Biology subjects

Clemente, J.

Publications and source records attributed to Clemente, J..

2 recordsLinked to original sources

bioRxiv2020

Detecting and phasing minor single-nucleotide variants from long-read sequencing data

Cellular genetic heterogeneity is common in many biological conditions including cancer, microbiome, co-infection of multiple pathogens. Detecting and phasing minor variants, which is to determine whether multiple variants are from the same haplotype, play an instrumental role in deciphering cellular genetic heterogeneity, but are still difficult because of technological limitations. Recently, long-read sequencing technologies, including those by Pacific Biosciences and Oxford Nanopore, have provided an unprecedented opportunity to tackle these challenges. However, high error rates make it difficult to take full advantage of these technologies. To fill this gap, we introduce iGDA, an open-source tool that can accurately detect and phase minor single-nucleotide variants (SNVs), whose frequencies are as low as 0.2%, from raw long-read sequencing data. We also demonstrated that iGDA can accurately reconstruct haplotypes in closely-related strains of the same species (divergence[≥] 0.011%) from long-read metagenomic data. Our approach, therefore, presents a significant advance towards the complete deciphering of cellular genetic heterogeneity.

bioinformatics↗

bioRxiv2018

Heat-stress triggers MAPK crosstalk to turn on the hyper-osmotic response pathway

Cells make decisions based on a combination of external and internal signals. In yeast, the high osmolarity response (HOG) is a mitogen-activated protein kinase (MAPK) pathway that responds to a variety of stimuli, and it is central to the general stress response. Here we studied the effect of heat-stress (HS) on HOG. Using live-cell reporters and genetics, we show that HS promotes Hog1 phosphorylation and gene expression, exclusively via the Sln1 phosphorelay branch, and that the strength of the activation is larger in yeast adapted to high external osmolarity. HS stimulation of HOG is indirect. First, we found that it depends on the operation of a second MAPK pathway, the cell-wall integrity (CWI), a well-known mediator of HS. Second, we show that HS causes glycerol loss via the channel Fps1, and that strictly requires the CWI MAPK Slt2. Third, blocking glycerol efflux also blocks HOG activation, strongly suggesting that it is the resulting loss of turgor by the loss of the accompanying water what causes HOG stimulation. Thus, taken together, our findings highlight a central role for Fps1, and the metabolism of glycerol, in the communication between the yeast MAPK pathways, essential for survival and reproduction in changing environments.

cell biology↗