PMID: 12798677Jun 12, 2003Paper

Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites

Journal of Molecular Biology
François Képès

Abstract

The organization of transcription within the eukaryotic nucleus may be expected to both depend on and determine the structure of the chromosomes. This study shows that, in yeast, genes that are controlled by the same sequence-specific transcription factor tend to be regularly spaced along the chromosome arms; a similar period characterizes the spacing of origins of replication, although periodicity is less pronounced. The same period is found for most transcription factors within a chromosome arm. However, different periods are observed for different chromosome arms, making it unlikely that periodicity is caused by dedicated scaffolding proteins. Such regularities are consistent with a genome-wide loop model of chromosomes, in which coregulated genes tend to dynamically colocalize in 3D. This colocalization may also involve co-regulated genes belonging to different chromosomes, as suggested by partial conservation of the respective positioning of different transcription factors around the loops. Thus, binding at genuine regulatory sites on DNA would be optimized by locally increasing the concentration of multimeric transcription factors. In this model, self-organization of transcriptional initiation plays a major role in the fu...Continue Reading

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Citations

May 8, 2004·Nature Reviews. Genetics·Laurence D HurstMartin J Lercher
Dec 18, 2012·Nucleic Acids Research·Mohamed ElatiFrançois Képès
Sep 14, 2010·Algorithms for Molecular Biology : AMB·Ivan JunierFrançois Képès
Nov 7, 2007·Genome Biology·Juan F Poyatos, Laurence D Hurst
Feb 20, 2010·PLoS Computational Biology·Ivan JunierFrançois Képès
Jul 16, 2011·PLoS Computational Biology·Jing KangJianfeng Feng
Apr 7, 2005·Médecine sciences : M/S·François Képès
Apr 10, 2012·FEBS Letters·François KépèsIvan Junier
Apr 25, 2006·Journal of Molecular Biology·Martin J Lercher, Laurence D Hurst
Mar 7, 2015·Molecular Biology and Evolution·Avazeh T Ghanbarian, Laurence D Hurst
May 7, 2016·Nucleic Acids Research·Costas BouyioukosFrançois Képès
Jun 15, 2016·BMC Bioinformatics·Costas BouyioukosFrançois Képès
Jun 16, 2016·Scientific Reports·Costas BouyioukosFrançois Képès
Dec 11, 2003·Yeast
Aug 23, 2006·Human Molecular Genetics·Hong SunRunsheng Chen
Jul 9, 2004·Journal of Molecular Biology·François Képès

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