Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 46, 2013, Pages 18602-18607

  Teytelman, Leonid ^a   Thurtle, Deborah M ^a   Rine, Jasper ^b   Van Oudenaarden, Alexander ^a,c  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c HUBRECHT INSTITUTE   (Netherlands)

Author keywords

ChIP chip; Hot regions; TRNA; Yeast

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; GREEN FLUORESCENT PROTEIN; RNA POLYMERASE II; SILENT INFORMATION REGULATOR PROTEIN; SIRTUIN 2; SIRTUIN 3; SIRTUIN 4;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; EUCHROMATIN; GENE EXPRESSION; GENETIC ASSOCIATION; IMMUNOPRECIPITATION; MATING TYPE; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN LOCALIZATION; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE;

CHIP-CHIP; HOT REGIONS; TRNA; YEAST;

ARTIFACTS; CHROMATIN IMMUNOPRECIPITATION; DNA PRIMERS; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; POLYMERASE CHAIN REACTION; SILENT INFORMATION REGULATOR PROTEINS, SACCHAROMYCES CEREVISIAE;

EID: 84887478181     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1316064110     Document Type: Article

References (28)

1. Hanlon SE, Lieb JD (2004) Progress and challenges in profiling the dynamics of chromatin and transcription factor binding with DNA microarrays. Curr Opin Genet Dev 14(6):697-705. (Pubitemid 39505377)
2. Park PJ (2009) ChIP-seq: Advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669-680.
3. Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13(12):840-852.
4. Ho JW, et al. (2011) ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis. BMC Genomics 12:134.
5. Chen Y, et al. (2012) Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods 9(6):609-614.
6. Kidder BL, Hu G, Zhao K (2011) ChIP-Seq: Technical considerations for obtaining high-quality data. Nat Immunol 12(10):918-922.
7. Rusche LN, Kirchmaier AL, Rine J (2003) The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem 72:481-516. (Pubitemid 36930453)
8. Teytelman L, Nishimura EA, Ozaydin B, Eisen MB, Rine J (2012) The enigmatic conservation of a Rap1 binding site in the Saccharomyces cerevisiae HMR-E silencer. G3 (Bethesda) 2(12):1555-1562.
9. Radman-Livaja M, et al. (2011) Dynamics of Sir3 spreading in budding yeast: Secondary recruitment sites and euchromatic localization. EMBO J 30(6):1012-1026.
10. Lieb JD, Liu X, Botstein D, Brown PO (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28(4):327-334. (Pubitemid 32702421)
11. Marchfelder U, Rateitschak K, Ehrenhofer-Murray AE (2003) SIR-dependent repression of non-telomeric genes in Saccharomyces cerevisiae? Yeast 20(9):797-801. (Pubitemid 36850045)
12. Barton AB, Kaback DB (2006) Telomeric silencing of an open reading frame in Saccharomyces cerevisiae. Genetics 173(2):1169-1173. (Pubitemid 43945928)
13. Gottschling DE, Aparicio OM, Billington BL, Zakian VA (1990) Position effect at S. cerevisiae telomeres: Reversible repression of Pol II transcription. Cell 63(4):751-762. (Pubitemid 120035048)
14. Vega-Palas MA, Martín-Figueroa E, Florencio FJ (2000) Telomeric silencing of a natural subtelomeric gene. Mol Gen Genet 263(2):287-291.
15. Wyrick JJ, et al. (1999) Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402(6760):418-421. (Pubitemid 129544830)
16. Lefrançois P, et al. (2009) Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics 10:37.
17. Dieci G, Sentenac A (1996) Facilitated recycling pathway for RNA polymerase III. Cell 84(2):245-252. (Pubitemid 26040844)
18. Roberts DN, Stewart AJ, Huff JT, Cairns BR (2003) The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc Natl Acad Sci USA 100(25):14695-14700. (Pubitemid 37517953)
19. Moqtaderi Z, Struhl K (2004) Genome-wide occupancy profile of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol Cell Biol 24(10):4118-4127. (Pubitemid 41070986)
20. Fan X, Struhl K (2009) Where does mediator bind in vivo? PLoS ONE 4(4):e5029.
21. Li M, Valsakumar V, Poorey K, Bekiranov S, Smith JS (2013) Genome-wide analysis of functional sirtuin chromatin targets in yeast. Genome Biol 14(5):R48.
22. Longtine MS, et al. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14(10):953-961. (Pubitemid 28328001)
23. Aparicio O, et al. (2005) Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Mol Biol Chap 21:Unit 21.3.
24. Zill OA, Scannell D, Teytelman L, Rine J (2010) Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol 8(11):e1000550.
25. Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18(11):1851-1858.
26. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5):589-595.
27. Li H, et al.; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078-2079.
28. Zhang Y, et al. (2008) Model-based analysis of ChIP-seq (MACS). Genome Biol 9(9):R137.