ArticleBMC genomics2007
Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Laboratory methods to decipher epigenetic signatures: a comparative review.Cellular & molecular biology letters · 2021Review
- More than a powerplant: the influence of mitochondrial transfer on the epigenome.Current opinion in physiology · 2018Article
- Transient DNMT1 suppression reveals hidden heritable marks in the genome.Nucleic acids research · 2015Article
- DNA hypermethylation of zygote arrest 1 (ZAR1) in hepatitis C virus positive related hepatocellular carcinoma.SpringerPlus · 2013Article
- Loss of DNMT1o disrupts imprinted X chromosome inactivation and accentuates placental defects in females.PLoS genetics · 2013Article
- Gene silencing of SLC5A8 identified by genome-wide methylation profiling in lung cancer.Lung cancer (Amsterdam, Netherlands) · 2013Article
- Mitochondrial regulation of epigenetics and its role in human diseases.Epigenetics · 2012Review
- Tissue specific DNA methylation of CpG islands in normal human adult somatic tissues distinguishes neural from non-neural tissues.Epigenetics · 2010Article
- Identification and analysis of an early diagnostic marker for malignant melanoma: ZAR1 intra-genic differential methylation.Journal of dermatological science · 2010Article
- Epigenetic regulation of the expression of genes involved in steroid hormone biosynthesis and action.Steroids · 2010Review
- Mild folate deficiency induces genetic and epigenetic instability and phenotype changes in prostate cancer cells.BMC biology · 2010Article
- DNA methylation of cancer genome.Birth defects research. Part C, Embryo today : reviews · 2009Review
- Epigenetic silencing of the kinase tumor suppressor WNK2 is tumor-type and tumor-grade specific.Neuro-oncology · 2009Article
- Tissue specific differentially methylated regions (TDMR): Changes in DNA methylation during development.Genomics · 2009Article
- Article
- A novel role for mitochondria in regulating epigenetic modification in the nucleus.Cancer biology & therapy · 2008Article
- Phenotype-specific CpG island methylation events in a murine model of prostate cancer.Cancer research · 2008Article
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Authors and funding
27 authors.
Funding
Abstract
backgroundRestriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning."
resultsWe report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation.
conclusionThe new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation.
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