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A reassessment of DNA-immunoprecipitation-based genomic profiling

Lentini, Antonio ; Lagerwall, Cathrine ; Vikingsson, Svante ; Mjoseng, Heidi K ; Douvlataniotis, Karolos ; Vogt, Hartmut ; Green, Henrik ; Meehan, Richard R ; Benson, Mikael ; Nestor, Colm E

Nature methods, 2018-07, Vol.15 (7), p.499-504 [Periódico revisado por pares]

United States: Nature Publishing Group

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Título:
A reassessment of DNA-immunoprecipitation-based genomic profiling
Autor: Lentini, Antonio ; Lagerwall, Cathrine ; Vikingsson, Svante ; Mjoseng, Heidi K ; Douvlataniotis, Karolos ; Vogt, Hartmut ; Green, Henrik ; Meehan, Richard R ; Benson, Mikael ; Nestor, Colm E
Assuntos: Analysis ; Animal genetics ; Animals ; Antibodies ; Biological activity ; Chromatin ; CpG Islands ; Criminal investigation ; Deoxyribonucleic acid ; DNA ; DNA - genetics ; DNA - immunology ; DNA fingerprinting ; DNA Fingerprinting - methods ; DNA Methylation ; DNA sequencing ; Embryo cells ; Embryonic Stem Cells ; Error correction ; Genetic research ; Genome ; Genomes ; Genomics ; Genomics - methods ; High-Throughput Nucleotide Sequencing - methods ; Immunoglobulin G ; Immunoprecipitation ; Immunoprecipitation - methods ; Male ; Methylation ; Mice ; Sequence Analysis, DNA - methods ; Stem cell transplantation ; Stem cells
É parte de: Nature methods, 2018-07, Vol.15 (7), p.499-504
Descrição: DNA immunoprecipitation followed by sequencing (DIP-seq) is a common enrichment method for profiling DNA modifications in mammalian genomes. However, the results of independent DIP-seq studies often show considerable variation between profiles of the same genome and between profiles obtained by alternative methods. Here we show that these differences are primarily due to the intrinsic affinity of IgG for short unmodified DNA repeats. This pervasive experimental error accounts for 50-99% of regions identified as 'enriched' for DNA modifications in DIP-seq data. Correction of this error profoundly altered DNA-modification profiles for numerous cell types, including mouse embryonic stem cells, and subsequently revealed novel associations among DNA modifications, chromatin modifications and biological processes. We conclude that both matched input and IgG controls are essential in order for the results of DIP-based assays to be interpreted correctly, and that complementary, non-antibody-based techniques should be used to validate DIP-based findings to avoid further misinterpretation of genome-wide profiling data.
Editor: United States: Nature Publishing Group
Idioma: Inglês

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A reassessment of DNA-immunoprecipitation-based genomic profiling

Lentini, Antonio ; Lagerwall, Cathrine ; Vikingsson, Svante ; Mjoseng, Heidi K ; Douvlataniotis, Karolos ; Vogt, Hartmut ; Green, Henrik ; Meehan, Richard R ; Benson, Mikael ; Nestor, Colm E

United States: Nature Publishing Group

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