MeDIP-Seq/DIP-seq

Methylated DNA Immunoprecipitation/DNA Immunoprecipitation Followed by High-Throughput Sequencing

MeDIP-seq is used to study 5mC modification (Weber et al., 2005). It is based on MeDIP, originally developed as an approach for immunocapturing methylated DNA followed by microarray analysis (Weber et al., 2005). A variation on this method detects 5hmC to provide a more complete view of cytosine modifications (see hMeDIP-seq) (Xu et al., 2011). In this method, anti-5mC antibodies are used to isolate methylated DNA from fragmented gDNA via immunoprecipitation. The isolated DNA fragments are purified and used to prepare a sequencing library. Deep sequencing provides greater genome coverage, representing the majority of immunoprecipitated methylated DNA.

Advantages:

  • Covers CpG and non-CpG 5mC throughout the genome
  • Covers 5mC in dense and less dense repeat regions
  • Antibody-based selection is independent of sequence and does not enrich for 5hmC due to antibody specificity
  • Can be a cost-effective approach when single-base resolution is not desired (Yong et al., 2016)

Disadvantages:

  • Base-pair resolution is lower (~150 bp), as opposed to single-base resolution with other methods
  • Antibody specificity and selectivity must be tested to avoid nonspecific interaction
  • Biased toward hypermethylated regions


Reagents:

Illumina Library prep and Array Kit Selector



Reviews:

Sharma G., Sowpati D. T., Singh P., et al. Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection. Sci Rep. 2016;6:25006

Soto J., Rodriguez-Antolin C., Vallespin E., de Castro Carpeno J. and Ibanez de Caceres I. The impact of next-generation sequencing on the DNA methylation-based translational cancer research. Transl Res. 2016;169:1-18 e11

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

Yong W. S., Hsu F. M. and Chen P. Y. Profiling genome-wide DNA methylation. Epigenetics Chromatin. 2016;9:26



References:

Staunstrup N. H., Starnawska A., Nyegaard M., et al. Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots. Clin Epigenetics. 2016;8:81

Tang A., Huang Y., Li Z., et al. Analysis of a four generation family reveals the widespread sequence-dependent maintenance of allelic DNA methylation in somatic and germ cells. Sci Rep. 2016;6:19260

Han B., Li W., Chen Z., et al. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure. PLoS One. 2016;11:e0160358

Halder R., Hennion M., Vidal R. O., et al. DNA methylation changes in plasticity genes accompany the formation and maintenance of memory. Nat Neurosci. 2016;19:102-110

Chowdhury B., Seetharam A., Wang Z., et al. A Study of Alterations in DNA Epigenetic Modifications (5mC and 5hmC) and Gene Expression Influenced by Simulated Microgravity in Human Lymphoblastoid Cells. PLoS One. 2016;11:e0147514

Lucas E. S., Dyer N. P., Murakami K., et al. Loss of Endometrial Plasticity in Recurrent Pregnancy Loss. Stem Cells. 2016;34:346-356

Pheiffer C., Erasmus R. T., Kengne A. P. and Matsha T. E. Differential DNA methylation of microRNAs within promoters, intergenic and intragenic regions of type 2 diabetic, pre-diabetic and non-diabetic individuals. Clin Biochem. 2016;49:433-438

Su Y., Fan Z., Wu X., et al. Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs. BMC Genomics. 2016;17:134

Sun L. X., Wang Y. Y., Zhao Y., Wang H., Li N. and Ji X. S. Global DNA Methylation Changes in Nile Tilapia Gonads during High Temperature-Induced Masculinization. PLoS One. 2016;11:e0158483

Yang Y., Zhou R., Mu Y., Hou X., Tang Z., et al. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep. 2016;6:30160

Zeng Y., Yao B., Shin J., et al. Lin28A Binds Active Promoters and Recruits Tet1 to Regulate Gene Expression. Mol Cell. 2016;61:153-160