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Evolutionary changes in promoter and enhancer activity during corticogenesis (non-human)

ABSTRACT: Evolutionary changes in promoter and enhancer activity during corticogenesis (non-human)

PROVIDER: PRJNA259649 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1560370.fastq.gz	Fastqsanger.gz
	SRR1560380.fastq.gz	Fastqsanger.gz
	SRR1560390.fastq.gz	Fastqsanger.gz
	SRR1560400.fastq.gz	Fastqsanger.gz
	SRR1560371.fastq.gz	Fastqsanger.gz

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Evolutionary changes in promoter and enhancer activity during human corticogenesis (human)

Project description:Evolutionary changes in gene regulation during cortical development likely contributed to the expansion and specialization of the cortex in humans. However, the lack of a regulatory map of the human embryonic cortex has hindered identification of these changes and the biological processes they influenced. We performed genome-wide epigenetic profiling to compare promoter and enhancer activity during corticogenesis in human, rhesus, and mouse. We identified 2,855 promoters and 8,996 enhancers that have gained activity in human based on increased epigenetic marking. To detect biological pathways enriched for these changes, we mapped promoters and enhancers exhibiting epigenetic gains onto modules of co-expressed genes constructed using spatio-temporally rich expression data from developing human cortex. We identified multiple modules enriched in human lineage epigenetic gains. Gains in enriched modules were associated with genes functioning in neuronal proliferation and migration, cortical patterning, and the extracellular matrix. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes in corticogenesis, providing insight into human cortical evolution.

2015-03-06 | GSE63648 | GEO

Evolutionary changes in promoter and enhancer activity during corticogenesis (non-human)

Project description:Evolutionary changes in gene regulation during cortical development likely contributed to the expansion and specialization of the cortex. However, the lack of a regulatory map of the embryonic cortex has hindered identification of these changes and the biological processes they influenced. We performed genome-wide epigenetic profiling to compare promoter and enhancer activity during corticogenesis in rhesus and mouse. We identified 2,855 promoters and 8,996 enhancers that have gained activity in based on increased epigenetic marking. To detect biological pathways enriched for these changes, we mapped promoters and enhancers exhibiting epigenetic gains onto modules of co-expressed genes constructed using spatio-temporally rich expression data from developing cortex. We identified multiple modules enriched in lineage epigenetic gains. Gains in enriched modules were associated with genes functioning in neuronal proliferation and migration, cortical patterning, and the extracellular matrix. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes in corticogenesis, providing insight into cortical evolution.

2015-03-06 | GSE60838 | GEO

Evolutionary genomics. Evolutionary changes in promoter and enhancer activity during human corticogenesis.

Project description:Human higher cognition is attributed to the evolutionary expansion and elaboration of the human cerebral cortex. However, the genetic mechanisms contributing to these developmental changes are poorly understood. We used comparative epigenetic profiling of human, rhesus macaque, and mouse corticogenesis to identify promoters and enhancers that have gained activity in humans. These gains are significantly enriched in modules of coexpressed genes in the cortex that function in neuronal proliferation, migration, and cortical-map organization. Gain-enriched modules also showed correlated gene expression patterns and similar transcription factor binding site enrichments in promoters and enhancers, suggesting that they are connected by common regulatory mechanisms. Our results reveal coordinated patterns of potential regulatory changes associated with conserved developmental processes during corticogenesis, providing insight into human cortical evolution.

| S-EPMC4426903 | biostudies-literature

Project description:Evolutionary changes in promoter and enhancer activity during human corticogenesis

| PRJNA268527 | ENA

Evolutionary changes in promoter and enhancer activity during human corticogenesis

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

2015-03-06 | GSE63649 | GEO

Homo sapiens

Project description:Evolutionary changes in promoter and enhancer activity during human corticogenesis (human)

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Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

Project description:Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

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CpG island turnover is associated with evolutionary changes in enhancer activity

Project description:CpG island turnover is associated with evolutionary changes in enhancer activity

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Analysis of enhancer-promoter connectivity alterations

Project description:The study uncovers epigenomic changes associated with dexamethasone response heterogeneity in myeloma cells, revealing rewired promoter-enhancer interactions and DNA loop stabilization

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High-throughput functional comparison of promoter and enhancer activities

Project description:Promoters initiate RNA synthesis, and enhancers stimulate promoter activity. Whether promoter and enhancer activities are encoded distinctly in DNA sequences is unknown. We measured the enhancer and promoter activities of thousands of DNA fragments transduced into mouse neurons. We focused on genomic loci bound by the neuronal activity-regulated co-activator CREBBP, and we measured enhancer and promoter activities both before and after neuronal activation. We find that the same sequences typically encode both enhancer and promoter activities. However, gene promoters generate more promoter activity than distal enhancers, despite generating similar enhancer activity. Surprisingly, the greater promoter activity of gene promoters is not due to conventional core promoter elements or splicing signals. Instead, we find that particular transcription factor binding motifs are intrinsically biased toward the generation of promoter activity, while others are not. While the specific biases we observe may be dependent on experimental or cellular context, our results suggest that gene promoters are distinguished from distal enhancers by specific complements of transcriptional activators.

2016-05-23 | GSE77213 | GEO

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