Method for detecting methylated CpG islands

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C435S091200

Reexamination Certificate

active

07425415

ABSTRACT:
The present invention provides new and improved assay for detection of genomic methylated CpG islands. This new method is termed the methylated-CpG island recovery assay (MIRA). In accordance with one embodiment, MIRA comprises the steps of: (a) incubating genomic DNA fragments with a methylated CpG island binding protein in the presence of a binding partner for the binding protein to produce bound DNA containing methylated CpG islands, (b) isolating the bound DNA, and (c) detecting CpG island methylation by gene-specific amplification reactions. In accordance with a preferred embodiment, MIRA comprises the steps of: (a) incubating sonicated genomic DNA with a matrix containing a fusion protein of glutathione S-transferase (GST) and MBD2b (GST-MBD2b) in the presence of MBD3L1 to produce bound DNA containing methylated CpG islands, (b) eluting bound DNA from the matrix, and (c) detecting CpG island methylation by gene-specific amplification reactions.

REFERENCES:
patent: 2006/0204988 (2006-09-01), Fassbender et al.
Matarazzo et al., “In vivo analysis of DNA methylation patterns recognized by specific proteins: coupling ChIP and bisulfite analysis,” Biotechniques, Oct. 2004, vol. 37, No. 4.
Jiang et al., “MBD3L1 Is a Transcriptional Repressor That Interacts with Methyl-CpG-binding Protein 2 (MBD2) and Components of the NuRD Complex,” J.Biol.Chem, Dec. 2004, vol. 279, No. 50, pp. 52456-52464.
Ballestar et al., “Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer,” EMBO journal, 2003, vol. 22, No. 23, pp. 6335-6345.
Yan et al., “Use of CpG island microarrays to identify colorectal tumors with a high degree of concurrent methylation,” Methods, 2002, vol. 27, pp. 162-169.
Cross, S., et al, “Purification of CpG Islands Using a Methylated DNA Binding Column,”Nature Genetics, vol. 6, Mar. 1994, pp. 236-244, 1994 Nature Publishing Group; Institute of Cell and Molecular Biology, University of Edinburgh, Kings Buildings, Edinburgh, Scotland, UK.
Shiraishi, M., et al, “Isolation of DNA Fragments Associated With Methylated CpG Islands in Human Adenocarcinomas of the Lung Using a Methylated DNA Binding Column and Denaturing Gradient Gel Electrophoresis,”Proceedings of National Academy of Sciences, USA, vol. 96, pp. 2913-2918, Mar. 1999 Genetics.
Jiang, C., et al, “MBD3L1 Is a Transcriptional Repressor That Interacts With Methyl-CpG-Binding Protein 2 (MBD2) and Components of the NuRD Complex,”The Journal of Biological Chemistry, 2004 by The American Society for Biochemistry and Molecular Biology, Inc., vol. 279, No. 50, issue of Dec. 10, pp. 52456-52464, 2004, USA.
Rauch T., et al, “Methylated-CpG Island Recovery Assay: A New Technique for the Rapid Detection of Methylated-CpG Islands in Cancer,”Laboratory Investigation 2005, vol. 85, pp. 1172-1180, 2005 USCAP, Inc.; Division of Biology, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
Hendrich B., et al, “Mammalian Methyltransferases and Methyl-CpG-Binding Domains: Proteins Involved in DNA Methylation,” Mol. and Cell. Biol., 1998, pp. 6538-6547.
Wade, P., “Methyl CpG Binding Proteins: Coupling Chromatin Architecture to Gene Regulation,”Oncogene(2001), vol. 20, pp. 3166-3173, 2001 Nature Publishing Group; Emory University School of Medicine, Department of Pathology and Laboratory Medicine, Woodruff Memorial Research Building, Atlanta, Georgia, USA.
Hendrich, B. et al, “Identification and Characterization of a Family of Mammalian Methyl-CpG Binding Proteins,”Molecular and Cellular Biology, Nov. 1998, pp. 6538-6547, 1998 American Society for Microbiology; Institute of Cell and Molecular Biology, University of Edinburgh, Edinburgh, Scotland.
Costello, J., et al, “Aberrant CpG-Island Methylation has Non-Random and Tumour-Type-Specific Patterns,”Nature Genetics, vol. 25, Feb. 2000, pp. 132-138, 2000 Nature America Inc., USA.
Fraga, M. et al, “DNA Methylation: A Profile of Methods and Applications,”BioTechniques, vol. 33, No. 3, pp. 632-649 (Sep. 2002); Spanish National Cancer Research Center (CNIO), Madrid, Spain.
Shiraishi, M., et al, “An Overview of the Analysis of DNA Methylation in Mammalian Genomes,”Biol. Chem., vol. 383, pp. 893-906, Jun. 2002; DNA Methylation and Genome Function Project, National Cancer Center Research Institute, Tokyo, Japan.
Pfeifer, G., et al, “Genomic Sequencing and Methylation Analysis by Ligation Mediated PCR,”Science, vol. 246, Nov. 10, 1989, pp. 810-813; Molecular Biology Section, Beckman Research Institute of the City of Hope, Duarte, CA; California Institute of Technology, Division of Biology, Pasadena, CA.
Clark, S. et al, “High Sensitivity Mapping of Methylated Cytosines,”Nucleic Acids Research, 1994, vol. 22, No. 15, pp. 2990-2997; Kanematsu Laboratories, Royal Prince Alfred Hospital, Sydney, Australia; CSIRO Division of Biomolecular Engineering, Sydney Laboratory, Sydney, Australia; School of Biological Sciences, A12, University of Sydney, Australia.
Frommer, M., et al, “A Genomic Sequencing Protocol That Yields a Positive Display of 5-Methylcytosine Residues in Individual DNA Strands,”Proceedings of National Academy of Sciences, USA, vol. 89, pp. 1827-1831, Mar. 1992, Genetics; The Kanematsu Laboratories, Royal Prince Alfred Hospital, Sydney, Australia; Division of Biomolecular Engineering, Laboratory for Molecular Biology, Commonwealth Scientific and Industrial Research Organization, Australia.
Xiong, Z., et al, “COBRA: A Sensitive and Quantitative DNA Methylation Assay,”Nucleic Acids Research, 1997, vol. 25, No. 12, pp. 2532-2534, 1997 Oxford University Press; Department of Surgery and Department of Biochemistry and Molecular Biology, University of Southern California School of Medicine, The Norris Comprehensive Cancer Center, Los Angeles, California, USA.
Herman, J., et al, “Methylation-Specific PCR: A Novel PCR Assay for Methylation Status of CpG Islands,”Proceedings of National Academy of Sciencies, USA, vol. 93, pp. 9821-9826, Sep. 1996, Medical Sciences; Oncology Center and Department of Medicine, The Johns Hopkins Medical Institutions, Baltimore, Maryland.

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Method for detecting methylated CpG islands does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Method for detecting methylated CpG islands, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method for detecting methylated CpG islands will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3969916

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.