NDLI: Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

Please wait, while we are loading the content...

Inhibition of class I histone deacetylases in non-small cell lung cancer by honokiol leads to suppression of cancer cell growth and induction of cell death in vitro and in vivo

DNA demethylation and histone H3K9 acetylation determine the active transcription of the NKG2D gene in human CD8+ T and NK cells

Epigenetic regulation of planarian stem cells by the SET1/MLL family of histone methyltransferases

The epigenome of AML stem and progenitor cells

Aberrant Keap1 methylation in breast cancer and association with clinicopathological features

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

Year: 2012, Volume: 7

Year: 2011, Volume: 6

Year: 2010, Volume: 5

Year: 2009, Volume: 4

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

Content Provider	PubMed Central
Author	Ross, Jason P. Shaw, Jan M. Molloy, Peter L.
Copyright Year	2013
Abstract	We have developed a method that enriches for methylated cytosines by capturing the fraction of bisulfite-treated DNA with unconverted cytosines. The method, called streptavidin bisulfite ligand methylation enrichment (SuBLiME), involves the specific labeling (using a biotin-labeled nucleotide ligand) of methylated cytosines in bisulfite-converted DNA. This step is then followed by affinity capture, using streptavidin-coupled magnetic beads. SuBLiME is highly adaptable and can be combined with deep sequencing library generation and/or genomic complexity-reduction. In this pilot study, we enriched methylated DNA from Csp6I-cut complexity-reduced genomes of colorectal cancer cell lines (HCT-116, HT-29 and SW-480) and normal blood leukocytes with the aim of discovering colorectal cancer biomarkers. Enriched libraries were sequenced with SOLiD-3 technology. In pairwise comparisons, we scored a total of 1,769 gene loci and 33 miRNA loci as differentially methylated between the cell lines and leukocytes. Of these, 516 loci were differently methylated in at least two promoter-proximal CpG sites over two discrete Csp6I fragments. Identified methylated gene loci were associated with anatomical development, differentiation and cell signaling. The data correlated with good agreement to a number of published colorectal cancer DNA methylation biomarkers and genomic data sets. SuBLiME is effective in the enrichment of methylated nucleic acid and in the detection of known and novel biomarkers.
Related Links	http://dx.doi.org/10.4161/epi.23330
Ending Page	127
Page Count	15
Starting Page	113
File Format	PDF
ISSN	15592294
e-ISSN	15592308
Journal	Epigenetics
Issue Number	1
Volume Number	8
Language	English
Publisher	Landes Bioscience
Publisher Date	2013-01-01
Access Restriction	Open
Rights Holder	Landes Bioscience
Subject Keyword	Cancer Research Molecular Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Cancer Research

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data

Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species

A Parallel Tool for the Identification of Differentially Methylated Regions in Genomic Analyses

MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation

Thousands of CpGs Show DNA Methylation Differences in ACPA-Positive Individuals

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

The bisulfite genomic sequencing protocol

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing

Similar Documents

Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data

Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species

A Parallel Tool for the Identification of Differentially Methylated Regions in Genomic Analyses

MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation

Thousands of CpGs Show DNA Methylation Differences in ACPA-Positive Individuals

Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus

Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

The bisulfite genomic sequencing protocol

Identification of differentially methylated regions using streptavidin bisulfite ligand methylation enrichment (SuBLiME), a new method to enrich for methylated DNA prior to deep bisulfite genomic sequencing