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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

ABSTRACT: Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

PROVIDER: PRJNA267839 | ENA |

REPOSITORIES: ENA

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Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Project description:To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I–hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.

2014-11-20 | GSE51336 | GEO

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

Project description: Not available

| S-EPMC4337786 | biostudies-other

Enhancer divergence and cis-regulatory evolution in the human and chimpanzee neural crest

Project description:Here we derive human and chimpanzee cranial neural crest cells (CNCCs) and profile histone modifications, transcription factors, chromatin accessibility and gene expression to systematically and quantitatively annotate evolutionary divergence of craniofacial cis-regulatory landscapes. Histone modifications (H3K27ac, H3K4me1, H3K4me3, H3K27me3), chromatin modifiers (p300), transcription factors (NR2F1, TFAP2A), chromatin accessibility (ATACseq) and gene expression (RNAseq) were assayed in CNCCs derived from iPSCs/ESCs from 2 chimpanzee and 3 human individuals.

2015-09-11 | E-GEOD-70751 | biostudies-arrayexpress

Enhancer divergence and cis-regulatory evolution in the human and chimpanzee neural crest

2015-09-11 | GSE70751 | GEO

The role of cis regulatory evolution in Zea Mays domestication

Project description:Modification of cis regulatory elements to produce differences in gene expression level, localization, and timing is an important mechanism by which organisms evolve divergent adaptations. To examine gene regulatory change during the domestication of maize from its wild progenitor, teosinte, we assessed allele-specific expression in a collection of maize and teosinte inbreds and their F1 hybrids using three tissues from different developmental stages. Our use of F1 hybrids represents the first study in a domesticated crop and wild progenitor that dissects cis and trans regulatory effects to examine characteristics of genes under various cis and trans regulatory regimes. We find evidence for consistent cis regulatory divergence that differentiates maize from teosinte in approximately 4% of genes. These genes are significantly correlated with genes under selection during domestication and crop improvement, suggesting an important role for cis regulatory elements in maize evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem) followed by assessment of allele-specific gene expression.

2014-11-06 | E-GEOD-61810 | biostudies-arrayexpress

Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

Project description:Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis

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Runx3 pioneers chromatin accessibility of cis-regulatory landscapes that drive memory CTL formation

Project description:Runx3 pioneers chromatin accessibility of cis-regulatory landscapes that drive memory CTL formation

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The Role of cis Regulatory Evolution in Maize Domestication

2014-11-06 | GSE61810 | GEO

Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic

Project description:Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic

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Runx3 pioneers chromatin accessibility of cis-regulatory landscapes that drive memory CTL formation

Project description:T cell receptor (TCR) stimulation of naïve CD8+ T cells initiates reprogramming of cis-regulatory landscapes that specify effector and memory cytotoxic T lymphocyte (CTL) differentiation. We mapped regions of hyper-accessible chromatin in naïve cells during TCR stimulation and discovered that the transcription factor (TF) Runx3 controls de novo access to memory CTL-specific cistromes prior to the first cell division, and is essential for memory CTL differentiation. Runx3 specifically promotes accessibility of cis-acting regions highly enriched with IRF, bZIP and Prdm1-like family TF motifs, upregulates IRF4 and establishes feed-forward transcriptional circuits that induce fundamental CTL attributes in memory precursor cells. Runx3 drives uncoupling from the naïve cell state, but subsequently restrains terminal differentiation of nascent CTL by preventing high expression of the TF T-bet and slowing effector cell proliferation. Enforced Runx3 expression enhances memory CTL differentiation and increases their numbers during iterative infections. Thus, Runx3 functions in a pioneering role to initialize and then ensure memory CTL differentiate. This SuperSeries is composed of the SubSeries listed below.

2018-04-19 | GSE111149 | GEO

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