Unknown,Transcriptomics,Genomics,Proteomics

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H3K4me3, H3K27ac and H3K4me1 ChIP-seq in 4 tissues of 10 mammals

ABSTRACT: To study the tissue-specific evolution of regulatory elements in the mammalian lineage, we created a comprehensive map of promoters and enhancers in 4 tissues of 10 mammalian species. To map in-vivo promoters and enhancers, we performed ChIP-seq experiments for H3K4me3, H3K27ac and H3K4me1 in adult liver, muscle, brain and testis of all 10 species. The species included in the study are: macaque, marmoset, mouse, rat, rabbit, pig, dog, cat, horse and opossum. To correlate regulatory evolution to expression, we also performed RNA-seq experiments in all tissues and species submitted separately to ArrayExpress.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Monodelphis domestica

SUBMITTER: Maša Roller

PROVIDER: E-MTAB-7127 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Chromatin accessibility is an important functional genomics phenotype that influences transcription factor binding and gene expression. Genome-scale technologies allow chromatin accessibility to be mapped with high-resolution, facilitating detailed analyses into the genetic architecture and evolution of chromatin structure within and between species. We performed Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-Seq) to map chromatin accessibility in two parental haploid yeast species, Saccharomyces cerevisiae and Saccharomyces paradoxus and their diploid hybrid. We show that although broad-scale characteristics of the chromatin landscape are well conserved between these species, accessibility is significantly different for 947 regions upstream of genes that are enriched for GO terms such as intracellular transport and protein localization exhibit. We also develop new statistical methods to investigate the genetic architecture of variation in chromatin accessibility between species, and find that cis effects are more common and of greater magnitude than trans effects. Interestingly, we find that cis and trans effects at individual genes are often negatively correlated, suggesting widespread compensatory evolution to stabilize levels of chromatin accessibility. Finally, we demonstrate that the relationship between chromatin accessibility and gene expression levels is complex, and a significant proportion of differences in chromatin accessibility might be functionally benign. There are 20 samples in total. These consist of 10 FAIRE-seq samples, specifically 6 haploid samples, S. cerevisiae strain UWOPS05_217_3 replicates 1 and 2, S. cerevisiae strain DBVPG1373 replicates 1 and 2, and S. paradoxus strain CBS432 replicates 1 and 2. There are also 4 diploid hybrid samples, hybrid between S. cerevisiae strain UWOPS05_217_3 and S. paradoxus strain CBS432 replicates 1 and 2, and the hybrid between S. cerevisiae strain DBVPG1373 and S. paradoxus strain CBS432 replicates 1 and 2. There are also RNA-seq samples for each of these 10 samples.

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H3K4me3, H3K27ac and H3K4me1 ChIP-seq in 4 tissues of 10 mammals

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