Journal Title
Title of Journal: Chromosoma
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Publisher
Springer Berlin Heidelberg
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Authors: Corinna Lieleg Nils Krietenstein Maria Walker Philipp Korber
Publish Date: 2014/12/23
Volume: 124, Issue: 2, Pages: 131-151
Abstract
Eukaryotic nuclear DNA is packaged into nucleosomes During the past decade genomewide nucleosome mapping across species revealed the high degree of order in nucleosome positioning There is a conserved stereotypical nucleosome organization around transcription start sites TSSs with a nucleosomedepleted region NDR upstream of the TSS and a TSSaligned regular array of evenly spaced nucleosomes downstream over the gene body As nucleosomes largely impede access to DNA and thereby provide an important level of genome regulation it is of general interest to understand the mechanisms generating nucleosome positioning and especially the stereotypical NDRarray pattern We focus here on the most advanced models unicellular yeasts and review the progress in mapping nucleosomes and which nucleosome positioning mechanisms are discussed There are four mechanistic aspects How are NDRs generated How are individual nucleosomes positioned especially those flanking the NDRs How are nucleosomes evenly spaced leading to regular arrays How are regular arrays aligned at TSSs The main candidates for nucleosome positioning determinants are intrinsic DNA binding preferences of the histone octamer specific DNA binding factors nucleosome remodeling enzymes transcription and statistical positioning We summarize the state of the art in an integrative model where nucleosomes are positioned by a combination of all these candidate determinants We highlight the predominance of active mechanisms involving nucleosome remodeling enzymes which may be recruited by DNA binding factors and the transcription machinery While this mechanistic framework emerged clearly during recent years the involved factors and their mechanisms are still poorly understood and require future efforts combining in vivo and in vitro approachesWe apologize to all colleagues whose work we could not cite because of space restrictions This work was funded by the German Research Community DFG through the Collaborative Research Cluster SFB1064 and by the Bavarian State Ministry of Education and Culture Science and the Arts through the Bavarian Research Network for Molecular Biosystems BioSysNet
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