Nucleosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes

Hebert Charles, Roest

Description

The position of a nucleosome, both translational along the DNA molecule and rotational between the histone core and the DNA, is controlled by many factors, including the regular occurrence of specific dinucleotides with a period of approximately 10 bp, important for the rotational setting of the DNA around the histone octamer. Results We show that such a 10 bp periodic signal of purine-purine dinucleotides occurs in phase with the transcription start site (TSS) of human genes and is centered on the position of the first (+1) nucleosome downstream of the TSS. These data support a direct link between transcription and the rotational setting of the nucleosome. The periodic signal is most prevalent in genes that contain CpG islands that are expressed at low levels in a tissue-specific manner and are involved in the control of transcription. Conclusions These results, together with several lines of evidence from the recent literature, support a new model whereby the +1 nucleosome could be more efficiently disassembled from gene promoters by H3K56 acetylation marks if the periodic signal specifies an optimal rotational setting.

Informations

• Publié par: biomed
• Publié le: 01 janvier 2010
• Nombre de lectures: 5
• Langue: English
• Poids de l'ouvrage: 3 Mo

Extrait

Hebert and Roest Crollius Genome Biology 2010, 11 :R51 http://genomebiology.com/2010/11/5/R51

R E S E A R C H  Open Access R N ese u ar c c l h eosome rotational setting is associated with transcriptional regulation in promoters of tissue-specific human genes Charles Hebert and Hugues Roest Crollius*

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Background nucleosome mapping data in different organisms [4-7]. Nucleosomes, composed of 147 bp of DNA wrapped These results, while primarily focusing on the transla- around a histone octamer, play a fundamental role of tional positions of nucleosomes along the DNA molecule, compacting DNA molecules inside the nucleus of eukary- also show that the rotational position of the histone otic cells [1], but also in the regulation of gene expression octamer with respect to the DNA molecule is important. [2,3]. Elucidating the molecular mechanisms that specify High-resolution maps indicate that individual the position of nucleosomes in a genome is important to nucleosomes tend to settle at approximately 10-bp inter- understand their role at the crossroads of essential cellu- vals around an average position in the genome [4,6,8]. lar functions. Histone cores, when forming a nucleosome with the Factors influencing nucleosome positioning likely DNA, thus appear to locally select one of several alterna- include DNA sequence-based information (either to tive positions on the DNA, as long as they are separated specify a favorable or unfavorable DNA structure or to by distances multiple of a helical turn. Importantly, allow for DNA-histone interactions), contacts between selecting one position rather than the next will translate neighboring nucleosomes, and chromatin remodeling the nucleosome by 10 bp, but will not change the rota- proteins. The extent and the modalities of these contribu- tional angle of the histone core with respect to the DNA tions are still being investigated, and different models molecule and its molecular environment. To wedge his- have been proposed to explain whole genome tones in their preferred rotational setting, the main theo- retic constraint is a periodic occurrence of specific * D   y C o or g r e es n p G o r n o d u e p n , c I e n : s h t r it c u @ t e d n e s.   f B r iologie de l'Ecole Normale Supérieure (IBENS), 46 dinucleotides at approximately 10-bp interval l s     i i s  n  si p g h n a if s i e rue d'Ulm, CNRS UMR8197, INSERM U1024, 75005 Paris Cedex 05, France with nucleosome positions [9-11]. This signa - Full list of author information is available at the end of the article cantly different between species. In yeast, it has been

© 2010 Hebert and Roest Crollius; licensee BioMed Central Ltd. This is an open access article distributed under the terms of th e Creative Bio Med  Central Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and rep ro- duction in any medium, provided the original work is properly cited.