FAIRE-seq/Sono-Seq
Formaldehyde-Assisted Isolation of Regulatory Elements / Sonication of Crosslinked Chromatin
FAIRE-seq (Giresi et al., 2009) (Hogan et al., 2006) and Sono-Seq (Auerbach et al., 2009) are based on differences in crosslinking efficiencies between DNA and nucleosomes or sequence-specific DNA-binding proteins. In this method, DNA-protein complexes are crosslinked briefly in vivo using formaldehyde. The sample is then lysed and sonicated. After phenol/chloroform extraction, the DNA in the aqueous phase is purified and sequenced. Sequencing provides information for regions of DNA that are not occupied by histones.
Advantages:
- Simple and highly reproducible protocol
- Does not require antibodies
- Does not require enzymes, such as DNase or MNase, avoiding the optimization and extra steps necessary for enzymatic processing
- Does not require a single-cell suspension or nuclear isolation, so it is easily adapted for use on tissue samples (Simon et al., 2012)
Disadvantages:
- Cannot identify regulatory proteins bound to DNA
- DNase-Seq may be better at identifying nucleosome-depleted promoters of highly expressed genes (Song et al., 2011)
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109
References:
Lavender C. A., Cannady K. R., Hoffman J. A., Trotter K. W., Gilchrist D. A., et al. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. PLoS Genet. 2016;12:e1006224
Behura S. K., Sarro J., Li P., et al. High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. BMC Genomics. 2016;17:341
Verfaillie A., Imrichova H., Atak Z. K., et al. Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. Nat Commun. 2015;6:6683
Ackermann A. M., Wang Z., Schug J., Naji A. and Kaestner K. H. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol Metab. 2016;5:233-244
de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116
Du J., Leung A., Trac C., et al. Chromatin variation associated with liver metabolism is mediated by transposable elements. Epigenetics Chromatin. 2016;9:28
Fabrizius A., Andre D., Laufs T., et al. Critical re-evaluation of neuroglobin expression reveals conserved patterns among mammals. Neuroscience. 2016;337:339-354
Nevedomskaya E., Stelloo S., van der Poel H. G., et al. Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer. Genom Data. 2016;7:124-126
Bicker A., Brahmer A. M., Meller S., Kristiansen G., Gorr T. A. and Hankeln T. The Distinct Gene Regulatory Network of Myoglobin in Prostate and Breast Cancer. PLoS One. 2015;10:e0142662
Davie K., Jacobs J., Atkins M., et al. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet. 2015;11:e1004994
Naval-Sanchez M., Potier D., Hulselmans G., Christiaens V. and Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Mol Biol Evol. 2015;32:2441-2455
Reschen M. E., Gaulton K. J., Lin D., et al. Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding. PLoS Genet. 2015;11:e1005061
Related
History: FAIRE-seq/Sono-Seq
Revision by sbrumpton on 2017-06-21 09:34:59 - Show/Hide
Formaldehyde-Assisted Isolation of Regulatory Elements / Sonication of Crosslinked Chromatin
FAIRE-seq (Giresi et al., 2009) (Hogan et al., 2006) and Sono-Seq (Auerbach et al., 2009) are based on differences in crosslinking efficiencies between DNA and nucleosomes or sequence-specific DNA-binding proteins. In this method, DNA-protein complexes are crosslinked briefly in vivo using formaldehyde. The sample is then lysed and sonicated. After phenol/chloroform extraction, the DNA in the aqueous phase is purified and sequenced. Sequencing provides information for regions of DNA that are not occupied by histones.
Advantages:- Simple and highly reproducible protocol
- Does not require antibodies
- Does not require enzymes, such as DNase or MNase, avoiding the optimization and extra steps necessary for enzymatic processing
- Does not require a single-cell suspension or nuclear isolation, so it is easily adapted for use on tissue samples (Simon et al., 2012)
Disadvantages:- Cannot identify regulatory proteins bound to DNA
- DNase-Seq may be better at identifying nucleosome-depleted promoters of highly expressed genes (Song et al., 2011)
Reagents:Illumina Library prep and Array Kit SelectorReviews:Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109References:Lavender C. A., Cannady K. R., Hoffman J. A., Trotter K. W., Gilchrist D. A., et al. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters. PLoS Genet. 2016;12:e1006224Behura S. K., Sarro J., Li P., et al. High-throughput cis-regulatory element discovery in the vector mosquito Aedes aegypti. BMC Genomics. 2016;17:341Verfaillie A., Imrichova H., Atak Z. K., et al. Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. Nat Commun. 2015;6:6683Ackermann A. M., Wang Z., Schug J., Naji A. and Kaestner K. H. Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes. Mol Metab. 2016;5:233-244de Dieuleveult M., Yen K., Hmitou I., Depaux A., Boussouar F., et al. Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Nature. 2016;530:113-116Du J., Leung A., Trac C., et al. Chromatin variation associated with liver metabolism is mediated by transposable elements. Epigenetics Chromatin. 2016;9:28Fabrizius A., Andre D., Laufs T., et al. Critical re-evaluation of neuroglobin expression reveals conserved patterns among mammals. Neuroscience. 2016;337:339-354Nevedomskaya E., Stelloo S., van der Poel H. G., et al. Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer. Genom Data. 2016;7:124-126Bicker A., Brahmer A. M., Meller S., Kristiansen G., Gorr T. A. and Hankeln T. The Distinct Gene Regulatory Network of Myoglobin in Prostate and Breast Cancer. PLoS One. 2015;10:e0142662Davie K., Jacobs J., Atkins M., et al. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet. 2015;11:e1004994Naval-Sanchez M., Potier D., Hulselmans G., Christiaens V. and Aerts S. Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Mol Biol Evol. 2015;32:2441-2455Reschen M. E., Gaulton K. J., Lin D., et al. Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding. PLoS Genet. 2015;11:e1005061