Advertisement

Yeast Genetics pp 231-255 | Cite as

Global Analysis of Transcription Factor-Binding Sites in Yeast Using ChIP-Seq

  • Philippe Lefrançois
  • Jennifer E. G. Gallagher
  • Michael SnyderEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1205)

Abstract

Transcription factors influence gene expression through their ability to bind DNA at specific regulatory elements. Specific DNA-protein interactions can be isolated through the chromatin immunoprecipitation (ChIP) procedure, in which DNA fragments bound by the protein of interest are recovered. ChIP is followed by high-throughput DNA sequencing (Seq) to determine the genomic provenance of ChIP DNA fragments and their relative abundance in the sample. This chapter describes a ChIP-Seq strategy adapted for budding yeast to enable the genome-wide characterization of binding sites of transcription factors (TFs) and other DNA-binding proteins in an efficient and cost-effective way.

Yeast strains with epitope-tagged TFs are most commonly used for ChIP-Seq, along with their matching untagged control strains. The initial step of ChIP involves the cross-linking of DNA and proteins. Next, yeast cells are lysed and sonicated to shear chromatin into smaller fragments. An antibody against an epitope-tagged TF is used to pull down chromatin complexes containing DNA and the TF of interest. DNA is then purified and proteins degraded. Specific barcoded adapters for multiplex DNA sequencing are ligated to ChIP DNA. Short DNA sequence reads (28–36 base pairs) are parsed according to the barcode and aligned against the yeast reference genome, thus generating a nucleotide-resolution map of transcription factor-binding sites and their occupancy.

Key words

ChIP-Seq ChIP Yeast Chromatin Transcription factor Binding site Genomics Multiplex 

References

  1. 1.
    Costanzo MC, Hogan JD, Cusick ME et al (2000) The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res 28:73–76PubMedCrossRefPubMedCentralGoogle Scholar
  2. 2.
    Prakash A, Tompa M (2009) Assessing the discordance of multiple sequence alignments. IEEE/ACM Trans Comput Biol Bioinform 6: 542–551PubMedCrossRefGoogle Scholar
  3. 3.
    Borneman AR, Gianoulis TA, Zhang ZD et al (2007) Divergence of transcription factor binding sites across related yeast species. Science 317:815–819PubMedCrossRefGoogle Scholar
  4. 4.
    Gilmour DS, Lis JT (1984) Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes. Proc Natl Acad Sci U S A 81:4275–4279PubMedCrossRefPubMedCentralGoogle Scholar
  5. 5.
    Orlando V, Strutt H, Paro R (1997) Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 11:205–214PubMedCrossRefGoogle Scholar
  6. 6.
    Horak CE, Snyder M (2002) ChIP-chip: a genomic approach for identifying transcription factor binding sites. Methods Enzymol 350: 469–483PubMedCrossRefGoogle Scholar
  7. 7.
    Harbison C, Gordon DB, Lee TI et al (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431:99–104PubMedCrossRefPubMedCentralGoogle Scholar
  8. 8.
    Johnson DS, Mortazavi A, Myers RM et al (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502PubMedCrossRefGoogle Scholar
  9. 9.
    Robertson G, Hirst M, Bainbridge M et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651–657PubMedCrossRefGoogle Scholar
  10. 10.
    Euskirchen GM, Rozowsky JS, Wei CL et al (2007) Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res 17:898–909PubMedCrossRefPubMedCentralGoogle Scholar
  11. 11.
    Birney E, Stamatoyannopoulos JA, Dutta A et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816PubMedCrossRefGoogle Scholar
  12. 12.
    Celniker SE, Dillon LA, Gerstein MB et al (2009) Unlocking the secrets of the genome. Nature 459:927–930PubMedCrossRefPubMedCentralGoogle Scholar
  13. 13.
    Lefrancois P, Euskirchen GM, Auerbach RK et al (2009) Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics 10:37PubMedCrossRefPubMedCentralGoogle Scholar
  14. 14.
    Teytelman L, Ozaydin B, Zill O et al (2009) Impact of chromatin structures on DNA processing for genomic analyses. PLoS One 4:e6700PubMedCrossRefPubMedCentralGoogle Scholar
  15. 15.
    Auerbach RK, Euskirchen G, Rozowsky J et al (2009) Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci U S A 106:14926–14931PubMedCrossRefPubMedCentralGoogle Scholar
  16. 16.
    Preti M, Ribeyre C, Pascali C et al (2010) The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae. Mol Cell 38:614–620PubMedCrossRefGoogle Scholar
  17. 17.
    Huber A, French SL, Tekotte H et al (2011) Sch9 regulates ribosome biogenesis via Stb3, Dot6 and Tod6 and the histone deacetylase complex RPD3L. EMBO J 30:3052–3064PubMedCrossRefPubMedCentralGoogle Scholar
  18. 18.
    Zill OA, Scannell D, Teytelman L et al (2010) Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol 8:e1000550PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    van Dijk EL, Chen CL, d’Aubenton-Carafa Y et al (2011) XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast. Nature 475:114–117PubMedCrossRefGoogle Scholar
  20. 20.
    Batta K, Zhang Z, Yen K et al (2011) Genome-wide function of H2B ubiquitylation in promoter and genic regions. Genes Dev 25: 2254–2265PubMedCrossRefPubMedCentralGoogle Scholar
  21. 21.
    Zhou X, O’Shea EK (2011) Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol Cell 42:826–836PubMedCrossRefPubMedCentralGoogle Scholar
  22. 22.
    Cai L, Sutter BM, Li B et al (2011) Acetyl-CoA induces cell growth and proliferation by promoting the acetylation of histones at growth genes. Mol Cell 42:426–437PubMedCrossRefPubMedCentralGoogle Scholar
  23. 23.
    Eaton ML, Galani K, Kang S et al (2010) Conserved nucleosome positioning defines replication origins. Genes Dev 24:748–753PubMedCrossRefPubMedCentralGoogle Scholar
  24. 24.
    Zheng W, Zhao H, Mancera E et al (2010) Genetic analysis of variation in transcription factor binding in yeast. Nature 464: 1187–1191PubMedCrossRefPubMedCentralGoogle Scholar
  25. 25.
    Haynes BC, Skowyra ML, Spencer SJ et al (2011) Toward an integrated model of capsule regulation in Cryptococcus neoformans. PLoS Pathog 7:e1002411PubMedCrossRefPubMedCentralGoogle Scholar
  26. 26.
    Smith KM, Phatale PA, Sullivan CM et al (2011) Heterochromatin is required for normal distribution of Neurospora crassa CenH3. Mol Cell Biol 31:2528–2542PubMedCrossRefPubMedCentralGoogle Scholar
  27. 27.
    Venters BJ, Wachi S, Mavrich TN et al (2011) A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces. Mol Cell 41:480–492PubMedCrossRefPubMedCentralGoogle Scholar
  28. 28.
    Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680PubMedCrossRefPubMedCentralGoogle Scholar
  29. 29.
    Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858PubMedCrossRefPubMedCentralGoogle Scholar
  30. 30.
    Li R, Li Y, Kristiansen K et al (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714PubMedCrossRefGoogle Scholar
  31. 31.
    Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25PubMedCrossRefPubMedCentralGoogle Scholar
  32. 32.
    Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760PubMedCrossRefPubMedCentralGoogle Scholar
  33. 33.
    Nicol JW, Helt GA, Blanchard SG Jr et al (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25:2730–2731PubMedCrossRefPubMedCentralGoogle Scholar
  34. 34.
    Wilbanks EG, Facciotti MT (2010) Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One 5:e11471PubMedCrossRefPubMedCentralGoogle Scholar
  35. 35.
    Rozowsky J, Euskirchen G, Auerbach RK et al (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27:66–75PubMedCrossRefPubMedCentralGoogle Scholar
  36. 36.
    Euskirchen GM, Auerbach RK, Davidov E et al (2011) Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet 7:e1002008PubMedCrossRefPubMedCentralGoogle Scholar
  37. 37.
    Zhu LJ, Gazin C, Lawson ND et al (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11:237PubMedCrossRefPubMedCentralGoogle Scholar
  38. 38.
    Ji H, Jiang H, Ma W et al (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293–1300PubMedCrossRefPubMedCentralGoogle Scholar
  39. 39.
    Janke C, Magiera MM, Rathfelder N et al (2004) A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21:947–962PubMedCrossRefGoogle Scholar
  40. 40.
    Pfaffl M (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45PubMedCrossRefPubMedCentralGoogle Scholar
  41. 41.
    Quail MA, Kozarewa I, Smith F et al (2008) A large genome center’s improvements to the Illumina sequencing system. Nat Methods 5:1005–1010PubMedCrossRefPubMedCentralGoogle Scholar
  42. 42.
    Cronn R, Liston A, Parks M et al (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Res 36:e122PubMedCrossRefPubMedCentralGoogle Scholar
  43. 43.
    Craig DW, Pearson JV, Szelinger S et al (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 5:887–893PubMedCrossRefPubMedCentralGoogle Scholar
  44. 44.
    Wong KH, Struhl K (2011) The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein. Genes Dev 25:2525–2539PubMedCrossRefPubMedCentralGoogle Scholar
  45. 45.
    Fejes AP, Robertson G, Bilenky M et al (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24: 1729–1730PubMedCrossRefPubMedCentralGoogle Scholar
  46. 46.
    Jothi R, Cuddapah S, Barski A et al (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 36:5221–5231PubMedCrossRefPubMedCentralGoogle Scholar
  47. 47.
    Valouev A, Johnson DS, Sundquist A et al (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5:829–834PubMedCrossRefPubMedCentralGoogle Scholar
  48. 48.
    Zhang Y, Liu T, Meyer CA et al (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9:R137PubMedCrossRefPubMedCentralGoogle Scholar
  49. 49.
    Nix DA, Courdy SJ, Boucher KM (2008) Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9:523PubMedCrossRefPubMedCentralGoogle Scholar
  50. 50.
    Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628PubMedCrossRefGoogle Scholar
  51. 51.
    Kharchenko PV, Tolstorukov MY, Park PJ (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26:1351–1359PubMedCrossRefPubMedCentralGoogle Scholar
  52. 52.
    Qin ZS, Yu J, Shen J et al (2010) HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics 11:369PubMedCrossRefPubMedCentralGoogle Scholar
  53. 53.
    Blahnik KR, Dou L, O’Geen H et al (2010) Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res 38:e13PubMedCrossRefPubMedCentralGoogle Scholar
  54. 54.
    Feng X, Grossman R, Stein L (2011) PeakRanger: a cloud-enabled peak caller for ChIP-seq data. BMC Bioinformatics 12:139PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Philippe Lefrançois
    • 1
  • Jennifer E. G. Gallagher
    • 2
  • Michael Snyder
    • 3
    Email author
  1. 1.Department of Molecular, Cellular and Developmental BiologyYale UniversityNew HavenUSA
  2. 2.Department of BiologyWest Virginia UniversityMorgantownUSA
  3. 3.Department of Genetics, MC: 5120Stanford University School of MedicineStanfordUSA

Personalised recommendations