Publication Date:
2011-05-24
Description:
Nucleosomes are the basic packaging units of chromatin, modulating accessibility of regulatory proteins to DNA and thus influencing eukaryotic gene regulation. Elaborate chromatin remodelling mechanisms have evolved that govern nucleosome organization at promoters, regulatory elements, and other functional regions in the genome. Analyses of chromatin landscape have uncovered a variety of mechanisms, including DNA sequence preferences, that can influence nucleosome positions. To identify major determinants of nucleosome organization in the human genome, we used deep sequencing to map nucleosome positions in three primary human cell types and in vitro. A majority of the genome showed substantial flexibility of nucleosome positions, whereas a small fraction showed reproducibly positioned nucleosomes. Certain sites that position in vitro can anchor the formation of nucleosomal arrays that have cell type-specific spacing in vivo. Our results unveil an interplay of sequence-based nucleosome preferences and non-nucleosomal factors in determining nucleosome organization within mammalian cells.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212987/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212987/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valouev, Anton -- Johnson, Steven M -- Boyd, Scott D -- Smith, Cheryl L -- Fire, Andrew Z -- Sidow, Arend -- R01 GM037706/GM/NIGMS NIH HHS/ -- R01 GM037706-24/GM/NIGMS NIH HHS/ -- R01 GM037706-25/GM/NIGMS NIH HHS/ -- R01 GM037706-26/GM/NIGMS NIH HHS/ -- R01 GM037706-27/GM/NIGMS NIH HHS/ -- R01GM37706/GM/NIGMS NIH HHS/ -- T32HG00044/HG/NHGRI NIH HHS/ -- U01HG004695/HG/NHGRI NIH HHS/ -- England -- Nature. 2011 May 22;474(7352):516-20. doi: 10.1038/nature10002.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21602827" target="_blank"〉PubMed〈/a〉
Keywords:
CD4-Positive T-Lymphocytes/metabolism
;
CD8-Positive T-Lymphocytes/metabolism
;
Cells, Cultured
;
Chromatin Assembly and Disassembly/*physiology
;
*Gene Expression Regulation
;
Genome, Human/genetics
;
Granulocytes/metabolism
;
High-Throughput Nucleotide Sequencing
;
Humans
;
Micrococcal Nuclease/metabolism
;
Nucleosomes/chemistry/genetics/*metabolism
;
Organ Specificity
;
Transcription, Genetic
Print ISSN:
0028-0836
Electronic ISSN:
1476-4687
Topics:
Biology
,
Chemistry and Pharmacology
,
Medicine
,
Natural Sciences in General
,
Physics
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