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Literature DB >> 32822040

Genome-Wide Mapping of DNA Methylation 5mC by Methylated DNA Immunoprecipitation (MeDIP)-Sequencing.

Millissia Ben Maamar¹, Ingrid Sadler-Riggleman¹, Daniel Beck¹, Michael K Skinner².

Abstract

Methylated DNA immunoprecipitation is a large scale purification technique. It enables the isolation of methylated DNA fragments for subsequent locus-specific or genome-wide analysis. Here we describe an immunoprecipitation protocol using a monoclonal mouse anti 5-methyl-cytidine antibody followed by next-generation sequencing (MeDIP-Seq).

Entities: Chemical

Keywords: DNA methylation; Epigenetics; Immuno-precipitation; Methylated DNA immunoprecipitation; Next generation sequencing; Review

Mesh：

Substances：

Year: 2021 PMID： 32822040 PMCID： PMC8285090 DOI： 10.1007/978-1-0716-0876-0_23

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

13 in total

Review 1. DNA methylation patterns and epigenetic memory.

Authors: Adrian Bird
Journal: Genes Dev Date: 2002-01-01 Impact factor: 11.361

2. Fast gapped-read alignment with Bowtie 2.

Authors: Ben Langmead; Steven L Salzberg
Journal: Nat Methods Date: 2012-03-04 Impact factor: 28.547

3. The Sequence Alignment/Map format and SAMtools.

Authors: Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal: Bioinformatics Date: 2009-06-08 Impact factor: 6.937

4. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome.

Authors: Carlos Guerrero-Bosagna; Matthew Settles; Ben Lucker; Michael K Skinner
Journal: PLoS One Date: 2010-09-30 Impact factor: 3.240

Review 5. Finding the fifth base: genome-wide sequencing of cytosine methylation.

Authors: Ryan Lister; Joseph R Ecker
Journal: Genome Res Date: 2009-03-09 Impact factor: 9.043

6. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.

Authors: Steffen Durinck; Paul T Spellman; Ewan Birney; Wolfgang Huber
Journal: Nat Protoc Date: 2009-07-23 Impact factor: 13.491

7. Generational comparisons (F1 versus F3) of vinclozolin induced epigenetic transgenerational inheritance of sperm differential DNA methylation regions (epimutations) using MeDIP-Seq.

Authors: Daniel Beck; Ingrid Sadler-Riggleman; Michael K Skinner
Journal: Environ Epigenet Date: 2017-08-29

5. Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations.

Authors: Eric Nilsson; Ingrid Sadler-Riggleman; Daniel Beck; Michael K Skinner
Journal: Environ Epigenet Date: 2021-05-19

5 in total

Genome-Wide Mapping of DNA Methylation 5mC by Methylated DNA Immunoprecipitation (MeDIP)-Sequencing.

Review 1. DNA methylation patterns and epigenetic memory.

2. Fast gapped-read alignment with Bowtie 2.

3. The Sequence Alignment/Map format and SAMtools.

4. Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome.

Review 5. Finding the fifth base: genome-wide sequencing of cytosine methylation.

6. Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt.

7. Generational comparisons (F1 versus F3) of vinclozolin induced epigenetic transgenerational inheritance of sperm differential DNA methylation regions (epimutations) using MeDIP-Seq.

8. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

9. MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.

10. Trimmomatic: a flexible trimmer for Illumina sequence data.

Review 1. A Comprehensive Toolbox to Analyze Enhancer-Promoter Functions.

2. Preterm birth buccal cell epigenetic biomarkers to facilitate preventative medicine.

3. Genome-wide CpG density and DNA methylation analysis method (MeDIP, RRBS, and WGBS) comparisons.

Review 4. Update on the Molecular Aspects and Methods Underlying the Complex Architecture of FSHD.

5. Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations.