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Cis-regulatory variation affects gene expression dynamics

ABSTRACT: Cis-regulatory variation affects gene expression dynamics

PROVIDER: PRJNA695016 | ENA |

REPOSITORIES: ENA

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Cis-regulatory variation affects gene expression dynamics

Project description:This study examined allele-specific expression dynamics in yeast. Gene expression was measured by an RNA-seq time-course over the diauxic shift for three strains of Saccharomcyes cerevisiae and two inter-specific hybrids of S. cerevisiae with S. paradoxus and S. uvarum.

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Impact of Regulatory Variation from RNA to Protein

Project description:Genetic variants that impact gene regulation are important contributors to human phenotypic variation. For this reason, considerable efforts have been made to identify genetic associations with differences in mRNA levels of nearby genes, namely, cis expression quantitative trait loci (eQTLs). The phenotypic consequences of eQTLs are presumably due, in most cases, to their ultimate effects on protein expression levels. Yet, only few studies have quantified the impact of genetic variation on proteins levels directly. It remains unclear how faithfully eQTLs are reflected at the protein level, and whether there is a significant layer of cis regulatory variation acting primarily on translation or steady state protein levels. To address these questions, we measured ribosome occupancy by high-throughput sequencing, and relative protein levels by high-resolution quantitative mass spectrometry, in a panel of lymphoblastoid cell lines (LCLs) in which we had previously measured transcript expression using RNA sequencing. We then mapped genetic variants that are associated with changes in transcript expression (eQTLs), ribosome occupancy (rQTLs), or protein abundance (pQTLs). Most of the QTLs we detected are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, we found that eQTLs tend to have significantly reduced effect sizes on protein levels, suggesting that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we confirmed the presence of a class of cis QTLs that specifically affect protein abundance with little or no effect on mRNA levels; most of these QTLs have little effect on ribosome occupancy, and hence may arise from differences in post-translational regulation.

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Histone turnover marks the boundaries of cis-regulatory domains

Project description:Cellular memory is maintained at the Drosophila homeotic gene clusters by cis-regulatory elements who mechanism of action is unknown. We have examined chromatin dynamics in the Drosophila genome by measuring histone turnover levels at high resolution. Surprisingly, homeotic gene clusters display characteristic histone turnover profiles with conspicuous peaks at boundaries of cis-regulatory domains superimposed over regions of very low turnover. Peaks of histone turnover precisely correspond to nuclease hypersensitive sites for epigenetic silencing proteins. Our results suggest that epigenetic regulation is facilitated by histone turnover, which maintains continuous accessibility ov cis-regulatory DNA. Keywords: Chromatin affinity-purification on microarray

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Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana

Project description:We mapped DNaseI hypersensitive sites (DHSs) and applied genomic footprinting to define in vivo transcription factor (TF) occupancy at nucleotide resolution across the A. thaliana genome in whole seedlings during heat- and light-response states. We find that trait-associated variation localizes within DHSs, and that extensive TF occupancy within protein-coding exons has shaped A. thaliana codon usage. Analysis of >700,000 TF footprints disclosed an extensive cis-regulatory lexicon, and enabled construction of large-scale TF cross-regulatory networks. Although the cis- and trans-regulatory repertoire is markedly distinct from mammals, the architecture of A. thaliana TF networks is strikingly similar to those of human. Analysis of the DHS landscape and TF network dynamics during heat shock and photomorphogenesis revealed thousands of conditionally-sensitive elements and enabled mapping of key regulatory circuits. Our results provide an extensive resource for understanding and enabling diverse aspects of A. thaliana biology. Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old dark-grown seedlings exposed to 0hr light, 30min light, 3hr light or 24hr LD conditions. Chromatin accessibility profiling (Dnase I-seq) and RNA-seq of 7-day-old LD-grown seedlings treated with a brief sever heat shock or kept under control conditions. Replicates are included when available; controls and read-normalized samples (samples that were subsampled to the same read-depth) are also included here.

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