RRBS-Seq
Reduced-Representation Bisulfite Sequencing
RRBS uses one or multiple restriction enzymes on the genomic DNA to produce sequence-specific fragmentation (Meissner et al., 2005). The fragmented genomic DNA is treated with bisulfite and sequenced. This is the method of choice to study specific regions of interest. It is particularly effective where methylation levels are high, such as in promoters and repeat regions.
Advantages:
- Provides genome-wide coverage of CpGs in islands at single-base resolution
- Covers CpG methylation in dense regions
Disadvantages:
- Restriction enzymes cut at specific sites, providing biased sequence selection
- Method measures 10-15% of all CpGs in the genome
- Cannot distinguish between 5mC and 5hmC
- Does not cover non-CpG areas, genome-wide CpGs, and CpGs in areas without the enzyme restriction site
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
Devall M., Roubroeks J., Mill J., Weedon M. and Lunnon K. Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies. Neurosci Lett. 2016;625:47-55
Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26
References:
Auclair G., Borgel J., Sanz L. A., et al. EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos. Genome Res. 2016;26:192-202
Day S. E., Coletta R. L., Kim J. Y., et al. Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes. Clin Epigenetics. 2016;8:77
Heller G., Topakian T., Altenberger C., et al. Next-generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia. Leukemia. 2016;30:1861-1868
Baheti S., Kanwar R., Goelzenleuchter M., Kocher J. P., Beutler A. S. and Sun Z. Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data. BMC Genomics. 2016;17:149
Flinders C., Lam L., Rubbi L., et al. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med. 2016;8:54
Orlanski S., Labi V., Reizel Y., et al. Tissue-specific DNA demethylation is required for proper B-cell differentiation and function. Proc Natl Acad Sci U S A. 2016;113:5018-5023
Page A., Paoli P., Moran Salvador E., White S., French J. and Mann J. Hepatic stellate cell transdifferentiation involves genome-wide remodeling of the DNA methylation landscape. J Hepatol. 2016;64:661-673
Pegoraro M., Bafna A., Davies N. J., Shuker D. M. and Tauber E. DNA methylation changes induced by long and short photoperiods in Nasonia. Genome Res. 2016;26:203-210
Yuan X. L., Gao N., Xing Y., et al. Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing. Sci Rep. 2016;6:22138
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History: RRBS-Seq
Revision by sbrumpton on 2017-06-21 07:50:20 - Show/Hide
Reduced-Representation Bisulfite Sequencing
RRBS uses one or multiple restriction enzymes on the genomic DNA to produce sequence-specific fragmentation (Meissner et al., 2005). The fragmented genomic DNA is treated with bisulfite and sequenced. This is the method of choice to study specific regions of interest. It is particularly effective where methylation levels are high, such as in promoters and repeat regions.
Advantages:- Provides genome-wide coverage of CpGs in islands at single-base resolution
- Covers CpG methylation in dense regions
Disadvantages:- Restriction enzymes cut at specific sites, providing biased sequence selection
- Method measures 10-15% of all CpGs in the genome
- Cannot distinguish between 5mC and 5hmC
- Does not cover non-CpG areas, genome-wide CpGs, and CpGs in areas without the enzyme restriction site
Reagents:Illumina Library prep and Array Kit SelectorReviews:Devall M., Roubroeks J., Mill J., Weedon M. and Lunnon K. Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies. Neurosci Lett. 2016;625:47-55Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26References:Auclair G., Borgel J., Sanz L. A., et al. EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos. Genome Res. 2016;26:192-202Day S. E., Coletta R. L., Kim J. Y., et al. Next-generation sequencing methylation profiling of subjects with obesity identifies novel gene changes. Clin Epigenetics. 2016;8:77Heller G., Topakian T., Altenberger C., et al. Next-generation sequencing identifies major DNA methylation changes during progression of Ph+ chronic myeloid leukemia. Leukemia. 2016;30:1861-1868Baheti S., Kanwar R., Goelzenleuchter M., Kocher J. P., Beutler A. S. and Sun Z. Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data. BMC Genomics. 2016;17:149Flinders C., Lam L., Rubbi L., et al. Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Med. 2016;8:54Orlanski S., Labi V., Reizel Y., et al. Tissue-specific DNA demethylation is required for proper B-cell differentiation and function. Proc Natl Acad Sci U S A. 2016;113:5018-5023Page A., Paoli P., Moran Salvador E., White S., French J. and Mann J. Hepatic stellate cell transdifferentiation involves genome-wide remodeling of the DNA methylation landscape. J Hepatol. 2016;64:661-673Pegoraro M., Bafna A., Davies N. J., Shuker D. M. and Tauber E. DNA methylation changes induced by long and short photoperiods in Nasonia. Genome Res. 2016;26:203-210Yuan X. L., Gao N., Xing Y., et al. Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing. Sci Rep. 2016;6:22138