Literature DB >> 19007886

Eukaryotic gene regulation in three dimensions and its impact on genome evolution.

M Madan Babu1, Sarath Chandra Janga, Ines de Santiago, Ana Pombo.   

Abstract

Recent advances in molecular techniques and high-resolution imaging are beginning to provide exciting insights into the higher order chromatin organization within the cell nucleus and its influence on eukaryotic gene regulation. This improved understanding of gene regulation also raises fundamental questions about how spatial features might have constrained the organization of genes on eukaryotic chromosomes and how mutations that affect these processes might contribute to disease conditions. In this review, we discuss recent studies that highlight the role of spatial components in gene regulation and their impact on genome evolution. We then address implications for human diseases and outline new directions for future research.

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Mesh:

Year:  2008        PMID: 19007886     DOI: 10.1016/j.gde.2008.10.002

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


  20 in total

1.  The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome.

Authors:  Subhajyoti De; Sarah A Teichmann; M Madan Babu
Journal:  Genome Res       Date:  2009-02-19       Impact factor: 9.043

2.  Did the modulation of expression noise shape the evolution of three dimensional genome organizations in eukaryotes?

Authors:  Kuljeet Singh Sandhu
Journal:  Nucleus       Date:  2012-05-01       Impact factor: 4.197

Review 3.  Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information.

Authors:  Georgi Muskhelishvili; Andrew Travers
Journal:  Cell Mol Life Sci       Date:  2013-06-15       Impact factor: 9.261

4.  Comparison of diverse developmental transcriptomes reveals that coexpression of gene neighbors is not evolutionarily conserved.

Authors:  Itai Yanai; Craig P Hunter
Journal:  Genome Res       Date:  2009-09-10       Impact factor: 9.043

Review 5.  Bioinformatics and systems biology.

Authors:  Prahlad T Ram; John Mendelsohn; Gordon B Mills
Journal:  Mol Oncol       Date:  2012-02-17       Impact factor: 6.603

6.  A 3,000-loci transcription map of chromosome 3B unravels the structural and functional features of gene islands in hexaploid wheat.

Authors:  Camille Rustenholz; Frédéric Choulet; Christel Laugier; Jan Safár; Hana Simková; Jaroslav Dolezel; Federica Magni; Simone Scalabrin; Federica Cattonaro; Sonia Vautrin; Arnaud Bellec; Hélène Bergès; Catherine Feuillet; Etienne Paux
Journal:  Plant Physiol       Date:  2011-10-27       Impact factor: 8.340

7.  Evolutionary tinkering with conserved components of a transcriptional regulatory network.

Authors:  Hugo Lavoie; Hervé Hogues; Jaideep Mallick; Adnane Sellam; André Nantel; Malcolm Whiteway
Journal:  PLoS Biol       Date:  2010-03-09       Impact factor: 8.029

8.  Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions.

Authors:  Wei-Hua Chen; Juliette de Meaux; Martin J Lercher
Journal:  BMC Genomics       Date:  2010-03-16       Impact factor: 3.969

9.  Neighbourhood continuity is not required for correct testis gene expression in Drosophila.

Authors:  Lisa A Meadows; Yuk Sang Chan; John Roote; Steven Russell
Journal:  PLoS Biol       Date:  2010-11-30       Impact factor: 8.029

10.  HIV promoter integration site primarily modulates transcriptional burst size rather than frequency.

Authors:  Ron Skupsky; John C Burnett; Jonathan E Foley; David V Schaffer; Adam P Arkin
Journal:  PLoS Comput Biol       Date:  2010-09-30       Impact factor: 4.475

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