Literature DB >> 23374338

Genomes on the edge: programmed genome instability in ciliates.

John R Bracht1, Wenwen Fang, Aaron David Goldman, Egor Dolzhenko, Elizabeth M Stein, Laura F Landweber.   

Abstract

Ciliates are an ancient and diverse group of microbial eukaryotes that have emerged as powerful models for RNA-mediated epigenetic inheritance. They possess extensive sets of both tiny and long noncoding RNAs that, together with a suite of proteins that includes transposases, orchestrate a broad cascade of genome rearrangements during somatic nuclear development. This Review emphasizes three important themes: the remarkable role of RNA in shaping genome structure, recent discoveries that unify many deeply diverged ciliate genetic systems, and a surprising evolutionary "sign change" in the role of small RNAs between major species groups.
Copyright © 2013 Elsevier Inc. All rights reserved.

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Year:  2013        PMID： 23374338      PMCID： PMC3725814          DOI： 10.1016/j.cell.2013.01.005

Source DB:  PubMed          Journal:  Cell        ISSN： 0092-8674            Impact factor:   41.582


  104 in total

1.  Mobile elements bounded by C4A4 telomeric repeats in Oxytricha fallax.

Authors:  G Herrick; S Cartinhour; D Dawson; D Ang; R Sheets; A Lee; K Williams
Journal:  Cell       Date:  1985-12       Impact factor: 41.582

2.  Genetic consequences of programmed genome rearrangement.

Authors:  Jeramiah J Smith; Carl Baker; Evan E Eichler; Chris T Amemiya
Journal:  Curr Biol       Date:  2012-07-19       Impact factor: 10.834

3.  A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena.

Authors:  E H Blackburn; J G Gall
Journal:  J Mol Biol       Date:  1978-03-25       Impact factor: 5.469

Review 4.  RNA-Mediated Epigenetic Programming of Genome Rearrangements.

Authors:  Mariusz Nowacki; Keerthi Shetty; Laura F Landweber
Journal:  Annu Rev Genomics Hum Genet       Date:  2011       Impact factor: 8.929

5.  Analysis of a piwi-related gene implicates small RNAs in genome rearrangement in tetrahymena.

Authors:  Kazufumi Mochizuki; Noah A Fine; Toshitaka Fujisawa; Martin A Gorovsky
Journal:  Cell       Date:  2002-09-20       Impact factor: 41.582

6.  Developmentally regulated chromosome fragmentation linked to imprecise elimination of repeated sequences in paramecia.

Authors:  Anne Le Mouël; Alain Butler; François Caron; Eric Meyer
Journal:  Eukaryot Cell       Date:  2003-10

7.  Lia1p, a novel protein required during nuclear differentiation for genome-wide DNA rearrangements in Tetrahymena thermophila.

Authors:  Charles H Rexer; Douglas L Chalker
Journal:  Eukaryot Cell       Date:  2007-06-22

8.  Homology-dependent maternal inhibition of developmental excision of internal eliminated sequences in Paramecium tetraurelia.

Authors:  S Duharcourt; A M Keller; E Meyer
Journal:  Mol Cell Biol       Date:  1998-12       Impact factor: 4.272

9.  Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Authors:  Jonathan A Eisen; Robert S Coyne; Martin Wu; Dongying Wu; Mathangi Thiagarajan; Jennifer R Wortman; Jonathan H Badger; Qinghu Ren; Paolo Amedeo; Kristie M Jones; Luke J Tallon; Arthur L Delcher; Steven L Salzberg; Joana C Silva; Brian J Haas; William H Majoros; Maryam Farzad; Jane M Carlton; Roger K Smith; Jyoti Garg; Ronald E Pearlman; Kathleen M Karrer; Lei Sun; Gerard Manning; Nels C Elde; Aaron P Turkewitz; David J Asai; David E Wilkes; Yufeng Wang; Hong Cai; Kathleen Collins; B Andrew Stewart; Suzanne R Lee; Katarzyna Wilamowska; Zasha Weinberg; Walter L Ruzzo; Dorota Wloga; Jacek Gaertig; Joseph Frankel; Che-Chia Tsao; Martin A Gorovsky; Patrick J Keeling; Ross F Waller; Nicola J Patron; J Michael Cherry; Nicholas A Stover; Cynthia J Krieger; Christina del Toro; Hilary F Ryder; Sondra C Williamson; Rebecca A Barbeau; Eileen P Hamilton; Eduardo Orias
Journal:  PLoS Biol       Date:  2006-09       Impact factor: 8.029

10.  The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences.

Authors:  Olivier Arnaiz; Nathalie Mathy; Céline Baudry; Sophie Malinsky; Jean-Marc Aury; Cyril Denby Wilkes; Olivier Garnier; Karine Labadie; Benjamin E Lauderdale; Anne Le Mouël; Antoine Marmignon; Mariusz Nowacki; Julie Poulain; Malgorzata Prajer; Patrick Wincker; Eric Meyer; Sandra Duharcourt; Laurent Duret; Mireille Bétermier; Linda Sperling
Journal:  PLoS Genet       Date:  2012-10-04       Impact factor: 5.917
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  40 in total

Review 1.  Nuclear Noncoding RNAs and Genome Stability.

Authors:  Jasbeer S Khanduja; Isabel A Calvo; Richard I Joh; Ian T Hill; Mo Motamedi
Journal:  Mol Cell       Date:  2016-07-07       Impact factor: 17.970

Review 2.  Origin, structure and function of millions of chromosomes present in the macronucleus of unicellular eukaryotic ciliate, Oxytricha trifallax: a model organism for transgenerationally programmed genome rearrangements.

Authors:  Sushil Kumar; Renu Kumari
Journal:  J Genet       Date:  2015-06       Impact factor: 1.166

3.  Identification of a DNA N6-Adenine Methyltransferase Complex and Its Impact on Chromatin Organization.

Authors:  Leslie Y Beh; Galia T Debelouchina; Derek M Clay; Robert E Thompson; Kelsi A Lindblad; Elizabeth R Hutton; John R Bracht; Robert P Sebra; Tom W Muir; Laura F Landweber
Journal:  Cell       Date:  2019-05-16       Impact factor: 41.582

Review 4.  Living Organisms Author Their Read-Write Genomes in Evolution.

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

Review 5.  Programmed Genome Rearrangements in the Ciliate Oxytricha.

Authors:  V Talya Yerlici; Laura F Landweber
Journal:  Microbiol Spectr       Date:  2014-12

6.  Recurring patterns among scrambled genes in the encrypted genome of the ciliate Oxytricha trifallax.

Authors:  Jonathan Burns; Denys Kukushkin; Xiao Chen; Laura F Landweber; Masahico Saito; Nataša Jonoska
Journal:  J Theor Biol       Date:  2016-09-02       Impact factor: 2.691

7.  Beyond transcriptional silencing: is methylcytosine a widely conserved eukaryotic DNA elimination mechanism?

Authors:  John R Bracht
Journal:  Bioessays       Date:  2014-02-12       Impact factor: 4.345

Review 8.  Programmed DNA elimination in multicellular organisms.

Authors:  Jianbin Wang; Richard E Davis
Journal:  Curr Opin Genet Dev       Date:  2014-06-02       Impact factor: 5.578

Review 9.  Gene silencing and sex determination by programmed DNA elimination in parasitic nematodes.

Authors:  Adrian Streit; Jianbin Wang; Yuanyuan Kang; Richard E Davis
Journal:  Curr Opin Microbiol       Date:  2016-06-14       Impact factor: 7.934

10.  Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome.

Authors:  Eileen P Hamilton; Aurélie Kapusta; Piroska E Huvos; Shelby L Bidwell; Nikhat Zafar; Haibao Tang; Michalis Hadjithomas; Vivek Krishnakumar; Jonathan H Badger; Elisabet V Caler; Carsten Russ; Qiandong Zeng; Lin Fan; Joshua Z Levin; Terrance Shea; Sarah K Young; Ryan Hegarty; Riza Daza; Sharvari Gujja; Jennifer R Wortman; Bruce W Birren; Chad Nusbaum; Jainy Thomas; Clayton M Carey; Ellen J Pritham; Cédric Feschotte; Tomoko Noto; Kazufumi Mochizuki; Romeo Papazyan; Sean D Taverna; Paul H Dear; Donna M Cassidy-Hanley; Jie Xiong; Wei Miao; Eduardo Orias; Robert S Coyne
Journal:  Elife       Date:  2016-11-28       Impact factor: 8.140
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