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Series GSE95793 Query DataSets for GSE95793
Status Public on Mar 22, 2017
Title Sirtuin 1-chromatin-binding dynamics point to a common mechanism regulating microglial inflammatory targets in SIV infection and in the aging brain
Organism Macaca mulatta
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Microglia are critical regulators in neurodegenerative disorders. Since HIV infection results in neurological perturbations that are similar to those in aging, we examined microglial changes that might resemble aging, using SIV infection in rhesus macaques to model neuroAIDS. We found that Sirt-1, a molecule that impacts survival and health in many models, was decreased in infected macaques. The role of Sirt-1 in neuroAIDS is unknown. We hypothesized that Sirt-1 silencing functions are affected by SIV. Mapping of Sirt-1 binding patterns to chromatin revealed that the number of Sirt-1-bound genes was 29.6% increased in microglia from infected animals with mild neuropathology, but 51% was decreased in severe neuropathology, compared to controls. Sirt-1-bound genes in controls largely participate on neuroinflammation. Promoters of type I IFN pathway genes IRF7, IRF1, IFIT1, and AIF1, showed Sirt-1 binding in controls, which was consistently lost after infection, together with higher transcription. This was also found in brains from old uninfected animals, suggesting a common regulation. Sirt-1 blockage in vitro modulated IRF7, IRF1 and AIF1 levels. Our data suggests that Sirt-1-inflammatory gene silencing is disturbed by SIV, resembling aging in brains. These findings may impact neurological consequences of HIV infection, aggravated and overlapping with the aging process.
Overall design We investigated the hypothesis that in SIV infection a Sirt-1-regulated gene network may be involved in producing phenotypic changes in innate immune cells of the CNS, which are associated to the development of an inflammatory environment, and that may resemble the phenotype found in the aging population. To understand that, we used Chromatin Immunoprecipitation (ChIP) and NextGen ChIP-sequence9 to investigate genome-wide Sirt-1 binding targets, in microglia from control and SIV-infected macaques, and the changes produced by infection were compared in animals that exhibited or not severe encephalitis. After the identification of relevant targets, we further investigated the protein expression and distribution of selected candidate molecules in the brain of uninfected but aging monkeys (>19 years old). A ChIP reaction was carried out with 30ug of microglia chromatin and anti-Sirt-1 antibody (Millipore) extracted from 6 older rhesus macaques and 6 younger rhesus macaques. The ChIP DNA was processed into an Illumina ChIP-Seq library and sequenced to generate >2 million reads, which were aligned to the M.mulatta genome annotation (MacaM/Oct 2014 assembly) and 6.2 million unique aligns (removed duplicates) were obtained.
Contributor(s) Marcondes MG, Bortell N
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Submission date Mar 07, 2017
Last update date May 15, 2019
Contact name Maria Cecilia Marcondes
Phone 858-200-7197
Organization name San Diego Biomedical Research Institute
Street address 10865 Road to the Cure, Suite 100
City San Diego
State/province CA
ZIP/Postal code 92121
Country USA
Platforms (2)
GPL19129 Illumina HiSeq 2500 (Macaca mulatta)
GPL21120 Illumina NextSeq 500 (Macaca mulatta)
Samples (8)
GSM2526068 516_Sirt1_i8
GSM2526069 404_Sirt1_i73
GSM2526070 417_Sirt1_i94
BioProject PRJNA378414
SRA SRP101511

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Supplementary file Size Download File type/resource
GSE95793_RAW.tar 761.1 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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