Transcription factor binding site identification in yeast: A comparison of high-density oligonucleotide and PCR-based microarray platforms

Anthony R. Borneman, Zhengdong Zhang, Joel Rozowsky, Michael R. Seringhaus, Mark Gerstein, Michael Snyder

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

In recent years, techniques have been developed to map transcription factor binding sites using chromatin immunoprecipitation combined with DNA microarrays (chIP chip). Initially, polymerase chain reaction (PCR)-based DNA arrays were used for the chIP chip procedure, however, high-density oligonucleotide (HDO) arrays, which allow for the production of thousands more features per array, have emerged as a competing array platform. To compare the two platforms, data from chIP chip analysis performed for three factors (Tec1, Ste12, and Sok2) using both HDO and PCR arrays under identical experimental conditions were compared. HDO arrays provided increased reproducibility and sensitivity, detecting approximately three times more binding events than the PCR arrays while also showing increased accuracy. The increased resolution provided by the HDO arrays also allowed for the identification of multiple binding peaks in close proximity and of novel binding events such as binding within ORFs. The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available.

Original languageEnglish (US)
Pages (from-to)335-345
Number of pages11
JournalFunctional and Integrative Genomics
Volume7
Issue number4
DOIs
StatePublished - Oct 2007
Externally publishedYes

Fingerprint

Oligonucleotide Array Sequence Analysis
Transcription Factors
Yeasts
Binding Sites
Polymerase Chain Reaction
Chromatin Immunoprecipitation
ribonucleotide polymerase
Open Reading Frames

Keywords

  • Chromatin immunoprecipitation
  • Microarray
  • Tiling array
  • Yeast

ASJC Scopus subject areas

  • Genetics

Cite this

Transcription factor binding site identification in yeast : A comparison of high-density oligonucleotide and PCR-based microarray platforms. / Borneman, Anthony R.; Zhang, Zhengdong; Rozowsky, Joel; Seringhaus, Michael R.; Gerstein, Mark; Snyder, Michael.

In: Functional and Integrative Genomics, Vol. 7, No. 4, 10.2007, p. 335-345.

Research output: Contribution to journalArticle

Borneman, Anthony R. ; Zhang, Zhengdong ; Rozowsky, Joel ; Seringhaus, Michael R. ; Gerstein, Mark ; Snyder, Michael. / Transcription factor binding site identification in yeast : A comparison of high-density oligonucleotide and PCR-based microarray platforms. In: Functional and Integrative Genomics. 2007 ; Vol. 7, No. 4. pp. 335-345.
@article{3bc183103fb14cce8f754ce71aa0b715,
title = "Transcription factor binding site identification in yeast: A comparison of high-density oligonucleotide and PCR-based microarray platforms",
abstract = "In recent years, techniques have been developed to map transcription factor binding sites using chromatin immunoprecipitation combined with DNA microarrays (chIP chip). Initially, polymerase chain reaction (PCR)-based DNA arrays were used for the chIP chip procedure, however, high-density oligonucleotide (HDO) arrays, which allow for the production of thousands more features per array, have emerged as a competing array platform. To compare the two platforms, data from chIP chip analysis performed for three factors (Tec1, Ste12, and Sok2) using both HDO and PCR arrays under identical experimental conditions were compared. HDO arrays provided increased reproducibility and sensitivity, detecting approximately three times more binding events than the PCR arrays while also showing increased accuracy. The increased resolution provided by the HDO arrays also allowed for the identification of multiple binding peaks in close proximity and of novel binding events such as binding within ORFs. The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available.",
keywords = "Chromatin immunoprecipitation, Microarray, Tiling array, Yeast",
author = "Borneman, {Anthony R.} and Zhengdong Zhang and Joel Rozowsky and Seringhaus, {Michael R.} and Mark Gerstein and Michael Snyder",
year = "2007",
month = "10",
doi = "10.1007/s10142-007-0054-7",
language = "English (US)",
volume = "7",
pages = "335--345",
journal = "Functional and Integrative Genomics",
issn = "1438-793X",
publisher = "Springer Verlag",
number = "4",

}

TY - JOUR

T1 - Transcription factor binding site identification in yeast

T2 - A comparison of high-density oligonucleotide and PCR-based microarray platforms

AU - Borneman, Anthony R.

AU - Zhang, Zhengdong

AU - Rozowsky, Joel

AU - Seringhaus, Michael R.

AU - Gerstein, Mark

AU - Snyder, Michael

PY - 2007/10

Y1 - 2007/10

N2 - In recent years, techniques have been developed to map transcription factor binding sites using chromatin immunoprecipitation combined with DNA microarrays (chIP chip). Initially, polymerase chain reaction (PCR)-based DNA arrays were used for the chIP chip procedure, however, high-density oligonucleotide (HDO) arrays, which allow for the production of thousands more features per array, have emerged as a competing array platform. To compare the two platforms, data from chIP chip analysis performed for three factors (Tec1, Ste12, and Sok2) using both HDO and PCR arrays under identical experimental conditions were compared. HDO arrays provided increased reproducibility and sensitivity, detecting approximately three times more binding events than the PCR arrays while also showing increased accuracy. The increased resolution provided by the HDO arrays also allowed for the identification of multiple binding peaks in close proximity and of novel binding events such as binding within ORFs. The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available.

AB - In recent years, techniques have been developed to map transcription factor binding sites using chromatin immunoprecipitation combined with DNA microarrays (chIP chip). Initially, polymerase chain reaction (PCR)-based DNA arrays were used for the chIP chip procedure, however, high-density oligonucleotide (HDO) arrays, which allow for the production of thousands more features per array, have emerged as a competing array platform. To compare the two platforms, data from chIP chip analysis performed for three factors (Tec1, Ste12, and Sok2) using both HDO and PCR arrays under identical experimental conditions were compared. HDO arrays provided increased reproducibility and sensitivity, detecting approximately three times more binding events than the PCR arrays while also showing increased accuracy. The increased resolution provided by the HDO arrays also allowed for the identification of multiple binding peaks in close proximity and of novel binding events such as binding within ORFs. The HDO array platform provides a far more robust array system by all measures than PCR-based arrays, all of which is directly attributable to the large number of probes available.

KW - Chromatin immunoprecipitation

KW - Microarray

KW - Tiling array

KW - Yeast

UR - http://www.scopus.com/inward/record.url?scp=34548359013&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34548359013&partnerID=8YFLogxK

U2 - 10.1007/s10142-007-0054-7

DO - 10.1007/s10142-007-0054-7

M3 - Article

C2 - 17638031

AN - SCOPUS:34548359013

VL - 7

SP - 335

EP - 345

JO - Functional and Integrative Genomics

JF - Functional and Integrative Genomics

SN - 1438-793X

IS - 4

ER -