Literature DB >> 21266347

Next generation sequencing based approaches to epigenomics.

Martin Hirst1, Marco A Marra.   

Abstract

Next generation sequencing has brought epigenomic studies to the forefront of current research. The power of massively parallel sequencing coupled to innovative molecular and computational techniques has allowed researchers to profile the epigenome at resolutions that were unimaginable only a few years ago. With early proof of concept studies published, the field is now moving into the next phase where the importance of method standardization and rigorous quality control are becoming paramount. In this review we will describe methodologies that have been developed to profile the epigenome using next generation sequencing platforms. We will discuss these in terms of library preparation, sequence platforms and analysis techniques.

Mesh:

Year:  2010        PMID: 21266347      PMCID: PMC3080743          DOI: 10.1093/bfgp/elq035

Source DB:  PubMed          Journal:  Brief Funct Genomics        ISSN: 2041-2649            Impact factor:   4.241


  79 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.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.

Authors:  M Frommer; L E McDonald; D S Millar; C M Collis; F Watt; G W Grigg; P L Molloy; C L Paul
Journal:  Proc Natl Acad Sci U S A       Date:  1992-03-01       Impact factor: 11.205

3.  A massively parallel PicoTiterPlate based platform for discrete picoliter-scale polymerase chain reactions.

Authors:  John H Leamon; William L Lee; Karrie R Tartaro; Janna R Lanza; Gary J Sarkis; Alex D deWinter; Jan Berka; Michael Weiner; Jonathan M Rothberg; Kenton L Lohman
Journal:  Electrophoresis       Date:  2003-11       Impact factor: 3.535

4.  Chromatin structure: a repeating unit of histones and DNA.

Authors:  R D Kornberg
Journal:  Science       Date:  1974-05-24       Impact factor: 47.728

Review 5.  Genome-scale DNA methylation analysis.

Authors:  Shaun D Fouse; Raman O Nagarajan; Joseph F Costello
Journal:  Epigenomics       Date:  2010-02       Impact factor: 4.778

6.  The NIH Roadmap Epigenomics Mapping Consortium.

Authors:  Bradley E Bernstein; John A Stamatoyannopoulos; Joseph F Costello; Bing Ren; Aleksandar Milosavljevic; Alexander Meissner; Manolis Kellis; Marco A Marra; Arthur L Beaudet; Joseph R Ecker; Peggy J Farnham; Martin Hirst; Eric S Lander; Tarjei S Mikkelsen; James A Thomson
Journal:  Nat Biotechnol       Date:  2010-10       Impact factor: 54.908

7.  BigWig and BigBed: enabling browsing of large distributed datasets.

Authors:  W J Kent; A S Zweig; G Barber; A S Hinrichs; D Karolchik
Journal:  Bioinformatics       Date:  2010-07-17       Impact factor: 6.937

8.  Identification of 5-methylcytosine in DNA fragments immobilized on nitrocellulose paper.

Authors:  H Sano; H D Royer; R Sager
Journal:  Proc Natl Acad Sci U S A       Date:  1980-06       Impact factor: 11.205

9.  Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene.

Authors:  M J Solomon; P L Larsen; A Varshavsky
Journal:  Cell       Date:  1988-06-17       Impact factor: 41.582

10.  Histone H4 acetylation distinguishes coding regions of the human genome from heterochromatin in a differentiation-dependent but transcription-independent manner.

Authors:  L P O'Neill; B M Turner
Journal:  EMBO J       Date:  1995-08-15       Impact factor: 11.598

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  25 in total

1.  The decade of the epigenomes?

Authors:  Joost H A Martens; Hendrik G Stunnenberg; Colin Logie
Journal:  Genes Cancer       Date:  2011-06

Review 2.  Space, the final frontier: A critical review of recent experiments performed in microgravity.

Authors:  Joshua P Vandenbrink; John Z Kiss
Journal:  Plant Sci       Date:  2015-11-07       Impact factor: 4.729

Review 3.  Methods of integrating data to uncover genotype-phenotype interactions.

Authors:  Marylyn D Ritchie; Emily R Holzinger; Ruowang Li; Sarah A Pendergrass; Dokyoon Kim
Journal:  Nat Rev Genet       Date:  2015-01-13       Impact factor: 53.242

Review 4.  -Omic and Electronic Health Record Big Data Analytics for Precision Medicine.

Authors:  Po-Yen Wu; Chih-Wen Cheng; Chanchala D Kaddi; Janani Venugopalan; Ryan Hoffman; May D Wang
Journal:  IEEE Trans Biomed Eng       Date:  2016-10-10       Impact factor: 4.538

Review 5.  Prostate cancer epigenome.

Authors:  Swathi Chinaranagari; Pankaj Sharma; Nathan J Bowen; Jaideep Chaudhary
Journal:  Methods Mol Biol       Date:  2015

Review 6.  Deciphering bacterial epigenomes using modern sequencing technologies.

Authors:  John Beaulaurier; Eric E Schadt; Gang Fang
Journal:  Nat Rev Genet       Date:  2019-03       Impact factor: 53.242

Review 7.  Functional genomics data: privacy risk assessment and technological mitigation.

Authors:  Gamze Gürsoy; Tianxiao Li; Susanna Liu; Eric Ni; Charlotte M Brannon; Mark B Gerstein
Journal:  Nat Rev Genet       Date:  2021-11-10       Impact factor: 53.242

8.  Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data.

Authors:  Bo Hu; Yuan Ji; Yaomin Xu; Angela H Ting
Journal:  Stat Biosci       Date:  2013-05

9.  Promoter Hypomethylation and Expression Is Conserved in Mouse Chronic Lymphocytic Leukemia Induced by Decreased or Inactivated Dnmt3a.

Authors:  Staci L Haney; G Michael Upchurch; Jana Opavska; David Klinkebiel; Ryan A Hlady; Abhinav Suresh; Samuel J Pirruccello; Vipul Shukla; Runqing Lu; Stefan Costinean; Angie Rizzino; Adam R Karpf; Shantaram Joshi; Patrick Swanson; Rene Opavsky
Journal:  Cell Rep       Date:  2016-04-28       Impact factor: 9.423

10.  Aberrantly methylated-differentially genes and pathways among Iranian patients with colorectal cancer.

Authors:  Mahla Ghorbani; Marjan Azghandi; Mohammad Amin Kerachian
Journal:  Cancer Cell Int       Date:  2021-07-03       Impact factor: 5.722

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