

[32]  K. Thurow,et al.  Future and frontiers of automated screening in plant sciences , 2010 .

[33]  Q. Shen,et al.  WRKY transcription factors. , 2010, Trends in plant science.

[34]  Jong-Chan Hong,et al.  The arabidopsis bZIP1 transcription factor is involved in sugar signaling, protein networking, and DNA binding. , 2010, Molecular plant.

[35]  O. Kohlbacher,et al.  The role of phosphorylatable serine residues in the DNA-binding domain of Arabidopsis bZIP transcription factors. , 2010, European journal of cell biology.

[36]  Sarah A. Teichmann,et al.  FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database , 2009, Nucleic Acids Res..

[37]  D. Stillman.  Nhp6: a small but powerful effector of chromatin structure in Saccharomyces cerevisiae. , 2010, Biochimica et biophysica acta.

[38]  M. Djordjevic.  Inferring protein-DNA interaction parameters from SELEX experiments. , 2010, Methods in molecular biology.

[39]  Jens Boch,et al.  Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors , 2009, Science.

[40]  H. Flores-Rozas,et al.  Modulation of the DNA-binding activity of Saccharomyces cerevisiae MSH2–MSH6 complex by the high-mobility group protein NHP6A, in vitro , 2009, Nucleic acids research.

[41]  R. Mann,et al.  The role of DNA shape in protein-DNA recognition , 2009, Nature.

[42]  N. Mermod,et al.  Protein-binding microarrays: probing disease markers at the interface of proteomics and genomics. , 2009, Trends in molecular medicine.

[43]  Daniel E. Newburger,et al.  Diversity and Complexity in DNA Recognition by Transcription Factors , 2009, Science.

[44]  Daniel E. Newburger,et al.  High-resolution DNA-binding specificity analysis of yeast transcription factors. , 2009, Genome research.

[45]  M. Berger,et al.  Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors , 2009, Nature Protocols.

[46]  Hoo Sun Chung,et al.  A Critical Role for the TIFY Motif in Repression of Jasmonate Signaling by a Stabilized Splice Variant of the JASMONATE ZIM-Domain Protein JAZ10 in Arabidopsis[C][W] , 2009, The Plant Cell Online.

[47]  Martha L. Bulyk,et al.  UniPROBE: an online database of protein binding microarray data on protein–DNA interactions , 2008, Nucleic Acids Res..

[48]  K. Harter,et al.  Analysis of plant regulatory DNA sequences by the yeast-one-hybrid assay. , 2009, Methods in molecular biology.

[49]  K. Harter,et al.  Analysis of plant regulatory DNA sequences by transient protoplast assays and computer aided sequence evaluation. , 2009, Methods in molecular biology.

[50]  D. Wanke,et al.  Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function , 2008, Plant Molecular Biology.

[51]  C. Massie,et al.  ChIPping away at gene regulation , 2008, EMBO reports.

[52]  E. Segal,et al.  Predicting expression patterns from regulatory sequence in Drosophila segmentation , 2008, Nature.

[53]  Ole Winther,et al.  JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update , 2007, Nucleic Acids Res..

[54]  L. Hellman,et al.  Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions , 2007, Nature Protocols.

[55]  T. Kohchi,et al.  The tify family previously known as ZIM. , 2007, Trends in plant science.

[56]  M. Djordjevic.  SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways. , 2007, Biomolecular engineering.

[57]  Rachel Patton McCord,et al.  Inferring condition-specific transcription factor function from DNA binding and gene expression data , 2007, Molecular systems biology.

[58]  D. Vaux,et al.  Error bars in experimental biology , 2007, The Journal of cell biology.

[59]  Martha L Bulyk,et al.  Protein binding microarrays for the characterization of DNA-protein interactions. , 2007, Advances in biochemical engineering/biotechnology.

[60]  M. Snyder,et al.  High-throughput methods of regulatory element discovery. , 2006, BioTechniques.

[61]  Klaus Harter,et al.  Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves , 2006, BMC Bioinformatics.

[62]  L. Aravind,et al.  The natural history of the WRKY–GCM1 zinc fingers and the relationship between transcription factors and transposons , 2006, Nucleic acids research.

[63]  K. Harter,et al.  bZIP10‐LSD1 antagonism modulates basal defense and cell death in Arabidopsis following infection , 2006, The EMBO journal.

[64]  Amos Tanay,et al.  Extensive low-affinity transcriptional interactions in the yeast genome. , 2006, Genome research.

[65]  Sjef Smeekens,et al.  Two-hybrid protein-protein interaction analysis in Arabidopsis protoplasts: establishment of a heterodimerization map of group C and group S bZIP transcription factors. , 2006, The Plant journal : for cell and molecular biology.

[66]  M. Berger,et al.  Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. , 2006, Methods in molecular biology.

[67]  Martha L Bulyk,et al.  Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays. , 2006, Methods in enzymology.

[68]  G. Cumming,et al.  Inference by eye: confidence intervals and how to read pictures of data. , 2005, The American psychologist.

[69]  J. Wengel,et al.  LNA (locked nucleic acid): high-affinity targeting of complementary RNA and DNA. , 2004, Biochemistry.

[70]  D. Stillman,et al.  Role for Nhp6, Gcn5, and the Swi/Snf Complex in Stimulating Formation of the TATA-Binding Protein-TFIIA-DNA Complex , 2004, Molecular and Cellular Biology.

[71]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[72]  Jonathan L. Gross,et al.  Handbook of graph theory , 2007, Discrete mathematics and its applications.

[73]  Rodolfo Ghirlando,et al.  Determinants of GATA-1 Binding to DNA , 2003, Journal of Biological Chemistry.

[74]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[75]  E. Paleček,et al.  New ELISA technique for analysis of p53 protein/DNA binding properties. , 2002, Journal of immunological methods.

[76]  P. Bucher,et al.  High-throughput SELEX–SAGE method for quantitative modeling of transcription-factor binding sites , 2002, Nature Biotechnology.

[77]  S. Orkin,et al.  Transcriptional regulation of erythropoiesis: an affair involving multiple partners , 2002, Oncogene.

[78]  I. Somssich,et al.  Synthetic Plant Promoters Containing Defined Regulatory Elements Provide Novel Insights into Pathogen- and Wound-Induced Signaling Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010412. , 2002, The Plant Cell Online.

[79]  F. Ausubel,et al.  MAP kinase signalling cascade in Arabidopsis innate immunity , 2002, Nature.

[80]  Patricia Renard,et al.  Development of a sensitive multi-well colorimetric assay for active NFκB , 2001 .

[81]  J. Remacle,et al.  Development of a sensitive multi-well colorimetric assay for active NFkappaB. , 2001, Nucleic acids research.

[82]  T. Eulgem,et al.  The WRKY superfamily of plant transcription factors. , 2000, Trends in plant science.

[83]  B. Weisshaar,et al.  Transactivation properties of parsley proline-rich bZIP transcription factors. , 2000, The Plant journal : for cell and molecular biology.

[84]  William R. Atchley,et al.  Molecular Evolution of the GATA Family of Transcription Factors: Conservation Within the DNA-Binding Domain , 2000, Journal of Molecular Evolution.

[85]  Xin Chen,et al.  TRANSFAC: an integrated system for gene expression regulation , 2000, Nucleic Acids Res..

[86]  Michael S. German,et al.  Paired-Homeodomain Transcription Factor PAX4 Acts as a Transcriptional Repressor in Early Pancreatic Development , 1999, Molecular and Cellular Biology.

[87]  T. Eulgem,et al.  Early nuclear events in plant defence signalling: rapid gene activation by WRKY transcription factors , 1999, The EMBO journal.

[88]  Martha L. Bulyk,et al.  Quantifying DNA–protein interactions by double-stranded DNA arrays , 1999, Nature Biotechnology.

[89]  F. Allain,et al.  Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non‐sequence‐specific binding , 1999, The EMBO journal.

[90]  B. Müller-Hill,et al.  Dimerisation mutants of Lac repressor. I. A monomeric mutant, L251A, that binds Lac operator DNA as a dimer. , 1999, Journal of molecular biology.

[91]  M F Hoylaerts,et al.  Nonisotopic quantitative analysis of protein-DNA interactions at equilibrium. , 1997, Analytical biochemistry.

[92]  F. Nagy,et al.  A plant in vitro system for the nuclear import of proteins. , 1996, The Plant journal : for cell and molecular biology.

[93]  I. Somssich,et al.  Interaction of elicitor‐induced DNA‐binding proteins with elicitor response elements in the promoters of parsley PR1 genes. , 1996, The EMBO journal.

[94]  P. Abarzúa,et al.  Nonradioactive assay for sequence-specific DNA binding proteins. , 1995, BioTechniques.

[95]  M. Hibma,et al.  A non-radioactive assay for the detection and quantitation of a DNA binding protein. , 1994, Nucleic acids research.

[96]  S. Orkin,et al.  DNA-binding specificity of GATA family transcription factors , 1993, Molecular and cellular biology.

[97]  B. Müller-Hill,et al.  The roles of residues 5 and 9 of the recognition helix of Lac repressor in lac operator binding. , 1991, Journal of molecular biology.

[98]  B. Müller-Hill,et al.  The three operators of the lac operon cooperate in repression. , 1990, The EMBO journal.

[99]  B. Müller-Hill,et al.  Recognition helices of lac and lambda repressor are oriented in opposite directions and recognize similar DNA sequences. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[100]  Steven Skiena,et al.  The Algorithm Design Manual , 2020, Texts in Computer Science.

[101]  M. Pfahl,et al.  How lac Repressor Binds to DNA , 1972, Nature.