Dataset Information

Three distinct mechanisms of long-distance modulation of gene expression in yeast.

ABSTRACT: Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression level of a reporter gene as well as its cell-to-cell variability (noise). We ectopically inserted an insulated MET3 promoter (MET3pr) flanked by ~1kb invariable sequences into thousands of genomic loci, allowing it to make contacts with different parts of the genome, and assayed the MET3pr activity in single cells. Changes of MET3pr activity in this case necessarily involve mechanisms that function over a distance. MET3pr has similar activities at most locations. However, at some locations, they deviate from the norm and exhibit three distinct patterns including low expression / high noise, low expression / low noise, and high expression / low noise. We provided evidence that these three patterns of MET3pr expression are caused by Sir2-mediated silencing, transcriptional interference, and 3D clustering. The clustering also occurs in the native genome and enhances the transcription of endogenous Met4-targeted genes. Overall, our results demonstrate that a small fraction of long-distance chromosomal interactions can affect gene expression in yeast.

SUBMITTER: Du M

PROVIDER: S-EPMC5417705 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Three distinct mechanisms of long-distance modulation of gene expression in yeast.

Du Manyu M Zhang Qian Q Bai Lu L

PLoS genetics 20170420 4

Recent Hi-C measurements have revealed numerous intra- and inter-chromosomal interactions in various eukaryotic cells. To what extent these interactions regulate gene expression is not clear. This question is particularly intriguing in budding yeast because it has extensive long-distance chromosomal interactions but few cases of gene regulation over-a-distance. Here, we developed a medium-throughput assay to screen for functional long-distance interactions that affect the average expression leve ...[more]

PMID: 28426659

Similar Datasets

Project description:BackgroundGene expression profiling has been used to define molecular phenotypes of complex diseases such as breast cancer. The luminal A and basal-like subtypes have been repeatedly identified and validated as the two main subtypes out of a total of five molecular subtypes of breast cancer. These two are associated with distinctly different gene expression patterns and more importantly, a significant difference in clinical outcome. To further validate and more thoroughly characterize these two subtypes at the molecular level in tumors at an early stage, we report a gene expression profiling study using three different DNA microarray platforms.ResultsExpression data from 20 tumor biopsies of early stage breast carcinomas were generated on three different DNA microarray platforms; Applied Biosystems Human Genome Survey Microarrays, Stanford cDNA Microarrays and Agilent's Whole Human Genome Oligo Microarrays, and the resulting gene expression patterns were analyzed. Both unsupervised and supervised analyses identified the different clinically relevant subtypes of breast tumours, and the results were consistent across all three platforms. Gene classification and biological pathway analyses of the genes differentially expressed between the two main subtypes revealed different molecular mechanisms descriptive of the two expression-based subtypes: Signature genes of the luminal A subtype were over-represented by genes involved in fatty acid metabolism and steroid hormone-mediated signaling pathways, in particular estrogen receptor signaling, while signature genes of the basal-like subtype were over-represented by genes involved in cell proliferation and differentiation, p21-mediated pathway, and G1-S checkpoint of cell cycle-signaling pathways. A minimal set of 54 genes that best discriminated the two subtypes was identified using the combined data sets generated from the three different array platforms. These predictor genes were further verified by TaqMan Gene Expression assays.ConclusionWe have identified and validated the two main previously defined clinically relevant subtypes, luminal A and basal-like, in a small set of early stage breast carcinomas. Signature genes characterizing these two subtypes revealed that distinct molecular mechanisms might have been pre-programmed at an early stage in different subtypes of the disease. Our results provide further evidence that these breast tumor subtypes represent biologically distinct disease entities and may require different therapeutic strategies. Finally, validated by multiple gene expression platforms, including quantitative PCR, the set of 54 predictor genes identified in this study may define potential prognostic molecular markers for breast cancer.

Project description:Introduction:Alliaria petiolata, an herbaceous plant, has invaded woodlands in North America. Its ecology has been thoroughly studied, but an overlooked aspect of its biology is seed dispersal distances and mechanisms. We measured seed dispersal distances in the field and tested if epizoochory is a potential mechanism for long-distance seed dispersal. Methods:Dispersal distances were measured by placing seed traps in a sector design around three seed point sources, which consisted of 15 second-year plants transplanted within a 0.25 m radius circle. Traps were placed at intervals ranging from 0.25-3.25 m from the point source. Traps remained in the field until a majority of seeds were dispersed. Eight probability density functions were fitted to seed trap counts via maximum likelihood. Epizoochory was tested as a potential seed dispersal mechanism for A. petiolata through a combination of field and laboratory experiments. To test if small mammals transport A. petiolata seeds in their fur, experimental blocks were placed around dense A. petiolata patches. Each block contained a mammal inclusion treatment (MIT) and control. The MIT consisted of a wood-frame (31 × 61× 31 cm) covered in wire mesh, except for the two 31 × 31 cm ends, placed over a germination tray filled with potting soil. A pan filled with bait was placed in the center of the tray. The control frame (11 × 31 × 61 cm) was placed over a germination tray and completely covered in wire mesh to exclude animal activity. Treatments were in the field for peak seed dispersal. In March, trays were moved to a greenhouse and A. petiolata seedlings were counted and then compared between treatments. To determine if A. petiolata seeds attach to raccoon (Procyon lotor) and white-tailed deer (Odocoileus virginianus) fur, wet and dry seeds were dropped onto wet and dry fur. Furs were rotated 180 degrees and the seeds that remained attached were counted. To measure seed retention, seeds were dropped on furs and rotated as before, then the furs were agitated for one hour. The seeds retained in the fur were counted. Results:For the seed dispersal experiment, the 2Dt function provided the best fit and was the most biologically meaningful. It predicted that seed density rapidly declined with distance from the point source. Mean dispersal distance was 0.52 m and 95% of seeds dispersed within 1.14 m. The epizoochory field experiment showed increased mammal activity and A. petiolata seedlings in germination trays of the MIT compared to control. Laboratory studies showed 3-26% of seeds were attached and retained by raccoon and deer fur. Retention significantly increased if either seed or fur were wet (57-98%). Discussion:Without animal seed vectors, most seeds fall within a short distance of the seed source; however, long distance dispersal may be accomplished by epizoochory. Our data are consistent with A. petiolata's widespread distribution and development of dense clusters of the species in invaded areas.

Dataset Information

Three distinct mechanisms of long-distance modulation of gene expression in yeast.

Publications

Three distinct mechanisms of long-distance modulation of gene expression in yeast.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets