Literature DB >> 21963133

Seeing elegance in gene regulatory networks of the worm.

Eric L Van Nostrand1, Stuart K Kim.   

Abstract

There has been a recent explosion in the wealth of genomic data available to C. elegans researchers, as efforts to characterize gene expression and its regulators at a molecular level have borne significant fruit. Detailed measurement of gene expression at a variety of developmental stages, and in numerous individual tissues, has dramatically increased our understanding of cell-type-specific gene expression networks. Characterization of the targets of transcription factors, chromatin-binding proteins, and miRNAs has provided genome-wide insights into the mechanisms governing gene expression. Development of new techniques have allowed this characterization to begin to shift from whole-organism studies to tissue-level, and even single-cell-level profiling, creating a first glimpse into gene regulatory circuits at the single-cell level in a living organism. Integration of these datasets has yielded novel insights into evolution, gene expression regulation, and the link between sequence and phenotype.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21963133      PMCID: PMC3224770          DOI: 10.1016/j.gde.2011.08.007

Source DB:  PubMed          Journal:  Curr Opin Genet Dev        ISSN: 0959-437X            Impact factor:   5.578


  67 in total

1.  Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase.

Authors:  B van Steensel; S Henikoff
Journal:  Nat Biotechnol       Date:  2000-04       Impact factor: 54.908

2.  A global profile of germline gene expression in C. elegans.

Authors:  V Reinke; H E Smith; J Nance; J Wang; C Van Doren; R Begley; S J Jones; E B Davis; S Scherer; S Ward; S K Kim
Journal:  Mol Cell       Date:  2000-09       Impact factor: 17.970

3.  A gene expression map for Caenorhabditis elegans.

Authors:  S K Kim; J Lund; M Kiraly; K Duke; M Jiang; J M Stuart; A Eizinger; B N Wylie; G S Davidson
Journal:  Science       Date:  2001-09-14       Impact factor: 47.728

4.  Broad chromosomal domains of histone modification patterns in C. elegans.

Authors:  Tao Liu; Andreas Rechtsteiner; Thea A Egelhofer; Anne Vielle; Isabel Latorre; Ming-Sin Cheung; Sevinc Ercan; Kohta Ikegami; Morten Jensen; Paulina Kolasinska-Zwierz; Heidi Rosenbaum; Hyunjin Shin; Scott Taing; Teruaki Takasaki; A Leonardo Iniguez; Arshad Desai; Abby F Dernburg; Hiroshi Kimura; Jason D Lieb; Julie Ahringer; Susan Strome; X Shirley Liu
Journal:  Genome Res       Date:  2010-12-22       Impact factor: 9.043

5.  Regulation of organogenesis by the Caenorhabditis elegans FoxA protein PHA-4.

Authors:  J Gaudet; S E Mango
Journal:  Science       Date:  2002-02-01       Impact factor: 47.728

6.  Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.

Authors:  Wei Niu; Zhi John Lu; Mei Zhong; Mihail Sarov; John I Murray; Cathleen M Brdlik; Judith Janette; Chao Chen; Pedro Alves; Elicia Preston; Cindie Slightham; Lixia Jiang; Anthony A Hyman; Stuart K Kim; Robert H Waterston; Mark Gerstein; Michael Snyder; Valerie Reinke
Journal:  Genome Res       Date:  2010-12-22       Impact factor: 9.043

7.  Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning.

Authors:  Sam Guoping Gu; Andrew Fire
Journal:  Chromosoma       Date:  2009-08-25       Impact factor: 4.316

8.  Analysis of cell fate from single-cell gene expression profiles in C. elegans.

Authors:  Xiao Liu; Fuhui Long; Hanchuan Peng; Sarah J Aerni; Min Jiang; Adolfo Sánchez-Blanco; John I Murray; Elicia Preston; Barbara Mericle; Serafim Batzoglou; Eugene W Myers; Stuart K Kim
Journal:  Cell       Date:  2009-10-30       Impact factor: 41.582

9.  Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans.

Authors:  Dimitrios G Zisoulis; Michael T Lovci; Melissa L Wilbert; Kasey R Hutt; Tiffany Y Liang; Amy E Pasquinelli; Gene W Yeo
Journal:  Nat Struct Mol Biol       Date:  2010-01-10       Impact factor: 15.369

10.  Co-regulation of alternative splicing by diverse splicing factors in Caenorhabditis elegans.

Authors:  Sergio Barberan-Soler; Pedro Medina; Jeffrey Estella; James Williams; Alan M Zahler
Journal:  Nucleic Acids Res       Date:  2010-08-30       Impact factor: 16.971

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  7 in total

Review 1.  The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit.

Authors:  Xiao Xu; Stuart K Kim
Journal:  Nat Rev Genet       Date:  2011-10-04       Impact factor: 53.242

Review 2.  Transcriptional regulation of gene expression in C. elegans.

Authors:  Valerie Reinke; Michael Krause; Peter Okkema
Journal:  WormBook       Date:  2013-06-04

Review 3.  The embryo as a laboratory: quantifying transcription in Drosophila.

Authors:  Thomas Gregor; Hernan G Garcia; Shawn C Little
Journal:  Trends Genet       Date:  2014-07-06       Impact factor: 11.639

4.  Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.

Authors:  M S Vijayabaskar; Debbie K Goode; Nadine Obier; Monika Lichtinger; Amber M L Emmett; Fatin N Zainul Abidin; Nisar Shar; Rebecca Hannah; Salam A Assi; Michael Lie-A-Ling; Berthold Gottgens; Georges Lacaud; Valerie Kouskoff; Constanze Bonifer; David R Westhead
Journal:  PLoS Comput Biol       Date:  2019-11-04       Impact factor: 4.475

5.  Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.

Authors:  Stephen M Blazie; Cody Babb; Henry Wilky; Alan Rawls; Jin G Park; Marco Mangone
Journal:  BMC Biol       Date:  2015-01-20       Impact factor: 7.431

6.  Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation.

Authors:  Debbie K Goode; Nadine Obier; M S Vijayabaskar; Michael Lie-A-Ling; Andrew J Lilly; Rebecca Hannah; Monika Lichtinger; Kiran Batta; Magdalena Florkowska; Rahima Patel; Mairi Challinor; Kirstie Wallace; Jane Gilmour; Salam A Assi; Pierre Cauchy; Maarten Hoogenkamp; David R Westhead; Georges Lacaud; Valerie Kouskoff; Berthold Göttgens; Constanze Bonifer
Journal:  Dev Cell       Date:  2016-02-25       Impact factor: 12.270

7.  Ectopic hbox12 Expression Evoked by Histone Deacetylase Inhibition Disrupts Axial Specification of the Sea Urchin Embryo.

Authors:  Vincenzo Cavalieri; Giovanni Spinelli
Journal:  PLoS One       Date:  2015-11-30       Impact factor: 3.240

  7 in total

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