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Eskiw, C. H.

Publications and source records attributed to Eskiw, C. H..

2 recordsLinked to original sources

Rapid nuclear exclusion of Hcm1 in aging Saccharomyces cerevisiae leads to vacuolar alkalization and replicative senescence

Yeast cells, like other higher eukaryotic cells, undergo a finite number of cell divisions before exiting the cell cycle due to the effects of aging. Here, we show that yeast aging begins with the nuclear exclusion of Hcm1 in young cells, resulting in loss of acidic vacuoles. Autophagy is required for healthy aging in yeast, with proteins targeted for turnover by autophagy directed to the vacuole. Consistent with this, vacuolar acidity is necessary for vacuolar function and yeast longevity. Using yeast genetics and immunofluorescence microscopy, we confirm that vacuolar acidity plays a critical role in cell health and lifespan, and is potentially maintained by a series of Forkhead Box (Fox) transcription factors. An interconnected transcriptional network involving the Fox proteins (Fkh1, Fkh2 and Hcm1) are required for transcription of v-ATPase subunits and vacuolar acidity. As cells age, Hcm1 is rapidly excluded from the nucleus in young cells, blocking the expression of Hcm1 targets (Fkh1 and Fkh2), leading to loss of v-ATPase gene expression, reduced vacuolar acidification, increased -syn-GFP vacuolar accumulation, and finally, diminished replicative lifespan (RLS). Loss of vacuolar acidity occurs about the same time as Hcm1 nuclear exclusion and is conserved; we have recently demonstrated that lysosomal alkalization similarly contributes to aging in C. elegans following a transition from progeny producing to post-reproductive life. Our data points to a molecular mechanism regulating vacuolar acidity that signals the end of RLS when acidification is lost.

genetics

GrapHi-C: Graph-based visualization of Hi-C Datasets

BackgroundHi-C is a proximity-based ligation reaction used to detect regions of the genome that are close in 3D space (or \"interacting\"). Typically, results from Hi-C experiments (whole-genome contact maps) are visualized as heatmaps or Circos plots. While informative, these visualizations do not intuitively represent the complex organization and folding of the genome in 3D space, making the interpretation of the underlying 3D genomic organization difficult. Our objective was to utilize existing tools to generate a graph-based representation of a whole-genome contact map that leads to a more intuitive visualization.\n\nMethodologyWhole-genome contact maps were converted into graphs where each vertex represented a genomic region and each edge represented a detected or known interaction between two vertices. Three types of interactions were represented in the graph: linear, intra-chromosomal (cis-), and inter-chromosomal (trans-) interactions. Each edge had an associated weight related to the linear distance (Hi-C experimental resolution) or the associated interaction frequency from the contact map. Graphs were generated based on this representation scheme for whole-genome contact maps from a fission yeast dataset where yeast mutants were used to identify specific principles influencing genome organization (GEO accession: GSE56849). Graphs were visualized in Cytoscape with an edge-weighted spring embedded layout where vertices and linear interaction edges were coloured according to their corresponding chromosome.\n\nResultsThe graph-based visualizations (compared to the equivalent heatmaps) more intuitively represented the effects of the rad21 mutant on genome organization. Specifically, the graph based visualizations clearly highlighted the loss of structural globules and a greater intermingling of chromosomes in the mutant strain when compared to the wild-type. The graph-based representation and visualization protocol developed here will aid in understanding the complex organization and folding of the genome.

bioinformatics