Optimization of transcription factor binding map accuracy utilizing knockout-mouse models.
Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify 'hyper ChIPable regions' as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany.
Wolfgang
W
Krebs
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany.
Susanne V
SV
Schmidt
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Alon
A
Goren
Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany.
Dominic
D
De Nardo
Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany.
Larisa
L
Labzin
Institute for Applied Mathematics, University of Bonn, 53115 Bonn, Germany.
Anton
A
Bovier
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany.
Thomas
T
Ulas
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany.
Heidi
H
Theis
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany.
Michael
M
Kraut
Institute of Innate Immunity, University Hospitals, University of Bonn, 53127 Bonn, Germany Division of Infectious Diseases and Immunology, UMass Medical School, Worcester, MA 01605, USA German Center of Neurodegenerative Diseases (DZNE), 53175 Bonn, Germany.
Eicke
E
Latz
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany.
Marc
M
Beyer
Genomics and Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany j.schultze@uni-bonn.de.
Joachim L
JL
Schultze
D000465:Algorithms; D000818:Animals; D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008810:Mice, Inbred C57BL; D018345:Mice, Knockout; D023421:Models, Animal; D059372:Nucleotide Motifs; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
D014157:Transcription Factors