Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq.
BMC Genomics
; 16: 46, 2015 Feb 05.
Article
em En
| MEDLINE
| ID: mdl-25652644
ABSTRACT
BACKGROUND:
Chromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low cell numbers.RESULTS:
We describe a robust, simple and scalable methodology for ChIP-seq of low-abundant cell populations, verified down to 10,000 cells. By employing non-mammalian genome mapping bacterial carrier DNA during amplification, we reliably amplify down to 50 pg of ChIP DNA from transcription factor (CEBPA) and histone mark (H3K4me3) ChIP. We further demonstrate that genomic profiles are highly resilient to changes in carrier DNA to ChIP DNA ratios.CONCLUSIONS:
This represents a significant advance compared to existing technologies, which involve either complex steps of pre-selection for nucleosome-containing chromatin or pre-amplification of precipitated DNA, making them prone to introduce experimental biases.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Fatores de Transcrição
/
Análise de Sequência com Séries de Oligonucleotídeos
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Técnicas de Amplificação de Ácido Nucleico
/
Imunoprecipitação da Cromatina
Limite:
Animals
Idioma:
En
Revista:
BMC Genomics
Ano de publicação:
2015
Tipo de documento:
Article