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| Status |
Public on Aug 07, 2015 |
| Title |
Nucleosome Repositioning: Nicotine- and Cocaine-induced Changes |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by array
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| Summary |
SH-SY5Y, neuroblastoma cells, were exposed to nicotine for 10, 60, and 90 minutes or cocaine for 5, 20, 40, and 60 minutes. Drugs of abuse modify behavior by altering gene expression in the brain. Gene expression can be regulated by changes in DNA methylation as well as by histone modifications, which alter chromatin structure, DNA compaction and DNA accessibility. In order to better understand the molecular mechanisms directing drug-induced changes in chromatin structure, we examined DNA-nucleosome interactions within promoter regions of 858 genes in human neuroblastoma cells (SH-SY5Y) exposed to nicotine or cocaine. Widespread, drug- and time-resolved repositioning of nucleosomes was identified at the transcription start site and promoter region of multiple genes. Nicotine and cocaine produced unique and shared changes in terms of the numbers and types of genes affected, as well as repositioning of nucleosomes at sites which could increase or decrease the probability of gene expression based on DNA accessibility. Half of the drug-induced nucleosome positions approximated a theoretical model of nucleosome occupancy based on physical and chemical characteristics of the DNA sequence, whereas the basal or drug-naive positions were generally DNA sequence independent. Thus we suggest that nucleosome repositioning represents an initial dynamic genome-wide alteration of the transcriptional landscape preceding more selective downstream transcriptional reprogramming, which ultimately characterizes the cell- and tissue-specific responses to drugs of abuse.
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| Overall design |
SH-SY5Y, neuroblastoma cells, were exposed to nicotine for 10, 60, and 90 minutes or cocaine for 5, 20, 40, and 60 minutes. Two independently grown biological replicates for each time point and condition, and two controls were processed.
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| Contributor(s) |
Brown AN, Vied C, Dennis JH, Bhide PG |
| Citation(s) |
26414157 |
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| Submission date |
Aug 06, 2015 |
| Last update date |
Oct 12, 2015 |
| Contact name |
Cynthia Vied |
| E-mail(s) |
cynthia.vied@med.fsu.edu
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| Organization name |
Florida State University
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| Department |
Translational Science Laboratory
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| Street address |
1115 W. Call St
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| City |
Tallahassee |
| State/province |
Florida |
| ZIP/Postal code |
32306 |
| Country |
USA |
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| Platforms (1) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA292096 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE71795_RAW.tar |
185.5 Mb |
(http)(custom) |
TAR (of GFF, PAIR) |
| Processed data provided as supplementary file |
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