Literature DB >> 23876611

How life changes itself: the Read-Write (RW) genome.

James A Shapiro1.   

Abstract

The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.
© 2013 Elsevier B.V. All rights reserved.

Keywords:  A; BER; C; CDS; CNE; CRISPR; CRM; CSR; DS; Epigenetics; G; Genome inscriptions; I; K; LTR; MB; MGE; Mobile genetic elements (MGEs); NER; NGE; NHEJ; Natural genetic engineering (NGE); R; RITS; RNA interference by transcriptional silencing; Rec; T; TF; TIR; TPRT; U; WGD; adenine; arginine; base excision repair; cis-regulatory module; class switch recombination; clustered regularly interspaced short palindromic repeats; coding sequence; conserved nucleotide element; cytosine; double-strand; guanine; inosine; long terminal repeat; lysine; mega-base-pairs; mobile genetic element; natural genetic engineering; nc; non-coding; non-homologous end joining; nucleotide excision repair; recombination; target-primed reverse transcription; terminal inverted repeat; thymine; transcription factor; uracil; whole genome duplication

Mesh:

Year:  2013        PMID: 23876611     DOI: 10.1016/j.plrev.2013.07.001

Source DB:  PubMed          Journal:  Phys Life Rev        ISSN: 1571-0645            Impact factor:   11.025


  21 in total

1.  You cannot tell a book by looking at the cover: Cryptic complexity in bacterial evolution.

Authors:  Qiucen Zhang; Julia Bos; Grigory Tarnopolskiy; James C Sturm; Hyunsung Kim; Nader Pourmand; Robert H Austin
Journal:  Biomicrofluidics       Date:  2014-09-09       Impact factor: 2.800

Review 2.  Pragmatic turn in biology: From biological molecules to genetic content operators.

Authors:  Guenther Witzany
Journal:  World J Biol Chem       Date:  2014-08-26

Review 3.  Physiology of the read-write genome.

Authors:  James A Shapiro
Journal:  J Physiol       Date:  2014-06-01       Impact factor: 5.182

Review 4.  From gene action to reactive genomes.

Authors:  Evelyn Fox Keller
Journal:  J Physiol       Date:  2014-06-01       Impact factor: 5.182

Review 5.  A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles.

Authors:  Janine Aucamp; Abel J Bronkhorst; Christoffel P S Badenhorst; Piet J Pretorius
Journal:  Cell Mol Life Sci       Date:  2016-09-20       Impact factor: 9.261

6.  Stochasticity and determinism in cancer creation and progression.

Authors:  Paul C Davies; David B Agus
Journal:  Converg Sci Phys Oncol       Date:  2016-01-07

Review 7.  Biological action in Read-Write genome evolution.

Authors:  James A Shapiro
Journal:  Interface Focus       Date:  2017-08-18       Impact factor: 3.906

Review 8.  Living Organisms Author Their Read-Write Genomes in Evolution.

Authors:  James A Shapiro
Journal:  Biology (Basel)       Date:  2017-12-06

9.  Evolution: life has evolved to evolve: comment on "How life changes itself: the Read-Write (RW) genome" by James Shapiro.

Authors:  Michael W Deem
Journal:  Phys Life Rev       Date:  2013-07-10       Impact factor: 11.025

10.  Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.

Authors:  Jacopo Grilli; Mariacristina Romano; Federico Bassetti; Marco Cosentino Lagomarsino
Journal:  Nucleic Acids Res       Date:  2014-05-14       Impact factor: 16.971

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