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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

ABSTRACT: Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

PROVIDER: PRJNA339582 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3098590_1.fastq.gz	Fastqsanger.gz
	SRR3098590_2.fastq.gz	Fastqsanger.gz
	SRR3098600_1.fastq.gz	Fastqsanger.gz
	SRR3098600_2.fastq.gz	Fastqsanger.gz
	SRR3098610_1.fastq.gz	Fastqsanger.gz

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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [methylation]

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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution.

Project description:How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further examining 38 human-specific DMRs using targeted deep genomic and bisulfite sequencing in an independent panel of 37 individuals from five primate species. Our unbiased genome-scan identified human brain differentially methylated regions (DMRs), irrespective of their associations with annotated genes. Remarkably, over half of the newly identified DMRs locate in intergenic regions or gene bodies. Nevertheless, their regulatory potential is on par with those of promoter DMRs. An intriguing observation is that DMRs are enriched in active chromatin loops, suggesting human-specific evolutionary remodeling at a higher-order chromatin structure. These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions.

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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-08-20 | GSE85868 | GEO

Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

Project description:We report the application of DNA sequencing technology for high-throughput sequencing of mix bis-PCR products totally 38 based on bisulfate treated DNA from human, chimpanzee, gibbon, macaque and crab eating macaque profrontal cortex tissues. Mix bisulfate PCR products from 1 tissues, 23 individula humans, 2 individual chimpanzees, 1 individual gibbons, 7 individual rhesus macaques and 5 crab eating macaques were sequenced by using MiSeq

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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [methylation]

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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [SNP]

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Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution [SNP]

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Project description:In order to determine the impact of the epigenetic response to traumatic stress on post-traumatic stress disorder (PTSD), this study examined longitudinal changes of genome-wide blood DNA methylation profiles in relation to the development of PTSD symptoms in two prospective military cohorts (one discovery and one replication data set). In the first cohort consisting of male Dutch military servicemen (n=93), the emergence of PTSD symptoms over a deployment period to a combat zone was significantly associated with alterations in DNA methylation levels at 17 genomic positions and 12 genomic regions. Evidence for mediation of the relation between combat trauma and PTSD symptoms by longitudinal changes in DNA methylation was observed at several positions and regions. Bioinformatic analyses of the reported associations identified significant enrichment in several pathways relevant for symptoms of PTSD. Targeted analyses of the significant findings from the discovery sample in an independent prospective cohort of male US marines (n=98) replicated the observed relation between decreases in DNA methylation levels and PTSD symptoms at genomic regions in ZFP57, RNF39 and HIST1H2APS2. Together, our study pinpoints three novel genomic regions where longitudinal decreases in DNA methylation across the period of exposure to combat trauma marks susceptibility for PTSD.

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