Epigenetics: Core misconcept

A recent issue of PNAS opened with an unfortunate Core Concepts article titled “Epigenetics” (1). The author, a science writer, began promisingly enough:

[1]  Kevin Struhl,et al.  An Epigenetic Switch Involving NF-κB, Lin28, Let-7 MicroRNA, and IL6 Links Inflammation to Cell Transformation , 2009, Cell.

[2]  R. B. Azevedo,et al.  On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE , 2013, Genome biology and evolution.

[3]  Mark Ptashne,et al.  On the use of the word ‘epigenetic’ , 2007, Current Biology.

[4]  M. Ptashne.  Faddish Stuff: Epigenetics and the Inheritance of Acquired Characteristics , 2013, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[5]  T. Perlmann,et al.  Maintaining differentiated cellular identity , 2012, Nature Reviews Genetics.

[6]  S. Schreiber,et al.  Dimeric ligands define a role for transcriptional activation domains in reinitiation , 1996, Nature.

[7]  R. Paro,et al.  Polycomb/Trithorax response elements and epigenetic memory of cell identity , 2007, Development.

[8]  W. Doolittle.  Is junk DNA bunk? A critique of ENCODE , 2013, Proceedings of the National Academy of Sciences.

[9]  M. Gartenberg,et al.  Yeast heterochromatin is a dynamic structure that requires silencers continuously. , 2000, Genes & development.

[10]  O. Rando,et al.  Combinatorial complexity in chromatin structure and function: revisiting the histone code. , 2012, Current opinion in genetics & development.

[11]  Oliver Hobert,et al.  Transgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans , 2011, Cell.

[12]  E. Davidson.  The Regulatory Genome: Gene Regulatory Networks In Development And Evolution , 2006 .

[13]  Steven Henikoff,et al.  Histone modification: cause or cog? , 2011, Trends in genetics : TIG.

[14]  N. Friedman,et al.  Replication and Active Demethylation Represent Partially Overlapping Mechanisms for Erasure of H3K4me3 in Budding Yeast , 2010, PLoS genetics.

[15]  S. Henikoff,et al.  Genome-Wide Kinetics of Nucleosome Turnover Determined by Metabolic Labeling of Histones , 2010, Science.

[16]  K. Struhl,et al.  Dynamics of global histone acetylation and deacetylation in vivo: rapid restoration of normal histone acetylation status upon removal of activators and repressors. , 2002, Genes & development.

[17]  D. Moazed.  Small RNAs in transcriptional gene silencing and genome defence , 2009, Nature.

[18]  Eric H. Davidson,et al.  Transcriptional Network Logic: The Systems Biology of Development , 2013 .

[19]  T. Enver,et al.  Forcing cells to change lineages , 2009, Nature.

[20]  M. Grunstein.  Histone function in transcription. , 1990, Annual review of cell biology.

[21]  S. Eddy.  The ENCODE project: Missteps overshadowing a success , 2013, Current Biology.

[22]  J. Workman,et al.  reSETting chromatin during transcription elongation , 2013, Epigenetics.

[23]  S. Yamanaka,et al.  Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors , 2006, Cell.

[24]  O. Hobert.  Maintaining a memory by transcriptional autoregulation , 2011, Current Biology.