Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Epigenetic modifications are associated with inter-species gene expression variation in primates

ABSTRACT: Epigenetic modifications are associated with inter-species gene expression variation in primates

PROVIDER: PRJNA257893 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1541030.fastq.gz	Fastqsanger.gz
	SRR1541040.fastq.gz	Fastqsanger.gz
	SRR1541050.fastq.gz	Fastqsanger.gz
	SRR1541060.fastq.gz	Fastqsanger.gz
	SRR1541070.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 98

Similar Datasets

Epigenetic modifications are associated with inter-species gene expression variation in primates

Project description:Changes in gene regulation level have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels yet we know much less about the extent to which regulatory mechanisms differ between species. To begin addressing this gap, we performed a comparative epigenetic study in primate lymphoblastoid cell lines (LCLs), to query the contribution of RNA polymerase II (Pol II) and four histone modifications (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) to inter-species variation in gene expression levels. We found that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also found that first-order interactions among the histone marks and Pol II do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution.

2014-11-09 | GSE60269 | GEO

Epigenetic modifications are associated with inter-species gene expression variation in primates.

Project description:BackgroundChanges in gene regulation have long been thought to play an important role in evolution and speciation, especially in primates. Over the past decade, comparative genomic studies have revealed extensive inter-species differences in gene expression levels, yet we know much less about the extent to which regulatory mechanisms differ between species.ResultsTo begin addressing this gap, we perform a comparative epigenetic study in primate lymphoblastoid cell lines, to query the contribution of RNA polymerase II and four histone modifications, H3K4me1, H3K4me3, H3K27ac, and H3K27me3, to inter-species variation in gene expression levels. We find that inter-species differences in mark enrichment near transcription start sites are significantly more often associated with inter-species differences in the corresponding gene expression level than expected by chance alone. Interestingly, we also find that first-order interactions among the five marks, as well as chromatin states, do not markedly contribute to the degree of association between the marks and inter-species variation in gene expression levels, suggesting that the marginal effects of the five marks dominate this contribution.ConclusionsOur observations suggest that epigenetic modifications are substantially associated with changes in gene expression levels among primates and may represent important molecular mechanisms in primate evolution.

| S-EPMC4290387 | biostudies-literature

Intra-species variation of H3K14ac in S. cerevisiae

Project description:Quantitative variation of epigenetic marks, such as histone modifications, can modify gene expression and eventually contribute to inter-individual phenotypic variation. Our goal is to investigate natural inter-individual variation of the epigenome in a quantitative manner. To probe the degree of natural epigenomic diversity in S. cerevisiae, we compared two unrelated wild strains using replicated Mnase-seq and ChIP-seq profiling at mononucleosomal resolution for H3K14 acetylation.

2015-07-22 | E-MTAB-2671 | biostudies-arrayexpress

Human milk dynamics: Inter-individual variation in peptidome

Project description:The aim of this study was to map inter-individual variation in the human milk peptidome and to investigate relationships between these data and possible explanations for observed variation.

2022-05-04 | PXD028294 | Pride

Human milk dynamics: Inter-individual variation in milk proteome

Project description:The aim of this study was to map inter-individual variation in the human milk proteome and to investigate relationships between these data and possible explanations for observed variation.

2022-05-04 | PXD028280 | Pride

Pilot study to identify technical variation in microarray data of mouse lungs in the context of inter-animal variation

Project description:Prior to generation of microarray data for a Top-down Systems analysis of influenza A infection, we evaluated the degree and origin of technical variation in gene expression microarray data from mouse lungs and compared this to inter-animal variation. Technical variation in these microarray data in the context of inter-animal variation supported a choice of biological rather than technical replicates.

2013-07-03 | GSE42521 | GEO

Inter-individual variation among worms in a shared environment

Project description:Isogenic individuals growing in the same environment often show substantial phenotypic variation. The causes, consequences and molecular bases of inter-individual variation are usually poorly understood. To characterize molecular differences between isogenic individuals, we measured genome-wide expression profiles in synchronized single young adult C. elegans worms.

2017-12-05 | GSE98747 | GEO

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels

Project description:Analysis of the extent to which inter-individual variation in mRNA decay contributes to inter-individual variation in gene expression levels in humans. The study examines properties of genome-wide decay rates and the relationship between mRNA decay and gene expression across genes, across individuals, and finally across genotype classes.

2012-10-01 | GSE37451 | GEO

Gene expression differences among primates are associated with changes in a histone epigenetic modification

Project description:Changes in gene regulation are thought to play an important role in speciation and adaptation, especially in primates. However, we still know relatively little about the mechanisms underlying regulatory evolution. In particular, the extent to which epigenetic modifications underlie gene expression differences between primates is not yet known. Our study focuses on an epigenetic histone modification, H3K4me3, which is thought to promote transcription. To investigate the contribution of H3K4me3 to regulatory differences between species, we collected gene expression data and identified H3K4me3-associated genomic regions in lymphoblastoid cell lines (LCLs) from humans, chimpanzees, and rhesus macaques, using three cell lines from each species. We found strong evidence for conservation of H3K4me3 localization in primates. Moreover, regardless of species, H3K4me3 is consistently enriched near annotated transcription start sites (TSS), and highly expressed genes are more likely than lowly expressed genes to have the histone modification near their TSS. Interestingly, we observed an enrichment of interspecies differences in H3K4me3 at the TSS of genes that are differentially expressed between species. We estimate that as much as 7% of gene expression differences between the LCLs of humans, chimpanzees, and rhesus macaques may be explained, at least in part, by changes in the status of H3K4me3 histone modifications. Our results suggest a modest, yet important role for epigenetic changes in gene expression differences between primates. Examination of H3K4me3 profiles in lymphoblastoid cell lines (LCLs) from three primate species (human, chimpanzee, and rhesus macaque), using 3 samples from each species, compared to a pooled input control from each species. Expression profiling was also done in the same LCL samples.

2011-02-15 | E-GEOD-24111 | biostudies-arrayexpress

Primates

Project description:Primates

| PRJNA551411 | ENA