Literature DB >> 20434563

DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP).

Masako Suzuki1, John M Greally.   

Abstract

The HELP assay is a technique that allows genome-wide analysis of cytosine methylation. Here we describe the assay, its relative strengths and weaknesses, and the transition of the assay from a microarray to massively-parallel sequencing-based foundation.
Copyright © 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID： 20434563      PMCID： PMC2954265          DOI： 10.1016/j.ymeth.2010.04.013

Source DB:  PubMed          Journal:  Methods        ISSN： 1046-2023            Impact factor:   3.608


  27 in total

1.  Comparative isoschizomer profiling of cytosine methylation: the HELP assay.

Authors:  Batbayar Khulan; Reid F Thompson; Kenny Ye; Melissa J Fazzari; Masako Suzuki; Edyta Stasiek; Maria E Figueroa; Jacob L Glass; Quan Chen; Cristina Montagna; Eli Hatchwell; Rebecca R Selzer; Todd A Richmond; Roland D Green; Ari Melnick; John M Greally
Journal:  Genome Res       Date:  2006-06-29       Impact factor: 9.043

2.  Heritable rather than age-related environmental and stochastic factors dominate variation in DNA methylation of the human IGF2/H19 locus.

Authors:  Bastiaan T Heijmans; Dennis Kremer; Elmar W Tobi; Dorret I Boomsma; P Eline Slagboom
Journal:  Hum Mol Genet       Date:  2007-03-05       Impact factor: 6.150

3.  An analytical pipeline for genomic representations used for cytosine methylation studies.

Authors:  Reid F Thompson; Mark Reimers; Batbayar Khulan; Mathieu Gissot; Todd A Richmond; Quan Chen; Xin Zheng; Kami Kim; John M Greally
Journal:  Bioinformatics       Date:  2008-03-18       Impact factor: 6.937

4.  Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation.

Authors:  Mathieu Gissot; Sang-Woon Choi; Reid F Thompson; John M Greally; Kami Kim
Journal:  Eukaryot Cell       Date:  2008-01-04

5.  Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats.

Authors:  Reid F Thompson; Melissa J Fazzari; Hongshun Niu; Nir Barzilai; Rebecca A Simmons; John M Greally
Journal:  J Biol Chem       Date:  2010-03-01       Impact factor: 5.157

6.  Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

Authors:  Daniel Zilberman; Mary Gehring; Robert K Tran; Tracy Ballinger; Steven Henikoff
Journal:  Nat Genet       Date:  2006-11-26       Impact factor: 38.330

7.  Highly integrated single-base resolution maps of the epigenome in Arabidopsis.

Authors:  Ryan Lister; Ronan C O'Malley; Julian Tonti-Filippini; Brian D Gregory; Charles C Berry; A Harvey Millar; Joseph R Ecker
Journal:  Cell       Date:  2008-05-02       Impact factor: 41.582

8.  An integrative genomic and epigenomic approach for the study of transcriptional regulation.

Authors:  Maria E Figueroa; Mark Reimers; Reid F Thompson; Kenny Ye; Yushan Li; Rebecca R Selzer; Jakob Fridriksson; Elisabeth Paietta; Peter Wiernik; Roland D Green; John M Greally; Ari Melnick
Journal:  PLoS One       Date:  2008-03-26       Impact factor: 3.240

9.  Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning.

Authors:  Shawn J Cokus; Suhua Feng; Xiaoyu Zhang; Zugen Chen; Barry Merriman; Christian D Haudenschild; Sriharsa Pradhan; Stanley F Nelson; Matteo Pellegrini; Steven E Jacobsen
Journal:  Nature       Date:  2008-02-17       Impact factor: 49.962

10.  CG dinucleotide clustering is a species-specific property of the genome.

Authors:  Jacob L Glass; Reid F Thompson; Batbayar Khulan; Maria E Figueroa; Emmanuel N Olivier; Erin J Oakley; Gary Van Zant; Eric E Bouhassira; Ari Melnick; Aaron Golden; Melissa J Fazzari; John M Greally
Journal:  Nucleic Acids Res       Date:  2007-10-10       Impact factor: 16.971
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  14 in total

Review 1.  Using DNA methylation to understand biological consequences of genetic variability.

Authors:  Dena G Hernandez; Andrew B Singleton
Journal:  Neurodegener Dis       Date:  2011-11-26       Impact factor: 2.977

Review 2.  Epigenomics: the science of no-longer-junk DNA. Why study it in chronic kidney disease?

Authors:  Yi-An Ko; Katalin Susztak
Journal:  Semin Nephrol       Date:  2013-07       Impact factor: 5.299

Review 3.  Advances in epigenetics and epigenomics for neurodegenerative diseases.

Authors:  Irfan A Qureshi; Mark F Mehler
Journal:  Curr Neurol Neurosci Rep       Date:  2011-10       Impact factor: 5.081

Review 4.  Epigenome-wide association studies for common human diseases.

Authors:  Vardhman K Rakyan; Thomas A Down; David J Balding; Stephan Beck
Journal:  Nat Rev Genet       Date:  2011-07-12       Impact factor: 53.242

5.  MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case--control samples.

Authors:  Karolina A Aberg; Joseph L McClay; Srilaxmi Nerella; Lin Y Xie; Shaunna L Clark; Alexandra D Hudson; Jozsef Bukszár; Daniel Adkins; Christina M Hultman; Patrick F Sullivan; Patrik K E Magnusson; Edwin J C G van den Oord
Journal:  Epigenomics       Date:  2012-12       Impact factor: 4.778

6.  The RUNX1/IL-34/CSF-1R axis is an autocrinally regulated modulator of resistance to BRAF-V600E inhibition in melanoma.

Authors:  Orsi Giricz; Yongkai Mo; Kimberly B Dahlman; Xiomaris M Cotto-Rios; Chiara Vardabasso; Hoa Nguyen; Bernice Matusow; Matthias Bartenstein; Veronika Polishchuk; Douglas B Johnson; Tushar D Bhagat; Rafe Shellooe; Elizabeth Burton; James Tsai; Chao Zhang; Gaston Habets; John M Greally; Yiting Yu; Paraic A Kenny; Gregg B Fields; Kith Pradhan; E Richard Stanley; Emily Bernstein; Gideon Bollag; Evripidis Gavathiotis; Brian L West; Jeffrey A Sosman; Amit K Verma
Journal:  JCI Insight       Date:  2018-07-26

Review 7.  Anticancer activity of green tea polyphenols in prostate gland.

Authors:  Pierpaola Davalli; Federica Rizzi; Andrea Caporali; Davide Pellacani; Serena Davoli; Saverio Bettuzzi; Maurizio Brausi; Domenico D'Arca
Journal:  Oxid Med Cell Longev       Date:  2012-05-15       Impact factor: 6.543

8.  Differential epigenome-wide DNA methylation patterns in childhood obesity-associated asthma.

Authors:  Deepa Rastogi; Masako Suzuki; John M Greally
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

9.  Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.

Authors:  Bo Zhang; Yan Zhou; Nan Lin; Rebecca F Lowdon; Chibo Hong; Raman P Nagarajan; Jeffrey B Cheng; Daofeng Li; Michael Stevens; Hyung Joo Lee; Xiaoyun Xing; Jia Zhou; Vasavi Sundaram; Ginell Elliott; Junchen Gu; Taoping Shi; Philippe Gascard; Mahvash Sigaroudinia; Thea D Tlsty; Theresa Kadlecek; Arthur Weiss; Henriette O'Geen; Peggy J Farnham; Cécile L Maire; Keith L Ligon; Pamela A F Madden; Angela Tam; Richard Moore; Martin Hirst; Marco A Marra; Baoxue Zhang; Joseph F Costello; Ting Wang
Journal:  Genome Res       Date:  2013-06-26       Impact factor: 9.043

10.  Intrauterine Programming of Diabetes Induced Cardiac Embryopathy.

Authors:  Rolanda Lister; Alyssa Chamberlain; Francine Einstein; Bingruo Wu; DeYou Zheng; Bin Zhou
Journal:  Diabetes Obes Int J       Date:  2019-05-06
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