Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq
| Autor: | Anne-Katrine Frank, Johannes Waage, Frederik Otzen Bagger, Bo T. Porse, Mikkel Bruhn Schuster, Kristoffer Vitting-Seerup, Marie Sigurd Hasemann, Janus S. Jakobsen |
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| Rok vydání: | 2015 |
| Předmět: |
DNA
Bacterial Chromatin Immunoprecipitation Computational biology Biology Deep sequencing chemistry.chemical_compound Genetics Animals Oligonucleotide Array Sequence Analysis Methodology Article Epigenetic profile Histone mark Multiple displacement amplification High-Throughput Nucleotide Sequencing Sequence Analysis DNA Nucleic acid amplification technique Chromatin Sequencing by ligation ChIP-sequencing ChIP-seq chemistry Transcription factor DNA microarray Nucleic Acid Amplification Techniques Genome Bacterial Pico-scale DNA Transcription Factors Biotechnology |
| Zdroj: | BMC Genomics Jakobsen, J S, Bagger, F O, Hasemann, M S, Schuster, M B, Frank, A-K, Waage, J, Vitting-Seerup, K & Porse, B T 2015, ' Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq ', BMC Genomics, vol. 16, pp. 46 . https://doi.org/10.1186/s12864-014-1195-4 |
| ISSN: | 1471-2164 |
| Popis: | 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1195-4) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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