Literature DB >> 21941622

The decade of the epigenomes?

Joost H A Martens1, Hendrik G Stunnenberg, Colin Logie.   

Abstract

The beginning of this century was not only marked by the publication of the first draft of the human genome but also set off a decade of intense research on epigenetic phenomena. Apart from DNA methylation, it became clear that many other factors including a wide range of histone modifications, different shades of chromatin accessibility, and a vast suite of noncoding RNAs comprise the epigenome. With the recent advances in sequencing technologies, it has now become possible to analyze many of these features in depth, allowing for the first time the establishment of complete epigenomic profiles for basically every cell type of interest. Here, we will discuss the recent advances that allow comprehensive epigenetic mapping, highlight several projects that set out to better understand the epigenome, and discuss the impact that epigenomic mapping can have on our understanding of both healthy and diseased cells.

Entities:  

Keywords:  ChIP-seq; DNA methylation; RNA-seq; chromatin accessibility; epigenome

Year:  2011        PMID: 21941622      PMCID: PMC3174262          DOI: 10.1177/1947601911417860

Source DB:  PubMed          Journal:  Genes Cancer        ISSN: 1947-6019


  40 in total

1.  NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation.

Authors:  Gaetano Gargiulo; Samuel Levy; Gabriele Bucci; Mauro Romanenghi; Lorenzo Fornasari; Karen Y Beeson; Susanne M Goldberg; Matteo Cesaroni; Marco Ballarini; Fabio Santoro; Natalie Bezman; Gianmaria Frigè; Philip D Gregory; Michael C Holmes; Robert L Strausberg; Pier Giuseppe Pelicci; Fyodor D Urnov; Saverio Minucci
Journal:  Dev Cell       Date:  2009-03       Impact factor: 12.270

2.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

Authors:  Paul G Giresi; Jonghwan Kim; Ryan M McDaniell; Vishwanath R Iyer; Jason D Lieb
Journal:  Genome Res       Date:  2006-12-19       Impact factor: 9.043

Review 3.  Transgenerational epigenetic effects.

Authors:  Neil A Youngson; Emma Whitelaw
Journal:  Annu Rev Genomics Hum Genet       Date:  2008       Impact factor: 8.929

Review 4.  Epigenetics and the environmental regulation of the genome and its function.

Authors:  Tie-Yuan Zhang; Michael J Meaney
Journal:  Annu Rev Psychol       Date:  2010       Impact factor: 24.137

5.  DNMT3A mutations in acute myeloid leukemia.

Authors:  Timothy J Ley; Li Ding; Matthew J Walter; Michael D McLellan; Tamara Lamprecht; David E Larson; Cyriac Kandoth; Jacqueline E Payton; Jack Baty; John Welch; Christopher C Harris; Cheryl F Lichti; R Reid Townsend; Robert S Fulton; David J Dooling; Daniel C Koboldt; Heather Schmidt; Qunyuan Zhang; John R Osborne; Ling Lin; Michelle O'Laughlin; Joshua F McMichael; Kim D Delehaunty; Sean D McGrath; Lucinda A Fulton; Vincent J Magrini; Tammi L Vickery; Jasreet Hundal; Lisa L Cook; Joshua J Conyers; Gary W Swift; Jerry P Reed; Patricia A Alldredge; Todd Wylie; Jason Walker; Joelle Kalicki; Mark A Watson; Sharon Heath; William D Shannon; Nobish Varghese; Rakesh Nagarajan; Peter Westervelt; Michael H Tomasson; Daniel C Link; Timothy A Graubert; John F DiPersio; Elaine R Mardis; Richard K Wilson
Journal:  N Engl J Med       Date:  2010-11-10       Impact factor: 91.245

6.  Discovery and characterization of chromatin states for systematic annotation of the human genome.

Authors:  Jason Ernst; Manolis Kellis
Journal:  Nat Biotechnol       Date:  2010-07-25       Impact factor: 54.908

7.  A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.

Authors:  Thomas A Down; Vardhman K Rakyan; Daniel J Turner; Paul Flicek; Heng Li; Eugene Kulesha; Stefan Gräf; Nathan Johnson; Javier Herrero; Eleni M Tomazou; Natalie P Thorne; Liselotte Bäckdahl; Marlis Herberth; Kevin L Howe; David K Jackson; Marcos M Miretti; John C Marioni; Ewan Birney; Tim J P Hubbard; Richard Durbin; Simon Tavaré; Stephan Beck
Journal:  Nat Biotechnol       Date:  2008-07       Impact factor: 54.908

8.  Acquired mutations in TET2 are common in myelodysplastic syndromes.

Authors:  Saskia M C Langemeijer; Roland P Kuiper; Marieke Berends; Ruth Knops; Mariam G Aslanyan; Marion Massop; Ellen Stevens-Linders; Patricia van Hoogen; Ad Geurts van Kessel; Reinier A P Raymakers; Eveline J Kamping; Gregor E Verhoef; Estelle Verburgh; Anne Hagemeijer; Peter Vandenberghe; Theo de Witte; Bert A van der Reijden; Joop H Jansen
Journal:  Nat Genet       Date:  2009-05-31       Impact factor: 38.330

9.  Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Authors:  Gordon Robertson; Martin Hirst; Matthew Bainbridge; Misha Bilenky; Yongjun Zhao; Thomas Zeng; Ghia Euskirchen; Bridget Bernier; Richard Varhol; Allen Delaney; Nina Thiessen; Obi L Griffith; Ann He; Marco Marra; Michael Snyder; Steven Jones
Journal:  Nat Methods       Date:  2007-06-11       Impact factor: 28.547

10.  Transcriptome sequencing to detect gene fusions in cancer.

Authors:  Christopher A Maher; Chandan Kumar-Sinha; Xuhong Cao; Shanker Kalyana-Sundaram; Bo Han; Xiaojun Jing; Lee Sam; Terrence Barrette; Nallasivam Palanisamy; Arul M Chinnaiyan
Journal:  Nature       Date:  2009-01-11       Impact factor: 49.962

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  5 in total

1.  BLUEPRINT: mapping human blood cell epigenomes.

Authors:  Joost H A Martens; Hendrik G Stunnenberg
Journal:  Haematologica       Date:  2013-10       Impact factor: 9.941

Review 2.  Personalized medicine: Genetic risk prediction of drug response.

Authors:  Ge Zhang; Daniel W Nebert
Journal:  Pharmacol Ther       Date:  2017-02-14       Impact factor: 12.310

3.  Is this the right normalization? A diagnostic tool for ChIP-seq normalization.

Authors:  Claudia Angelini; Ruth Heller; Rita Volkinshtein; Daniel Yekutieli
Journal:  BMC Bioinformatics       Date:  2015-05-09       Impact factor: 3.169

4.  Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses.

Authors:  Angela Nebbioso; Rosaria Benedetti; Mariarosaria Conte; Vincenzo Carafa; Floriana De Bellis; Jani Shaik; Filomena Matarese; Bartolomeo Della Ventura; Felice Gesuele; Raffaele Velotta; Joost H A Martens; Hendrik G Stunnenberg; Carlo Altucci; Lucia Altucci
Journal:  Sci Rep       Date:  2017-09-15       Impact factor: 4.379

5.  Scrutinizing the epigenetics revolution.

Authors:  Maurizio Meloni; Giuseppe Testa
Journal:  Biosocieties       Date:  2014-11
  5 in total

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